Starting phenix.real_space_refine on Fri Mar 15 11:11:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyj_0544/03_2024/6nyj_0544.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyj_0544/03_2024/6nyj_0544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyj_0544/03_2024/6nyj_0544.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyj_0544/03_2024/6nyj_0544.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyj_0544/03_2024/6nyj_0544.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyj_0544/03_2024/6nyj_0544.pdb" } resolution = 3.2 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= 0.090 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 42948 2.51 5 N 12060 2.21 5 O 13512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 68664 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "B" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "C" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "D" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "E" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "F" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "G" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "H" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "I" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "J" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "K" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "L" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Time building chain proxies: 27.25, per 1000 atoms: 0.40 Number of scatterers: 68664 At special positions: 0 Unit cell: (299.98, 293.62, 119.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 13512 8.00 N 12060 7.00 C 42948 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 749 " distance=2.03 Simple disulfide: pdb=" SG CYS G 738 " - pdb=" SG CYS G 749 " distance=2.03 Simple disulfide: pdb=" SG CYS H 738 " - pdb=" SG CYS H 749 " distance=2.03 Simple disulfide: pdb=" SG CYS I 738 " - pdb=" SG CYS I 749 " distance=2.03 Simple disulfide: pdb=" SG CYS J 738 " - pdb=" SG CYS J 749 " distance=2.03 Simple disulfide: pdb=" SG CYS K 738 " - pdb=" SG CYS K 749 " distance=2.03 Simple disulfide: pdb=" SG CYS L 738 " - pdb=" SG CYS L 749 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 19.70 Conformation dependent library (CDL) restraints added in 10.7 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 180 sheets defined 6.1% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.10 Creating SS restraints... Processing helix chain 'A' and resid 29 through 38 removed outlier: 3.668A pdb=" N ALA A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 removed outlier: 4.211A pdb=" N GLU A 59 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE A 60 " --> pdb=" O PHE A 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 56 through 60' Processing helix chain 'A' and resid 71 through 75 removed outlier: 3.808A pdb=" N SER A 74 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 720 removed outlier: 3.856A pdb=" N GLU A 720 " --> pdb=" O ASN A 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 717 through 720' Processing helix chain 'A' and resid 721 through 726 Processing helix chain 'A' and resid 744 through 754 removed outlier: 4.325A pdb=" N ALA A 748 " --> pdb=" O ASP A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 765 removed outlier: 3.523A pdb=" N ASN A 764 " --> pdb=" O ASN A 761 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR A 765 " --> pdb=" O PRO A 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 761 through 765' Processing helix chain 'B' and resid 29 through 38 removed outlier: 3.668A pdb=" N ALA B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 removed outlier: 4.212A pdb=" N GLU B 59 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE B 60 " --> pdb=" O PHE B 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 56 through 60' Processing helix chain 'B' and resid 71 through 75 removed outlier: 3.808A pdb=" N SER B 74 " --> pdb=" O LEU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 720 removed outlier: 3.856A pdb=" N GLU B 720 " --> pdb=" O ASN B 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 717 through 720' Processing helix chain 'B' and resid 721 through 726 Processing helix chain 'B' and resid 744 through 754 removed outlier: 4.325A pdb=" N ALA B 748 " --> pdb=" O ASP B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 removed outlier: 3.523A pdb=" N ASN B 764 " --> pdb=" O ASN B 761 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYR B 765 " --> pdb=" O PRO B 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 761 through 765' Processing helix chain 'C' and resid 29 through 38 removed outlier: 3.667A pdb=" N ALA C 35 " --> pdb=" O GLY C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 removed outlier: 4.211A pdb=" N GLU C 59 " --> pdb=" O GLY C 56 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE C 60 " --> pdb=" O PHE C 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 56 through 60' Processing helix chain 'C' and resid 71 through 75 removed outlier: 3.808A pdb=" N SER C 74 " --> pdb=" O LEU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 720 removed outlier: 3.856A pdb=" N GLU C 720 " --> pdb=" O ASN C 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 717 through 720' Processing helix chain 'C' and resid 721 through 726 Processing helix chain 'C' and resid 744 through 754 removed outlier: 4.325A pdb=" N ALA C 748 " --> pdb=" O ASP C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 765 removed outlier: 3.524A pdb=" N ASN C 764 " --> pdb=" O ASN C 761 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYR C 765 " --> pdb=" O PRO C 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 761 through 765' Processing helix chain 'D' and resid 29 through 38 removed outlier: 3.667A pdb=" N ALA D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 removed outlier: 4.211A pdb=" N GLU D 59 " --> pdb=" O GLY D 56 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE D 60 " --> pdb=" O PHE D 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 56 through 60' Processing helix chain 'D' and resid 71 through 75 removed outlier: 3.809A pdb=" N SER D 74 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 720 removed outlier: 3.855A pdb=" N GLU D 720 " --> pdb=" O ASN D 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 717 through 720' Processing helix chain 'D' and resid 721 through 726 Processing helix chain 'D' and resid 744 through 754 removed outlier: 4.326A pdb=" N ALA D 748 " --> pdb=" O ASP D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 765 removed outlier: 3.524A pdb=" N ASN D 764 " --> pdb=" O ASN D 761 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR D 765 " --> pdb=" O PRO D 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 761 through 765' Processing helix chain 'E' and resid 29 through 38 removed outlier: 3.668A pdb=" N ALA E 35 " --> pdb=" O GLY E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 60 removed outlier: 4.211A pdb=" N GLU E 59 " --> pdb=" O GLY E 56 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE E 60 " --> pdb=" O PHE E 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 56 through 60' Processing helix chain 'E' and resid 71 through 75 removed outlier: 3.808A pdb=" N SER E 74 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 717 through 720 removed outlier: 3.855A pdb=" N GLU E 720 " --> pdb=" O ASN E 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 717 through 720' Processing helix chain 'E' and resid 721 through 726 Processing helix chain 'E' and resid 744 through 754 removed outlier: 4.325A pdb=" N ALA E 748 " --> pdb=" O ASP E 744 " (cutoff:3.500A) Processing helix chain 'E' and resid 761 through 765 removed outlier: 3.523A pdb=" N ASN E 764 " --> pdb=" O ASN E 761 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR E 765 " --> pdb=" O PRO E 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 761 through 765' Processing helix chain 'F' and resid 29 through 38 removed outlier: 3.668A pdb=" N ALA F 35 " --> pdb=" O GLY F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 60 removed outlier: 4.211A pdb=" N GLU F 59 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE F 60 " --> pdb=" O PHE F 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 56 through 60' Processing helix chain 'F' and resid 71 through 75 removed outlier: 3.808A pdb=" N SER F 74 " --> pdb=" O LEU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 717 through 720 removed outlier: 3.856A pdb=" N GLU F 720 " --> pdb=" O ASN F 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 717 through 720' Processing helix chain 'F' and resid 721 through 726 Processing helix chain 'F' and resid 744 through 754 removed outlier: 4.325A pdb=" N ALA F 748 " --> pdb=" O ASP F 744 " (cutoff:3.500A) Processing helix chain 'F' and resid 761 through 765 removed outlier: 3.524A pdb=" N ASN F 764 " --> pdb=" O ASN F 761 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYR F 765 " --> pdb=" O PRO F 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 761 through 765' Processing helix chain 'G' and resid 29 through 38 removed outlier: 3.667A pdb=" N ALA G 35 " --> pdb=" O GLY G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 60 removed outlier: 4.211A pdb=" N GLU G 59 " --> pdb=" O GLY G 56 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE G 60 " --> pdb=" O PHE G 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 56 through 60' Processing helix chain 'G' and resid 71 through 75 removed outlier: 3.809A pdb=" N SER G 74 " --> pdb=" O LEU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 717 through 720 removed outlier: 3.856A pdb=" N GLU G 720 " --> pdb=" O ASN G 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 717 through 720' Processing helix chain 'G' and resid 721 through 726 Processing helix chain 'G' and resid 744 through 754 removed outlier: 4.325A pdb=" N ALA G 748 " --> pdb=" O ASP G 744 " (cutoff:3.500A) Processing helix chain 'G' and resid 761 through 765 removed outlier: 3.523A pdb=" N ASN G 764 " --> pdb=" O ASN G 761 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR G 765 " --> pdb=" O PRO G 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 761 through 765' Processing helix chain 'H' and resid 29 through 38 removed outlier: 3.667A pdb=" N ALA H 35 " --> pdb=" O GLY H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 60 removed outlier: 4.211A pdb=" N GLU H 59 " --> pdb=" O GLY H 56 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE H 60 " --> pdb=" O PHE H 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 56 through 60' Processing helix chain 'H' and resid 71 through 75 removed outlier: 3.808A pdb=" N SER H 74 " --> pdb=" O LEU H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 717 through 720 removed outlier: 3.856A pdb=" N GLU H 720 " --> pdb=" O ASN H 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 717 through 720' Processing helix chain 'H' and resid 721 through 726 Processing helix chain 'H' and resid 744 through 754 removed outlier: 4.326A pdb=" N ALA H 748 " --> pdb=" O ASP H 744 " (cutoff:3.500A) Processing helix chain 'H' and resid 761 through 765 removed outlier: 3.523A pdb=" N ASN H 764 " --> pdb=" O ASN H 761 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR H 765 " --> pdb=" O PRO H 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 761 through 765' Processing helix chain 'I' and resid 29 through 38 removed outlier: 3.668A pdb=" N ALA I 35 " --> pdb=" O GLY I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 60 removed outlier: 4.210A pdb=" N GLU I 59 " --> pdb=" O GLY I 56 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE I 60 " --> pdb=" O PHE I 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 56 through 60' Processing helix chain 'I' and resid 71 through 75 removed outlier: 3.809A pdb=" N SER I 74 " --> pdb=" O LEU I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 717 through 720 removed outlier: 3.856A pdb=" N GLU I 720 " --> pdb=" O ASN I 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 717 through 720' Processing helix chain 'I' and resid 721 through 726 Processing helix chain 'I' and resid 744 through 754 removed outlier: 4.325A pdb=" N ALA I 748 " --> pdb=" O ASP I 744 " (cutoff:3.500A) Processing helix chain 'I' and resid 761 through 765 removed outlier: 3.524A pdb=" N ASN I 764 " --> pdb=" O ASN I 761 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR I 765 " --> pdb=" O PRO I 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 761 through 765' Processing helix chain 'J' and resid 29 through 38 removed outlier: 3.667A pdb=" N ALA J 35 " --> pdb=" O GLY J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 60 removed outlier: 4.211A pdb=" N GLU J 59 " --> pdb=" O GLY J 56 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE J 60 " --> pdb=" O PHE J 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 56 through 60' Processing helix chain 'J' and resid 71 through 75 removed outlier: 3.808A pdb=" N SER J 74 " --> pdb=" O LEU J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 717 through 720 removed outlier: 3.857A pdb=" N GLU J 720 " --> pdb=" O ASN J 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 717 through 720' Processing helix chain 'J' and resid 721 through 726 Processing helix chain 'J' and resid 744 through 754 removed outlier: 4.325A pdb=" N ALA J 748 " --> pdb=" O ASP J 744 " (cutoff:3.500A) Processing helix chain 'J' and resid 761 through 765 removed outlier: 3.524A pdb=" N ASN J 764 " --> pdb=" O ASN J 761 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR J 765 " --> pdb=" O PRO J 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 761 through 765' Processing helix chain 'K' and resid 29 through 38 removed outlier: 3.668A pdb=" N ALA K 35 " --> pdb=" O GLY K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 60 removed outlier: 4.211A pdb=" N GLU K 59 " --> pdb=" O GLY K 56 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE K 60 " --> pdb=" O PHE K 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 56 through 60' Processing helix chain 'K' and resid 71 through 75 removed outlier: 3.808A pdb=" N SER K 74 " --> pdb=" O LEU K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 717 through 720 removed outlier: 3.856A pdb=" N GLU K 720 " --> pdb=" O ASN K 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 717 through 720' Processing helix chain 'K' and resid 721 through 726 Processing helix chain 'K' and resid 744 through 754 removed outlier: 4.325A pdb=" N ALA K 748 " --> pdb=" O ASP K 744 " (cutoff:3.500A) Processing helix chain 'K' and resid 761 through 765 removed outlier: 3.524A pdb=" N ASN K 764 " --> pdb=" O ASN K 761 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYR K 765 " --> pdb=" O PRO K 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 761 through 765' Processing helix chain 'L' and resid 29 through 38 removed outlier: 3.667A pdb=" N ALA L 35 " --> pdb=" O GLY L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 60 removed outlier: 4.211A pdb=" N GLU L 59 " --> pdb=" O GLY L 56 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE L 60 " --> pdb=" O PHE L 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 56 through 60' Processing helix chain 'L' and resid 71 through 75 removed outlier: 3.808A pdb=" N SER L 74 " --> pdb=" O LEU L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 717 through 720 removed outlier: 3.856A pdb=" N GLU L 720 " --> pdb=" O ASN L 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 717 through 720' Processing helix chain 'L' and resid 721 through 726 Processing helix chain 'L' and resid 744 through 754 removed outlier: 4.324A pdb=" N ALA L 748 " --> pdb=" O ASP L 744 " (cutoff:3.500A) Processing helix chain 'L' and resid 761 through 765 removed outlier: 3.524A pdb=" N ASN L 764 " --> pdb=" O ASN L 761 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR L 765 " --> pdb=" O PRO L 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 761 through 765' Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 126 removed outlier: 8.278A pdb=" N ASN A 126 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL A 101 " --> pdb=" O ASN A 126 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TRP A 49 " --> pdb=" O GLU A 100 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASP A 102 " --> pdb=" O TRP A 49 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE A 51 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ARG A 50 " --> pdb=" O GLN B 343 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE B 345 " --> pdb=" O ARG A 50 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLN A 52 " --> pdb=" O ILE B 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 79 removed outlier: 3.539A pdb=" N HIS A 88 " --> pdb=" O GLY A 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 142 removed outlier: 6.455A pdb=" N ASN A 140 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU A 168 " --> pdb=" O SER A 204 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE A 203 " --> pdb=" O TRP A 225 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL A 224 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU A 257 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU A 280 " --> pdb=" O ASN A 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 155 through 157 removed outlier: 6.630A pdb=" N VAL A 155 " --> pdb=" O THR A 188 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU A 187 " --> pdb=" O ASN A 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 252 through 253 removed outlier: 6.296A pdb=" N VAL A 252 " --> pdb=" O HIS A 276 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 269 through 270 removed outlier: 6.730A pdb=" N ILE A 269 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 381 " --> pdb=" O GLU A 407 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 343 through 345 removed outlier: 6.368A pdb=" N TRP F 49 " --> pdb=" O GLU F 100 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASP F 102 " --> pdb=" O TRP F 49 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE F 51 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N ASN F 126 " --> pdb=" O LEU F 99 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL F 101 " --> pdb=" O ASN F 126 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 476 through 477 removed outlier: 6.457A pdb=" N ILE A 476 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU A 500 " --> pdb=" O ILE A 518 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU A 517 " --> pdb=" O ARG A 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 530 through 535 removed outlier: 3.587A pdb=" N LYS A 562 " --> pdb=" O PHE A 532 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLU A 534 " --> pdb=" O LYS A 562 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 541 through 542 removed outlier: 3.833A pdb=" N LEU A 567 " --> pdb=" O ASN A 587 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 589 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL A 588 " --> pdb=" O THR A 614 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 572 through 573 removed outlier: 6.283A pdb=" N PHE A 572 " --> pdb=" O ALA A 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 621 through 623 removed outlier: 3.626A pdb=" N LEU A 645 " --> pdb=" O TYR A 623 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE A 642 " --> pdb=" O LYS A 680 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASN A 682 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR A 644 " --> pdb=" O ASN A 682 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 662 through 664 Processing sheet with id=AB5, first strand: chain 'A' and resid 691 through 697 removed outlier: 4.067A pdb=" N THR A 691 " --> pdb=" O TYR A 791 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR A 791 " --> pdb=" O THR A 691 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE A 787 " --> pdb=" O LEU A 695 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 729 through 730 Processing sheet with id=AB7, first strand: chain 'A' and resid 737 through 740 removed outlier: 3.684A pdb=" N TRP A 773 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 771 " --> pdb=" O VAL A 740 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 125 through 126 removed outlier: 8.279A pdb=" N ASN B 126 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL B 101 " --> pdb=" O ASN B 126 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TRP B 49 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASP B 102 " --> pdb=" O TRP B 49 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE B 51 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ARG B 50 " --> pdb=" O GLN C 343 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE C 345 " --> pdb=" O ARG B 50 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLN B 52 " --> pdb=" O ILE C 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 78 through 79 removed outlier: 3.539A pdb=" N HIS B 88 " --> pdb=" O GLY B 79 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 140 through 142 removed outlier: 6.455A pdb=" N ASN B 140 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU B 168 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE B 203 " --> pdb=" O TRP B 225 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL B 224 " --> pdb=" O THR B 258 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU B 257 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU B 280 " --> pdb=" O ASN B 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 155 through 157 removed outlier: 6.630A pdb=" N VAL B 155 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU B 187 " --> pdb=" O ASN B 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 252 through 253 removed outlier: 6.297A pdb=" N VAL B 252 " --> pdb=" O HIS B 276 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 269 through 270 removed outlier: 6.730A pdb=" N ILE B 269 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR B 381 " --> pdb=" O GLU B 407 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 476 through 477 removed outlier: 6.457A pdb=" N ILE B 476 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU B 500 " --> pdb=" O ILE B 518 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU B 517 " --> pdb=" O ARG B 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 530 through 535 removed outlier: 3.587A pdb=" N LYS B 562 " --> pdb=" O PHE B 532 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLU B 534 " --> pdb=" O LYS B 562 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 541 through 