Starting phenix.real_space_refine on Fri Mar 15 11:05:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyg_0543/03_2024/6nyg_0543.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyg_0543/03_2024/6nyg_0543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyg_0543/03_2024/6nyg_0543.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyg_0543/03_2024/6nyg_0543.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyg_0543/03_2024/6nyg_0543.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyg_0543/03_2024/6nyg_0543.pdb" } resolution = 3.9 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= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 42948 2.51 5 N 12060 2.21 5 O 13512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-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: 25.77, per 1000 atoms: 0.38 Number of scatterers: 68664 At special positions: 0 Unit cell: (297.86, 297.86, 117.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 13512 8.00 N 12060 7.00 C 42948 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 749 " distance=2.02 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 749 " distance=2.03 Simple disulfide: pdb=" SG CYS G 738 " - pdb=" SG CYS G 749 " distance=2.03 Simple disulfide: pdb=" SG CYS H 738 " - pdb=" SG CYS H 749 " distance=2.02 Simple disulfide: pdb=" SG CYS I 738 " - pdb=" SG CYS I 749 " distance=2.02 Simple disulfide: pdb=" SG CYS J 738 " - pdb=" SG CYS J 749 " distance=2.03 Simple disulfide: pdb=" SG CYS K 738 " - pdb=" SG CYS K 749 " distance=2.02 Simple disulfide: pdb=" SG CYS L 738 " - pdb=" SG CYS L 749 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.26 Conformation dependent library (CDL) restraints added in 9.7 seconds 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16080 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 192 sheets defined 5.5% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.31 Creating SS restraints... Processing helix chain 'A' and resid 29 through 34 Processing helix chain 'A' and resid 35 through 38 removed outlier: 3.600A pdb=" N ALA A 38 " --> pdb=" O ALA A 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 35 through 38' Processing helix chain 'A' and resid 56 through 60 removed outlier: 3.789A pdb=" N GLU A 59 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N PHE A 60 " --> pdb=" O PHE A 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 56 through 60' Processing helix chain 'A' and resid 721 through 725 removed outlier: 3.873A pdb=" N ARG A 725 " --> pdb=" O GLN A 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 721 through 725' Processing helix chain 'A' and resid 744 through 754 removed outlier: 4.038A pdb=" N ALA A 748 " --> pdb=" O ASP A 744 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 752 " --> pdb=" O ALA A 748 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE A 753 " --> pdb=" O CYS A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 759 removed outlier: 3.752A pdb=" N MET A 758 " --> pdb=" O ASN A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 765 removed outlier: 3.512A pdb=" N ASN A 764 " --> pdb=" O ASN A 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 38 removed outlier: 3.601A pdb=" N ALA B 38 " --> pdb=" O ALA B 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 35 through 38' Processing helix chain 'B' and resid 56 through 60 removed outlier: 3.789A pdb=" N GLU B 59 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N PHE B 60 " --> pdb=" O PHE B 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 56 through 60' Processing helix chain 'B' and resid 721 through 725 removed outlier: 3.872A pdb=" N ARG B 725 " --> pdb=" O GLN B 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 721 through 725' Processing helix chain 'B' and resid 744 through 754 removed outlier: 4.040A pdb=" N ALA B 748 " --> pdb=" O ASP B 744 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA B 752 " --> pdb=" O ALA B 748 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE B 753 " --> pdb=" O CYS B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 759 removed outlier: 3.753A pdb=" N MET B 758 " --> pdb=" O ASN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 removed outlier: 3.512A pdb=" N ASN B 764 " --> pdb=" O ASN B 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 35 through 38 removed outlier: 3.601A pdb=" N ALA C 38 " --> pdb=" O ALA C 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 35 through 38' Processing helix chain 'C' and resid 56 through 60 removed outlier: 3.789A pdb=" N GLU C 59 " --> pdb=" O GLY C 56 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N PHE C 60 " --> pdb=" O PHE C 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 56 through 60' Processing helix chain 'C' and resid 721 through 725 removed outlier: 3.873A pdb=" N ARG C 725 " --> pdb=" O GLN C 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 721 through 725' Processing helix chain 'C' and resid 744 through 754 removed outlier: 4.039A pdb=" N ALA C 748 " --> pdb=" O ASP C 744 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA C 752 " --> pdb=" O ALA C 748 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE C 753 " --> pdb=" O CYS C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 759 removed outlier: 3.752A pdb=" N MET C 758 " --> pdb=" O ASN C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 765 removed outlier: 3.512A pdb=" N ASN C 764 " --> pdb=" O ASN C 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'D' and resid 35 through 38 removed outlier: 3.600A pdb=" N ALA D 38 " --> pdb=" O ALA D 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 35 through 38' Processing helix chain 'D' and resid 56 through 60 removed outlier: 3.789A pdb=" N GLU D 59 " --> pdb=" O GLY D 56 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N PHE D 60 " --> pdb=" O PHE D 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 56 through 60' Processing helix chain 'D' and resid 721 through 725 removed outlier: 3.872A pdb=" N ARG D 725 " --> pdb=" O GLN D 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 721 through 725' Processing helix chain 'D' and resid 744 through 754 removed outlier: 4.039A pdb=" N ALA D 748 " --> pdb=" O ASP D 744 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA D 752 " --> pdb=" O ALA D 748 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE D 753 " --> pdb=" O CYS D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 755 through 759 removed outlier: 3.752A pdb=" N MET D 758 " --> pdb=" O ASN D 755 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 765 removed outlier: 3.512A pdb=" N ASN D 764 " --> pdb=" O ASN D 761 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 35 through 38 removed outlier: 3.600A pdb=" N ALA E 38 " --> pdb=" O ALA E 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 35 through 38' Processing helix chain 'E' and resid 56 through 60 removed outlier: 3.788A pdb=" N GLU E 59 " --> pdb=" O GLY E 56 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N PHE E 60 " --> pdb=" O PHE E 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 56 through 60' Processing helix chain 'E' and resid 721 through 725 removed outlier: 3.872A pdb=" N ARG E 725 " --> pdb=" O GLN E 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 721 through 725' Processing helix chain 'E' and resid 744 through 754 removed outlier: 4.039A pdb=" N ALA E 748 " --> pdb=" O ASP E 744 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA E 752 " --> pdb=" O ALA E 748 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE E 753 " --> pdb=" O CYS E 749 " (cutoff:3.500A) Processing helix chain 'E' and resid 755 through 759 removed outlier: 3.752A pdb=" N MET E 758 " --> pdb=" O ASN E 755 " (cutoff:3.500A) Processing helix chain 'E' and resid 761 through 765 removed outlier: 3.513A pdb=" N ASN E 764 " --> pdb=" O ASN E 761 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 34 Processing helix chain 'F' and resid 35 through 38 removed outlier: 3.600A pdb=" N ALA F 38 " --> pdb=" O ALA F 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 35 through 38' Processing helix chain 'F' and resid 56 through 60 removed outlier: 3.788A pdb=" N GLU F 59 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N PHE F 60 " --> pdb=" O PHE F 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 56 through 60' Processing helix chain 'F' and resid 721 through 725 removed outlier: 3.873A pdb=" N ARG F 725 " --> pdb=" O GLN F 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 721 through 725' Processing helix chain 'F' and resid 744 through 754 removed outlier: 4.039A pdb=" N ALA F 748 " --> pdb=" O ASP F 744 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA F 752 " --> pdb=" O ALA F 748 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE F 753 " --> pdb=" O CYS F 749 " (cutoff:3.500A) Processing helix chain 'F' and resid 755 through 759 removed outlier: 3.752A pdb=" N MET F 758 " --> pdb=" O ASN F 755 " (cutoff:3.500A) Processing helix chain 'F' and resid 761 through 765 removed outlier: 3.512A pdb=" N ASN F 764 " --> pdb=" O ASN F 761 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 35 through 38 removed outlier: 3.601A pdb=" N ALA G 38 " --> pdb=" O ALA G 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 35 through 38' Processing helix chain 'G' and resid 56 through 60 removed outlier: 3.788A pdb=" N GLU G 59 " --> pdb=" O GLY G 56 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE G 60 " --> pdb=" O PHE G 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 56 through 60' Processing helix chain 'G' and resid 721 through 725 removed outlier: 3.873A pdb=" N ARG G 725 " --> pdb=" O GLN G 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 721 through 725' Processing helix chain 'G' and resid 744 through 754 removed outlier: 4.040A pdb=" N ALA G 748 " --> pdb=" O ASP G 744 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA G 752 " --> pdb=" O ALA G 748 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE G 753 " --> pdb=" O CYS G 749 " (cutoff:3.500A) Processing helix chain 'G' and resid 755 through 759 removed outlier: 3.753A pdb=" N MET G 758 " --> pdb=" O ASN G 755 " (cutoff:3.500A) Processing helix chain 'G' and resid 761 through 765 removed outlier: 3.512A pdb=" N ASN G 764 " --> pdb=" O ASN G 761 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 34 Processing helix chain 'H' and resid 35 through 38 removed outlier: 3.600A pdb=" N ALA H 38 " --> pdb=" O ALA H 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 35 through 38' Processing helix chain 'H' and resid 56 through 60 removed outlier: 3.788A pdb=" N GLU H 59 " --> pdb=" O GLY H 56 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N PHE H 60 " --> pdb=" O PHE H 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 56 through 60' Processing helix chain 'H' and resid 721 through 725 removed outlier: 3.872A pdb=" N ARG H 725 " --> pdb=" O GLN H 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 721 through 725' Processing helix chain 'H' and resid 744 through 754 removed outlier: 4.040A pdb=" N ALA H 748 " --> pdb=" O ASP H 744 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA H 752 " --> pdb=" O ALA H 748 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE H 753 " --> pdb=" O CYS H 749 " (cutoff:3.500A) Processing helix chain 'H' and resid 755 through 759 removed outlier: 3.752A pdb=" N MET H 758 " --> pdb=" O ASN H 755 " (cutoff:3.500A) Processing helix chain 'H' and resid 761 through 765 removed outlier: 3.512A pdb=" N ASN H 764 " --> pdb=" O ASN H 761 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 34 Processing helix chain 'I' and resid 35 through 38 removed outlier: 3.600A pdb=" N ALA I 38 " --> pdb=" O ALA I 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 35 through 38' Processing helix chain 'I' and resid 56 through 60 removed outlier: 3.789A pdb=" N GLU I 59 " --> pdb=" O GLY I 56 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N PHE I 60 " --> pdb=" O PHE I 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 56 through 60' Processing helix chain 'I' and resid 721 through 725 removed outlier: 3.873A pdb=" N ARG I 725 " --> pdb=" O GLN I 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 721 through 725' Processing helix chain 'I' and resid 744 through 754 removed outlier: 4.040A pdb=" N ALA I 748 " --> pdb=" O ASP I 744 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA I 752 " --> pdb=" O ALA I 748 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE I 753 " --> pdb=" O CYS I 749 " (cutoff:3.500A) Processing helix chain 'I' and resid 755 through 759 removed outlier: 3.751A pdb=" N MET I 758 " --> pdb=" O ASN I 755 " (cutoff:3.500A) Processing helix chain 'I' and resid 761 through 765 removed outlier: 3.512A pdb=" N ASN I 764 " --> pdb=" O ASN I 761 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 34 Processing helix chain 'J' and resid 35 through 38 removed outlier: 3.600A pdb=" N ALA J 38 " --> pdb=" O ALA J 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 35 through 38' Processing helix chain 'J' and resid 56 through 60 removed outlier: 3.788A pdb=" N GLU J 59 " --> pdb=" O GLY J 56 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N PHE J 60 " --> pdb=" O PHE J 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 56 through 60' Processing helix chain 'J' and resid 721 through 725 removed outlier: 3.872A pdb=" N ARG J 725 " --> pdb=" O GLN J 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 721 through 725' Processing helix chain 'J' and resid 744 through 754 removed outlier: 4.039A pdb=" N ALA J 748 " --> pdb=" O ASP J 744 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA J 752 " --> pdb=" O ALA J 748 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE J 753 " --> pdb=" O CYS J 749 " (cutoff:3.500A) Processing helix chain 'J' and resid 755 through 759 removed outlier: 3.752A pdb=" N MET J 758 " --> pdb=" O ASN J 755 " (cutoff:3.500A) Processing helix chain 'J' and resid 761 through 765 removed outlier: 3.513A pdb=" N ASN J 764 " --> pdb=" O ASN J 761 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 34 Processing helix chain 'K' and resid 35 through 38 removed outlier: 3.600A pdb=" N ALA K 38 " --> pdb=" O ALA K 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 35 through 38' Processing helix chain 'K' and resid 56 through 60 removed outlier: 3.788A pdb=" N GLU K 59 " --> pdb=" O GLY K 56 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N PHE K 60 " --> pdb=" O PHE K 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 56 through 60' Processing helix chain 'K' and resid 721 through 725 removed outlier: 3.872A pdb=" N ARG K 725 " --> pdb=" O GLN K 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 721 through 725' Processing helix chain 'K' and resid 744 through 754 removed outlier: 4.039A pdb=" N ALA K 748 " --> pdb=" O ASP K 744 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA K 752 " --> pdb=" O ALA K 748 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE K 753 " --> pdb=" O CYS K 749 " (cutoff:3.500A) Processing helix chain 'K' and resid 755 through 759 removed outlier: 3.752A pdb=" N MET K 758 " --> pdb=" O ASN K 755 " (cutoff:3.500A) Processing helix chain 'K' and resid 761 through 765 removed outlier: 3.513A pdb=" N ASN K 764 " --> pdb=" O ASN K 761 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 34 Processing helix chain 'L' and resid 35 through 38 removed outlier: 3.601A pdb=" N ALA L 38 " --> pdb=" O ALA L 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 35 through 38' Processing helix chain 'L' and resid 56 through 60 removed outlier: 3.789A pdb=" N GLU L 59 " --> pdb=" O GLY L 56 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N PHE L 60 " --> pdb=" O PHE L 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 56 through 60' Processing helix chain 'L' and resid 721 through 725 removed outlier: 3.873A pdb=" N ARG L 725 " --> pdb=" O GLN L 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 721 through 725' Processing helix chain 'L' and resid 744 through 754 removed outlier: 4.039A pdb=" N ALA L 748 " --> pdb=" O ASP L 744 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA L 752 " --> pdb=" O ALA L 748 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE L 753 " --> pdb=" O CYS L 749 " (cutoff:3.500A) Processing helix chain 'L' and resid 755 through 759 removed outlier: 3.753A pdb=" N MET L 758 " --> pdb=" O ASN L 755 " (cutoff:3.500A) Processing helix chain 'L' and resid 761 through 765 removed outlier: 3.512A pdb=" N ASN L 764 " --> pdb=" O ASN L 761 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 212 removed outlier: 7.003A pdb=" N LEU A 187 " --> pdb=" O ASN A 212 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL A 155 " --> pdb=" O THR A 188 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 125 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N ASP A 124 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N LEU A 99 " --> pdb=" O ASP A 124 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASN A 126 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A 101 " --> pdb=" O ASN A 126 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS A 47 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU A 100 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N TRP A 49 " --> pdb=" O GLU A 100 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASP A 102 " --> pdb=" O TRP A 49 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE A 51 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL F 339 " --> pdb=" O ASP A 46 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL A 48 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG A 50 " --> pdb=" O PRO F 341 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 66 removed outlier: 6.095A pdb=" N GLY A 108 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ARG A 133 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TYR A 110 " --> pdb=" O ARG A 133 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 142 removed outlier: 3.572A pdb=" N GLU A 169 " --> pdb=" O ASN A 140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 218 through 224 removed outlier: 4.059A pdb=" N VAL A 252 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU A 220 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N PHE A 254 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY A 222 " --> pdb=" O PHE A 254 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS A 256 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ASN A 253 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE A 277 " --> pdb=" O ASN A 253 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASN A 255 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N HIS A 276 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N ARG A 361 " --> pdb=" O HIS A 276 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLY A 278 " --> pdb=" O ARG A 361 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ASN A 363 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU A 280 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 269 through 270 removed outlier: 6.305A pdb=" N ILE A 269 " --> pdb=" O ILE A 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 339 through 345 removed outlier: 5.466A pdb=" N VAL A 339 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ARG B 50 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N GLN B 52 " --> pdb=" O PRO A 341 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLN A 343 " --> pdb=" O GLN B 52 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LYS B 47 " --> pdb=" O LYS B 98 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU B 100 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N TRP B 49 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASP B 102 " --> pdb=" O TRP B 49 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE B 51 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N ASP B 124 " --> pdb=" O ASN B 97 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU B 99 " --> pdb=" O ASP B 124 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASN B 126 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL B 101 " --> pdb=" O ASN B 126 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 125 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL B 155 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU B 187 " --> pdb=" O ASN B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 377 through 379 removed outlier: 3.708A pdb=" N GLU A 407 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA A 435 " --> pdb=" O ASN A 463 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LYS A 465 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE A 437 " --> pdb=" O LYS A 465 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AA9, first strand: chain 'A' and resid 456 through 457 removed outlier: 7.159A pdb=" N ILE A 456 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE A 476 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU A 500 " --> pdb=" O ILE A 518 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU A 517 " --> pdb=" O ARG A 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 470 through 472 Processing sheet with id=AB2, first strand: chain 'A' and resid 530 through 532 Processing sheet with id=AB3, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AB4, first strand: chain 'A' and resid 572 through 574 removed outlier: 5.444A pdb=" N PHE A 572 " --> pdb=" O ALA A 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 589 through 590 removed outlier: 3.827A pdb=" N ILE A 636 " --> pdb=" O LEU A 613 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 621 through 622 removed outlier: 6.495A pdb=" N MET A 621 " --> pdb=" O ASN A 643 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ILE A 679 " --> pdb=" O ALA A 727 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 693 through 697 removed outlier: 7.701A pdb=" N ILE A 787 " --> pdb=" O LEU A 695 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 729 through 730 Processing sheet with id=AB9, first strand: chain 'B' and resid 65 through 66 removed outlier: 6.095A pdb=" N GLY B 108 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ARG B 133 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N TYR B 110 " --> pdb=" O ARG B 133 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 140 through 142 removed outlier: 3.573A pdb=" N GLU B 169 " --> pdb=" O ASN B 140 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 218 through 224 removed outlier: 4.059A pdb=" N VAL B 252 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU B 220 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N PHE B 254 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY B 222 " --> pdb=" O PHE B 254 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS B 256 " --> pdb=" O GLY B 222 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ASN B 253 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE B 277 " --> pdb=" O ASN B 253 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASN B 255 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N HIS B 276 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N ARG B 361 " --> pdb=" O HIS B 276 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLY B 278 " --> pdb=" O ARG B 361 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ASN B 363 " --> pdb=" O GLY B 278 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU B 280 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 269 through 270 removed outlier: 6.306A pdb=" N ILE B 269 " --> pdb=" O ILE B 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 339 through 345 removed outlier: 5.471A pdb=" N VAL B 339 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ARG C 50 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N GLN C 52 " --> pdb=" O PRO B 341 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLN B 343 " --> pdb=" O GLN C 52 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS C 47 " --> pdb=" O LYS C 98 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU C 100 " --> pdb=" O LYS C 47 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N TRP C 49 " --> pdb=" O GLU C 100 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASP C 102 " --> pdb=" O TRP C 49 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE C 51 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N ASP C 124 " --> pdb=" O ASN C 97 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N LEU C 99 " --> pdb=" O ASP C 124 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASN C 126 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL C 101 " --> pdb=" O ASN C 126 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL C 125 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL C 155 " --> pdb=" O THR C 188 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU C 187 " --> pdb=" O ASN C 212 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 377 through 379 removed outlier: 3.709A pdb=" N GLU B 407 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA B 435 " --> pdb=" O ASN B 463 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LYS B 465 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE B 437 " --> pdb=" O LYS B 465 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 387 through 388 Processing sheet with id=AC7, first strand: chain 'B' and resid 456 through 457 removed outlier: 7.159A pdb=" N ILE B 456 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE B 476 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU B 500 " --> pdb=" O ILE B 518 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU B 517 " --> pdb=" O ARG B 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 470 through 472 Processing sheet with id=AC9, first strand: chain 'B' and resid 530 through 532 Processing sheet with id=AD1, first strand: chain 'B' and resid 541 through 542 Processing sheet with id=AD2, first strand: chain 'B' and resid 572 through 574 removed outlier: 5.445A pdb=" N PHE B 572 " --> pdb=" O ALA B 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 589 through 590 removed outlier: 3.826A pdb=" N ILE B 636 " --> pdb=" O LEU B 613 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 621 through 622 removed outlier: 6.495A pdb=" N MET B 621 " --> pdb=" O ASN B 643 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ILE B 679 " --> pdb=" O ALA B 727 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 693 through 697 removed outlier: 7.700A pdb=" N ILE B 787 " --> pdb=" O LEU B 695 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 729 through 730 Processing sheet with id=AD7, first strand: chain 'C' and resid 65 through 66 removed outlier: 6.095A pdb=" N GLY C 108 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ARG C 133 " --> pdb=" O GLY C 108 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TYR C 110 " --> pdb=" O ARG C 133 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 140 through 142 removed outlier: 3.572A pdb=" N GLU C 169 " --> pdb=" O ASN C 140 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 218 through 224 removed outlier: 4.058A pdb=" N VAL C 252 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU C 220 " --> pdb=" O VAL C 252 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N PHE C 254 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY C 222 " --> pdb=" O PHE C 254 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS C 256 " --> pdb=" O GLY C 222 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ASN C 253 " --> pdb=" O THR C 275 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE C 277 " --> pdb=" O ASN C 253 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASN C 255 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N HIS C 276 " --> pdb=" O ILE C 359 " (cutoff:3.500A) removed outlier: 9.660A pdb=" N ARG C 361 " --> pdb=" O HIS C 276 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLY C 278 " --> pdb=" O ARG C 361 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ASN C 363 " --> pdb=" O GLY C 278 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU C 280 " --> pdb=" O ASN C 363 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 269 through 270 removed outlier: 6.306A pdb=" N ILE C 269 " --> pdb=" O ILE C 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 339 through 345 removed outlier: 5.652A pdb=" N VAL C 339 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ARG D 50 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLN D 52 " --> pdb=" O PRO C 341 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLN C 343 " --> pdb=" O GLN D 52 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS D 47 " --> pdb=" O LYS D 98 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU D 100 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N TRP D 49 " --> pdb=" O GLU D 100 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP D 102 " --> pdb=" O TRP D 49 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE D 51 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N ASP D 124 " --> pdb=" O ASN D 97 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU D 99 " --> pdb=" O ASP D 124 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASN D 126 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL D 101 " --> pdb=" O ASN D 126 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 125 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL D 155 " --> pdb=" O THR D 188 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU D 187 " --> pdb=" O ASN D 212 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 377 through 379 removed outlier: 3.707A pdb=" N GLU C 407 " --> pdb=" O LEU C 379 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA C 435 " --> pdb=" O ASN C 463 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LYS C 465 " --> pdb=" O ALA C 435 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE C 437 " --> pdb=" O LYS C 465 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 387 through 388 Processing sheet with id=AE5, first strand: chain 'C' and resid 456 through 457 removed outlier: 7.159A pdb=" N ILE C 456 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE C 476 " --> pdb=" O ILE C 501 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU C 500 " --> pdb=" O ILE C 518 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU C 517 " --> pdb=" O ARG C 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 470 through 472 Processing sheet with id=AE7, first strand: chain 'C' and resid 530 through 532 Processing sheet with id=AE8, first strand: chain 'C' and resid 541 through 542 Processing sheet with id=AE9, first strand: chain 'C' and resid 572 through 574 removed outlier: 5.445A pdb=" N PHE C 572 " --> pdb=" O ALA C 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'C' and resid 589 through 590 removed outlier: 3.827A pdb=" N ILE C 636 " --> pdb=" O LEU C 613 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 621 through 622 removed outlier: 6.495A pdb=" N MET C 621 " --> pdb=" O ASN C 643 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE C 679 " --> pdb=" O ALA C 727 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 693 through 697 removed outlier: 7.701A pdb=" N ILE C 787 " --> pdb=" O LEU C 695 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 729 through 730 Processing sheet with id=AF5, first strand: chain 'D' and resid 65 through 66 removed outlier: 6.095A pdb=" N GLY D 108 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ARG D 133 " --> pdb=" O GLY D 108 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N TYR D 110 " --> pdb=" O ARG D 133 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 140 through 142 removed outlier: 3.572A pdb=" N GLU D 169 " --> pdb=" O ASN D 140 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 218 through 224 removed outlier: 4.059A pdb=" N VAL D 252 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU D 220 " --> pdb=" O VAL D 252 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N PHE D 254 " --> pdb=" O LEU D 220 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY D 222 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS D 256 " --> pdb=" O GLY D 222 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ASN D 253 " --> pdb=" O THR D 275 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE D 277 " --> pdb=" O ASN D 253 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASN D 255 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N HIS D 276 " --> pdb=" O ILE D 359 " (cutoff:3.500A) removed outlier: 9.660A pdb=" N ARG D 361 " --> pdb=" O HIS D 276 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY D 278 " --> pdb=" O ARG D 361 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ASN D 363 " --> pdb=" O GLY D 278 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU D 280 " --> pdb=" O ASN D 363 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 269 through 270 removed outlier: 6.306A pdb=" N ILE D 269 " --> pdb=" O ILE D 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'D' and resid 339 through 345 removed outlier: 5.608A pdb=" N VAL D 339 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ARG E 50 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N GLN E 52 " --> pdb=" O PRO D 341 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLN D 343 " --> pdb=" O GLN E 52 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS E 47 " --> pdb=" O LYS E 98 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU E 100 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N TRP E 49 " --> pdb=" O GLU E 100 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP E 102 " --> pdb=" O TRP E 49 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE E 51 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N ASP E 124 " --> pdb=" O ASN E 97 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N LEU E 99 " --> pdb=" O ASP E 124 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASN E 126 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL E 101 " --> pdb=" O ASN E 126 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL E 125 " --> pdb=" O ASP E 156 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL E 155 " --> pdb=" O THR E 188 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU E 187 " --> pdb=" O ASN E 212 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 377 through 379 removed outlier: 3.707A pdb=" N GLU D 407 " --> pdb=" O LEU D 379 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA D 435 " --> pdb=" O ASN D 463 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LYS D 465 " --> pdb=" O ALA D 435 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE D 437 " --> pdb=" O LYS D 465 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 387 through 388 Processing sheet with id=AG3, first strand: chain 'D' and resid 456 through 457 removed outlier: 7.158A pdb=" N ILE D 456 " --> pdb=" O ASP D 477 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE D 476 " --> pdb=" O ILE D 501 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU D 500 " --> pdb=" O ILE D 518 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU D 517 " --> pdb=" O ARG D 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'D' and resid 470 through 472 Processing sheet with id=AG5, first strand: chain 'D' and resid 530 through 532 Processing sheet with id=AG6, first strand: chain 'D' and resid 541 through 542 Processing sheet with id=AG7, first strand: chain 'D' and resid 572 through 574 removed outlier: 5.446A pdb=" N PHE D 572 " --> pdb=" O ALA D 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'D' and resid 589 through 590 removed outlier: 3.827A pdb=" N ILE D 636 " --> pdb=" O LEU D 613 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 621 through 622 removed outlier: 6.495A pdb=" N MET D 621 " --> pdb=" O ASN D 643 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE D 679 " --> pdb=" O ALA D 727 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 693 through 697 removed outlier: 7.701A pdb=" N ILE D 787 " --> pdb=" O LEU D 695 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'D' and resid 729 through 730 Processing sheet with id=AH3, first strand: chain 'E' and resid 65 through 66 removed outlier: 6.096A pdb=" N GLY E 108 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N ARG E 133 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TYR E 110 " --> pdb=" O ARG E 133 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 140 through 142 removed outlier: 3.572A pdb=" N GLU E 169 " --> pdb=" O ASN E 140 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 218 through 224 removed outlier: 4.059A pdb=" N VAL E 252 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU E 220 " --> pdb=" O VAL E 252 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N PHE E 254 " --> pdb=" O LEU E 220 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY E 222 " --> pdb=" O PHE E 254 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS E 256 " --> pdb=" O GLY E 222 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ASN E 253 " --> pdb=" O THR E 275 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE E 277 " --> pdb=" O ASN E 253 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASN E 255 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N HIS E 276 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 9.660A pdb=" N ARG E 361 " --> pdb=" O HIS E 276 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY E 278 " --> pdb=" O ARG E 361 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ASN E 363 " --> pdb=" O GLY E 278 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU E 280 " --> pdb=" O ASN E 363 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E' and resid 269 through 270 removed outlier: 6.306A pdb=" N ILE E 269 " --> pdb=" O ILE E 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH6 Processing sheet with id=AH7, first strand: chain 'E' and resid 339 through 345 removed outlier: 5.408A pdb=" N VAL E 339 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ARG F 50 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N GLN F 52 " --> pdb=" O PRO E 341 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLN E 343 " --> pdb=" O GLN F 52 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS F 47 " --> pdb=" O LYS F 98 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU F 100 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N TRP F 49 " --> pdb=" O GLU F 100 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP F 102 " --> pdb=" O TRP F 49 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE F 51 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N ASP F 124 " --> pdb=" O ASN F 97 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU F 99 " --> pdb=" O ASP F 124 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASN F 126 " --> pdb=" O LEU F 99 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL F 101 " --> pdb=" O ASN F 126 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL F 125 " --> pdb=" O ASP F 156 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL F 155 " --> pdb=" O THR F 188 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU F 187 " --> pdb=" O ASN F 212 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'E' and resid 377 through 379 removed outlier: 3.708A pdb=" N GLU E 407 " --> pdb=" O LEU E 379 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA E 435 " --> pdb=" O ASN E 463 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LYS E 465 " --> pdb=" O ALA E 435 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE E 437 " --> pdb=" O LYS E 465 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'E' and resid 387 through 388 Processing sheet with id=AI1, first strand: chain 'E' and resid 456 through 457 removed outlier: 7.159A pdb=" N ILE E 456 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE E 476 " --> pdb=" O ILE E 501 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU E 500 " --> pdb=" O ILE E 518 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU E 517 " --> pdb=" O ARG E 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI1 Processing sheet with id=AI2, first strand: chain 'E' and resid 470 through 472 Processing sheet with id=AI3, first strand: chain 'E' and resid 530 through 532 Processing sheet with id=AI4, first strand: chain 'E' and resid 541 through 542 Processing sheet with id=AI5, first strand: chain 'E' and resid 572 through 574 removed outlier: 5.444A pdb=" N PHE E 572 " --> pdb=" O ALA E 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI5 Processing sheet with id=AI6, first strand: chain 'E' and resid 589 through 590 removed outlier: 3.826A pdb=" N ILE E 636 " --> pdb=" O LEU E 613 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'E' and resid 621 through 622 removed outlier: 6.496A pdb=" N MET E 621 " --> pdb=" O ASN E 643 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE E 679 " --> pdb=" O ALA E 727 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'E' and resid 693 through 697 removed outlier: 7.701A pdb=" N ILE E 787 " --> pdb=" O LEU E 695 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'E' and resid 729 through 730 Processing sheet with id=AJ1, first strand: chain 'F' and resid 65 through 66 removed outlier: 6.095A pdb=" N GLY F 108 " --> pdb=" O THR F 131 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ARG F 133 " --> pdb=" O GLY F 108 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N TYR F 110 " --> pdb=" O ARG F 133 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'F' and resid 140 through 142 removed outlier: 3.572A pdb=" N GLU F 169 " --> pdb=" O ASN F 140 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'F' and resid 218 through 224 removed outlier: 4.058A pdb=" N VAL F 252 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU F 220 " --> pdb=" O VAL F 252 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N PHE F 254 " --> pdb=" O LEU F 220 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY F 222 " --> pdb=" O PHE F 254 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS F 256 " --> pdb=" O GLY F 222 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ASN F 253 " --> pdb=" O THR F 275 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE F 277 " --> pdb=" O ASN F 253 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASN F 255 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N HIS F 276 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 9.660A pdb=" N ARG F 361 " --> pdb=" O HIS F 276 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY F 278 " --> pdb=" O ARG F 361 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ASN F 363 " --> pdb=" O GLY F 278 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU F 280 " --> pdb=" O ASN F 363 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'F' and resid 269 through 270 removed outlier: 6.306A pdb=" N ILE F 269 " --> pdb=" O ILE F 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ4 Processing sheet with id=AJ5, first strand: chain 'F' and resid 377 through 379 removed outlier: 3.708A pdb=" N GLU F 407 " --> pdb=" O LEU F 379 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA F 435 " --> pdb=" O ASN F 463 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LYS F 465 " --> pdb=" O ALA F 435 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE F 437 " --> pdb=" O LYS F 465 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'F' and resid 387 through 388 Processing sheet