542 removed outlier: 3.833A pdb=" N LEU B 567 " --> pdb=" O ASN B 587 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU B 589 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL B 588 " --> pdb=" O THR B 614 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 572 through 573 removed outlier: 6.284A pdb=" N PHE B 572 " --> pdb=" O ALA B 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 621 through 623 removed outlier: 3.626A pdb=" N LEU B 645 " --> pdb=" O TYR B 623 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE B 642 " --> pdb=" O LYS B 680 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASN B 682 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR B 644 " --> pdb=" O ASN B 682 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 662 through 664 Processing sheet with id=AD2, first strand: chain 'B' and resid 691 through 697 removed outlier: 4.067A pdb=" N THR B 691 " --> pdb=" O TYR B 791 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR B 791 " --> pdb=" O THR B 691 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE B 787 " --> pdb=" O LEU B 695 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 729 through 730 Processing sheet with id=AD4, first strand: chain 'B' and resid 737 through 740 removed outlier: 3.684A pdb=" N TRP B 773 " --> pdb=" O CYS B 738 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 771 " --> pdb=" O VAL B 740 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 125 through 126 removed outlier: 8.278A pdb=" N ASN C 126 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL C 101 " --> pdb=" O ASN C 126 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TRP C 49 " --> pdb=" O GLU C 100 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASP C 102 " --> pdb=" O TRP C 49 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE C 51 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ARG C 50 " --> pdb=" O GLN D 343 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ILE D 345 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLN C 52 " --> pdb=" O ILE D 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'C' and resid 78 through 79 removed outlier: 3.539A pdb=" N HIS C 88 " --> pdb=" O GLY C 79 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 140 through 142 removed outlier: 6.456A pdb=" N ASN C 140 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU C 168 " --> pdb=" O SER C 204 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE C 203 " --> pdb=" O TRP C 225 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL C 224 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU C 257 " --> pdb=" O ASP C 281 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU C 280 " --> pdb=" O ASN C 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'C' and resid 155 through 157 removed outlier: 6.630A pdb=" N VAL C 155 " --> pdb=" O THR C 188 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU C 187 " --> pdb=" O ASN C 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 252 through 253 removed outlier: 6.296A pdb=" N VAL C 252 " --> pdb=" O HIS C 276 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 269 through 270 removed outlier: 6.729A pdb=" N ILE C 269 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR C 381 " --> pdb=" O GLU C 407 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 476 through 477 removed outlier: 6.457A pdb=" N ILE C 476 " --> pdb=" O ILE C 501 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU C 500 " --> pdb=" O ILE C 518 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU C 517 " --> pdb=" O ARG C 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 530 through 535 removed outlier: 3.587A pdb=" N LYS C 562 " --> pdb=" O PHE C 532 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLU C 534 " --> pdb=" O LYS C 562 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 541 through 542 removed outlier: 3.834A pdb=" N LEU C 567 " --> pdb=" O ASN C 587 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU C 589 " --> pdb=" O LEU C 567 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL C 588 " --> pdb=" O THR C 614 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 572 through 573 removed outlier: 6.283A pdb=" N PHE C 572 " --> pdb=" O ALA C 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 621 through 623 removed outlier: 3.626A pdb=" N LEU C 645 " --> pdb=" O TYR C 623 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE C 642 " --> pdb=" O LYS C 680 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ASN C 682 " --> pdb=" O ILE C 642 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR C 644 " --> pdb=" O ASN C 682 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 662 through 664 Processing sheet with id=AE8, first strand: chain 'C' and resid 691 through 697 removed outlier: 4.068A pdb=" N THR C 691 " --> pdb=" O TYR C 791 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR C 791 " --> pdb=" O THR C 691 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILE C 787 " --> pdb=" O LEU C 695 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 729 through 730 Processing sheet with id=AF1, first strand: chain 'C' and resid 737 through 740 removed outlier: 3.684A pdb=" N TRP C 773 " --> pdb=" O CYS C 738 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS C 771 " --> pdb=" O VAL C 740 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 125 through 126 removed outlier: 8.278A pdb=" N ASN D 126 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL D 101 " --> pdb=" O ASN D 126 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TRP D 49 " --> pdb=" O GLU D 100 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASP D 102 " --> pdb=" O TRP D 49 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE D 51 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ARG D 50 " --> pdb=" O GLN E 343 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ILE E 345 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLN D 52 " --> pdb=" O ILE E 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'D' and resid 78 through 79 removed outlier: 3.539A pdb=" N HIS D 88 " --> pdb=" O GLY D 79 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 140 through 142 removed outlier: 6.456A pdb=" N ASN D 140 " --> pdb=" O GLU D 169 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU D 168 " --> pdb=" O SER D 204 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE D 203 " --> pdb=" O TRP D 225 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL D 224 " --> pdb=" O THR D 258 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU D 257 " --> pdb=" O ASP D 281 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU D 280 " --> pdb=" O ASN D 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'D' and resid 155 through 157 removed outlier: 6.630A pdb=" N VAL D 155 " --> pdb=" O THR D 188 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU D 187 " --> pdb=" O ASN D 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'D' and resid 252 through 253 removed outlier: 6.296A pdb=" N VAL D 252 " --> pdb=" O HIS D 276 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 269 through 270 removed outlier: 6.729A pdb=" N ILE D 269 " --> pdb=" O ILE D 291 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR D 381 " --> pdb=" O GLU D 407 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 476 through 477 removed outlier: 6.457A pdb=" N ILE D 476 " --> pdb=" O ILE D 501 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU D 500 " --> pdb=" O ILE D 518 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU D 517 " --> pdb=" O ARG D 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'D' and resid 530 through 535 removed outlier: 3.586A pdb=" N LYS D 562 " --> pdb=" O PHE D 532 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLU D 534 " --> pdb=" O LYS D 562 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 541 through 542 removed outlier: 3.833A pdb=" N LEU D 567 " --> pdb=" O ASN D 587 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU D 589 " --> pdb=" O LEU D 567 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL D 588 " --> pdb=" O THR D 614 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 572 through 573 removed outlier: 6.283A pdb=" N PHE D 572 " --> pdb=" O ALA D 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'D' and resid 621 through 623 removed outlier: 3.625A pdb=" N LEU D 645 " --> pdb=" O TYR D 623 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE D 642 " --> pdb=" O LYS D 680 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASN D 682 " --> pdb=" O ILE D 642 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR D 644 " --> pdb=" O ASN D 682 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 662 through 664 Processing sheet with id=AG5, first strand: chain 'D' and resid 691 through 697 removed outlier: 4.067A pdb=" N THR D 691 " --> pdb=" O TYR D 791 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TYR D 791 " --> pdb=" O THR D 691 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE D 787 " --> pdb=" O LEU D 695 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 729 through 730 Processing sheet with id=AG7, first strand: chain 'D' and resid 737 through 740 removed outlier: 3.683A pdb=" N TRP D 773 " --> pdb=" O CYS D 738 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS D 771 " --> pdb=" O VAL D 740 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 125 through 126 removed outlier: 8.278A pdb=" N ASN E 126 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL E 101 " --> pdb=" O ASN E 126 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TRP E 49 " --> pdb=" O GLU E 100 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASP E 102 " --> pdb=" O TRP E 49 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE E 51 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ARG E 50 " --> pdb=" O GLN F 343 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ILE F 345 " --> pdb=" O ARG E 50 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLN E 52 " --> pdb=" O ILE F 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'E' and resid 78 through 79 removed outlier: 3.539A pdb=" N HIS E 88 " --> pdb=" O GLY E 79 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 140 through 142 removed outlier: 6.455A pdb=" N ASN E 140 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU E 168 " --> pdb=" O SER E 204 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE E 203 " --> pdb=" O TRP E 225 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL E 224 " --> pdb=" O THR E 258 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU E 257 " --> pdb=" O ASP E 281 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU E 280 " --> pdb=" O ASN E 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'E' and resid 155 through 157 removed outlier: 6.630A pdb=" N VAL E 155 " --> pdb=" O THR E 188 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU E 187 " --> pdb=" O ASN E 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'E' and resid 252 through 253 removed outlier: 6.296A pdb=" N VAL E 252 " --> pdb=" O HIS E 276 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 269 through 270 removed outlier: 6.730A pdb=" N ILE E 269 " --> pdb=" O ILE E 291 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR E 381 " --> pdb=" O GLU E 407 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 476 through 477 removed outlier: 6.457A pdb=" N ILE E 476 " --> pdb=" O ILE E 501 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU E 500 " --> pdb=" O ILE E 518 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU E 517 " --> pdb=" O ARG E 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'E' and resid 530 through 535 removed outlier: 3.586A pdb=" N LYS E 562 " --> pdb=" O PHE E 532 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLU E 534 " --> pdb=" O LYS E 562 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'E' and resid 541 through 542 removed outlier: 3.834A pdb=" N LEU E 567 " --> pdb=" O ASN E 587 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU E 589 " --> pdb=" O LEU E 567 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL E 588 " --> pdb=" O THR E 614 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'E' and resid 572 through 573 removed outlier: 6.283A pdb=" N PHE E 572 " --> pdb=" O ALA E 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'E' and resid 621 through 623 removed outlier: 3.626A pdb=" N LEU E 645 " --> pdb=" O TYR E 623 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE E 642 " --> pdb=" O LYS E 680 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ASN E 682 " --> pdb=" O ILE E 642 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR E 644 " --> pdb=" O ASN E 682 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'E' and resid 662 through 664 Processing sheet with id=AI2, first strand: chain 'E' and resid 691 through 697 removed outlier: 4.067A pdb=" N THR E 691 " --> pdb=" O TYR E 791 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TYR E 791 " --> pdb=" O THR E 691 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE E 787 " --> pdb=" O LEU E 695 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'E' and resid 729 through 730 Processing sheet with id=AI4, first strand: chain 'E' and resid 737 through 740 removed outlier: 3.683A pdb=" N TRP E 773 " --> pdb=" O CYS E 738 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS E 771 " --> pdb=" O VAL E 740 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'F' and resid 78 through 79 removed outlier: 3.539A pdb=" N HIS F 88 " --> pdb=" O GLY F 79 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'F' and resid 140 through 142 removed outlier: 6.456A pdb=" N ASN F 140 " --> pdb=" O GLU F 169 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU F 168 " --> pdb=" O SER F 204 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE F 203 " --> pdb=" O TRP F 225 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL F 224 " --> pdb=" O THR F 258 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU F 257 " --> pdb=" O ASP F 281 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU F 280 " --> pdb=" O ASN F 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'F' and resid 155 through 157 removed outlier: 6.631A pdb=" N VAL F 155 " --> pdb=" O THR F 188 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU F 187 " --> pdb=" O ASN F 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI7 Processing sheet with id=AI8, first strand: chain 'F' and resid 252 through 253 removed outlier: 6.297A pdb=" N VAL F 252 " --> pdb=" O HIS F 276 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'F' and resid 269 through 270 removed outlier: 6.730A pdb=" N ILE F 269 " --> pdb=" O ILE F 291 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR F 381 " --> pdb=" O GLU F 407 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'F' and resid 476 through 477 removed outlier: 6.457A pdb=" N ILE F 476 " --> pdb=" O ILE F 501 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU F 500 " --> pdb=" O ILE F 518 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU F 517 " --> pdb=" O ARG F 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ1 Processing sheet with id=AJ2, first strand: chain 'F' and resid 530 through 535 removed outlier: 3.587A pdb=" N LYS F 562 " --> pdb=" O PHE F 532 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLU F 534 " --> pdb=" O LYS F 562 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'F' and resid 541 through 542 removed outlier: 3.833A pdb=" N LEU F 567 " --> pdb=" O ASN F 587 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU F 589 " --> pdb=" O LEU F 567 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL F 588 " --> pdb=" O THR F 614 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'F' and resid 572 through 573 removed outlier: 6.283A pdb=" N PHE F 572 " --> pdb=" O ALA F 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ4 Processing sheet with id=AJ5, first strand: chain 'F' and resid 621 through 623 removed outlier: 3.626A pdb=" N LEU F 645 " --> pdb=" O TYR F 623 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE F 642 " --> pdb=" O LYS F 680 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ASN F 682 " --> pdb=" O ILE F 642 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR F 644 " --> pdb=" O ASN F 682 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'F' and resid 662 through 664 Processing sheet with id=AJ7, first strand: chain 'F' and resid 691 through 697 removed outlier: 4.067A pdb=" N THR F 691 " --> pdb=" O TYR F 791 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR F 791 " --> pdb=" O THR F 691 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE F 787 " --> pdb=" O LEU F 695 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'F' and resid 729 through 730 Processing sheet with id=AJ9, first strand: chain 'F' and resid 737 through 740 removed outlier: 3.684A pdb=" N TRP F 773 " --> pdb=" O CYS F 738 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS F 771 " --> pdb=" O VAL F 740 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'G' and resid 125 through 126 removed outlier: 8.278A pdb=" N ASN G 126 " --> pdb=" O LEU G 99 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL G 101 " --> pdb=" O ASN G 126 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TRP G 49 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASP G 102 " --> pdb=" O TRP G 49 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE G 51 " --> pdb=" O ASP G 102 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ARG G 50 " --> pdb=" O GLN H 343 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ILE H 345 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLN G 52 " --> pdb=" O ILE H 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK1 Processing sheet with id=AK2, first strand: chain 'G' and resid 78 through 79 removed outlier: 3.539A pdb=" N HIS G 88 " --> pdb=" O GLY G 79 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'G' and resid 140 through 142 removed outlier: 6.455A pdb=" N ASN G 140 " --> pdb=" O GLU G 169 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU G 168 " --> pdb=" O SER G 204 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE G 203 " --> pdb=" O TRP G 225 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL G 224 " --> pdb=" O THR G 258 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU G 257 " --> pdb=" O ASP G 281 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU G 280 " --> pdb=" O ASN G 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK3 Processing sheet with id=AK4, first strand: chain 'G' and resid 155 through 157 removed outlier: 6.630A pdb=" N VAL G 155 " --> pdb=" O THR G 188 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU G 187 " --> pdb=" O ASN G 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK4 Processing sheet with id=AK5, first strand: chain 'G' and resid 252 through 253 removed outlier: 6.297A pdb=" N VAL G 252 " --> pdb=" O HIS G 276 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'G' and resid 269 through 270 removed outlier: 6.730A pdb=" N ILE G 269 " --> pdb=" O ILE G 291 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR G 381 " --> pdb=" O GLU G 407 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'G' and resid 343 through 345 removed outlier: 6.368A pdb=" N TRP L 49 " --> pdb=" O GLU L 100 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASP L 102 " --> pdb=" O TRP L 49 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE L 51 " --> pdb=" O ASP L 102 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N ASN L 126 " --> pdb=" O LEU L 99 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL L 101 " --> pdb=" O ASN L 126 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'G' and resid 476 through 477 removed outlier: 6.456A pdb=" N ILE G 476 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU G 500 " --> pdb=" O ILE G 518 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU G 517 " --> pdb=" O ARG G 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK8 Processing sheet with id=AK9, first strand: chain 'G' and resid 530 through 535 removed outlier: 3.586A pdb=" N LYS G 562 " --> pdb=" O PHE G 532 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLU G 534 " --> pdb=" O LYS G 562 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'G' and resid 541 through 542 removed outlier: 3.834A pdb=" N LEU G 567 " --> pdb=" O ASN G 587 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU G 589 " --> pdb=" O LEU G 567 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL G 588 " --> pdb=" O THR G 614 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'G' and resid 572 through 573 removed outlier: 6.283A pdb=" N PHE G 572 " --> pdb=" O ALA G 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL2 Processing sheet with id=AL3, first strand: chain 'G' and resid 621 through 623 removed outlier: 3.625A pdb=" N LEU G 645 " --> pdb=" O TYR G 623 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE G 642 " --> pdb=" O LYS G 680 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ASN G 682 " --> pdb=" O ILE G 642 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR G 644 " --> pdb=" O ASN G 682 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'G' and resid 662 through 664 Processing sheet with id=AL5, first strand: chain 'G' and resid 691 through 697 removed outlier: 4.067A pdb=" N THR G 691 " --> pdb=" O TYR G 791 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR G 791 " --> pdb=" O THR G 691 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE G 787 " --> pdb=" O LEU G 695 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'G' and resid 729 through 730 Processing sheet with id=AL7, first strand: chain 'G' and resid 737 through 740 removed outlier: 3.684A pdb=" N TRP G 773 " --> pdb=" O CYS G 738 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS G 771 " --> pdb=" O VAL G 740 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'H' and resid 125 through 126 removed outlier: 8.278A pdb=" N ASN H 126 " --> pdb=" O LEU H 99 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL H 101 " --> pdb=" O ASN H 126 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TRP H 49 " --> pdb=" O GLU H 100 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASP H 102 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE H 51 " --> pdb=" O ASP H 102 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ARG H 50 " --> pdb=" O GLN I 343 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE I 