with id=AJ7, first strand: chain 'F' and resid 456 through 457 removed outlier: 7.159A pdb=" N ILE F 456 " --> pdb=" O ASP F 477 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE F 476 " --> pdb=" O ILE F 501 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU F 500 " --> pdb=" O ILE F 518 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU F 517 " --> pdb=" O ARG F 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ7 Processing sheet with id=AJ8, first strand: chain 'F' and resid 470 through 472 Processing sheet with id=AJ9, first strand: chain 'F' and resid 530 through 532 Processing sheet with id=AK1, first strand: chain 'F' and resid 541 through 542 Processing sheet with id=AK2, first strand: chain 'F' and resid 572 through 574 removed outlier: 5.445A pdb=" N PHE F 572 " --> pdb=" O ALA F 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK2 Processing sheet with id=AK3, first strand: chain 'F' and resid 589 through 590 removed outlier: 3.826A pdb=" N ILE F 636 " --> pdb=" O LEU F 613 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'F' and resid 621 through 622 removed outlier: 6.495A pdb=" N MET F 621 " --> pdb=" O ASN F 643 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE F 679 " --> pdb=" O ALA F 727 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'F' and resid 693 through 697 removed outlier: 7.700A pdb=" N ILE F 787 " --> pdb=" O LEU F 695 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'F' and resid 729 through 730 Processing sheet with id=AK7, first strand: chain 'G' and resid 210 through 212 removed outlier: 7.003A pdb=" N LEU G 187 " --> pdb=" O ASN G 212 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL G 155 " --> pdb=" O THR G 188 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL G 125 " --> pdb=" O ASP G 156 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N ASP G 124 " --> pdb=" O ASN G 97 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N LEU G 99 " --> pdb=" O ASP G 124 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASN G 126 " --> pdb=" O LEU G 99 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL G 101 " --> pdb=" O ASN G 126 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS G 47 " --> pdb=" O LYS G 98 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU G 100 " --> pdb=" O LYS G 47 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N TRP G 49 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP G 102 " --> pdb=" O TRP G 49 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE G 51 " --> pdb=" O ASP G 102 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N VAL L 339 " --> pdb=" O ASP G 46 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N VAL G 48 " --> pdb=" O VAL L 339 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ARG G 50 " --> pdb=" O PRO L 341 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'G' and resid 65 through 66 removed outlier: 6.095A pdb=" N GLY G 108 " --> pdb=" O THR G 131 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ARG G 133 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TYR G 110 " --> pdb=" O ARG G 133 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'G' and resid 140 through 142 removed outlier: 3.572A pdb=" N GLU G 169 " --> pdb=" O ASN G 140 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'G' and resid 218 through 224 removed outlier: 4.059A pdb=" N VAL G 252 " --> pdb=" O VAL G 218 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU G 220 " --> pdb=" O VAL G 252 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N PHE G 254 " --> pdb=" O LEU G 220 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY G 222 " --> pdb=" O PHE G 254 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS G 256 " --> pdb=" O GLY G 222 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ASN G 253 " --> pdb=" O THR G 275 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE G 277 " --> pdb=" O ASN G 253 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASN G 255 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N HIS G 276 " --> pdb=" O ILE G 359 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N ARG G 361 " --> pdb=" O HIS G 276 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLY G 278 " --> pdb=" O ARG G 361 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ASN G 363 " --> pdb=" O GLY G 278 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU G 280 " --> pdb=" O ASN G 363 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'G' and resid 269 through 270 removed outlier: 6.306A pdb=" N ILE G 269 " --> pdb=" O ILE G 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL2 Processing sheet with id=AL3, first strand: chain 'G' and resid 339 through 345 removed outlier: 5.535A pdb=" N VAL G 339 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ARG H 50 " --> pdb=" O VAL G 339 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLN H 52 " --> pdb=" O PRO G 341 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLN G 343 " --> pdb=" O GLN H 52 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS H 47 " --> pdb=" O LYS H 98 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU H 100 " --> pdb=" O LYS H 47 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N TRP H 49 " --> pdb=" O GLU H 100 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP H 102 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE H 51 " --> pdb=" O ASP H 102 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N ASP H 124 " --> pdb=" O ASN H 97 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU H 99 " --> pdb=" O ASP H 124 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASN H 126 " --> pdb=" O LEU H 99 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL H 101 " --> pdb=" O ASN H 126 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL H 125 " --> pdb=" O ASP H 156 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL H 155 " --> pdb=" O THR H 188 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU H 187 " --> pdb=" O ASN H 212 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'G' and resid 377 through 379 removed outlier: 3.708A pdb=" N GLU G 407 " --> pdb=" O LEU G 379 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA G 435 " --> pdb=" O ASN G 463 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LYS G 465 " --> pdb=" O ALA G 435 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE G 437 " --> pdb=" O LYS G 465 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'G' and resid 387 through 388 Processing sheet with id=AL6, first strand: chain 'G' and resid 456 through 457 removed outlier: 7.159A pdb=" N ILE G 456 " --> pdb=" O ASP G 477 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE G 476 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU G 500 " --> pdb=" O ILE G 518 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU G 517 " --> pdb=" O ARG G 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL6 Processing sheet with id=AL7, first strand: chain 'G' and resid 470 through 472 Processing sheet with id=AL8, first strand: chain 'G' and resid 530 through 532 Processing sheet with id=AL9, first strand: chain 'G' and resid 541 through 542 Processing sheet with id=AM1, first strand: chain 'G' and resid 572 through 574 removed outlier: 5.444A pdb=" N PHE G 572 " --> pdb=" O ALA G 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM1 Processing sheet with id=AM2, first strand: chain 'G' and resid 589 through 590 removed outlier: 3.826A pdb=" N ILE G 636 " --> pdb=" O LEU G 613 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'G' and resid 621 through 622 removed outlier: 6.495A pdb=" N MET G 621 " --> pdb=" O ASN G 643 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ILE G 679 " --> pdb=" O ALA G 727 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'G' and resid 693 through 697 removed outlier: 7.702A pdb=" N ILE G 787 " --> pdb=" O LEU G 695 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'G' and resid 729 through 730 Processing sheet with id=AM6, first strand: chain 'H' and resid 65 through 66 removed outlier: 6.096A pdb=" N GLY H 108 " --> pdb=" O THR H 131 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ARG H 133 " --> pdb=" O GLY H 108 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N TYR H 110 " --> pdb=" O ARG H 133 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'H' and resid 140 through 142 removed outlier: 3.572A pdb=" N GLU H 169 " --> pdb=" O ASN H 140 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'H' and resid 218 through 224 removed outlier: 4.059A pdb=" N VAL H 252 " --> pdb=" O VAL H 218 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU H 220 " --> pdb=" O VAL H 252 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N PHE H 254 " --> pdb=" O LEU H 220 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY H 222 " --> pdb=" O PHE H 254 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS H 256 " --> pdb=" O GLY H 222 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ASN H 253 " --> pdb=" O THR H 275 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE H 277 " --> pdb=" O ASN H 253 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASN H 255 " --> pdb=" O ILE H 277 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N HIS H 276 " --> pdb=" O ILE H 359 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N ARG H 361 " --> pdb=" O HIS H 276 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLY H 278 " --> pdb=" O ARG H 361 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ASN H 363 " --> pdb=" O GLY H 278 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU H 280 " --> pdb=" O ASN H 363 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'H' and resid 269 through 270 removed outlier: 6.306A pdb=" N ILE H 269 " --> pdb=" O ILE H 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM9 Processing sheet with id=AN1, first strand: chain 'H' and resid 339 through 345 removed outlier: 5.445A pdb=" N VAL H 339 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ARG I 50 " --> pdb=" O VAL H 339 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLN I 52 " --> pdb=" O PRO H 341 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN H 343 " --> pdb=" O GLN I 52 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS I 47 " --> pdb=" O LYS I 98 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLU I 100 " --> pdb=" O LYS I 47 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N TRP I 49 " --> pdb=" O GLU I 100 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP I 102 " --> pdb=" O TRP I 49 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE I 51 " --> pdb=" O ASP I 102 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N ASP I 124 " --> pdb=" O ASN I 97 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU I 99 " --> pdb=" O ASP I 124 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASN I 126 " --> pdb=" O LEU I 99 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL I 101 " --> pdb=" O ASN I 126 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL I 125 " --> pdb=" O ASP I 156 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL I 155 " --> pdb=" O THR I 188 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU I 187 " --> pdb=" O ASN I 212 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'H' and resid 377 through 379 removed outlier: 3.707A pdb=" N GLU H 407 " --> pdb=" O LEU H 379 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA H 435 " --> pdb=" O ASN H 463 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LYS H 465 " --> pdb=" O ALA H 435 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N PHE H 437 " --> pdb=" O LYS H 465 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'H' and resid 387 through 388 Processing sheet with id=AN4, first strand: chain 'H' and resid 456 through 457 removed outlier: 7.160A pdb=" N ILE H 456 " --> pdb=" O ASP H 477 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE H 476 " --> pdb=" O ILE H 501 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU H 500 " --> pdb=" O ILE H 518 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU H 517 " --> pdb=" O ARG H 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN4 Processing sheet with id=AN5, first strand: chain 'H' and resid 470 through 472 Processing sheet with id=AN6, first strand: chain 'H' and resid 530 through 532 Processing sheet with id=AN7, first strand: chain 'H' and resid 541 through 542 Processing sheet with id=AN8, first strand: chain 'H' and resid 572 through 574 removed outlier: 5.445A pdb=" N PHE H 572 " --> pdb=" O ALA H 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN8 Processing sheet with id=AN9, first strand: chain 'H' and resid 589 through 590 removed outlier: 3.827A pdb=" N ILE H 636 " --> pdb=" O LEU H 613 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain 'H' and resid 621 through 622 removed outlier: 6.495A pdb=" N MET H 621 " --> pdb=" O ASN H 643 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE H 679 " --> pdb=" O ALA H 727 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'H' and resid 693 through 697 removed outlier: 7.701A pdb=" N ILE H 787 " --> pdb=" O LEU H 695 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'H' and resid 729 through 730 Processing sheet with id=AO4, first strand: chain 'I' and resid 65 through 66 removed outlier: 6.096A pdb=" N GLY I 108 " --> pdb=" O THR I 131 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ARG I 133 " --> pdb=" O GLY I 108 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TYR I 110 " --> pdb=" O ARG I 133 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'I' and resid 140 through 142 removed outlier: 3.572A pdb=" N GLU I 169 " --> pdb=" O ASN I 140 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'I' and resid 218 through 224 removed outlier: 4.059A pdb=" N VAL I 252 " --> pdb=" O VAL I 218 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU I 220 " --> pdb=" O VAL I 252 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N PHE I 254 " --> pdb=" O LEU I 220 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY I 222 " --> pdb=" O PHE I 254 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS I 256 " --> pdb=" O GLY I 222 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ASN I 253 " --> pdb=" O THR I 275 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE I 277 " --> pdb=" O ASN I 253 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASN I 255 " --> pdb=" O ILE I 277 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N HIS I 276 " --> pdb=" O ILE I 359 " (cutoff:3.500A) removed outlier: 9.660A pdb=" N ARG I 361 " --> pdb=" O HIS I 276 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLY I 278 " --> pdb=" O ARG I 361 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ASN I 363 " --> pdb=" O GLY I 278 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU I 280 " --> pdb=" O ASN I 363 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'I' and resid 269 through 270 removed outlier: 6.306A pdb=" N ILE I 269 " --> pdb=" O ILE I 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AO7 Processing sheet with id=AO8, first strand: chain 'I' and resid 339 through 345 removed outlier: 5.542A pdb=" N VAL I 339 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ARG J 50 " --> pdb=" O VAL I 339 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N GLN J 52 " --> pdb=" O PRO I 341 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLN I 343 " --> pdb=" O GLN J 52 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LYS J 47 " --> pdb=" O LYS J 98 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU J 100 " --> pdb=" O LYS J 47 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N TRP J 49 " --> pdb=" O GLU J 100 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP J 102 " --> pdb=" O TRP J 49 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE J 51 " --> pdb=" O ASP J 102 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N ASP J 124 " --> pdb=" O ASN J 97 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N LEU J 99 " --> pdb=" O ASP J 124 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASN J 126 " --> pdb=" O LEU J 99 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL J 101 " --> pdb=" O ASN J 126 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL J 125 " --> pdb=" O ASP J 156 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL J 155 " --> pdb=" O THR J 188 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU J 187 " --> pdb=" O ASN J 212 " (cutoff:3.500A) Processing sheet with id=AO9, first strand: chain 'I' and resid 377 through 379 removed outlier: 3.708A pdb=" N GLU I 407 " --> pdb=" O LEU I 379 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA I 435 " --> pdb=" O ASN I 463 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LYS I 465 " --> pdb=" O ALA I 435 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE I 437 " --> pdb=" O LYS I 465 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'I' and resid 387 through 388 Processing sheet with id=AP2, first strand: chain 'I' and resid 456 through 457 removed outlier: 7.159A pdb=" N ILE I 456 " --> pdb=" O ASP I 477 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE I 476 " --> pdb=" O ILE I 501 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU I 500 " --> pdb=" O ILE I 518 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU I 517 " --> pdb=" O ARG I 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AP2 Processing sheet with id=AP3, first strand: chain 'I' and resid 470 through 472 Processing sheet with id=AP4, first strand: chain 'I' and resid 530 through 532 Processing sheet with id=AP5, first strand: chain 'I' and resid 541 through 542 Processing sheet with id=AP6, first strand: chain 'I' and resid 572 through 574 removed outlier: 5.445A pdb=" N PHE I 572 " --> pdb=" O ALA I 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AP6 Processing sheet with id=AP7, first strand: chain 'I' and resid 589 through 590 removed outlier: 3.826A pdb=" N ILE I 636 " --> pdb=" O LEU I 613 " (cutoff:3.500A) Processing sheet with id=AP8, first strand: chain 'I' and resid 621 through 622 removed outlier: 6.495A pdb=" N MET I 621 " --> pdb=" O ASN I 643 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE I 679 " --> pdb=" O ALA I 727 " (cutoff:3.500A) Processing sheet with id=AP9, first strand: chain 'I' and resid 693 through 697 removed outlier: 7.701A pdb=" N ILE I 787 " --> pdb=" O LEU I 695 " (cutoff:3.500A) Processing sheet with id=AQ1, first strand: chain 'I' and resid 729 through 730 Processing sheet with id=AQ2, first strand: chain 'J' and resid 65 through 66 removed outlier: 6.096A pdb=" N GLY J 108 " --> pdb=" O THR J 131 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ARG J 133 " --> pdb=" O GLY J 108 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TYR J 110 " --> pdb=" O ARG J 133 " (cutoff:3.500A) Processing sheet with id=AQ3, first strand: chain 'J' and resid 140 through 142 removed outlier: 3.572A pdb=" N GLU J 169 " --> pdb=" O ASN J 140 " (cutoff:3.500A) Processing sheet with id=AQ4, first strand: chain 'J' and resid 218 through 224 removed outlier: 4.059A pdb=" N VAL J 252 " --> pdb=" O VAL J 218 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU J 220 " --> pdb=" O VAL J 252 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N PHE J 254 " --> pdb=" O LEU J 220 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY J 222 " --> pdb=" O PHE J 254 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS J 256 " --> pdb=" O GLY J 222 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ASN J 253 " --> pdb=" O THR J 275 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE J 277 " --> pdb=" O ASN J 253 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASN J 255 " --> pdb=" O ILE J 277 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N HIS J 276 " --> pdb=" O ILE J 359 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N ARG J 361 " --> pdb=" O HIS J 276 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY J 278 " --> pdb=" O ARG J 361 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ASN J 363 " --> pdb=" O GLY J 278 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU J 280 " --> pdb=" O ASN J 363 " (cutoff:3.500A) Processing sheet with id=AQ5, first strand: chain 'J' and resid 269 through 270 removed outlier: 6.307A pdb=" N ILE J 269 " --> pdb=" O ILE J 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AQ5 Processing sheet with id=AQ6, first strand: chain 'J' and resid 339 through 345 removed outlier: 5.560A pdb=" N VAL J 339 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ARG K 50 " --> pdb=" O VAL J 339 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N GLN K 52 " --> pdb=" O PRO J 341 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLN J 343 " --> pdb=" O GLN K 52 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS K 47 " --> pdb=" O LYS K 98 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU K 100 " --> pdb=" O LYS K 47 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N TRP K 49 " --> pdb=" O GLU K 100 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP K 102 " --> pdb=" O TRP K 49 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE K 51 " --> pdb=" O ASP K 102 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N ASP K 124 " --> pdb=" O ASN K 97 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N LEU K 99 " --> pdb=" O ASP K 124 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASN K 126 " --> pdb=" O LEU K 99 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL K 101 " --> pdb=" O ASN K 126 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL K 125 " --> pdb=" O ASP K 156 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL K 155 " --> pdb=" O THR K 188 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU K 187 " --> pdb=" O ASN K 212 " (cutoff:3.500A) Processing sheet with id=AQ7, first strand: chain 'J' and resid 377 through 379 removed outlier: 3.708A pdb=" N GLU J 407 " --> pdb=" O LEU J 379 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA J 435 " --> pdb=" O ASN J 463 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LYS J 465 " --> pdb=" O ALA J 435 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE J 437 " --> pdb=" O LYS J 465 " (cutoff:3.500A) Processing sheet with id=AQ8, first strand: chain 'J' and resid 387 through 388 Processing sheet with id=AQ9, first strand: chain 'J' and resid 456 through 457 removed outlier: 7.159A pdb=" N ILE J 456 " --> pdb=" O ASP J 477 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE J 476 " --> pdb=" O ILE J 501 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU J 500 " --> pdb=" O ILE J 518 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU J 517 " --> pdb=" O ARG J 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AQ9 Processing sheet with id=AR1, first strand: chain 'J' and resid 470 through 472 Processing sheet with id=AR2, first strand: chain 'J' and resid 530 through 532 Processing sheet with id=AR3, first strand: chain 'J' and resid 541 through 542 Processing sheet with id=AR4, first strand: chain 'J' and resid 572 through 574 removed outlier: 5.445A pdb=" N PHE J 572 " --> pdb=" O ALA J 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AR4 Processing sheet with id=AR5, first strand: chain 'J' and resid 589 through 590 removed outlier: 3.827A pdb=" N ILE J 636 " --> pdb=" O LEU J 613 " (cutoff:3.500A) Processing sheet with id=AR6, first strand: chain 'J' and resid 621 through 622 removed outlier: 6.496A pdb=" N MET J 621 " --> pdb=" O ASN J 643 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ILE J 679 " --> pdb=" O ALA J 727 " (cutoff:3.500A) Processing sheet with id=AR7, first strand: chain 'J' and resid 693 through 697 removed outlier: 7.701A pdb=" N ILE J 787 " --> pdb=" O LEU J 695 " (cutoff:3.500A) Processing sheet with id=AR8, first strand: chain 'J' and resid 729 through 730 Processing sheet with id=AR9, first strand: chain 'K' and resid 65 through 66 removed outlier: 6.096A pdb=" N GLY K 108 " --> pdb=" O THR K 131 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N ARG K 133 " --> pdb=" O GLY K 108 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TYR K 110 " --> pdb=" O ARG K 133 " (cutoff:3.500A) Processing sheet with id=AS1, first strand: chain 'K' and resid 140 through 142 removed outlier: 3.572A pdb=" N GLU K 169 " --> pdb=" O ASN K 140 " (cutoff:3.500A) Processing sheet with id=AS2, first strand: chain 'K' and resid 218 through 224 removed outlier: 4.059A pdb=" N VAL K 252 " --> pdb=" O VAL K 218 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU K 220 " --> pdb=" O VAL K 252 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N PHE K 254 " --> pdb=" O LEU K 220 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY K 222 " --> pdb=" O PHE K 254 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS K 256 " --> pdb=" O GLY K 222 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ASN K 253 " --> pdb=" O THR K 275 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE K 277 " --> pdb=" O ASN K 253 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASN K 255 " --> pdb=" O ILE K 277 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N HIS K 276 " --> pdb=" O ILE K 359 " (cutoff:3.500A) removed outlier: 9.660A pdb=" N ARG K 361 " --> pdb=" O HIS K 276 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY K 278 " --> pdb=" O ARG K 361 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ASN K 363 " --> pdb=" O GLY K 278 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU K 280 " --> pdb=" O ASN K 363 " (cutoff:3.500A) Processing sheet with id=AS3, first strand: chain 'K' and resid 269 through 270 removed outlier: 6.306A pdb=" N ILE K 269 " --> pdb=" O ILE K 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AS3 Processing sheet with id=AS4, first strand: chain 'K' and resid 339 through 345 removed outlier: 5.385A pdb=" N VAL K 339 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ARG L 50 " --> pdb=" O VAL K 339 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N GLN L 52 " --> pdb=" O PRO K 341 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLN K 343 " --> pdb=" O GLN L 52 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS L 47 " --> pdb=" O LYS L 98 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU L 100 " --> pdb=" O LYS L 47 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N TRP L 49 " --> pdb=" O GLU L 100 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP L 102 " --> pdb=" O TRP L 49 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE L 51 " --> pdb=" O ASP L 102 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N ASP L 124 " --> pdb=" O ASN L 97 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU L 99 " --> pdb=" O ASP L 124 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASN L 126 " --> pdb=" O LEU L 99 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL L 101 " --> pdb=" O ASN L 126 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL L 125 " --> pdb=" O ASP L 156 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL L 155 " --> pdb=" O THR L 188 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU L 187 " --> pdb=" O ASN L 212 " (cutoff:3.500A) Processing sheet with id=AS5, first strand: chain 'K' and resid 377 through 379 removed outlier: 3.708A pdb=" N GLU K 407 " --> pdb=" O LEU K 379 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA K 435 " --> pdb=" O ASN K 463 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LYS K 465 " --> pdb=" O ALA K 435 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE K 437 " --> pdb=" O LYS K 465 " (cutoff:3.500A) Processing sheet with id=AS6, first strand: chain 'K' and resid 387 through 388 Processing sheet with id=AS7, first strand: chain 'K' and resid 456 through 457 removed outlier: 7.159A pdb=" N ILE K 456 " --> pdb=" O ASP K 477 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE K 476 " --> pdb=" O ILE K 501 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU K 500 " --> pdb=" O ILE K 518 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU K 517 " --> pdb=" O ARG K 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AS7 Processing sheet with id=AS8, first strand: chain 'K' and resid 470 through 472 Processing sheet with id=AS9, first strand: chain 'K' and resid 530 through 532 Processing sheet with id=AT1, first strand: chain 'K' and resid 541 through 542 Processing sheet with id=AT2, first strand: chain 'K' and resid 572 through 574 removed outlier: 5.444A pdb=" N PHE K 572 " --> pdb=" O ALA K 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AT2 Processing sheet with id=AT3, first strand: chain 'K' and resid 589 through 590 removed outlier: 3.826A pdb=" N ILE K 636 " --> pdb=" O LEU K 613 " (cutoff:3.500A) Processing sheet with id=AT4, first strand: chain 'K' and resid 621 through 622 removed outlier: 6.496A pdb=" N MET K 621 " --> pdb=" O ASN K 643 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE K 679 " --> pdb=" O ALA K 727 " (cutoff:3.500A) Processing sheet with id=AT5, first strand: chain 'K' and resid 693 through 697 removed outlier: 7.701A pdb=" N ILE K 787 " --> pdb=" O LEU K 695 " (cutoff:3.500A) Processing sheet with id=AT6, first strand: chain 'K' and resid 729 through 730 Processing sheet with id=AT7, first strand: chain 'L' and resid 65 through 66 removed outlier: 6.095A pdb=" N GLY L 108 " --> pdb=" O THR L 131 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ARG L 133 " --> pdb=" O GLY L 108 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TYR L 110 " --> pdb=" O ARG L 133 " (cutoff:3.500A) Processing sheet with id=AT8, first strand: chain 'L' and resid 140 through 142 removed outlier: 3.572A pdb=" N GLU L 169 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AT9, first strand: chain 'L' and resid 218 through 224 removed outlier: 4.058A pdb=" N VAL L 252 " --> pdb=" O VAL L 218 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU L 220 " --> pdb=" O VAL L 252 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N PHE L 254 " --> pdb=" O LEU L 220 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY L 222 " --> pdb=" O PHE L 254 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS L 256 " --> pdb=" O GLY L 222 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ASN L 253 " --> pdb=" O THR L 275 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE L 277 " --> pdb=" O ASN L 253 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASN L 255 " --> pdb=" O ILE L 277 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N HIS L 276 " --> pdb=" O ILE L 359 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N ARG L 361 " --> pdb=" O HIS L 276 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY L 278 " --> pdb=" O ARG L 361 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ASN L 363 " --> pdb=" O GLY L 278 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU L 280 " --> pdb=" O ASN L 363 " (cutoff:3.500A) Processing sheet with id=AU1, first strand: chain 'L' and resid 269 through 270 removed outlier: 6.306A pdb=" N ILE L 269 " --> pdb=" O ILE L 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AU1 Processing sheet with id=AU2, first strand: chain 'L' and resid 377 through 379 removed outlier: 3.708A pdb=" N GLU L 407 " --> pdb=" O LEU L 379 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA L 435 " --> pdb=" O ASN L 463 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LYS L 465 " --> pdb=" O ALA L 435 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE L 437 " --> pdb=" O LYS L 465 " (cutoff:3.500A) Processing sheet with id=AU3, first strand: chain 'L' and resid 387 through 388 Processing sheet with id=AU4, first strand: chain 'L' and resid 456 through 457 removed outlier: 7.159A pdb=" N ILE L 456 " --> pdb=" O ASP L 477 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE L 476 " --> pdb=" O ILE L 501 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU L 500 " --> pdb=" O ILE L 518 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU L 517 " --> pdb=" O ARG L 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AU4 Processing sheet with id=AU5, first strand: chain 'L' and resid 470 through 472 Processing sheet with id=AU6, first strand: chain 'L' and resid 530 through 532 Processing sheet with id=AU7, first strand: chain 'L' and resid 541 through 542 Processing sheet with id=AU8, first strand: chain 'L' and resid 572 through 574 removed outlier: 5.445A pdb=" N PHE L 572 " --> pdb=" O ALA L 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AU8 Processing sheet with id=AU9, first strand: chain 'L' and resid 589 through 590 removed outlier: 3.827A pdb=" N ILE L 636 " --> pdb=" O LEU L 613 " (cutoff:3.500A) Processing sheet with id=AV1, first strand: chain 'L' and resid 621 through 622 removed outlier: 6.496A pdb=" N MET L 621 " --> pdb=" O ASN L 643 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE L 679 " --> pdb=" O ALA L 727 " (cutoff:3.500A) Processing sheet with id=AV2, first strand: chain 'L' and resid 693 through 697 removed outlier: 7.701A pdb=" N ILE L 787 " --> pdb=" O LEU L 695 " (cutoff:3.500A) Processing sheet with id=AV3, first strand: chain 'L' and resid 729 through 730 522 hydrogen bonds defined for protein. 1350 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 35.93 Time building geometry restraints manager: 22.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 22846 1.34 - 1.46: 13485 1.46 - 1.58: 33245 1.58 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 69840 Sorted by residual: bond pdb=" CB ASN C 273 " pdb=" CG ASN C 273 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.50e-02 1.60e+03 3.80e+00 bond pdb=" CB ASN H 273 " pdb=" CG ASN H 273 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.50e-02 1.60e+03 3.80e+00 bond pdb=" CB ASN E 273 " pdb=" CG ASN E 273 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.50e-02 1.60e+03 3.78e+00 bond pdb=" CB ASN K 273 " pdb=" CG ASN K 273 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.50e-02 1.60e+03 3.78e+00 bond pdb=" CB ASN B 273 " pdb=" CG ASN B 273 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.50e-02 1.60e+03 3.78e+00 ... (remaining 69835 not shown) Histogram of bond angle deviations from ideal: 99.91 - 106.74: 1574 106.74 - 113.57: 38399 113.57 - 120.40: 24107 120.40 - 127.23: 29899 127.23 - 134.06: 605 Bond angle restraints: 94584 Sorted by residual: angle pdb=" C GLY F 83 " pdb=" N ASN F 84 " pdb=" CA ASN F 84 " ideal model delta sigma weight residual 121.54 130.65 -9.11 1.91e+00 2.74e-01 2.28e+01 angle pdb=" C GLY I 83 " pdb=" N ASN I 84 " pdb=" CA ASN I 84 " ideal model delta sigma weight residual 121.54 130.65 -9.11 1.91e+00 2.74e-01 2.27e+01 angle pdb=" C GLY A 83 " pdb=" N ASN A 84 " pdb=" CA ASN A 84 " ideal model delta sigma weight residual 121.54 130.61 -9.07 1.91e+00 2.74e-01 2.25e+01 angle pdb=" C GLY B 83 " pdb=" N ASN B 84 " pdb=" CA ASN B 84 " ideal model delta sigma weight residual 121.54 130.60 -9.06 1.91e+00 2.74e-01 2.25e+01 angle pdb=" C GLY E 83 " pdb=" N ASN E 84 " pdb=" CA ASN E 84 " ideal model delta sigma weight residual 121.54 130.59 -9.05 1.91e+00 2.74e-01 2.24e+01 ... (remaining 94579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.32: 38733 16.32 - 32.64: 2077 32.64 - 48.96: 302 48.96 - 65.28: 24 65.28 - 81.60: 36 Dihedral angle restraints: 41172 sinusoidal: 15828 harmonic: 25344 Sorted by residual: dihedral pdb=" CB CYS H 738 " pdb=" SG CYS H 738 " pdb=" SG CYS H 749 " pdb=" CB CYS H 749 " ideal model delta sinusoidal sigma weight residual -86.00 -167.60 81.60 1 1.00e+01 1.00e-02 8.20e+01 dihedral pdb=" CB CYS F 738 " pdb=" SG CYS F 738 " pdb=" SG CYS F 749 " pdb=" CB CYS F 749 " ideal model delta sinusoidal sigma weight residual -86.00 -167.60 81.60 1 1.00e+01 1.00e-02 8.20e+01 dihedral pdb=" CB CYS E 738 " pdb=" SG CYS E 738 " pdb=" SG CYS E 749 " pdb=" CB CYS E 749 " ideal model delta sinusoidal sigma weight residual -86.00 -167.57 81.57 1 1.00e+01 1.00e-02 8.19e+01 ... (remaining 41169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 6591 0.047 - 0.094: 2758 0.094 - 0.141: 1116 0.141 - 0.188: 119 0.188 - 0.235: 36 Chirality restraints: 10620 Sorted by residual: chirality pdb=" CA ASN L 84 " pdb=" N ASN L 84 " pdb=" C ASN L 84 " pdb=" CB ASN L 84 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA ASN G 84 " pdb=" N ASN G 84 " pdb=" C ASN G 84 " pdb=" CB ASN G 84 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA ASN H 84 " pdb=" N ASN H 84 " pdb=" C ASN H 84 " pdb=" CB ASN H 84 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 10617 not shown) Planarity restraints: 12396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU K 163 " 0.010 2.00e-02 2.50e+03 2.15e-02 4.62e+00 pdb=" C LEU K 163 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU K 163 " 0.014 2.00e-02 2.50e+03 pdb=" N ILE K 164 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 163 " 0.010 2.00e-02 2.50e+03 2.15e-02 4.62e+00 pdb=" C LEU E 163 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU E 163 " 0.014 2.00e-02 2.50e+03 pdb=" N ILE E 164 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 163 " -0.010 2.00e-02 2.50e+03 2.14e-02 4.60e+00 pdb=" C LEU B 163 " 0.037 2.00e-02 2.50e+03 pdb=" O LEU B 163 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE B 164 " -0.012 2.00e-02 2.50e+03 ... (remaining 12393 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 13030 2.77 - 3.31: 65906 3.31 - 3.84: 119118 3.84 - 4.37: 138948 4.37 - 4.90: 237978 Nonbonded interactions: 574980 Sorted by model distance: nonbonded pdb=" OG1 THR D 153 " pdb=" OG1 THR D 185 " model vdw 2.242 2.440 nonbonded pdb=" OG1 THR A 153 " pdb=" OG1 THR A 185 " model vdw 2.242 2.440 nonbonded pdb=" OG1 THR B 153 " pdb=" OG1 THR B 185 " model vdw 2.242 2.440 nonbonded pdb=" OG1 THR C 153 " pdb=" OG1 THR C 185 " model vdw 2.242 2.440 nonbonded pdb=" OG1 THR F 153 " pdb=" OG1 THR F 185 " model vdw 2.242 2.440 ... (remaining 574975 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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: 2.890 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: 13.760 Check model and map are aligned: 0.750 Set scattering table: 0.500 Process input model: 147.910 Find NCS groups from input model: 3.680 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:2.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 172.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6317 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 69840 Z= 0.344 Angle : 0.972 9.413 94584 Z= 0.547 Chirality : 0.058 0.235 10620 Planarity : 0.005 0.041 12396 Dihedral : 10.451 69.840 25056 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.10 % Favored : 85.90 % Rotamer: Outliers : 0.16 % Allowed : 2.94 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.66 (0.07), residues: 8952 helix: -3.66 (0.25), residues: 144 sheet: -3.25 (0.12), residues: 1476 loop : -3.38 (0.06), residues: 7332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP I 225 HIS 0.003 0.001 HIS F 385 PHE 0.021 0.003 PHE J 167 TYR 0.027 0.003 TYR F 574 ARG 0.004 0.001 ARG H 546 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 552 time to evaluate : 5.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 665 ASN cc_start: 0.6510 (OUTLIER) cc_final: 0.6300 (t0) REVERT: A 764 ASN cc_start: 0.8916 (t0) cc_final: 0.8690 (t0) REVERT: B 266 GLN cc_start: 0.9344 (mt0) cc_final: 0.9134 (mm110) REVERT: B 662 MET cc_start: 0.4136 (mtm) cc_final: 0.3854 (mpp) REVERT: B 665 ASN cc_start: 0.6232 (OUTLIER) cc_final: 0.6021 (t0) REVERT: B 764 ASN cc_start: 0.9028 (t0) cc_final: 0.8761 (t0) REVERT: C 266 GLN cc_start: 0.9174 (mt0) cc_final: 0.8892 (mm110) REVERT: D 764 ASN cc_start: 0.8801 (t0) cc_final: 0.8570 (t0) REVERT: E 662 MET cc_start: 0.4396 (mtm) cc_final: 0.4018 (mpp) REVERT: E 764 ASN cc_start: 0.8976 (t0) cc_final: 0.8728 (t0) REVERT: F 266 GLN cc_start: 0.9262 (mt0) cc_final: 0.9050 (mm110) REVERT: F 764 ASN cc_start: 0.8799 (t0) cc_final: 0.8526 (t0) REVERT: H 266 GLN cc_start: 0.9338 (mt0) cc_final: 0.9129 (mm110) REVERT: H 662 MET cc_start: 0.4310 (mtm) cc_final: 0.3936 (mpp) REVERT: H 764 ASN cc_start: 0.8932 (t0) cc_final: 0.8698 (t0) REVERT: I 266 GLN cc_start: 0.9146 (mt0) cc_final: 0.8869 (mm110) REVERT: K 266 GLN cc_start: 0.9261 (mt0) cc_final: 0.9044 (mm110) REVERT: K 662 MET cc_start: 0.4303 (mtm) cc_final: 0.3920 (mpp) REVERT: K 764 ASN cc_start: 0.9067 (t0) cc_final: 0.8805 (t0) REVERT: L 266 GLN cc_start: 0.9283 (mt0) cc_final: 0.9075 (mm110) REVERT: L 764 ASN cc_start: 0.8692 (t0) cc_final: 0.8428 (t0) outliers start: 12 outliers final: 0 residues processed: 564 average time/residue: 0.6942 time to fit residues: 675.3132 Evaluate side-chains 242 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 240 time to evaluate : 5.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 665 ASN Chi-restraints excluded: chain B residue 665 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 759 optimal weight: 5.9990 chunk 682 optimal weight: 7.9990 chunk 378 optimal weight: 10.0000 chunk 233 optimal weight: 8.9990 chunk 460 optimal weight: 10.0000 chunk 364 optimal weight: 2.9990 chunk 705 optimal weight: 30.0000 chunk 272 optimal weight: 20.0000 chunk 428 optimal weight: 8.9990 chunk 525 optimal weight: 10.0000 chunk 817 optimal weight: 50.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 665 ASN ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN ** B 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 618 ASN B 665 ASN ** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 ASN ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 617 GLN ** C 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 ASN ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 ASN ** D 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 755 ASN ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 ASN ** E 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 755 ASN ** F 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN ** F 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 755 ASN ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 ASN ** G 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 755 ASN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 422 ASN H 618 ASN ** H 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 755 ASN ** I 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 422 ASN I 617 GLN ** I 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 755 ASN ** J 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 422 ASN ** J 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 755 ASN ** K 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 422 ASN ** K 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 755 ASN ** L 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 422 ASN ** L 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 755 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 69840 Z= 0.368 Angle : 0.748 8.170 94584 Z= 0.396 Chirality : 0.050 0.161 10620 Planarity : 0.004 0.031 12396 Dihedral : 7.304 29.532 9520 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 22.