345 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLN H 52 " --> pdb=" O ILE I 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL8 Processing sheet with id=AL9, first strand: chain 'H' and resid 78 through 79 removed outlier: 3.540A pdb=" N HIS H 88 " --> pdb=" O GLY H 79 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'H' and resid 140 through 142 removed outlier: 6.456A pdb=" N ASN H 140 " --> pdb=" O GLU H 169 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU H 168 " --> pdb=" O SER H 204 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE H 203 " --> pdb=" O TRP H 225 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL H 224 " --> pdb=" O THR H 258 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU H 257 " --> pdb=" O ASP H 281 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU H 280 " --> pdb=" O ASN H 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM1 Processing sheet with id=AM2, first strand: chain 'H' and resid 155 through 157 removed outlier: 6.630A pdb=" N VAL H 155 " --> pdb=" O THR H 188 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU H 187 " --> pdb=" O ASN H 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM2 Processing sheet with id=AM3, first strand: chain 'H' and resid 252 through 253 removed outlier: 6.297A pdb=" N VAL H 252 " --> pdb=" O HIS H 276 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'H' and resid 269 through 270 removed outlier: 6.729A pdb=" N ILE H 269 " --> pdb=" O ILE H 291 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR H 381 " --> pdb=" O GLU H 407 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'H' and resid 476 through 477 removed outlier: 6.457A pdb=" N ILE H 476 " --> pdb=" O ILE H 501 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU H 500 " --> pdb=" O ILE H 518 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU H 517 " --> pdb=" O ARG H 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM5 Processing sheet with id=AM6, first strand: chain 'H' and resid 530 through 535 removed outlier: 3.587A pdb=" N LYS H 562 " --> pdb=" O PHE H 532 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLU H 534 " --> pdb=" O LYS H 562 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'H' and resid 541 through 542 removed outlier: 3.833A pdb=" N LEU H 567 " --> pdb=" O ASN H 587 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU H 589 " --> pdb=" O LEU H 567 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL H 588 " --> pdb=" O THR H 614 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'H' and resid 572 through 573 removed outlier: 6.282A pdb=" N PHE H 572 " --> pdb=" O ALA H 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM8 Processing sheet with id=AM9, first strand: chain 'H' and resid 621 through 623 removed outlier: 3.626A pdb=" N LEU H 645 " --> pdb=" O TYR H 623 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE H 642 " --> pdb=" O LYS H 680 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASN H 682 " --> pdb=" O ILE H 642 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR H 644 " --> pdb=" O ASN H 682 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'H' and resid 662 through 664 Processing sheet with id=AN2, first strand: chain 'H' and resid 691 through 697 removed outlier: 4.068A pdb=" N THR H 691 " --> pdb=" O TYR H 791 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR H 791 " --> pdb=" O THR H 691 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILE H 787 " --> pdb=" O LEU H 695 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'H' and resid 729 through 730 Processing sheet with id=AN4, first strand: chain 'H' and resid 737 through 740 removed outlier: 3.683A pdb=" N TRP H 773 " --> pdb=" O CYS H 738 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS H 771 " --> pdb=" O VAL H 740 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'I' and resid 125 through 126 removed outlier: 8.278A pdb=" N ASN I 126 " --> pdb=" O LEU I 99 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL I 101 " --> pdb=" O ASN I 126 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TRP I 49 " --> pdb=" O GLU I 100 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASP I 102 " --> pdb=" O TRP I 49 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE I 51 " --> pdb=" O ASP I 102 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ARG I 50 " --> pdb=" O GLN J 343 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE J 345 " --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLN I 52 " --> pdb=" O ILE J 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN5 Processing sheet with id=AN6, first strand: chain 'I' and resid 78 through 79 removed outlier: 3.539A pdb=" N HIS I 88 " --> pdb=" O GLY I 79 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'I' and resid 140 through 142 removed outlier: 6.456A pdb=" N ASN I 140 " --> pdb=" O GLU I 169 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU I 168 " --> pdb=" O SER I 204 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE I 203 " --> pdb=" O TRP I 225 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL I 224 " --> pdb=" O THR I 258 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU I 257 " --> pdb=" O ASP I 281 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU I 280 " --> pdb=" O ASN I 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN7 Processing sheet with id=AN8, first strand: chain 'I' and resid 155 through 157 removed outlier: 6.631A pdb=" N VAL I 155 " --> pdb=" O THR I 188 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU I 187 " --> pdb=" O ASN I 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN8 Processing sheet with id=AN9, first strand: chain 'I' and resid 252 through 253 removed outlier: 6.297A pdb=" N VAL I 252 " --> pdb=" O HIS I 276 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain 'I' and resid 269 through 270 removed outlier: 6.729A pdb=" N ILE I 269 " --> pdb=" O ILE I 291 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR I 381 " --> pdb=" O GLU I 407 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'I' and resid 476 through 477 removed outlier: 6.457A pdb=" N ILE I 476 " --> pdb=" O ILE I 501 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU I 500 " --> pdb=" O ILE I 518 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU I 517 " --> pdb=" O ARG I 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AO2 Processing sheet with id=AO3, first strand: chain 'I' and resid 530 through 535 removed outlier: 3.586A pdb=" N LYS I 562 " --> pdb=" O PHE I 532 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLU I 534 " --> pdb=" O LYS I 562 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'I' and resid 541 through 542 removed outlier: 3.833A pdb=" N LEU I 567 " --> pdb=" O ASN I 587 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU I 589 " --> pdb=" O LEU I 567 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL I 588 " --> pdb=" O THR I 614 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'I' and resid 572 through 573 removed outlier: 6.284A pdb=" N PHE I 572 " --> pdb=" O ALA I 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AO5 Processing sheet with id=AO6, first strand: chain 'I' and resid 621 through 623 removed outlier: 3.625A pdb=" N LEU I 645 " --> pdb=" O TYR I 623 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE I 642 " --> pdb=" O LYS I 680 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ASN I 682 " --> pdb=" O ILE I 642 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR I 644 " --> pdb=" O ASN I 682 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'I' and resid 662 through 664 Processing sheet with id=AO8, first strand: chain 'I' and resid 691 through 697 removed outlier: 4.067A pdb=" N THR I 691 " --> pdb=" O TYR I 791 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TYR I 791 " --> pdb=" O THR I 691 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE I 787 " --> pdb=" O LEU I 695 " (cutoff:3.500A) Processing sheet with id=AO9, first strand: chain 'I' and resid 729 through 730 Processing sheet with id=AP1, first strand: chain 'I' and resid 737 through 740 removed outlier: 3.684A pdb=" N TRP I 773 " --> pdb=" O CYS I 738 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS I 771 " --> pdb=" O VAL I 740 " (cutoff:3.500A) Processing sheet with id=AP2, first strand: chain 'J' and resid 125 through 126 removed outlier: 8.278A pdb=" N ASN J 126 " --> pdb=" O LEU J 99 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL J 101 " --> pdb=" O ASN J 126 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TRP J 49 " --> pdb=" O GLU J 100 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASP J 102 " --> pdb=" O TRP J 49 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE J 51 " --> pdb=" O ASP J 102 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ARG J 50 " --> pdb=" O GLN K 343 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE K 345 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLN J 52 " --> pdb=" O ILE K 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AP2 Processing sheet with id=AP3, first strand: chain 'J' and resid 78 through 79 removed outlier: 3.539A pdb=" N HIS J 88 " --> pdb=" O GLY J 79 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'J' and resid 140 through 142 removed outlier: 6.455A pdb=" N ASN J 140 " --> pdb=" O GLU J 169 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU J 168 " --> pdb=" O SER J 204 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE J 203 " --> pdb=" O TRP J 225 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL J 224 " --> pdb=" O THR J 258 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU J 257 " --> pdb=" O ASP J 281 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU J 280 " --> pdb=" O ASN J 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AP4 Processing sheet with id=AP5, first strand: chain 'J' and resid 155 through 157 removed outlier: 6.630A pdb=" N VAL J 155 " --> pdb=" O THR J 188 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU J 187 " --> pdb=" O ASN J 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AP5 Processing sheet with id=AP6, first strand: chain 'J' and resid 252 through 253 removed outlier: 6.298A pdb=" N VAL J 252 " --> pdb=" O HIS J 276 " (cutoff:3.500A) Processing sheet with id=AP7, first strand: chain 'J' and resid 269 through 270 removed outlier: 6.729A pdb=" N ILE J 269 " --> pdb=" O ILE J 291 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR J 381 " --> pdb=" O GLU J 407 " (cutoff:3.500A) Processing sheet with id=AP8, first strand: chain 'J' and resid 476 through 477 removed outlier: 6.457A pdb=" N ILE J 476 " --> pdb=" O ILE J 501 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU J 500 " --> pdb=" O ILE J 518 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU J 517 " --> pdb=" O ARG J 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AP8 Processing sheet with id=AP9, first strand: chain 'J' and resid 530 through 535 removed outlier: 3.587A pdb=" N LYS J 562 " --> pdb=" O PHE J 532 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLU J 534 " --> pdb=" O LYS J 562 " (cutoff:3.500A) Processing sheet with id=AQ1, first strand: chain 'J' and resid 541 through 542 removed outlier: 3.833A pdb=" N LEU J 