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.73 % Favored : 84.27 % Rotamer: Outliers : 2.26 % Allowed : 6.69 % Favored : 91.06 % 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: -4.58 (0.07), residues: 8952 helix: -3.73 (0.19), residues: 168 sheet: -3.26 (0.12), residues: 1536 loop : -3.28 (0.06), residues: 7248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 225 HIS 0.005 0.002 HIS F 256 PHE 0.019 0.002 PHE E 57 TYR 0.016 0.002 TYR G 65 ARG 0.005 0.001 ARG A 133 *********************** 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 399 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 232 time to evaluate : 6.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 PHE cc_start: 0.4486 (OUTLIER) cc_final: 0.4051 (m-10) REVERT: B 266 GLN cc_start: 0.9370 (mt0) cc_final: 0.9160 (mm110) REVERT: B 764 ASN cc_start: 0.9045 (t0) cc_final: 0.8728 (t0) REVERT: C 266 GLN cc_start: 0.9248 (mt0) cc_final: 0.8944 (mm110) REVERT: C 452 PHE cc_start: 0.4448 (OUTLIER) cc_final: 0.4075 (m-80) REVERT: C 470 THR cc_start: 0.6704 (m) cc_final: 0.6462 (p) REVERT: D 452 PHE cc_start: 0.4667 (OUTLIER) cc_final: 0.4232 (m-10) REVERT: D 758 MET cc_start: 0.4946 (mpt) cc_final: 0.3594 (ttm) REVERT: E 226 MET cc_start: 0.6956 (mmm) cc_final: 0.6698 (mmm) REVERT: E 764 ASN cc_start: 0.9025 (t0) cc_final: 0.8735 (t0) REVERT: F 226 MET cc_start: 0.6833 (mmm) cc_final: 0.6494 (mmm) REVERT: F 266 GLN cc_start: 0.9276 (mt0) cc_final: 0.9047 (mm110) REVERT: F 452 PHE cc_start: 0.4325 (OUTLIER) cc_final: 0.3939 (m-80) REVERT: F 621 MET cc_start: 0.5687 (ttt) cc_final: 0.5441 (tpt) REVERT: F 676 LYS cc_start: 0.7432 (OUTLIER) cc_final: 0.7193 (pttt) REVERT: G 452 PHE cc_start: 0.4592 (OUTLIER) cc_final: 0.4147 (m-10) REVERT: H 266 GLN cc_start: 0.9337 (mt0) cc_final: 0.9135 (mm110) REVERT: H 764 ASN cc_start: 0.8990 (t0) cc_final: 0.8674 (t0) REVERT: I 266 GLN cc_start: 0.9229 (mt0) cc_final: 0.8931 (mm110) REVERT: I 452 PHE cc_start: 0.4470 (OUTLIER) cc_final: 0.4088 (m-80) REVERT: I 470 THR cc_start: 0.6689 (m) cc_final: 0.6408 (p) REVERT: I 621 MET cc_start: 0.5544 (ttt) cc_final: 0.5333 (tpt) REVERT: J 452 PHE cc_start: 0.4388 (OUTLIER) cc_final: 0.3968 (m-10) REVERT: J 662 MET cc_start: 0.3222 (mpp) cc_final: 0.2774 (mpp) REVERT: K 266 GLN cc_start: 0.9310 (mt0) cc_final: 0.9044 (mm110) REVERT: K 764 ASN cc_start: 0.9104 (t0) cc_final: 0.8828 (t0) REVERT: L 226 MET cc_start: 0.6685 (mmm) cc_final: 0.6246 (mmm) REVERT: L 266 GLN cc_start: 0.9317 (mt0) cc_final: 0.9065 (mm110) REVERT: L 452 PHE cc_start: 0.4147 (OUTLIER) cc_final: 0.3782 (m-80) outliers start: 167 outliers final: 78 residues processed: 382 average time/residue: 0.6265 time to fit residues: 419.3090 Evaluate side-chains 275 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 188 time to evaluate : 5.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 510 LYS Chi-restraints excluded: chain C residue 513 ASN Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 452 PHE Chi-restraints excluded: chain D residue 513 ASN Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 452 PHE Chi-restraints excluded: chain E residue 510 LYS Chi-restraints excluded: chain E residue 742 ASN Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 452 PHE Chi-restraints excluded: chain F residue 510 LYS Chi-restraints excluded: chain F residue 513 ASN Chi-restraints excluded: chain F residue 676 LYS Chi-restraints excluded: chain F residue 742 ASN Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 452 PHE Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain H residue 199 LYS Chi-restraints excluded: chain H residue 277 ILE Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 452 PHE Chi-restraints excluded: chain H residue 510 LYS Chi-restraints excluded: chain H residue 742 ASN Chi-restraints excluded: chain I residue 46 ASP Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 277 ILE Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 452 PHE Chi-restraints excluded: chain I residue 510 LYS Chi-restraints excluded: chain I residue 513 ASN Chi-restraints excluded: chain J residue 46 ASP Chi-restraints excluded: chain J residue 127 MET Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 277 ILE Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 452 PHE Chi-restraints excluded: chain J residue 513 ASN Chi-restraints excluded: chain K residue 184 SER Chi-restraints excluded: chain K residue 277 ILE Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 452 PHE Chi-restraints excluded: chain K residue 510 LYS Chi-restraints excluded: chain K residue 742 ASN Chi-restraints excluded: chain L residue 46 ASP Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 277 ILE Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 452 PHE Chi-restraints excluded: chain L residue 510 LYS Chi-restraints excluded: chain L residue 513 ASN Chi-restraints excluded: chain L residue 742 ASN 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: 10.0000 chunk 680 optimal weight: 0.9990 chunk 556 optimal weight: 7.9990 chunk 225 optimal weight: 10.0000 chunk 818 optimal weight: 9.9990 chunk 884 optimal weight: 30.0000 chunk 729 optimal weight: 6.9990 chunk 811 optimal weight: 30.0000 chunk 279 optimal weight: 0.9990 chunk 656 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN A 705 ASN ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 ASN ** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 584 ASN ** C 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 584 ASN ** D 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 705 ASN ** D 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 584 ASN ** E 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 584 ASN ** F 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 705 ASN ** F 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 764 ASN ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 584 ASN ** G 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 584 ASN ** H 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 584 ASN ** I 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 705 ASN ** I 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 584 ASN ** J 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 705 ASN ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 584 ASN ** K 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 584 ASN ** L 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 705 ASN ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6343 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 69840 Z= 0.201 Angle : 0.632 11.791 94584 Z= 0.330 Chirality : 0.048 0.265 10620 Planarity : 0.003 0.028 12396 Dihedral : 6.537 27.799 9516 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.62 % Favored : 87.38 % Rotamer: Outliers : 1.59 % Allowed : 8.67 % Favored : 89.74 % 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: -4.49 (0.07), residues: 8952 helix: -3.19 (0.23), residues: 168 sheet: -3.30 (0.11), residues: 1788 loop : -3.16 (0.06), residues: 6996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 82 HIS 0.003 0.001 HIS F 256 PHE 0.012 0.001 PHE H 473 TYR 0.018 0.001 TYR L 765 ARG 0.003 0.000 ARG E 180 *********************** 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 327 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 209 time to evaluate : 6.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 MET cc_start: 0.5883 (tmm) cc_final: 0.5619 (tmm) REVERT: A 735 MET cc_start: 0.1277 (mtp) cc_final: 0.0919 (ptp) REVERT: A 758 MET cc_start: 0.6523 (mmm) cc_final: 0.4236 (ttt) REVERT: B 266 GLN cc_start: 0.9381 (mt0) cc_final: 0.9165 (mm110) REVERT: B 735 MET cc_start: 0.0747 (mtp) cc_final: 0.0145 (ptp) REVERT: B 758 MET cc_start: 0.5867 (mmm) cc_final: 0.3418 (ttm) REVERT: C 266 GLN cc_start: 0.9178 (mt0) cc_final: 0.8929 (mm110) REVERT: C 470 THR cc_start: 0.6708 (m) cc_final: 0.6394 (p) REVERT: C 735 MET cc_start: 0.2352 (mtp) cc_final: 0.1159 (ptp) REVERT: C 758 MET cc_start: 0.6537 (mpt) cc_final: 0.6120 (mmt) REVERT: D 72 LEU cc_start: 0.6657 (tp) cc_final: 0.6328 (tp) REVERT: D 662 MET cc_start: 0.3250 (mpp) cc_final: 0.2750 (mpp) REVERT: D 735 MET cc_start: 0.1533 (mtp) cc_final: 0.0969 (ptp) REVERT: D 758 MET cc_start: 0.5130 (mpt) cc_final: 0.3686 (ttt) REVERT: E 72 LEU cc_start: 0.6996 (OUTLIER) cc_final: 0.6740 (tp) REVERT: E 621 MET cc_start: 0.7240 (ttm) cc_final: 0.6959 (tmm) REVERT: E 735 MET cc_start: 0.1459 (mtp) cc_final: 0.1148 (ptp) REVERT: E 758 MET cc_start: 0.5888 (mmm) cc_final: 0.3090 (ttm) REVERT: E 764 ASN cc_start: 0.8645 (t0) cc_final: 0.8417 (t0) REVERT: F 266 GLN cc_start: 0.9307 (mt0) cc_final: 0.9061 (mm110) REVERT: F 735 MET cc_start: 0.1207 (mtp) cc_final: 0.0708 (ptp) REVERT: F 758 MET cc_start: 0.6549 (mpt) cc_final: 0.5033 (ttt) REVERT: G 72 LEU cc_start: 0.6892 (tp) cc_final: 0.6596 (tp) REVERT: G 621 MET cc_start: 0.4510 (OUTLIER) cc_final: 0.3978 (ppp) REVERT: G 735 MET cc_start: 0.1756 (mtp) cc_final: 0.1300 (ptp) REVERT: H 266 GLN cc_start: 0.9371 (mt0) cc_final: 0.9149 (mm110) REVERT: H 735 MET cc_start: 0.1020 (mtp) cc_final: 0.0115 (ptp) REVERT: H 758 MET cc_start: 0.6163 (mmm) cc_final: 0.3538 (ttm) REVERT: I 266 GLN cc_start: 0.9157 (mt0) cc_final: 0.8913 (mm110) REVERT: I 470 THR cc_start: 0.6857 (m) cc_final: 0.6490 (p) REVERT: I 662 MET cc_start: 0.2750 (OUTLIER) cc_final: 0.2476 (mpt) REVERT: J 621 MET cc_start: 0.4999 (OUTLIER) cc_final: 0.4791 (tmm) REVERT: J 735 MET cc_start: 0.1018 (mtp) cc_final: 0.0427 (ptp) REVERT: J 758 MET cc_start: 0.6594 (mpt) cc_final: 0.5099 (mtp) REVERT: K 266 GLN cc_start: 0.9344 (mt0) cc_final: 0.9085 (mm110) REVERT: K 621 MET cc_start: 0.7115 (ttm) cc_final: 0.6861 (tmm) REVERT: K 735 MET cc_start: 0.1314 (mtp) cc_final: 0.1030 (ptp) REVERT: K 758 MET cc_start: 0.5678 (mmm) cc_final: 0.2994 (ttm) REVERT: L 266 GLN cc_start: 0.9319 (mt0) cc_final: 0.9080 (mm110) REVERT: L 621 MET cc_start: 0.5987 (ttt) cc_final: 0.5781 (tmm) REVERT: L 735 MET cc_start: 0.1141 (mtp) cc_final: 0.0782 (ptp) REVERT: L 758 MET cc_start: 0.6355 (mpt) cc_final: 0.4876 (ttt) outliers start: 118 outliers final: 93 residues processed: 307 average time/residue: 0.5850 time to fit residues: 322.5370 Evaluate side-chains 281 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 184 time to evaluate : 5.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 480 ASN Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 480 ASN Chi-restraints excluded: chain B residue 646 VAL Chi-restraints excluded: chain B residue 742 ASN Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 480 ASN Chi-restraints excluded: chain C residue 513 ASN Chi-restraints excluded: chain C residue 646 VAL Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 480 ASN Chi-restraints excluded: chain D residue 513 ASN Chi-restraints excluded: chain D residue 646 VAL Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 480 ASN Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 742 ASN Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 513 ASN Chi-restraints excluded: chain F residue 646 VAL Chi-restraints excluded: chain F residue 700 ILE Chi-restraints excluded: chain F residue 742 ASN Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 137 PHE Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 480 ASN Chi-restraints excluded: chain G residue 621 MET Chi-restraints excluded: chain G residue 646 VAL Chi-restraints excluded: chain G residue 700 ILE Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 277 ILE Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 480 ASN Chi-restraints excluded: chain H residue 646 VAL Chi-restraints excluded: chain H residue 742 ASN Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 277 ILE Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 480 ASN Chi-restraints excluded: chain I residue 513 ASN Chi-restraints excluded: chain I residue 646 VAL Chi-restraints excluded: chain I residue 662 MET Chi-restraints excluded: chain I residue 700 ILE Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 127 MET Chi-restraints excluded: chain J residue 277 ILE Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 480 ASN Chi-restraints excluded: chain J residue 513 ASN Chi-restraints excluded: chain J residue 621 MET Chi-restraints excluded: chain J residue 646 VAL Chi-restraints excluded: chain K residue 46 ASP Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 184 SER Chi-restraints excluded: chain K residue 277 ILE Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 480 ASN Chi-restraints excluded: chain K residue 646 VAL Chi-restraints excluded: chain K residue 742 ASN Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 277 ILE Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 513 ASN Chi-restraints excluded: chain L residue 646 VAL Chi-restraints excluded: chain L residue 700 ILE Chi-restraints excluded: chain L residue 742 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 808 optimal weight: 40.0000 chunk 615 optimal weight: 2.9990 chunk 424 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 390 optimal weight: 1.9990 chunk 549 optimal weight: 9.9990 chunk 821 optimal weight: 0.5980 chunk 869 optimal weight: 20.0000 chunk 429 optimal weight: 4.9990 chunk 778 optimal weight: 9.9990 chunk 234 optimal weight: 9.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN B 705 ASN ** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 705 ASN ** E 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 ASN ** F 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 463 ASN ** G 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 705 ASN ** G 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 463 ASN ** H 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 705 ASN ** H 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 705 ASN ** K 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 463 ASN ** L 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6337 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 69840 Z= 0.181 Angle : 0.590 9.562 94584 Z= 0.309 Chirality : 0.046 0.203 10620 Planarity : 0.003 0.025 12396 Dihedral : 6.079 28.948 9516 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.95 % Favored : 87.05 % Rotamer: Outliers : 2.71 % Allowed : 8.77 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (0.08), residues: 8952 helix: -2.44 (0.28), residues: 168 sheet: -3.19 (0.11), residues: 1764 loop : -2.97 (0.07), residues: 7020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 82 HIS 0.003 0.001 HIS L 256 PHE 0.013 0.001 PHE F 594 TYR 0.015 0.001 TYR H 765 ARG 0.005 0.000 ARG I 734 *********************** 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 405 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 204 time to evaluate : 6.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LEU cc_start: 0.6928 (tp) cc_final: 0.6721 (tp) REVERT: A 621 MET cc_start: 0.5800 (tmm) cc_final: 0.5556 (tmm) REVERT: A 735 MET cc_start: 0.1298 (mtp) cc_final: 0.1026 (ptp) REVERT: A 758 MET cc_start: 0.6044 (mmm) cc_final: 0.3673 (ttt) REVERT: B 226 MET cc_start: 0.4982 (tpt) cc_final: 0.4755 (tpt) REVERT: B 266 GLN cc_start: 0.9405 (mt0) cc_final: 0.9173 (mm110) REVERT: B 510 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7821 (pptt) REVERT: B 735 MET cc_start: 0.1075 (mtp) cc_final: 0.0715 (ptp) REVERT: B 758 MET cc_start: 0.5548 (mmm) cc_final: 0.3015 (ttt) REVERT: C 226 MET cc_start: 0.5045 (tpt) cc_final: 0.4213 (tpt) REVERT: C 266 GLN cc_start: 0.9217 (mt0) cc_final: 0.8999 (mm110) REVERT: C 470 THR cc_start: 0.6827 (m) cc_final: 0.6499 (p) REVERT: C 735 MET cc_start: 0.2345 (mtp) cc_final: 0.0964 (ptp) REVERT: C 758 MET cc_start: 0.6635 (mpt) cc_final: 0.6124 (mmt) REVERT: D 72 LEU cc_start: 0.6607 (tp) cc_final: 0.6278 (tp) REVERT: D 735 MET cc_start: 0.1512 (mtp) cc_final: 0.0953 (ptp) REVERT: D 758 MET cc_start: 0.5041 (mpt) cc_final: 0.3544 (ttt) REVERT: E 412 ASN cc_start: 0.5997 (OUTLIER) cc_final: 0.4938 (p0) REVERT: E 662 MET cc_start: 0.5126 (mpp) cc_final: 0.4829 (mpp) REVERT: E 758 MET cc_start: 0.5249 (mmm) cc_final: 0.2500 (ttt) REVERT: E 764 ASN cc_start: 0.8638 (t0) cc_final: 0.8423 (t0) REVERT: F 266 GLN cc_start: 0.9300 (mt0) cc_final: 0.9071 (mm110) REVERT: F 735 MET cc_start: 0.1105 (mtp) cc_final: 0.0680 (ptp) REVERT: G 72 LEU cc_start: 0.6951 (tp) cc_final: 0.6644 (tp) REVERT: G 226 MET cc_start: 0.4581 (tpt) cc_final: 0.4281 (tpt) REVERT: G 266 GLN cc_start: 0.9256 (mt0) cc_final: 0.8956 (mm110) REVERT: G 735 MET cc_start: 0.1548 (mtp) cc_final: 0.1112 (ptp) REVERT: G 758 MET cc_start: 0.5993 (mpt) cc_final: 0.4805 (ttt) REVERT: H 226 MET cc_start: 0.4791 (tpt) cc_final: 0.4567 (tpt) REVERT: H 266 GLN cc_start: 0.9377 (mt0) cc_final: 0.9136 (mm110) REVERT: H 412 ASN cc_start: 0.5921 (OUTLIER) cc_final: 0.4944 (p0) REVERT: H 510 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7740 (pptt) REVERT: H 735 MET cc_start: 0.1235 (mtp) cc_final: 0.0535 (ptp) REVERT: H 758 MET cc_start: 0.5698 (mmm) cc_final: 0.3775 (ttt) REVERT: I 226 MET cc_start: 0.5059 (tpt) cc_final: 0.4225 (tpt) REVERT: I 470 THR cc_start: 0.6876 (m) cc_final: 0.6504 (p) REVERT: I 662 MET cc_start: 0.3028 (OUTLIER) cc_final: 0.2792 (mpt) REVERT: I 758 MET cc_start: 0.5280 (mmm) cc_final: 0.2569 (ttt) REVERT: J 735 MET cc_start: 0.1440 (mtp) cc_final: 0.0970 (ptp) REVERT: K 266 GLN cc_start: 0.9280 (mt0) cc_final: 0.9072 (mm110) REVERT: K 412 ASN cc_start: 0.5861 (OUTLIER) cc_final: 0.4848 (p0) REVERT: K 662 MET cc_start: 0.4985 (mpp) cc_final: 0.4709 (mpp) REVERT: K 758 MET cc_start: 0.5015 (mmm) cc_final: 0.2372 (ttt) REVERT: L 266 GLN cc_start: 0.9262 (mt0) cc_final: 0.9028 (mm110) REVERT: L 621 MET cc_start: 0.5973 (ttt) cc_final: 0.5727 (tmm) outliers start: 201 outliers final: 157 residues processed: 367 average time/residue: 0.5948 time to fit residues: 393.7047 Evaluate side-chains 347 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 184 time to evaluate : 5.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 480 ASN Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 480 ASN Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 513 ASN Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 646 VAL Chi-restraints excluded: chain B residue 742 ASN Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 412 ASN Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 480 ASN Chi-restraints excluded: chain C residue 510 LYS Chi-restraints excluded: chain C residue 513 ASN Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain C residue 646 VAL Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain C residue 710 THR Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 412 ASN Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 480 ASN Chi-restraints excluded: chain D residue 513 ASN Chi-restraints excluded: chain D residue 628 ASN Chi-restraints excluded: chain D residue 646 VAL Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 103 MET Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 170 ILE 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 480 ASN Chi-restraints excluded: chain E residue 513 ASN Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain E residue 628 ASN Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 700 ILE Chi-restraints excluded: chain E residue 742 ASN Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 412 ASN Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 480 ASN Chi-restraints excluded: chain F residue 510 LYS Chi-restraints excluded: chain F residue 513 ASN Chi-restraints excluded: chain F residue 628 ASN Chi-restraints excluded: chain F residue 646 VAL Chi-restraints excluded: chain F residue 700 ILE Chi-restraints excluded: chain F residue 742 ASN Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 137 PHE Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 480 ASN Chi-restraints excluded: chain G residue 513 ASN Chi-restraints excluded: chain G residue 628 ASN Chi-restraints excluded: chain G residue 646 VAL Chi-restraints excluded: chain G residue 700 ILE Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 277 ILE Chi-restraints excluded: chain H residue 412 ASN Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 480 ASN Chi-restraints excluded: chain H residue 510 LYS Chi-restraints excluded: chain H residue 513 ASN Chi-restraints excluded: chain H residue 613 LEU Chi-restraints excluded: chain H residue 628 ASN Chi-restraints excluded: chain H residue 646 VAL Chi-restraints excluded: chain H residue 742 ASN Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 164 ILE Chi-restraints excluded: chain I residue 277 ILE Chi-restraints excluded: chain I residue 412 ASN Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 480 ASN Chi-restraints excluded: chain I residue 510 LYS Chi-restraints excluded: chain I residue 513 ASN Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 628 ASN Chi-restraints excluded: chain I residue 646 VAL Chi-restraints excluded: chain I residue 662 MET Chi-restraints excluded: chain I residue 700 ILE Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 127 MET Chi-restraints excluded: chain J residue 277 ILE Chi-restraints excluded: chain J residue 412 ASN Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 480 ASN Chi-restraints excluded: chain J residue 513 ASN Chi-restraints excluded: chain J residue 613 LEU Chi-restraints excluded: chain J residue 628 ASN Chi-restraints excluded: chain J residue 646 VAL Chi-restraints excluded: chain K residue 46 ASP Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 137 PHE Chi-restraints excluded: chain K residue 164 ILE Chi-restraints excluded: chain K residue 170 ILE 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 480 ASN Chi-restraints excluded: chain K residue 513 ASN Chi-restraints excluded: chain K residue 613 LEU Chi-restraints excluded: chain K residue 628 ASN Chi-restraints excluded: chain K residue 646 VAL Chi-restraints excluded: chain K residue 700 ILE Chi-restraints excluded: chain K residue 742 ASN Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 164 ILE Chi-restraints excluded: chain L residue 170 ILE Chi-restraints excluded: chain L residue 277 ILE Chi-restraints excluded: chain L residue 412 ASN Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 480 ASN Chi-restraints excluded: chain L residue 510 LYS Chi-restraints excluded: chain L residue 513 ASN Chi-restraints excluded: chain L residue 628 ASN Chi-restraints excluded: chain L residue 646 VAL Chi-restraints excluded: chain L residue 742 ASN 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: 9.9990 chunk 12 optimal weight: 8.9990 chunk 647 optimal weight: 6.9990 chunk 358 optimal weight: 40.0000 chunk 742 optimal weight: 50.0000 chunk 601 optimal weight: 30.0000 chunk 1 optimal weight: 10.0000 chunk 444 optimal weight: 40.0000 chunk 780 optimal weight: 9.9990 chunk 219 optimal weight: 0.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 ASN ** D 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 705 ASN ** E 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 705 ASN ** F 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 705 ASN ** H 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 412 ASN ** J 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 705 ASN ** K 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 705 ASN ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6431 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 69840 Z= 0.383 Angle : 0.758 9.858 94584 Z= 0.400 Chirality : 0.051 0.259 10620 Planarity : 0.004 0.032 12396 Dihedral : 7.022 31.301 9516 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 29.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.15 % Favored : 80.85 % Rotamer: Outliers : 3.84 % Allowed : 11.14 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -4.39 (0.08), residues: 8952 helix: -2.85 (0.22), residues: 240 sheet: -3.13 (0.12), residues: 1608 loop : -3.14 (0.07), residues: 7104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP L 225 HIS 0.005 0.002 HIS G 276 PHE 0.021 0.002 PHE C 57 TYR 0.022 0.002 TYR C 765 ARG 0.006 0.001 ARG B 228 *********************** 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 469 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 284 poor density : 185 time to evaluate : 7.505 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: A 226 MET cc_start: 0.5385 (tpt) cc_final: 0.5110 (tpt) REVERT: A 452 PHE cc_start: 0.4448 (OUTLIER) cc_final: 0.4026 (m-10) REVERT: A 621 MET cc_start: 0.6406 (tmm) cc_final: 0.6047 (tmm) REVERT: A 758 MET cc_start: 0.6201 (mmm) cc_final: 0.3913 (ttt) REVERT: B 266 GLN cc_start: 0.9333 (mt0) cc_final: 0.9122 (mm110) REVERT: B 678 LEU cc_start: 0.7040 (OUTLIER) cc_final: 0.6780 (mp) REVERT: B 735 MET cc_start: 0.0961 (mtp) cc_final: 0.0264 (ptp) REVERT: B 758 MET cc_start: 0.5773 (mmm) cc_final: 0.3147 (ttt) REVERT: C 226 MET cc_start: 0.5916 (tpt) cc_final: 0.4791 (tpt) REVERT: C 266 GLN cc_start: 0.9136 (mt0) cc_final: 0.8930 (mm110) REVERT: C 452 PHE cc_start: 0.4656 (OUTLIER) cc_final: 0.3717 (m-10) REVERT: C 758 MET cc_start: 0.5975 (mpt) cc_final: 0.5725 (mmt) REVERT: D 67 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.7161 (tt) REVERT: D 452 PHE cc_start: 0.4478 (OUTLIER) cc_final: 0.4062 (m-10) REVERT: D 735 MET cc_start: 0.1162 (mtp) cc_final: 0.0774 (ptp) REVERT: D 758 MET cc_start: 0.5228 (mpt) cc_final: 0.3729 (ttm) REVERT: E 510 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7689 (pptt) REVERT: E 621 MET cc_start: 0.6382 (tmm) cc_final: 0.5957 (tmm) REVERT: E 678 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7164 (mp) REVERT: E 758 MET cc_start: 0.5428 (mmm) cc_final: 0.2647 (ttt) REVERT: E 764 ASN cc_start: 0.8747 (t0) cc_final: 0.8540 (t0) REVERT: F 266 GLN cc_start: 0.9261 (mt0) cc_final: 0.9018 (mm110) REVERT: F 452 PHE cc_start: 0.4295 (OUTLIER) cc_final: 0.3437 (m-10) REVERT: F 678 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7187 (mp) REVERT: G 452 PHE cc_start: 0.4534 (OUTLIER) cc_final: 0.4110 (m-10) REVERT: G 678 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6994 (mp) REVERT: G 758 MET cc_start: 0.6105 (mpt) cc_final: 0.5100 (mtp) REVERT: H 266 GLN cc_start: 0.9271 (mt0) cc_final: 0.9068 (mm110) REVERT: H 678 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.7049 (mp) REVERT: H 735 MET cc_start: 0.1112 (mtp) cc_final: -0.0153 (ptp) REVERT: H 758 MET cc_start: 0.5048 (mmm) cc_final: 0.3159 (tpp) REVERT: I 226 MET cc_start: 0.5795 (tpt) cc_final: 0.4657 (tpt) REVERT: I 452 PHE cc_start: 0.4658 (OUTLIER) cc_final: 0.3710 (m-10) REVERT: I 758 MET cc_start: 0.5318 (mmm) cc_final: 0.2958 (ttt) REVERT: J 67 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7156 (tt) REVERT: J 452 PHE cc_start: 0.4348 (OUTLIER) cc_final: 0.3944 (m-10) REVERT: J 735 MET cc_start: 0.1237 (mtp) cc_final: 0.0828 (ptp) REVERT: K 266 GLN cc_start: 0.9287 (mt0) cc_final: 0.9087 (mm110) REVERT: K 510 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7753 (pptt) REVERT: K 621 MET cc_start: 0.6273 (tmm) cc_final: 0.5875 (tmm) REVERT: K 678 LEU cc_start: 0.7292 (OUTLIER) cc_final: 0.6941 (mp) REVERT: K 758 MET cc_start: 0.5123 (mmm) cc_final: 0.2380 (ttt) REVERT: L 266 GLN cc_start: 0.9224 (mt0) cc_final: 0.9019 (mm110) REVERT: L 452 PHE cc_start: 0.4269 (OUTLIER) cc_final: 0.3341 (m-10) REVERT: L 621 MET cc_start: 0.6262 (ttt) cc_final: 0.5846 (tmm) REVERT: L 678 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6877 (mp) outliers start: 284 outliers final: 182 residues processed: 436 average time/residue: 0.6067 time to fit residues: 480.3531 Evaluate side-chains 372 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 171 time to evaluate : 6.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 480 ASN Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 513 ASN Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 646 VAL Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 742 ASN Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 412 ASN Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 480 ASN Chi-restraints excluded: chain C residue 510 LYS Chi-restraints excluded: chain C residue 513 ASN Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain C residue 710 THR Chi-restraints excluded: chain D residue 46 ASP 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 164 ILE Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 254 PHE Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 412 ASN Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 452 PHE Chi-restraints excluded: chain D residue 480 ASN Chi-restraints excluded: chain D residue 513 ASN Chi-restraints excluded: chain D residue 628 ASN Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 170 ILE 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 452 PHE Chi-restraints excluded: chain E residue 480 ASN Chi-restraints excluded: chain E residue 510 LYS Chi-restraints excluded: chain E residue 513 ASN Chi-restraints excluded: chain E residue 628 ASN Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 678 LEU Chi-restraints excluded: chain E residue 700 ILE Chi-restraints excluded: chain E residue 742 ASN Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 409 LEU Chi-restraints excluded: chain F residue 412 ASN Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 452 PHE Chi-restraints excluded: chain F residue 480 ASN Chi-restraints excluded: chain F residue 510 LYS Chi-restraints excluded: chain F residue 513 ASN Chi-restraints excluded: chain F residue 613 LEU Chi-restraints excluded: chain F residue 628 ASN Chi-restraints excluded: chain F residue 678 LEU Chi-restraints excluded: chain F residue 700 ILE Chi-restraints excluded: chain F residue 742 ASN Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 137 PHE Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 254 PHE Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 409 LEU Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 452 PHE Chi-restraints excluded: chain G residue 480 ASN Chi-restraints excluded: chain G residue 513 ASN Chi-restraints excluded: chain G residue 628 ASN Chi-restraints excluded: chain G residue 678 LEU Chi-restraints excluded: chain G residue 700 ILE Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 277 ILE Chi-restraints excluded: chain H residue 409 LEU Chi-restraints excluded: chain H residue 412 ASN Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 452 PHE Chi-restraints excluded: chain H residue 480 ASN Chi-restraints excluded: chain H residue 513 ASN Chi-restraints excluded: chain H residue 628 ASN Chi-restraints excluded: chain H residue 646 VAL Chi-restraints excluded: chain H residue 678 LEU Chi-restraints excluded: chain H residue 742 ASN Chi-restraints excluded: chain I residue 46 ASP Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 164 ILE Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 277 ILE Chi-restraints excluded: chain I residue 409 LEU Chi-restraints excluded: chain I residue 412 ASN Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 452 PHE Chi-restraints excluded: chain I residue 480 ASN Chi-restraints excluded: chain I residue 510 LYS Chi-restraints excluded: chain I residue 513 ASN Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 628 ASN Chi-restraints excluded: chain I residue 646 VAL Chi-restraints excluded: chain I residue 700 ILE Chi-restraints excluded: chain J residue 46 ASP Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 127 MET Chi-restraints excluded: chain J residue 164 ILE Chi-restraints excluded: chain J residue 184 SER Chi-restraints excluded: chain J residue 226 MET Chi-restraints excluded: chain J residue 254 PHE Chi-restraints excluded: chain J residue 277 ILE Chi-restraints excluded: chain J residue 409 LEU Chi-restraints excluded: chain J residue 412 ASN Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 452 PHE Chi-restraints excluded: chain J residue 480 ASN Chi-restraints excluded: chain J residue 513 ASN Chi-restraints excluded: chain J residue 628 ASN Chi-restraints excluded: chain K residue 46 ASP Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 137 PHE Chi-restraints excluded: chain K residue 164 ILE Chi-restraints excluded: chain K residue 170 ILE 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 452 PHE Chi-restraints excluded: chain K residue 480 ASN Chi-restraints excluded: chain K residue 510 LYS Chi-restraints excluded: chain K residue 513 ASN Chi-restraints excluded: chain K residue 628 ASN Chi-restraints excluded: chain K residue 646 VAL Chi-restraints excluded: chain K residue 678 LEU Chi-restraints excluded: chain K residue 700 ILE Chi-restraints excluded: chain K residue 742 ASN Chi-restraints excluded: chain L residue 46 ASP Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 137 PHE Chi-restraints excluded: chain L residue 164 ILE Chi-restraints excluded: chain L residue 170 ILE Chi-restraints excluded: chain L residue 277 ILE Chi-restraints excluded: chain L residue 379 LEU Chi-restraints excluded: chain L residue 409 LEU Chi-restraints excluded: chain L residue 412 ASN Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 452 PHE Chi-restraints excluded: chain L residue 480 ASN Chi-restraints excluded: chain L residue 510 LYS Chi-restraints excluded: chain L residue 513 ASN Chi-restraints excluded: chain L residue 613 LEU Chi-restraints excluded: chain L residue 628 ASN Chi-restraints excluded: chain L residue 646 VAL Chi-restraints excluded: chain L residue 678 LEU Chi-restraints excluded: chain L residue 700 ILE Chi-restraints excluded: chain L residue 742 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 292 optimal weight: 9.9990 chunk 783 optimal weight: 10.0000 chunk 171 optimal weight: 9.9990 chunk 510 optimal weight: 40.0000 chunk 214 optimal weight: 40.0000 chunk 870 optimal weight: 8.9990 chunk 722 optimal weight: 9.9990 chunk 403 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 288 optimal weight: 40.0000 chunk 457 optimal weight: 8.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 ASN ** B 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN ** C 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 387 ASN ** E 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN ** F 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 387 ASN ** H 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 387 ASN ** I 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 387 ASN ** K 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 387 ASN ** L 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 69840 Z= 0.419 Angle : 0.807 11.007 94584 Z= 0.423 Chirality : 0.052 0.183 10620 Planarity : 0.004 0.034 12396 Dihedral : 7.383 29.654 9516 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 31.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.86 % Favored : 80.14 % Rotamer: Outliers : 4.23 % Allowed : 12.51 % Favored : 83.27 % 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: -4.56 (0.08), residues: 8952 helix: -2.51 (0.26), residues: 240 sheet: -3.18 (0.12), residues: 1548 loop : -3.31 (0.07), residues: 7164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 225 HIS 0.004 0.001 HIS G 276 PHE 0.023 0.003 PHE I 57 TYR 0.018 0.002 TYR B 68 ARG 0.008 0.001 ARG F 460 *********************** 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 505 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 313 poor density : 192 time to evaluate : 6.270 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: A 67 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.6969 (tt) REVERT: A 150 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7485 (t70) REVERT: A 452 PHE cc_start: 0.4660 (OUTLIER) cc_final: 0.4205 (m-10) REVERT: A 621 MET cc_start: 0.6746 (tmm) cc_final: 0.6322 (tmm) REVERT: A 758 MET cc_start: 0.5987 (mmm) cc_final: 0.3606 (ttt) REVERT: B 621 MET cc_start: 0.7221 (tmm) cc_final: 0.6930 (tmm) REVERT: B 735 MET cc_start: 0.1106 (mtp) cc_final: 0.0651 (ptp) REVERT: B 758 MET cc_start: 0.5684 (mmm) cc_final: 0.2952 (ttm) REVERT: C 226 MET cc_start: 0.5931 (tpt) cc_final: 0.5459 (tpt) REVERT: C 452 PHE cc_start: 0.4708 (OUTLIER) cc_final: 0.3724 (m-80) REVERT: C 678 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6767 (mp) REVERT: D 67 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.7062 (tt) REVERT: D 412 ASN cc_start: 0.6238 (OUTLIER) cc_final: 0.5439 (p0) REVERT: D 452 PHE cc_start: 0.4650 (OUTLIER) cc_final: 0.4234 (m-10) REVERT: D 758 MET cc_start: 0.5344 (mpt) cc_final: 0.3955 (ttm) REVERT: E 226 MET cc_start: 0.5390 (tpt) cc_final: 0.4822 (tpt) REVERT: E 621 MET cc_start: 0.6190 (tmm) cc_final: 0.5767 (tmm) REVERT: E 678 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7247 (mp) REVERT: E 758 MET cc_start: 0.5507 (mmm) cc_final: 0.2771 (ttt) REVERT: E 764 ASN cc_start: 0.8773 (t0) cc_final: 0.8568 (t0) REVERT: F 452 PHE cc_start: 0.4508 (OUTLIER) cc_final: 0.3587 (m-80) REVERT: F 758 MET cc_start: 0.5334 (mpt) cc_final: 0.4186 (ttm) REVERT: G 67 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.6977 (tt) REVERT: G 452 PHE cc_start: 0.4735 (OUTLIER) cc_final: 0.4267 (m-10) REVERT: G 678 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6922 (mp) REVERT: G 735 MET cc_start: 0.1690 (mtp) cc_final: 0.1357 (ptm) REVERT: H 735 MET cc_start: 0.1125 (mtp) cc_final: -0.0408 (ptp) REVERT: H 758 MET cc_start: 0.5353 (mmm) cc_final: 0.3212 (ttt) REVERT: I 226 MET cc_start: 0.6034 (tpt) cc_final: 0.4870 (tpt) REVERT: I 452 PHE cc_start: 0.4709 (OUTLIER) cc_final: 0.3717 (m-80) REVERT: I 678 LEU cc_start: 0.7292 (OUTLIER) cc_final: 0.7030 (mp) REVERT: I 758 MET cc_start: 0.5381 (mmm) cc_final: 0.3416 (ttt) REVERT: J 67 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7146 (tt) REVERT: J 266 GLN cc_start: 0.9205 (mt0) cc_final: 0.8932 (mm-40) REVERT: J 412 ASN cc_start: 0.6235 (OUTLIER) cc_final: 0.5445 (p0) REVERT: J 452 PHE cc_start: 0.4557 (OUTLIER) cc_final: 0.4169 (m-10) REVERT: J 735 MET cc_start: 0.0942 (mtp) cc_final: 0.0511 (ptp) REVERT: J 758 MET cc_start: 0.6656 (mpt) cc_final: 0.5105 (ttm) REVERT: K 266 GLN cc_start: 0.9247 (mt0) cc_final: 0.9033 (mm110) REVERT: K 621 MET cc_start: 0.6082 (tmm) cc_final: 0.5684 (tmm) REVERT: K 678 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6995 (mp) REVERT: K 758 MET cc_start: 0.5317 (mmm) cc_final: 0.2506 (ttt) REVERT: L 226 MET cc_start: 0.6074 (tpt) cc_final: 0.5099 (tpt) REVERT: L 452 PHE cc_start: 0.4312 (OUTLIER) cc_final: 0.3397 (m-10) REVERT: L 621 MET cc_start: 0.6568 (ttt) cc_final: 0.5978 (tmm) REVERT: L 678 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6897 (mp) REVERT: L 758 MET cc_start: 0.5105 (mpt) cc_final: 0.4112 (ttm) outliers start: 313 outliers final: 195 residues processed: 483 average time/residue: 0.6028 time to fit residues: 528.1635 Evaluate side-chains 379 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 163 time to evaluate : 5.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP 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 164 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 480 ASN Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 480 ASN Chi-restraints excluded: chain B residue 513 ASN Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 646 VAL Chi-restraints excluded: chain B residue 742 ASN Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 412 ASN Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 510 LYS Chi-restraints excluded: chain C residue 513 ASN Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain C residue 646 VAL Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 67 LEU 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 164 ILE Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 254 PHE Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 412 ASN Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 452 PHE Chi-restraints excluded: chain D residue 513 ASN Chi-restraints excluded: chain D residue 628 ASN Chi-restraints excluded: chain D residue 646 VAL Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain D residue 761 ASN Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 412 ASN Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 452 PHE Chi-restraints excluded: chain E residue 513 ASN Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 628 ASN Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 678 LEU Chi-restraints excluded: chain E residue 700 ILE Chi-restraints excluded: chain E residue 742 ASN Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 412 ASN Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 452 PHE Chi-restraints excluded: chain F residue 480 ASN Chi-restraints excluded: chain F residue 510 LYS Chi-restraints excluded: chain F residue 513 ASN Chi-restraints excluded: chain F residue 628 ASN Chi-restraints excluded: chain F residue 646 VAL Chi-restraints excluded: chain F residue 700 ILE Chi-restraints excluded: chain F residue 742 ASN Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 137 PHE Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 254 PHE Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 452 PHE Chi-restraints excluded: chain G residue 513 ASN Chi-restraints excluded: chain G residue 628 ASN Chi-restraints excluded: chain G residue 646 VAL Chi-restraints excluded: chain G residue 678 LEU Chi-restraints excluded: chain G residue 700 ILE Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 199 LYS Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 277 ILE Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 412 ASN Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 452 PHE Chi-restraints excluded: chain H residue 480 ASN Chi-restraints excluded: chain H residue 513 ASN Chi-restraints excluded: chain H residue 628 ASN Chi-restraints excluded: chain H residue 646 VAL Chi-restraints excluded: chain H residue 742 ASN Chi-restraints excluded: chain I residue 46 ASP Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 164 ILE Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 277 ILE Chi-restraints excluded: chain I residue 379 LEU Chi-restraints excluded: chain I residue 412 ASN Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 452 PHE Chi-restraints excluded: chain I residue 510 LYS Chi-restraints excluded: chain I residue 513 ASN Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 628 ASN Chi-restraints excluded: chain I residue 646 VAL Chi-restraints excluded: chain I residue 678 LEU Chi-restraints excluded: chain I residue 700 ILE Chi-restraints excluded: chain J residue 46 ASP Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 72 LEU 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 164 ILE Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 254 PHE Chi-restraints excluded: chain J residue 277 ILE Chi-restraints excluded: chain J residue 412 ASN Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 452 PHE Chi-restraints excluded: chain J residue 513 ASN Chi-restraints excluded: chain J residue 628 ASN Chi-restraints excluded: chain J residue 646 VAL Chi-restraints excluded: chain J residue 700 ILE Chi-restraints excluded: chain K residue 46 ASP Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 137 PHE Chi-restraints excluded: chain K residue 164 ILE Chi-restraints excluded: chain K residue 170 ILE Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 277 ILE Chi-restraints excluded: chain K residue 412 ASN Chi-restraints excluded: chain K residue 416 ASP Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 452 PHE Chi-restraints excluded: chain K residue 513 ASN Chi-restraints excluded: chain K residue 567 LEU Chi-restraints excluded: chain K residue 628 ASN Chi-restraints excluded: chain K residue 646 VAL Chi-restraints excluded: chain K residue 678 LEU Chi-restraints excluded: chain K residue 700 ILE Chi-restraints excluded: chain K residue 742 ASN Chi-restraints excluded: chain L residue 46 ASP Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 137 PHE Chi-restraints excluded: chain L residue 164 ILE Chi-restraints excluded: chain L residue 170 ILE Chi-restraints excluded: chain L residue 277 ILE Chi-restraints excluded: chain L residue 409 LEU Chi-restraints excluded: chain L residue 412 ASN Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 452 PHE Chi-restraints excluded: chain L residue 510 LYS Chi-restraints excluded: chain L residue 513 ASN Chi-restraints excluded: chain L residue 628 ASN Chi-restraints excluded: chain L residue 646 VAL Chi-restraints excluded: chain L residue 678 LEU Chi-restraints excluded: chain L residue 700 ILE Chi-restraints excluded: chain L residue 742 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 839 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 496 optimal weight: 8.9990 chunk 635 optimal weight: 10.0000 chunk 492 optimal weight: 8.9990 chunk 733 optimal weight: 40.0000 chunk 486 optimal weight: 10.0000 chunk 867 optimal weight: 9.9990 chunk 542 optimal weight: 10.0000 chunk 528 optimal weight: 9.9990 chunk 400 optimal weight: 0.9980 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 ASN D 463 ASN ** D 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 412 ASN J 463 ASN ** J 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 69840 Z= 0.333 Angle : 0.746 12.275 94584 Z= 0.386 Chirality : 0.051 0.222 10620 Planarity : 0.004 0.029 12396 Dihedral : 7.075 28.874 9516 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 28.