567 " --> pdb=" O ASN J 587 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU J 589 " --> pdb=" O LEU J 567 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL J 588 " --> pdb=" O THR J 614 " (cutoff:3.500A) Processing sheet with id=AQ2, first strand: chain 'J' and resid 572 through 573 removed outlier: 6.283A pdb=" N PHE J 572 " --> pdb=" O ALA J 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AQ2 Processing sheet with id=AQ3, first strand: chain 'J' and resid 621 through 623 removed outlier: 3.625A pdb=" N LEU J 645 " --> pdb=" O TYR J 623 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE J 642 " --> pdb=" O LYS J 680 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ASN J 682 " --> pdb=" O ILE J 642 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR J 644 " --> pdb=" O ASN J 682 " (cutoff:3.500A) Processing sheet with id=AQ4, first strand: chain 'J' and resid 662 through 664 Processing sheet with id=AQ5, first strand: chain 'J' and resid 691 through 697 removed outlier: 4.067A pdb=" N THR J 691 " --> pdb=" O TYR J 791 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR J 791 " --> pdb=" O THR J 691 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE J 787 " --> pdb=" O LEU J 695 " (cutoff:3.500A) Processing sheet with id=AQ6, first strand: chain 'J' and resid 729 through 730 Processing sheet with id=AQ7, first strand: chain 'J' and resid 737 through 740 removed outlier: 3.684A pdb=" N TRP J 773 " --> pdb=" O CYS J 738 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS J 771 " --> pdb=" O VAL J 740 " (cutoff:3.500A) Processing sheet with id=AQ8, first strand: chain 'K' and resid 125 through 126 removed outlier: 8.279A pdb=" N ASN K 126 " --> pdb=" O LEU K 99 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL K 101 " --> pdb=" O ASN K 126 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TRP K 49 " --> pdb=" O GLU K 100 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASP K 102 " --> pdb=" O TRP K 49 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE K 51 " --> pdb=" O ASP K 102 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ARG K 50 " --> pdb=" O GLN L 343 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ILE L 345 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLN K 52 " --> pdb=" O ILE L 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AQ8 Processing sheet with id=AQ9, first strand: chain 'K' and resid 78 through 79 removed outlier: 3.539A pdb=" N HIS K 88 " --> pdb=" O GLY K 79 " (cutoff:3.500A) Processing sheet with id=AR1, first strand: chain 'K' and resid 140 through 142 removed outlier: 6.456A pdb=" N ASN K 140 " --> pdb=" O GLU K 169 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU K 168 " --> pdb=" O SER K 204 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE K 203 " --> pdb=" O TRP K 225 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL K 224 " --> pdb=" O THR K 258 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU K 257 " --> pdb=" O ASP K 281 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU K 280 " --> pdb=" O ASN K 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AR1 Processing sheet with id=AR2, first strand: chain 'K' and resid 155 through 157 removed outlier: 6.630A pdb=" N VAL K 155 " --> pdb=" O THR K 188 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU K 187 " --> pdb=" O ASN K 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AR2 Processing sheet with id=AR3, first strand: chain 'K' and resid 252 through 253 removed outlier: 6.297A pdb=" N VAL K 252 " --> pdb=" O HIS K 276 " (cutoff:3.500A) Processing sheet with id=AR4, first strand: chain 'K' and resid 269 through 270 removed outlier: 6.730A pdb=" N ILE K 269 " --> pdb=" O ILE K 291 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR K 381 " --> pdb=" O GLU K 407 " (cutoff:3.500A) Processing sheet with id=AR5, first strand: chain 'K' and resid 476 through 477 removed outlier: 6.457A pdb=" N ILE K 476 " --> pdb=" O ILE K 501 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU K 500 " --> pdb=" O ILE K 518 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU K 517 " --> pdb=" O ARG K 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AR5 Processing sheet with id=AR6, first strand: chain 'K' and resid 530 through 535 removed outlier: 3.586A pdb=" N LYS K 562 " --> pdb=" O PHE K 532 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLU K 534 " --> pdb=" O LYS K 562 " (cutoff:3.500A) Processing sheet with id=AR7, first strand: chain 'K' and resid 541 through 542 removed outlier: 3.834A pdb=" N LEU K 567 " --> pdb=" O ASN K 587 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU K 589 " --> pdb=" O LEU K 567 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL K 588 " --> pdb=" O THR K 614 " (cutoff:3.500A) Processing sheet with id=AR8, first strand: chain 'K' and resid 572 through 573 removed outlier: 6.283A pdb=" N PHE K 572 " --> pdb=" O ALA K 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AR8 Processing sheet with id=AR9, first strand: chain 'K' and resid 621 through 623 removed outlier: 3.625A pdb=" N LEU K 645 " --> pdb=" O TYR K 623 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE K 642 " --> pdb=" O LYS K 680 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASN K 682 " --> pdb=" O ILE K 642 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR K 644 " --> pdb=" O ASN K 682 " (cutoff:3.500A) Processing sheet with id=AS1, first strand: chain 'K' and resid 662 through 664 Processing sheet with id=AS2, first strand: chain 'K' and resid 691 through 697 removed outlier: 4.067A pdb=" N THR K 691 " --> pdb=" O TYR K 791 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR K 791 " --> pdb=" O THR K 691 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILE K 787 " --> pdb=" O LEU K 695 " (cutoff:3.500A) Processing sheet with id=AS3, first strand: chain 'K' and resid 729 through 730 Processing sheet with id=AS4, first strand: chain 'K' and resid 737 through 740 removed outlier: 3.683A pdb=" N TRP K 773 " --> pdb=" O CYS K 738 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS K 771 " --> pdb=" O VAL K 740 " (cutoff:3.500A) Processing sheet with id=AS5, first strand: chain 'L' and resid 78 through 79 removed outlier: 3.538A pdb=" N HIS L 88 " --> pdb=" O GLY L 79 " (cutoff:3.500A) Processing sheet with id=AS6, first strand: chain 'L' and resid 140 through 142 removed outlier: 6.455A pdb=" N ASN L 140 " --> pdb=" O GLU L 169 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU L 168 " --> pdb=" O SER L 204 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE L 203 " --> pdb=" O TRP L 225 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL L 224 " --> pdb=" O THR L 258 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU L 257 " --> pdb=" O ASP L 281 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU L 280 " --> pdb=" O ASN L 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AS6 Processing sheet with id=AS7, first strand: chain 'L' and resid 155 through 157 removed outlier: 6.630A pdb=" N VAL L 155 " --> pdb=" O THR L 188 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU L 187 " --> pdb=" O ASN L 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AS7 Processing sheet with id=AS8, first strand: chain 'L' and resid 252 through 253 removed outlier: 6.297A pdb=" N VAL L 252 " --> pdb=" O HIS L 276 " (cutoff:3.500A) Processing sheet with id=AS9, first strand: chain 'L' and resid 269 through 270 removed outlier: 6.729A pdb=" N ILE L 269 " --> pdb=" O ILE L 291 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR L 381 " --> pdb=" O GLU L 407 " (cutoff:3.500A) Processing sheet with id=AT1, first strand: chain 'L' and resid 476 through 477 removed outlier: 6.457A pdb=" N ILE L 476 " --> pdb=" O ILE L 501 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N LEU L 500 " --> pdb=" O ILE L 518 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU L 517 " --> pdb=" O ARG L 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AT1 Processing sheet with id=AT2, first strand: chain 'L' and resid 530 through 535 removed outlier: 3.587A pdb=" N LYS L 562 " --> pdb=" O PHE L 532 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLU L 534 " --> pdb=" O LYS L 562 " (cutoff:3.500A) Processing sheet with id=AT3, first strand: chain 'L' and resid 541 through 542 removed outlier: 3.834A pdb=" N LEU L 567 " --> pdb=" O ASN L 587 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU L 589 " --> pdb=" O LEU L 567 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL L 588 " --> pdb=" O THR L 614 " (cutoff:3.500A) Processing sheet with id=AT4, first strand: chain 'L' and resid 572 through 573 removed outlier: 6.283A pdb=" N PHE L 572 " --> pdb=" O ALA L 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AT4 Processing sheet with id=AT5, first strand: chain 'L' and resid 621 through 623 removed outlier: 3.626A pdb=" N LEU L 645 " --> pdb=" O TYR L 623 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE L 642 " --> pdb=" O LYS L 680 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASN L 682 " --> pdb=" O ILE L 642 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR L 644 " --> pdb=" O ASN L 682 " (cutoff:3.500A) Processing sheet with id=AT6, first strand: chain 'L' and resid 662 through 664 Processing sheet with id=AT7, first strand: chain 'L' and resid 691 through 697 removed outlier: 4.067A pdb=" N THR L 691 " --> pdb=" O TYR L 791 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR L 791 " --> pdb=" O THR L 691 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE L 787 " --> pdb=" O LEU L 695 " (cutoff:3.500A) Processing sheet with id=AT8, first strand: chain 'L' and resid 729 through 730 Processing sheet with id=AT9, first strand: chain 'L' and resid 737 through 740 removed outlier: 3.684A pdb=" N TRP L 773 " --> pdb=" O CYS L 738 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS L 771 " --> pdb=" O VAL L 740 " (cutoff:3.500A) 678 hydrogen bonds defined for protein. 1884 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 36.77 Time building geometry restraints manager: 21.