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.78 % Favored : 81.22 % Rotamer: Outliers : 3.84 % Allowed : 13.29 % Favored : 82.87 % 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: -4.49 (0.08), residues: 8952 helix: -2.33 (0.28), residues: 240 sheet: -3.13 (0.13), residues: 1548 loop : -3.28 (0.07), residues: 7164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 225 HIS 0.004 0.001 HIS L 256 PHE 0.017 0.002 PHE C 57 TYR 0.013 0.002 TYR F 428 ARG 0.006 0.001 ARG F 228 *********************** 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 463 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 284 poor density : 179 time to evaluate : 5.986 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 67 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.6990 (tt) REVERT: A 150 ASP cc_start: 0.7679 (OUTLIER) cc_final: 0.7340 (t70) REVERT: A 452 PHE cc_start: 0.4645 (OUTLIER) cc_final: 0.4137 (m-10) REVERT: A 621 MET cc_start: 0.6752 (tmm) cc_final: 0.6310 (tmm) REVERT: B 226 MET cc_start: 0.5667 (tpt) cc_final: 0.5406 (tpp) REVERT: B 476 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7590 (mm) REVERT: B 621 MET cc_start: 0.7233 (tmm) cc_final: 0.6816 (tmm) REVERT: B 735 MET cc_start: 0.0979 (mtp) cc_final: 0.0694 (ptp) REVERT: B 758 MET cc_start: 0.5410 (mmm) cc_final: 0.5094 (tpp) REVERT: C 226 MET cc_start: 0.5742 (tpt) cc_final: 0.5306 (tpt) REVERT: C 452 PHE cc_start: 0.4721 (OUTLIER) cc_final: 0.3667 (m-80) REVERT: C 470 THR cc_start: 0.7097 (m) cc_final: 0.6848 (p) REVERT: C 621 MET cc_start: 0.5679 (tpp) cc_final: 0.5236 (tpp) REVERT: C 678 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6666 (mp) REVERT: C 758 MET cc_start: 0.5753 (mpt) cc_final: 0.4634 (mtp) REVERT: D 67 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.7130 (tt) REVERT: D 452 PHE cc_start: 0.4714 (OUTLIER) cc_final: 0.4171 (m-10) REVERT: D 621 MET cc_start: 0.5742 (tmm) cc_final: 0.5358 (tmm) REVERT: D 735 MET cc_start: 0.1179 (mtp) cc_final: 0.0674 (ptp) REVERT: D 758 MET cc_start: 0.5465 (mpt) cc_final: 0.3974 (ttm) REVERT: E 226 MET cc_start: 0.4827 (tpt) cc_final: 0.4587 (tpt) REVERT: E 621 MET cc_start: 0.6779 (tmm) cc_final: 0.6391 (tmm) REVERT: E 758 MET cc_start: 0.5287 (mmm) cc_final: 0.2592 (ttt) REVERT: E 764 ASN cc_start: 0.8798 (t0) cc_final: 0.8594 (t0) REVERT: F 452 PHE cc_start: 0.4525 (OUTLIER) cc_final: 0.3503 (m-80) REVERT: F 678 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7080 (mp) REVERT: F 758 MET cc_start: 0.5301 (mpt) cc_final: 0.4031 (ttm) REVERT: G 452 PHE cc_start: 0.4735 (OUTLIER) cc_final: 0.4213 (m-10) REVERT: G 735 MET cc_start: 0.1583 (mtp) cc_final: 0.1329 (ptm) REVERT: H 476 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7530 (mm) REVERT: H 621 MET cc_start: 0.7412 (tmm) cc_final: 0.7052 (tmm) REVERT: H 735 MET cc_start: 0.1171 (mtp) cc_final: -0.0277 (ptp) REVERT: H 758 MET cc_start: 0.5213 (mmm) cc_final: 0.3815 (tpp) REVERT: I 226 MET cc_start: 0.5788 (tpt) cc_final: 0.5341 (tpt) REVERT: I 452 PHE cc_start: 0.4724 (OUTLIER) cc_final: 0.3657 (m-80) REVERT: I 470 THR cc_start: 0.7027 (m) cc_final: 0.6753 (p) REVERT: I 735 MET cc_start: -0.0385 (pmm) cc_final: -0.1392 (pmm) REVERT: I 758 MET cc_start: 0.5361 (mmm) cc_final: 0.3457 (ttt) REVERT: J 67 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.7075 (tt) REVERT: J 72 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6784 (tp) REVERT: J 452 PHE cc_start: 0.4564 (OUTLIER) cc_final: 0.4077 (m-10) REVERT: J 621 MET cc_start: 0.6199 (tmm) cc_final: 0.5698 (tmm) REVERT: J 735 MET cc_start: 0.0726 (mtp) cc_final: 0.0376 (ptp) REVERT: J 758 MET cc_start: 0.6124 (mpt) cc_final: 0.4877 (ttm) REVERT: K 226 MET cc_start: 0.5907 (tpt) cc_final: 0.4993 (tpt) REVERT: K 621 MET cc_start: 0.6669 (tmm) cc_final: 0.6310 (tmm) REVERT: K 758 MET cc_start: 0.4970 (mmm) cc_final: 0.2200 (ttt) REVERT: L 226 MET cc_start: 0.5429 (tpt) cc_final: 0.4371 (tpt) REVERT: L 452 PHE cc_start: 0.4399 (OUTLIER) cc_final: 0.3439 (m-80) REVERT: L 621 MET cc_start: 0.6605 (ttt) cc_final: 0.5779 (tmm) REVERT: L 678 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6839 (mp) REVERT: L 758 MET cc_start: 0.5132 (mpt) cc_final: 0.3986 (ttm) outliers start: 284 outliers final: 206 residues processed: 437 average time/residue: 0.5680 time to fit residues: 451.2506 Evaluate side-chains 383 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 159 time to evaluate : 6.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP 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 164 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 513 ASN Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 646 VAL Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 700 ILE Chi-restraints excluded: chain B residue 742 ASN Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 412 ASN Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 480 ASN Chi-restraints excluded: chain C residue 510 LYS Chi-restraints excluded: chain C residue 513 ASN Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain C residue 646 VAL Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain C residue 710 THR Chi-restraints excluded: chain D residue 46 ASP 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 137 PHE Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 452 PHE Chi-restraints excluded: chain D residue 513 ASN Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 628 ASN Chi-restraints excluded: chain D residue 646 VAL Chi-restraints excluded: chain D residue 662 MET Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 412 ASN Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 452 PHE Chi-restraints excluded: chain E residue 480 ASN Chi-restraints excluded: chain E residue 513 ASN Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 628 ASN Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 700 ILE Chi-restraints excluded: chain E residue 742 ASN Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 412 ASN Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 452 PHE Chi-restraints excluded: chain F residue 510 LYS Chi-restraints excluded: chain F residue 513 ASN Chi-restraints excluded: chain F residue 628 ASN Chi-restraints excluded: chain F residue 646 VAL Chi-restraints excluded: chain F residue 678 LEU Chi-restraints excluded: chain F residue 679 ILE Chi-restraints excluded: chain F residue 700 ILE Chi-restraints excluded: chain F residue 742 ASN Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 137 PHE Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 452 PHE Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 480 ASN Chi-restraints excluded: chain G residue 513 ASN Chi-restraints excluded: chain G residue 613 LEU Chi-restraints excluded: chain G residue 628 ASN Chi-restraints excluded: chain G residue 646 VAL Chi-restraints excluded: chain G residue 700 ILE Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain H residue 127 MET Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 277 ILE Chi-restraints excluded: chain H residue 409 LEU Chi-restraints excluded: chain H residue 412 ASN Chi-restraints excluded: chain H residue 416 ASP Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 452 PHE Chi-restraints excluded: chain H residue 476 ILE Chi-restraints excluded: chain H residue 513 ASN Chi-restraints excluded: chain H residue 628 ASN Chi-restraints excluded: chain H residue 646 VAL Chi-restraints excluded: chain H residue 662 MET Chi-restraints excluded: chain H residue 700 ILE Chi-restraints excluded: chain H residue 742 ASN Chi-restraints excluded: chain I residue 46 ASP Chi-restraints excluded: chain I residue 72 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 164 ILE Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 277 ILE Chi-restraints excluded: chain I residue 379 LEU Chi-restraints excluded: chain I residue 412 ASN Chi-restraints excluded: chain I residue 416 ASP Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 452 PHE Chi-restraints excluded: chain I residue 510 LYS Chi-restraints excluded: chain I residue 513 ASN Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 628 ASN Chi-restraints excluded: chain I residue 646 VAL Chi-restraints excluded: chain I residue 700 ILE Chi-restraints excluded: chain I residue 715 ASN Chi-restraints excluded: chain J residue 46 ASP Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 127 MET Chi-restraints excluded: chain J residue 137 PHE Chi-restraints excluded: chain J residue 164 ILE Chi-restraints excluded: chain J residue 277 ILE Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 452 PHE Chi-restraints excluded: chain J residue 513 ASN Chi-restraints excluded: chain J residue 628 ASN Chi-restraints excluded: chain J residue 646 VAL Chi-restraints excluded: chain J residue 662 MET Chi-restraints excluded: chain J residue 700 ILE Chi-restraints excluded: chain K residue 46 ASP Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 137 PHE Chi-restraints excluded: chain K residue 164 ILE Chi-restraints excluded: chain K residue 170 ILE Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 277 ILE Chi-restraints excluded: chain K residue 412 ASN Chi-restraints excluded: chain K residue 416 ASP Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 452 PHE Chi-restraints excluded: chain K residue 480 ASN Chi-restraints excluded: chain K residue 513 ASN Chi-restraints excluded: chain K residue 567 LEU Chi-restraints excluded: chain K residue 628 ASN Chi-restraints excluded: chain K residue 646 VAL Chi-restraints excluded: chain K residue 700 ILE Chi-restraints excluded: chain K residue 742 ASN Chi-restraints excluded: chain L residue 46 ASP Chi-restraints excluded: chain L residue 99 LEU Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 137 PHE Chi-restraints excluded: chain L residue 164 ILE Chi-restraints excluded: chain L residue 170 ILE Chi-restraints excluded: chain L residue 277 ILE Chi-restraints excluded: chain L residue 412 ASN Chi-restraints excluded: chain L residue 416 ASP Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 452 PHE Chi-restraints excluded: chain L residue 480 ASN Chi-restraints excluded: chain L residue 510 LYS Chi-restraints excluded: chain L residue 513 ASN Chi-restraints excluded: chain L residue 628 ASN Chi-restraints excluded: chain L residue 646 VAL Chi-restraints excluded: chain L residue 678 LEU Chi-restraints excluded: chain L residue 679 ILE Chi-restraints excluded: chain L residue 700 ILE Chi-restraints excluded: chain L residue 742 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 536 optimal weight: 5.9990 chunk 346 optimal weight: 20.0000 chunk 518 optimal weight: 40.0000 chunk 261 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 168 optimal weight: 1.9990 chunk 551 optimal weight: 6.9990 chunk 590 optimal weight: 0.2980 chunk 428 optimal weight: 0.6980 chunk 80 optimal weight: 40.0000 chunk 681 optimal weight: 0.3980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 775 ASN ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 775 ASN ** L 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 69840 Z= 0.162 Angle : 0.629 10.629 94584 Z= 0.322 Chirality : 0.048 0.174 10620 Planarity : 0.003 0.027 12396 Dihedral : 6.159 32.092 9516 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.38 % Favored : 88.62 % Rotamer: Outliers : 2.74 % Allowed : 13.99 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.08 (0.08), residues: 8952 helix: -1.97 (0.30), residues: 240 sheet: -2.51 (0.14), residues: 1296 loop : -3.08 (0.06), residues: 7416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 82 HIS 0.003 0.001 HIS H 276 PHE 0.014 0.001 PHE L 142 TYR 0.017 0.001 TYR J 428 ARG 0.004 0.000 ARG D 460 *********************** 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 407 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 204 time to evaluate : 6.011 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 67 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.7019 (tp) REVERT: A 150 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7577 (t70) REVERT: A 412 ASN cc_start: 0.5995 (OUTLIER) cc_final: 0.5144 (p0) REVERT: A 621 MET cc_start: 0.6597 (tmm) cc_final: 0.6119 (tmm) REVERT: A 758 MET cc_start: 0.6302 (mmm) cc_final: 0.5949 (tpp) REVERT: B 412 ASN cc_start: 0.5687 (OUTLIER) cc_final: 0.4715 (p0) REVERT: B 476 ILE cc_start: 0.7830 (OUTLIER) cc_final: 0.7486 (mm) REVERT: C 412 ASN cc_start: 0.6117 (OUTLIER) cc_final: 0.5147 (p0) REVERT: C 470 THR cc_start: 0.6939 (m) cc_final: 0.6550 (p) REVERT: D 735 MET cc_start: 0.0651 (mtp) cc_final: 0.0188 (ptp) REVERT: D 758 MET cc_start: 0.5127 (mpt) cc_final: 0.3695 (ttm) REVERT: E 226 MET cc_start: 0.4759 (tpt) cc_final: 0.4291 (tpt) REVERT: E 412 ASN cc_start: 0.5486 (OUTLIER) cc_final: 0.4786 (p0) REVERT: E 621 MET cc_start: 0.6476 (tmm) cc_final: 0.6166 (tmm) REVERT: E 758 MET cc_start: 0.4911 (mmm) cc_final: 0.2021 (ttt) REVERT: F 412 ASN cc_start: 0.5979 (OUTLIER) cc_final: 0.4980 (p0) REVERT: F 621 MET cc_start: 0.5389 (tpp) cc_final: 0.4916 (tpp) REVERT: F 758 MET cc_start: 0.5185 (mpt) cc_final: 0.3965 (mtp) REVERT: G 412 ASN cc_start: 0.6037 (OUTLIER) cc_final: 0.5186 (p0) REVERT: G 510 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8334 (ptmm) REVERT: G 621 MET cc_start: 0.6140 (tmm) cc_final: 0.5814 (tmm) REVERT: G 735 MET cc_start: 0.1411 (mtp) cc_final: 0.0966 (ptp) REVERT: H 226 MET cc_start: 0.4723 (tpt) cc_final: 0.3957 (tpt) REVERT: H 412 ASN cc_start: 0.5653 (OUTLIER) cc_final: 0.4689 (p0) REVERT: H 758 MET cc_start: 0.4958 (mmm) cc_final: 0.2852 (ttt) REVERT: I 412 ASN cc_start: 0.6027 (OUTLIER) cc_final: 0.5069 (p0) REVERT: I 470 THR cc_start: 0.6977 (m) cc_final: 0.6574 (p) REVERT: I 621 MET cc_start: 0.5265 (tpp) cc_final: 0.4780 (tpp) REVERT: I 735 MET cc_start: -0.0023 (pmm) cc_final: -0.1077 (pmm) REVERT: I 758 MET cc_start: 0.5288 (mmm) cc_final: 0.3500 (ttt) REVERT: J 72 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6757 (tp) REVERT: J 758 MET cc_start: 0.5895 (mpt) cc_final: 0.4429 (ttm) REVERT: K 412 ASN cc_start: 0.5350 (OUTLIER) cc_final: 0.4685 (p0) REVERT: K 621 MET cc_start: 0.6376 (tmm) cc_final: 0.6091 (tmm) REVERT: K 758 MET cc_start: 0.4562 (mmm) cc_final: 0.1587 (ttt) REVERT: L 412 ASN cc_start: 0.6129 (OUTLIER) cc_final: 0.5147 (p0) REVERT: L 735 MET cc_start: -0.1541 (pmm) cc_final: -0.2525 (pmm) REVERT: L 758 MET cc_start: 0.4962 (mpt) cc_final: 0.3871 (mtp) outliers start: 203 outliers final: 145 residues processed: 379 average time/residue: 0.5648 time to fit residues: 391.3465 Evaluate side-chains 329 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 169 time to evaluate : 6.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP 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 164 ILE Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 513 ASN Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 646 VAL Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 742 ASN Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 412 ASN Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 480 ASN Chi-restraints excluded: chain C residue 510 LYS Chi-restraints excluded: chain C residue 513 ASN Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain C residue 646 VAL Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain C residue 710 THR Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 480 ASN Chi-restraints excluded: chain D residue 513 ASN Chi-restraints excluded: chain D residue 628 ASN Chi-restraints excluded: chain D residue 646 VAL Chi-restraints excluded: chain D residue 662 MET Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 412 ASN Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 513 ASN Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 628 ASN Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 742 ASN Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 412 ASN Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 510 LYS Chi-restraints excluded: chain F residue 513 ASN Chi-restraints excluded: chain F residue 628 ASN Chi-restraints excluded: chain F residue 646 VAL Chi-restraints excluded: chain F residue 700 ILE Chi-restraints excluded: chain F residue 742 ASN Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 137 PHE Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 510 LYS Chi-restraints excluded: chain G residue 513 ASN Chi-restraints excluded: chain G residue 613 LEU Chi-restraints excluded: chain G residue 628 ASN Chi-restraints excluded: chain G residue 646 VAL Chi-restraints excluded: chain G residue 700 ILE Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 127 MET Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 412 ASN Chi-restraints excluded: chain H residue 416 ASP Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 513 ASN Chi-restraints excluded: chain H residue 628 ASN Chi-restraints excluded: chain H residue 646 VAL Chi-restraints excluded: chain H residue 662 MET Chi-restraints excluded: chain H residue 742 ASN Chi-restraints excluded: chain I residue 46 ASP Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 164 ILE Chi-restraints excluded: chain I residue 412 ASN Chi-restraints excluded: chain I residue 416 ASP Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 480 ASN Chi-restraints excluded: chain I residue 510 LYS Chi-restraints excluded: chain I residue 513 ASN Chi-restraints excluded: chain I residue 534 GLU Chi-restraints excluded: chain I residue 628 ASN Chi-restraints excluded: chain I residue 646 VAL Chi-restraints excluded: chain I residue 700 ILE Chi-restraints excluded: chain J residue 46 ASP Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 127 MET Chi-restraints excluded: chain J residue 137 PHE Chi-restraints excluded: chain J residue 164 ILE Chi-restraints excluded: chain J residue 226 MET Chi-restraints excluded: chain J residue 416 ASP Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 480 ASN Chi-restraints excluded: chain J residue 513 ASN Chi-restraints excluded: chain J residue 628 ASN Chi-restraints excluded: chain J residue 646 VAL Chi-restraints excluded: chain J residue 700 ILE Chi-restraints excluded: chain K residue 46 ASP Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 127 MET Chi-restraints excluded: chain K residue 137 PHE Chi-restraints excluded: chain K residue 164 ILE Chi-restraints excluded: chain K residue 170 ILE Chi-restraints excluded: chain K residue 412 ASN Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 513 ASN Chi-restraints excluded: chain K residue 567 LEU Chi-restraints excluded: chain K residue 628 ASN Chi-restraints excluded: chain K residue 646 VAL Chi-restraints excluded: chain K residue 742 ASN Chi-restraints excluded: chain L residue 46 ASP Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 137 PHE Chi-restraints excluded: chain L residue 164 ILE Chi-restraints excluded: chain L residue 170 ILE Chi-restraints excluded: chain L residue 412 ASN Chi-restraints excluded: chain L residue 416 ASP Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 510 LYS Chi-restraints excluded: chain L residue 513 ASN Chi-restraints excluded: chain L residue 628 ASN Chi-restraints excluded: chain L residue 646 VAL Chi-restraints excluded: chain L residue 700 ILE Chi-restraints excluded: chain L residue 742 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 789 optimal weight: 9.9990 chunk 831 optimal weight: 10.0000 chunk 758 optimal weight: 20.0000 chunk 808 optimal weight: 5.9990 chunk 830 optimal weight: 20.0000 chunk 486 optimal weight: 20.0000 chunk 352 optimal weight: 0.8980 chunk 634 optimal weight: 20.0000 chunk 248 optimal weight: 20.0000 chunk 730 optimal weight: 20.0000 chunk 764 optimal weight: 4.9990 overall best weight: 6.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 ASN ** C 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 412 ASN ** E 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 775 ASN ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 764 ASN ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 412 ASN I 463 ASN ** I 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 775 ASN ** L 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 764 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 69840 Z= 0.310 Angle : 0.714 10.273 94584 Z= 0.367 Chirality : 0.049 0.346 10620 Planarity : 0.003 0.027 12396 Dihedral : 6.613 31.049 9516 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 26.