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 22096 1.33 - 1.45: 10105 1.45 - 1.57: 37375 1.57 - 1.69: 0 1.69 - 1.80: 264 Bond restraints: 69840 Sorted by residual: bond pdb=" C ASN C 358 " pdb=" N ILE C 359 " ideal model delta sigma weight residual 1.334 1.302 0.032 1.29e-02 6.01e+03 5.99e+00 bond pdb=" C ASN L 358 " pdb=" N ILE L 359 " ideal model delta sigma weight residual 1.334 1.302 0.032 1.29e-02 6.01e+03 5.99e+00 bond pdb=" C ASN K 358 " pdb=" N ILE K 359 " ideal model delta sigma weight residual 1.334 1.303 0.031 1.29e-02 6.01e+03 5.92e+00 bond pdb=" C ASN E 358 " pdb=" N ILE E 359 " ideal model delta sigma weight residual 1.334 1.303 0.031 1.29e-02 6.01e+03 5.92e+00 bond pdb=" C ASN B 358 " pdb=" N ILE B 359 " ideal model delta sigma weight residual 1.334 1.303 0.031 1.29e-02 6.01e+03 5.92e+00 ... (remaining 69835 not shown) Histogram of bond angle deviations from ideal: 98.50 - 105.60: 891 105.60 - 112.71: 35795 112.71 - 119.82: 23467 119.82 - 126.92: 33764 126.92 - 134.03: 667 Bond angle restraints: 94584 Sorted by residual: angle pdb=" CA ASN I 273 " pdb=" CB ASN I 273 " pdb=" CG ASN I 273 " ideal model delta sigma weight residual 112.60 116.98 -4.38 1.00e+00 1.00e+00 1.92e+01 angle pdb=" CA ASN C 273 " pdb=" CB ASN C 273 " pdb=" CG ASN C 273 " ideal model delta sigma weight residual 112.60 116.98 -4.38 1.00e+00 1.00e+00 1.91e+01 angle pdb=" CA ASN E 273 " pdb=" CB ASN E 273 " pdb=" CG ASN E 273 " ideal model delta sigma weight residual 112.60 116.97 -4.37 1.00e+00 1.00e+00 1.91e+01 angle pdb=" CA ASN A 273 " pdb=" CB ASN A 273 " pdb=" CG ASN A 273 " ideal model delta sigma weight residual 112.60 116.95 -4.35 1.00e+00 1.00e+00 1.90e+01 angle pdb=" CA ASN H 273 " pdb=" CB ASN H 273 " pdb=" CG ASN H 273 " ideal model delta sigma weight residual 112.60 116.95 -4.35 1.00e+00 1.00e+00 1.89e+01 ... (remaining 94579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.22: 37804 14.22 - 28.43: 2673 28.43 - 42.65: 587 42.65 - 56.87: 60 56.87 - 71.08: 48 Dihedral angle restraints: 41172 sinusoidal: 15828 harmonic: 25344 Sorted by residual: dihedral pdb=" CB CYS I 738 " pdb=" SG CYS I 738 " pdb=" SG CYS I 749 " pdb=" CB CYS I 749 " ideal model delta sinusoidal sigma weight residual -86.00 -157.08 71.08 1 1.00e+01 1.00e-02 6.49e+01 dihedral pdb=" CB CYS G 738 " pdb=" SG CYS G 738 " pdb=" SG CYS G 749 " pdb=" CB CYS G 749 " ideal model delta sinusoidal sigma weight residual -86.00 -157.08 71.08 1 1.00e+01 1.00e-02 6.49e+01 dihedral pdb=" CB CYS E 738 " pdb=" SG CYS E 738 " pdb=" SG CYS E 749 " pdb=" CB CYS E 749 " ideal model delta sinusoidal sigma weight residual -86.00 -157.08 71.08 1 1.00e+01 1.00e-02 6.49e+01 ... (remaining 41169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 6784 0.055 - 0.110: 2984 0.110 - 0.165: 703 0.165 - 0.220: 114 0.220 - 0.275: 35 Chirality restraints: 10620 Sorted by residual: chirality pdb=" CB ILE J 345 " pdb=" CA ILE J 345 " pdb=" CG1 ILE J 345 " pdb=" CG2 ILE J 345 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CB ILE C 345 " pdb=" CA ILE C 345 " pdb=" CG1 ILE C 345 " pdb=" CG2 ILE C 345 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB ILE B 345 " pdb=" CA ILE B 345 " pdb=" CG1 ILE B 345 " pdb=" CG2 ILE B 345 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 10617 not shown) Planarity restraints: 12396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 225 " 0.014 2.00e-02 2.50e+03 1.51e-02 5.68e+00 pdb=" CG TRP H 225 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP H 225 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP H 225 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP H 225 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP H 225 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP H 225 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 225 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 225 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP H 225 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 225 " 0.014 2.00e-02 2.50e+03 1.51e-02 5.67e+00 pdb=" CG TRP I 225 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP I 225 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP I 225 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP I 225 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP I 225 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP I 225 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 225 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 225 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP I 225 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 225 " 0.014 2.00e-02 2.50e+03 1.50e-02 5.66e+00 pdb=" CG TRP J 225 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP J 225 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP J 225 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP J 225 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP J 225 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP J 225 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 225 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 225 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP J 225 " 0.001 2.00e-02 2.50e+03 ... (remaining 12393 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 15150 2.78 - 3.31: 63322 3.31 - 3.84: 114468 3.84 - 4.37: 135260 4.37 - 4.90: 238125 Nonbonded interactions: 566325 Sorted by model distance: nonbonded pdb=" O SER A 575 " pdb=" OG SER A 606 " model vdw 2.247 2.440 nonbonded pdb=" O SER J 575 " pdb=" OG SER J 606 " model vdw 2.247 2.440 nonbonded pdb=" O SER L 575 " pdb=" OG SER L 606 " model vdw 2.247 2.440 nonbonded pdb=" O SER B 575 " pdb=" OG SER B 606 " model vdw 2.247 2.440 nonbonded pdb=" O SER K 575 " pdb=" OG SER K 606 " model vdw 2.247 2.440 ... (remaining 566320 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.050 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: 0.070 Extract box with map and model: 13.770 Check model and map are aligned: 0.860 Set scattering table: 0.510 Process input model: 154.800 Find NCS groups from input model: 4.050 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 180.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 69840 Z= 0.536 Angle : 1.058 11.173 94584 Z= 0.595 Chirality : 0.064 0.275 10620 Planarity : 0.005 0.051 12396 Dihedral : 10.596 70.311 25056 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.18 % Favored : 84.82 % Rotamer: Outliers : 0.54 % Allowed : 2.54 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.28 (0.07), residues: 8952 helix: -4.59 (0.11), residues: 360 sheet: -3.42 (0.09), residues: 2556 loop : -3.70 (0.06), residues: 6036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP D 225 HIS 0.006 0.002 HIS C 256 PHE 0.023 0.003 PHE B 532 TYR 0.033 0.003 TYR B 574 ARG 0.008 0.001 ARG B 154 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 512 time to evaluate : 5.680 Fit side-chains REVERT: A 109 THR cc_start: 0.8681 (OUTLIER) cc_final: 0.8440 (p) REVERT: A 486 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7668 (mp) REVERT: A 658 ASN cc_start: 0.8243 (t0) cc_final: 0.7917 (t0) REVERT: A 662 MET cc_start: 0.5971 (mtm) cc_final: 0.5207 (mpp) REVERT: A 663 MET cc_start: 0.8169 (ttt) cc_final: 0.7886 (tmm) REVERT: A 768 LEU cc_start: 0.3369 (OUTLIER) cc_final: 0.3108 (mt) REVERT: B 109 THR cc_start: 0.8679 (OUTLIER) cc_final: 0.8382 (p) REVERT: B 609 MET cc_start: 0.6143 (ttt) cc_final: 0.5838 (mtp) REVERT: B 658 ASN cc_start: 0.8225 (t0) cc_final: 0.7881 (t0) REVERT: B 662 MET cc_start: 0.5843 (mtm) cc_final: 0.5255 (mpp) REVERT: B 665 ASN cc_start: 0.7548 (t160) cc_final: 0.7339 (t0) REVERT: C 592 ARG cc_start: 0.6968 (ptt90) cc_final: 0.6583 (ptm-80) REVERT: C 658 ASN cc_start: 0.8083 (t0) cc_final: 0.7861 (t0) REVERT: C 662 MET cc_start: 0.5863 (mtm) cc_final: 0.5476 (mpp) REVERT: C 663 MET cc_start: 0.8181 (ttt) cc_final: 0.7964 (tmm) REVERT: C 665 ASN cc_start: 0.7608 (t160) cc_final: 0.7174 (t0) REVERT: C 758 MET cc_start: 0.7194 (mpt) cc_final: 0.6678 (mpp) REVERT: D 486 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7814 (mp) REVERT: D 662 MET cc_start: 0.5946 (mtm) cc_final: 0.5406 (mpp) REVERT: D 665 ASN cc_start: 0.7570 (t160) cc_final: 0.7369 (t0) REVERT: E 486 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7850 (mp) REVERT: E 609 MET cc_start: 0.5977 (ttt) cc_final: 0.5615 (mtp) REVERT: E 658 ASN cc_start: 0.8253 (t0) cc_final: 0.8047 (t0) REVERT: E 662 MET cc_start: 0.6131 (mtm) cc_final: 0.5466 (mpp) REVERT: F 658 ASN cc_start: 0.8061 (t0) cc_final: 0.7854 (t0) REVERT: F 663 MET cc_start: 0.8084 (ttt) cc_final: 0.7786 (tmm) REVERT: F 665 ASN cc_start: 0.7620 (t160) cc_final: 0.7204 (t0) REVERT: F 758 MET cc_start: 0.6986 (mpt) cc_final: 0.6489 (mpp) REVERT: G 486 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7576 (mp) REVERT: G 658 ASN cc_start: 0.8303 (t0) cc_final: 0.8006 (t0) REVERT: G 662 MET cc_start: 0.5960 (mtm) cc_final: 0.5172 (mpp) REVERT: G 663 MET cc_start: 0.8130 (ttt) cc_final: 0.7880 (tmm) REVERT: G 665 ASN cc_start: 0.7432 (t160) cc_final: 0.7222 (t0) REVERT: H 33 LYS cc_start: 0.8080 (tptt) cc_final: 0.7737 (tppp) REVERT: H 486 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7891 (mp) REVERT: H 662 MET cc_start: 0.5721 (mtm) cc_final: 0.5222 (mpp) REVERT: H 665 ASN cc_start: 0.7427 (t160) cc_final: 0.7220 (t0) REVERT: I 580 PHE cc_start: 0.6535 (t80) cc_final: 0.6325 (t80) REVERT: I 592 ARG cc_start: 0.7158 (ptt90) cc_final: 0.6777 (ptm-80) REVERT: I 658 ASN cc_start: 0.8169 (t0) cc_final: 0.7946 (t0) REVERT: I 662 MET cc_start: 0.6157 (mtm) cc_final: 0.5762 (mpp) REVERT: I 663 MET cc_start: 0.8123 (ttt) cc_final: 0.7851 (tmm) REVERT: I 665 ASN cc_start: 0.7528 (t160) cc_final: 0.7119 (t0) REVERT: I 758 MET cc_start: 0.7140 (mpt) cc_final: 0.6631 (mpp) REVERT: J 486 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7787 (mp) REVERT: J 662 MET cc_start: 0.6149 (mtm) cc_final: 0.5452 (mpp) REVERT: J 663 MET cc_start: 0.8175 (ttt) cc_final: 0.7923 (tmm) REVERT: J 665 ASN cc_start: 0.7505 (t160) cc_final: 0.7295 (t0) REVERT: K 109 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8357 (p) REVERT: K 658 ASN cc_start: 0.8275 (t0) cc_final: 0.7931 (t0) REVERT: K 662 MET cc_start: 0.6134 (mtm) cc_final: 0.5540 (mpp) REVERT: K 665 ASN cc_start: 0.7285 (t160) cc_final: 0.7061 (t0) REVERT: L 109 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8386 (p) REVERT: L 580 PHE cc_start: 0.6384 (t80) cc_final: 0.6125 (t80) REVERT: L 658 ASN cc_start: 0.8211 (t0) cc_final: 0.7854 (t0) REVERT: L 663 MET cc_start: 0.8071 (ttt) cc_final: 0.7571 (tmm) REVERT: L 665 ASN cc_start: 0.7635 (t160) cc_final: 0.7226 (t0) REVERT: L 758 MET cc_start: 0.6871 (mpt) cc_final: 0.6389 (mpp) outliers start: 40 outliers final: 6 residues processed: 543 average time/residue: 0.6330 time to fit residues: 593.4150 Evaluate side-chains 278 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 261 time to evaluate : 5.