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.14 % Favored : 81.86 % Rotamer: Outliers : 2.98 % Allowed : 14.38 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.30 (0.08), residues: 8952 helix: -1.94 (0.30), residues: 240 sheet: -2.88 (0.13), residues: 1596 loop : -3.17 (0.07), residues: 7116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 225 HIS 0.004 0.001 HIS I 469 PHE 0.015 0.002 PHE C 57 TYR 0.013 0.002 TYR H 65 ARG 0.005 0.001 ARG L 228 *********************** 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 390 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 169 time to evaluate : 5.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6985 (tt) REVERT: A 150 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7646 (t70) REVERT: A 621 MET cc_start: 0.6725 (tmm) cc_final: 0.6221 (tmm) REVERT: A 758 MET cc_start: 0.6052 (mmm) cc_final: 0.5808 (tpp) REVERT: B 226 MET cc_start: 0.5284 (tpt) cc_final: 0.4456 (tpt) REVERT: B 476 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7596 (mm) REVERT: B 758 MET cc_start: 0.6178 (OUTLIER) cc_final: 0.3944 (ttm) REVERT: C 470 THR cc_start: 0.6914 (m) cc_final: 0.6613 (p) REVERT: C 510 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7470 (pptt) REVERT: C 621 MET cc_start: 0.5436 (tpp) cc_final: 0.4421 (tpp) REVERT: C 735 MET cc_start: -0.0320 (pmm) cc_final: -0.1306 (pmm) REVERT: C 758 MET cc_start: 0.5759 (mpt) cc_final: 0.4610 (mtp) REVERT: D 621 MET cc_start: 0.5997 (tmm) cc_final: 0.5744 (tmm) REVERT: D 735 MET cc_start: 0.1120 (mtp) cc_final: 0.0604 (ptp) REVERT: E 226 MET cc_start: 0.4983 (tpt) cc_final: 0.4586 (tpt) REVERT: E 621 MET cc_start: 0.6755 (tmm) cc_final: 0.6383 (tmm) REVERT: E 735 MET cc_start: -0.0556 (pmm) cc_final: -0.1787 (pmm) REVERT: E 758 MET cc_start: 0.4899 (mmm) cc_final: 0.1999 (ttt) REVERT: F 621 MET cc_start: 0.5451 (tpp) cc_final: 0.4528 (tpp) REVERT: F 758 MET cc_start: 0.5241 (mpt) cc_final: 0.4025 (mtp) REVERT: G 226 MET cc_start: 0.4839 (tpt) cc_final: 0.3890 (tpt) REVERT: G 510 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8358 (ptmm) REVERT: H 226 MET cc_start: 0.5084 (tpt) cc_final: 0.4689 (tpt) REVERT: H 476 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7545 (mm) REVERT: H 621 MET cc_start: 0.5587 (tmm) cc_final: 0.5127 (tmm) REVERT: H 758 MET cc_start: 0.5087 (mmm) cc_final: 0.2904 (ttt) REVERT: I 470 THR cc_start: 0.6957 (m) cc_final: 0.6639 (p) REVERT: I 510 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7431 (pptt) REVERT: I 621 MET cc_start: 0.5428 (tpp) cc_final: 0.4995 (tpp) REVERT: I 758 MET cc_start: 0.5463 (mmm) cc_final: 0.3575 (ttt) REVERT: J 72 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6767 (tp) REVERT: J 621 MET cc_start: 0.5606 (tmm) cc_final: 0.5324 (tmm) REVERT: J 735 MET cc_start: 0.0999 (mtp) cc_final: 0.0394 (ptp) REVERT: J 758 MET cc_start: 0.6175 (mpt) cc_final: 0.4812 (ttm) REVERT: K 226 MET cc_start: 0.5327 (tpt) cc_final: 0.4449 (tpt) REVERT: K 621 MET cc_start: 0.6649 (tmm) cc_final: 0.6304 (tmm) REVERT: K 678 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.7029 (mp) REVERT: K 735 MET cc_start: -0.0761 (pmm) cc_final: -0.1938 (pmm) REVERT: K 758 MET cc_start: 0.4775 (mmm) cc_final: 0.4553 (mmm) REVERT: L 621 MET cc_start: 0.5377 (tmm) cc_final: 0.5096 (tmm) REVERT: L 678 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6971 (mp) REVERT: L 758 MET cc_start: 0.5036 (mpt) cc_final: 0.3885 (ttm) outliers start: 221 outliers final: 173 residues processed: 364 average time/residue: 0.5683 time to fit residues: 378.0584 Evaluate side-chains 343 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 159 time to evaluate : 6.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP 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 164 ILE Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 513 ASN Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 646 VAL Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 700 ILE Chi-restraints excluded: chain B residue 742 ASN Chi-restraints excluded: chain B residue 758 MET Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 412 ASN Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 480 ASN Chi-restraints excluded: chain C residue 510 LYS Chi-restraints excluded: chain C residue 513 ASN Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain C residue 646 VAL Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain C residue 710 THR Chi-restraints excluded: chain C residue 764 ASN Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 137 PHE Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 480 ASN Chi-restraints excluded: chain D residue 513 ASN Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 628 ASN Chi-restraints excluded: chain D residue 646 VAL Chi-restraints excluded: chain D residue 662 MET Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 412 ASN Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 513 ASN Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain E residue 628 ASN Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 700 ILE Chi-restraints excluded: chain E residue 742 ASN Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 412 ASN Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 510 LYS Chi-restraints excluded: chain F residue 513 ASN Chi-restraints excluded: chain F residue 613 LEU Chi-restraints excluded: chain F residue 628 ASN Chi-restraints excluded: chain F residue 646 VAL Chi-restraints excluded: chain F residue 700 ILE Chi-restraints excluded: chain F residue 742 ASN Chi-restraints excluded: chain F residue 764 ASN Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 137 PHE Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 510 LYS Chi-restraints excluded: chain G residue 513 ASN Chi-restraints excluded: chain G residue 613 LEU Chi-restraints excluded: chain G residue 628 ASN Chi-restraints excluded: chain G residue 646 VAL Chi-restraints excluded: chain G residue 700 ILE Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 127 MET Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 412 ASN Chi-restraints excluded: chain H residue 416 ASP Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 476 ILE Chi-restraints excluded: chain H residue 513 ASN Chi-restraints excluded: chain H residue 613 LEU Chi-restraints excluded: chain H residue 628 ASN Chi-restraints excluded: chain H residue 646 VAL Chi-restraints excluded: chain H residue 662 MET Chi-restraints excluded: chain H residue 700 ILE Chi-restraints excluded: chain H residue 742 ASN Chi-restraints excluded: chain I residue 46 ASP Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 164 ILE Chi-restraints excluded: chain I residue 412 ASN Chi-restraints excluded: chain I residue 416 ASP Chi-restraints excluded: chain I residue 510 LYS Chi-restraints excluded: chain I residue 513 ASN Chi-restraints excluded: chain I residue 628 ASN Chi-restraints excluded: chain I residue 646 VAL Chi-restraints excluded: chain I residue 700 ILE Chi-restraints excluded: chain J residue 46 ASP Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 127 MET Chi-restraints excluded: chain J residue 137 PHE Chi-restraints excluded: chain J residue 164 ILE Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 226 MET Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 480 ASN Chi-restraints excluded: chain J residue 513 ASN Chi-restraints excluded: chain J residue 628 ASN Chi-restraints excluded: chain J residue 646 VAL Chi-restraints excluded: chain J residue 700 ILE Chi-restraints excluded: chain K residue 46 ASP Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 127 MET Chi-restraints excluded: chain K residue 137 PHE Chi-restraints excluded: chain K residue 164 ILE Chi-restraints excluded: chain K residue 170 ILE Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 412 ASN Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 513 ASN Chi-restraints excluded: chain K residue 567 LEU Chi-restraints excluded: chain K residue 613 LEU Chi-restraints excluded: chain K residue 628 ASN Chi-restraints excluded: chain K residue 646 VAL Chi-restraints excluded: chain K residue 678 LEU Chi-restraints excluded: chain K residue 700 ILE Chi-restraints excluded: chain K residue 742 ASN Chi-restraints excluded: chain L residue 46 ASP Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 137 PHE Chi-restraints excluded: chain L residue 164 ILE Chi-restraints excluded: chain L residue 170 ILE Chi-restraints excluded: chain L residue 412 ASN Chi-restraints excluded: chain L residue 416 ASP Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 510 LYS Chi-restraints excluded: chain L residue 513 ASN Chi-restraints excluded: chain L residue 613 LEU Chi-restraints excluded: chain L residue 628 ASN Chi-restraints excluded: chain L residue 646 VAL Chi-restraints excluded: chain L residue 678 LEU Chi-restraints excluded: chain L residue 700 ILE Chi-restraints excluded: chain L residue 742 ASN Chi-restraints excluded: chain L residue 764 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 805 optimal weight: 10.0000 chunk 530 optimal weight: 40.0000 chunk 854 optimal weight: 5.9990 chunk 521 optimal weight: 7.9990 chunk 405 optimal weight: 6.9990 chunk 594 optimal weight: 10.0000 chunk 896 optimal weight: 10.0000 chunk 825 optimal weight: 5.9990 chunk 713 optimal weight: 0.0050 chunk 74 optimal weight: 0.0870 chunk 551 optimal weight: 0.8980 overall best weight: 2.5976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6384 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 69840 Z= 0.191 Angle : 0.654 11.846 94584 Z= 0.332 Chirality : 0.048 0.273 10620 Planarity : 0.003 0.028 12396 Dihedral : 6.212 31.537 9516 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 23.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 2.57 % Allowed : 14.82 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -4.13 (0.08), residues: 8952 helix: -1.77 (0.31), residues: 240 sheet: -2.66 (0.13), residues: 1452 loop : -3.09 (0.07), residues: 7260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS I 469 PHE 0.016 0.002 PHE F 664 TYR 0.024 0.001 TYR B 765 ARG 0.003 0.000 ARG G 228 ********************** 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 360 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 170 time to evaluate : 6.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6972 (tp) REVERT: A 621 MET cc_start: 0.6704 (tmm) cc_final: 0.6210 (tmm) REVERT: A 735 MET cc_start: -0.0514 (pmm) cc_final: -0.1078 (pmm) REVERT: A 758 MET cc_start: 0.5917 (mmm) cc_final: 0.5700 (tpp) REVERT: B 226 MET cc_start: 0.4872 (tpt) cc_final: 0.4074 (tpt) REVERT: B 412 ASN cc_start: 0.6011 (OUTLIER) cc_final: 0.4922 (p0) REVERT: B 476 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.7528 (mm) REVERT: B 621 MET cc_start: 0.4700 (tmm) cc_final: 0.4215 (tmm) REVERT: B 758 MET cc_start: 0.6070 (OUTLIER) cc_final: 0.4227 (tpp) REVERT: C 412 ASN cc_start: 0.6588 (OUTLIER) cc_final: 0.5472 (p0) REVERT: C 470 THR cc_start: 0.7019 (m) cc_final: 0.6668 (p) REVERT: C 621 MET cc_start: 0.5427 (tpp) cc_final: 0.4511 (tpp) REVERT: C 735 MET cc_start: -0.0354 (pmm) cc_final: -0.1384 (pmm) REVERT: C 758 MET cc_start: 0.5841 (mpt) cc_final: 0.4580 (mtp) REVERT: D 621 MET cc_start: 0.5963 (tmm) cc_final: 0.5731 (tmm) REVERT: D 735 MET cc_start: 0.0908 (mtp) cc_final: 0.0469 (ptp) REVERT: E 226 MET cc_start: 0.4809 (tpt) cc_final: 0.4319 (tpt) REVERT: E 412 ASN cc_start: 0.5763 (OUTLIER) cc_final: 0.5045 (p0) REVERT: E 476 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7572 (mm) REVERT: E 621 MET cc_start: 0.6695 (tmm) cc_final: 0.6371 (tmm) REVERT: E 735 MET cc_start: -0.1009 (pmm) cc_final: -0.2208 (pmm) REVERT: E 758 MET cc_start: 0.4864 (mmm) cc_final: 0.1946 (ttt) REVERT: F 226 MET cc_start: 0.4605 (tpt) cc_final: 0.3613 (tpt) REVERT: F 412 ASN cc_start: 0.6653 (OUTLIER) cc_final: 0.5603 (p0) REVERT: F 621 MET cc_start: 0.5350 (tpp) cc_final: 0.4461 (tpp) REVERT: F 758 MET cc_start: 0.5134 (mpt) cc_final: 0.3926 (mtp) REVERT: G 510 LYS cc_start: 0.8721 (pptt) cc_final: 0.8324 (ptmm) REVERT: G 621 MET cc_start: 0.5771 (tmm) cc_final: 0.5404 (tmm) REVERT: G 758 MET cc_start: 0.4876 (mpt) cc_final: 0.3390 (ttm) REVERT: H 226 MET cc_start: 0.4900 (tpt) cc_final: 0.4372 (tpt) REVERT: H 412 ASN cc_start: 0.5831 (OUTLIER) cc_final: 0.4927 (p0) REVERT: H 476 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.7520 (mm) REVERT: H 621 MET cc_start: 0.5576 (tmm) cc_final: 0.5105 (tmm) REVERT: H 758 MET cc_start: 0.4927 (mmm) cc_final: 0.2817 (ttt) REVERT: I 412 ASN cc_start: 0.6392 (OUTLIER) cc_final: 0.5186 (p0) REVERT: I 470 THR cc_start: 0.7061 (m) cc_final: 0.6698 (p) REVERT: I 621 MET cc_start: 0.5378 (tpp) cc_final: 0.4981 (tpp) REVERT: I 758 MET cc_start: 0.5329 (mmm) cc_final: 0.3457 (ttt) REVERT: J 72 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6679 (tp) REVERT: J 621 MET cc_start: 0.5732 (tmm) cc_final: 0.5488 (tmm) REVERT: J 735 MET cc_start: 0.0558 (mtp) cc_final: 0.0055 (ptp) REVERT: J 758 MET cc_start: 0.6047 (mpt) cc_final: 0.4552 (ttm) REVERT: K 226 MET cc_start: 0.5304 (tpt) cc_final: 0.4575 (tpt) REVERT: K 412 ASN cc_start: 0.5580 (OUTLIER) cc_final: 0.4792 (p0) REVERT: K 476 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7608 (mm) REVERT: K 621 MET cc_start: 0.6588 (tmm) cc_final: 0.6289 (tmm) REVERT: K 678 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.7057 (mp) REVERT: K 735 MET cc_start: -0.1231 (pmm) cc_final: -0.2379 (pmm) REVERT: K 758 MET cc_start: 0.4539 (mmm) cc_final: 0.4309 (mmm) REVERT: L 226 MET cc_start: 0.4836 (tpt) cc_final: 0.3998 (tpt) REVERT: L 412 ASN cc_start: 0.6727 (OUTLIER) cc_final: 0.5717 (p0) REVERT: L 621 MET cc_start: 0.5467 (tmm) cc_final: 0.5186 (tmm) REVERT: L 758 MET cc_start: 0.4924 (mpt) cc_final: 0.3708 (ttm) outliers start: 190 outliers final: 167 residues processed: 337 average time/residue: 0.5664 time to fit residues: 348.6576 Evaluate side-chains 347 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 164 time to evaluate : 5.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP 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 164 ILE Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 513 ASN Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 646 VAL Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 700 ILE Chi-restraints excluded: chain B residue 742 ASN Chi-restraints excluded: chain B residue 758 MET Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 412 ASN Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 480 ASN Chi-restraints excluded: chain C residue 510 LYS Chi-restraints excluded: chain C residue 513 ASN Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain C residue 646 VAL Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain C residue 710 THR Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 480 ASN Chi-restraints excluded: chain D residue 513 ASN Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 628 ASN Chi-restraints excluded: chain D residue 646 VAL Chi-restraints excluded: chain D residue 662 MET Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 170 ILE 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 476 ILE Chi-restraints excluded: chain E residue 513 ASN Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain E residue 628 ASN Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 700 ILE Chi-restraints excluded: chain E residue 742 ASN Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 412 ASN Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 510 LYS Chi-restraints excluded: chain F residue 513 ASN Chi-restraints excluded: chain F residue 613 LEU Chi-restraints excluded: chain F residue 628 ASN Chi-restraints excluded: chain F residue 646 VAL Chi-restraints excluded: chain F residue 700 ILE Chi-restraints excluded: chain F residue 742 ASN Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 137 PHE Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 513 ASN Chi-restraints excluded: chain G residue 613 LEU Chi-restraints excluded: chain G residue 628 ASN Chi-restraints excluded: chain G residue 646 VAL Chi-restraints excluded: chain G residue 700 ILE Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 127 MET Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 277 ILE Chi-restraints excluded: chain H residue 412 ASN Chi-restraints excluded: chain H residue 416 ASP Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 476 ILE Chi-restraints excluded: chain H residue 513 ASN Chi-restraints excluded: chain H residue 613 LEU Chi-restraints excluded: chain H residue 628 ASN Chi-restraints excluded: chain H residue 646 VAL Chi-restraints excluded: chain H residue 662 MET Chi-restraints excluded: chain H residue 700 ILE Chi-restraints excluded: chain H residue 742 ASN Chi-restraints excluded: chain I residue 46 ASP Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 164 ILE Chi-restraints excluded: chain I residue 277 ILE Chi-restraints excluded: chain I residue 412 ASN Chi-restraints excluded: chain I residue 416 ASP Chi-restraints excluded: chain I residue 510 LYS Chi-restraints excluded: chain I residue 513 ASN Chi-restraints excluded: chain I residue 628 ASN Chi-restraints excluded: chain I residue 646 VAL Chi-restraints excluded: chain I residue 700 ILE Chi-restraints excluded: chain J residue 46 ASP Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 127 MET Chi-restraints excluded: chain J residue 137 PHE Chi-restraints excluded: chain J residue 164 ILE Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 226 MET Chi-restraints excluded: chain J residue 416 ASP Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 480 ASN Chi-restraints excluded: chain J residue 513 ASN Chi-restraints excluded: chain J residue 628 ASN Chi-restraints excluded: chain J residue 646 VAL Chi-restraints excluded: chain J residue 700 ILE Chi-restraints excluded: chain K residue 46 ASP Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 127 MET Chi-restraints excluded: chain K residue 137 PHE Chi-restraints excluded: chain K residue 164 ILE Chi-restraints excluded: chain K residue 170 ILE Chi-restraints excluded: chain K residue 210 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 476 ILE Chi-restraints excluded: chain K residue 513 ASN Chi-restraints excluded: chain K residue 567 LEU Chi-restraints excluded: chain K residue 613 LEU Chi-restraints excluded: chain K residue 628 ASN Chi-restraints excluded: chain K residue 646 VAL Chi-restraints excluded: chain K residue 678 LEU Chi-restraints excluded: chain K residue 700 ILE Chi-restraints excluded: chain K residue 742 ASN Chi-restraints excluded: chain L residue 46 ASP Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 137 PHE Chi-restraints excluded: chain L residue 164 ILE Chi-restraints excluded: chain L residue 170 ILE Chi-restraints excluded: chain L residue 412 ASN Chi-restraints excluded: chain L residue 416 ASP Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 510 LYS Chi-restraints excluded: chain L residue 513 ASN Chi-restraints excluded: chain L residue 628 ASN Chi-restraints excluded: chain L residue 646 VAL Chi-restraints excluded: chain L residue 700 ILE Chi-restraints excluded: chain L residue 742 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 437 optimal weight: 9.9990 chunk 567 optimal weight: 9.9990 chunk 760 optimal weight: 5.9990 chunk 218 optimal weight: 10.0000 chunk 658 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 198 optimal weight: 8.9990 chunk 715 optimal weight: 3.9990 chunk 299 optimal weight: 50.0000 chunk 734 optimal weight: 10.0000 chunk 90 optimal weight: 0.2980 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 732 ASN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 412 ASN ** E 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 732 ASN ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 764 ASN ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 ASN ** I 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 412 ASN ** K 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 732 ASN ** L 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 764 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.072397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.053494 restraints weight = 378884.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.054583 restraints weight = 226493.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.055338 restraints weight = 163212.026| |-----------------------------------------------------------------------------| r_work (final): 0.4274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 69840 Z= 0.272 Angle : 0.692 10.330 94584 Z= 0.355 Chirality : 0.049 0.223 10620 Planarity : 0.003 0.042 12396 Dihedral : 6.429 31.756 9516 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 25.60 Ramachandran Plot: Outliers : 0.01 % Allowed : 17.61 % Favored : 82.38 % Rotamer: Outliers : 2.80 % Allowed : 14.91 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.27 (0.08), residues: 8952 helix: -1.70 (0.32), residues: 240 sheet: -2.90 (0.13), residues: 1512 loop : -3.16 (0.07), residues: 7200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 577 HIS 0.003 0.001 HIS I 469 PHE 0.016 0.002 PHE F 664 TYR 0.023 0.002 TYR B 765 ARG 0.004 0.001 ARG L 228 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10878.66 seconds wall clock time: 197 minutes 24.41 seconds (11844.41 seconds total)