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain F residue 486 LEU Chi-restraints excluded: chain G residue 486 LEU Chi-restraints excluded: chain H residue 486 LEU Chi-restraints excluded: chain I residue 486 LEU Chi-restraints excluded: chain J residue 486 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 486 LEU Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 486 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 759 optimal weight: 0.9990 chunk 682 optimal weight: 0.7980 chunk 378 optimal weight: 3.9990 chunk 233 optimal weight: 2.9990 chunk 460 optimal weight: 0.8980 chunk 364 optimal weight: 0.0030 chunk 705 optimal weight: 5.9990 chunk 272 optimal weight: 9.9990 chunk 428 optimal weight: 4.9990 chunk 525 optimal weight: 1.9990 chunk 817 optimal weight: 20.0000 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 HIS A 387 ASN ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 665 ASN ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 ASN ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 HIS B 387 ASN ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 665 ASN ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 ASN ** B 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 ASN C 140 ASN C 256 HIS C 387 ASN ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 665 ASN ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 715 ASN ** C 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 ASN D 140 ASN D 256 HIS D 387 ASN ** D 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 665 ASN ** D 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 715 ASN ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 755 ASN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 HIS E 387 ASN ** E 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 715 ASN ** E 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 755 ASN F 140 ASN F 256 HIS F 387 ASN ** F 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 665 ASN ** F 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 715 ASN ** F 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 755 ASN G 140 ASN G 256 HIS G 387 ASN ** G 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 665 ASN ** G 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 715 ASN ** G 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 755 ASN ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 256 HIS H 387 ASN ** H 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 665 ASN ** H 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 715 ASN ** H 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 755 ASN I 140 ASN I 256 HIS I 387 ASN ** I 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 618 ASN I 665 ASN ** I 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 715 ASN ** I 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 755 ASN J 140 ASN J 256 HIS J 387 ASN ** J 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 665 ASN ** J 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 715 ASN ** J 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 755 ASN ** K 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 256 HIS K 387 ASN ** K 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 665 ASN ** K 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 715 ASN ** K 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 755 ASN L 140 ASN L 256 HIS L 387 ASN ** L 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 665 ASN ** L 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 715 ASN ** L 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 755 ASN Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 69840 Z= 0.149 Angle : 0.565 7.034 94584 Z= 0.301 Chirality : 0.046 0.162 10620 Planarity : 0.003 0.041 12396 Dihedral : 6.180 57.994 9546 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 0.84 % Allowed : 5.93 % Favored : 93.23 % 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: -4.88 (0.07), residues: 8952 helix: -3.44 (0.18), residues: 384 sheet: -3.49 (0.09), residues: 2904 loop : -3.21 (0.07), residues: 5664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.005 0.001 HIS B 88 PHE 0.022 0.001 PHE F 664 TYR 0.012 0.001 TYR L 574 ARG 0.007 0.000 ARG G 546 *********************** 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 414 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 352 time to evaluate : 7.312 Fit side-chains REVERT: A 109 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8283 (p) REVERT: A 621 MET cc_start: 0.6800 (mtp) cc_final: 0.6557 (mtp) REVERT: A 658 ASN cc_start: 0.8282 (t0) cc_final: 0.7967 (t0) REVERT: A 662 MET cc_start: 0.6416 (mtm) cc_final: 0.5790 (mpp) REVERT: A 663 MET cc_start: 0.8258 (ttt) cc_final: 0.7615 (tmm) REVERT: A 768 LEU cc_start: 0.3285 (OUTLIER) cc_final: 0.2933 (mt) REVERT: B 109 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8272 (p) REVERT: B 486 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7830 (mp) REVERT: B 658 ASN cc_start: 0.8227 (t0) cc_final: 0.7909 (t0) REVERT: B 662 MET cc_start: 0.5873 (mtm) cc_final: 0.5316 (mpp) REVERT: B 768 LEU cc_start: 0.4032 (OUTLIER) cc_final: 0.3618 (mt) REVERT: C 407 GLU cc_start: 0.7237 (tt0) cc_final: 0.7033 (tt0) REVERT: C 658 ASN cc_start: 0.8270 (t0) cc_final: 0.7879 (t0) REVERT: C 663 MET cc_start: 0.8241 (ttt) cc_final: 0.7841 (tmm) REVERT: C 665 ASN cc_start: 0.7865 (t0) cc_final: 0.7542 (t0) REVERT: C 758 MET cc_start: 0.7154 (mpt) cc_final: 0.6928 (mpt) REVERT: D 662 MET cc_start: 0.6145 (mtm) cc_final: 0.5274 (mpp) REVERT: D 663 MET cc_start: 0.8161 (tmm) cc_final: 0.7499 (tmm) REVERT: D 768 LEU cc_start: 0.3418 (OUTLIER) cc_final: 0.3166 (mt) REVERT: E 486 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7865 (mp) REVERT: E 658 ASN cc_start: 0.8290 (t0) cc_final: 0.7933 (t0) REVERT: E 662 MET cc_start: 0.6194 (mtm) cc_final: 0.5433 (mpp) REVERT: E 768 LEU cc_start: 0.4177 (OUTLIER) cc_final: 0.3805 (mt) REVERT: F 380 THR cc_start: 0.8486 (m) cc_final: 0.8262 (m) REVERT: F 580 PHE cc_start: 0.6511 (t80) cc_final: 0.6291 (t80) REVERT: F 658 ASN cc_start: 0.8260 (t0) cc_final: 0.7910 (t0) REVERT: F 663 MET cc_start: 0.8194 (ttt) cc_final: 0.7676 (tmm) REVERT: F 758 MET cc_start: 0.7117 (mpt) cc_final: 0.6873 (mpt) REVERT: F 768 LEU cc_start: 0.2945 (OUTLIER) cc_final: 0.2676 (mt) REVERT: G 658 ASN cc_start: 0.8276 (t0) cc_final: 0.7997 (t0) REVERT: G 662 MET cc_start: 0.6362 (mtm) cc_final: 0.5573 (mpp) REVERT: G 663 MET cc_start: 0.8346 (ttt) cc_final: 0.8067 (tmm) REVERT: G 768 LEU cc_start: 0.3267 (OUTLIER) cc_final: 0.3003 (mt) REVERT: H 33 LYS cc_start: 0.8218 (tptt) cc_final: 0.7985 (tppp) REVERT: H 103 MET cc_start: 0.7177 (mtt) cc_final: 0.6901 (mtt) REVERT: H 486 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7795 (mp) REVERT: H 662 MET cc_start: 0.6025 (mtm) cc_final: 0.5393 (mpp) REVERT: I 658 ASN cc_start: 0.8326 (t0) cc_final: 0.8111 (t0) REVERT: I 663 MET cc_start: 0.8241 (ttt) cc_final: 0.7750 (tmm) REVERT: I 665 ASN cc_start: 0.7717 (t0) cc_final: 0.7383 (t0) REVERT: J 621 MET cc_start: 0.6798 (mtp) cc_final: 0.6587 (mtp) REVERT: J 662 MET cc_start: 0.6468 (mtm) cc_final: 0.5748 (mpp) REVERT: J 663 MET cc_start: 0.8213 (ttt) cc_final: 0.7690 (tmm) REVERT: J 768 LEU cc_start: 0.3381 (OUTLIER) cc_final: 0.3088 (mt) REVERT: K 109 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8230 (p) REVERT: K 486 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7827 (mp) REVERT: K 658 ASN cc_start: 0.8297 (t0) cc_final: 0.7954 (t0) REVERT: K 662 MET cc_start: 0.6139 (mtm) cc_final: 0.5516 (mpp) REVERT: L 109 THR cc_start: 0.8504 (OUTLIER) cc_final: 0.8274 (p) REVERT: L 658 ASN cc_start: 0.8341 (t0) cc_final: 0.7975 (t0) REVERT: L 663 MET cc_start: 0.8108 (ttt) cc_final: 0.7742 (tmm) REVERT: L 768 LEU cc_start: 0.3296 (OUTLIER) cc_final: 0.2945 (mt) outliers start: 62 outliers final: 13 residues processed: 402 average time/residue: 0.6607 time to fit residues: 472.6128 Evaluate side-chains 306 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 277 time to evaluate : 6.032 ------------------------------------------------------------------------------- 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 768 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 768 LEU Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain E residue 768 LEU Chi-restraints excluded: chain F residue 768 LEU Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 455 ASP Chi-restraints excluded: chain G residue 768 LEU Chi-restraints excluded: chain H residue 486 LEU Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain J residue 103 MET Chi-restraints excluded: chain J residue 127 MET Chi-restraints excluded: chain J residue 455 ASP Chi-restraints excluded: chain J residue 613 LEU Chi-restraints excluded: chain J residue 768 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 486 LEU Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 455 ASP Chi-restraints excluded: chain L residue 768 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 454 optimal weight: 0.8980 chunk 253 optimal weight: 3.9990 chunk 680 optimal weight: 20.0000 chunk 556 optimal weight: 6.9990 chunk 225 optimal weight: 0.9980 chunk 818 optimal weight: 8.9990 chunk 884 optimal weight: 20.0000 chunk 729 optimal weight: 10.0000 chunk 811 optimal weight: 8.9990 chunk 279 optimal weight: 20.0000 chunk 656 optimal weight: 10.0000 overall best weight: 4.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 GLN A 340 GLN A 498 ASN ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 GLN B 340 GLN B 469 HIS B 498 ASN ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN C 284 GLN C 340 GLN C 498 ASN ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN D 284 GLN D 340 GLN D 498 ASN ** D 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 GLN ** E 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN F 284 GLN F 340 GLN F 498 ASN ** F 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 ASN G 284 GLN G 340 GLN G 498 ASN ** G 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 340 GLN H 498 ASN ** H 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 140 ASN I 284 GLN I 340 GLN I 498 ASN ** I 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 140 ASN J 284 GLN J 340 GLN J 498 ASN ** J 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 284 GLN K 340 GLN K 498 ASN ** K 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 140 ASN L 284 GLN L 340 GLN L 498 ASN ** L 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 69840 Z= 0.458 Angle : 0.717 8.379 94584 Z= 0.386 Chirality : 0.052 0.177 10620 Planarity : 0.004 0.040 12396 Dihedral : 6.490 54.585 9530 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 17.76 % Favored : 82.17 % Rotamer: Outliers : 2.19 % Allowed : 6.93 % Favored : 90.88 % 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: -4.69 (0.08), residues: 8952 helix: -2.32 (0.24), residues: 384 sheet: -3.54 (0.10), residues: 2376 loop : -3.18 (0.07), residues: 6192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 225 HIS 0.003 0.001 HIS D 88 PHE 0.026 0.003 PHE L 580 TYR 0.016 0.002 TYR E 574 ARG 0.006 0.001 ARG J 154 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 274 time to evaluate : 5.844 Fit side-chains REVERT: A 658 ASN cc_start: 0.8320 (t0) cc_final: 0.8034 (t0) REVERT: A 662 MET cc_start: 0.6594 (mtm) cc_final: 0.5796 (mpp) REVERT: A 663 MET cc_start: 0.8131 (ttt) cc_final: 0.7653 (tmm) REVERT: A 768 LEU cc_start: 0.3401 (OUTLIER) cc_final: 0.3085 (mt) REVERT: B 574 TYR cc_start: 0.6527 (m-80) cc_final: 0.6307 (m-80) REVERT: B 594 PHE cc_start: 0.6906 (t80) cc_final: 0.5627 (t80) REVERT: B 621 MET cc_start: 0.6587 (mtp) cc_final: 0.6217 (tpt) REVERT: B 658 ASN cc_start: 0.8296 (t0) cc_final: 0.7961 (t0) REVERT: B 662 MET cc_start: 0.6373 (mtm) cc_final: 0.5496 (mpp) REVERT: B 768 LEU cc_start: 0.4051 (OUTLIER) cc_final: 0.3593 (mt) REVERT: C 168 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8606 (tp) REVERT: C 658 ASN cc_start: 0.8368 (t0) cc_final: 0.7997 (t0) REVERT: C 663 MET cc_start: 0.8054 (ttt) cc_final: 0.7602 (tmm) REVERT: C 758 MET cc_start: 0.7433 (mpt) cc_final: 0.7000 (mpt) REVERT: D 662 MET cc_start: 0.6464 (mtm) cc_final: 0.5567 (mpp) REVERT: D 663 MET cc_start: 0.8063 (tmm) cc_final: 0.7370 (tmm) REVERT: D 768 LEU cc_start: 0.3340 (OUTLIER) cc_final: 0.3081 (mt) REVERT: E 609 MET cc_start: 0.4938 (ttt) cc_final: 0.4619 (mtp) REVERT: E 658 ASN cc_start: 0.8342 (t0) cc_final: 0.8007 (t0) REVERT: E 662 MET cc_start: 0.6476 (mtm) cc_final: 0.5421 (mpp) REVERT: F 168 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8602 (tp) REVERT: F 580 PHE cc_start: 0.6728 (t80) cc_final: 0.6515 (t80) REVERT: F 658 ASN cc_start: 0.8267 (t0) cc_final: 0.8064 (t0) REVERT: F 663 MET cc_start: 0.7989 (ttt) cc_final: 0.7771 (tmm) REVERT: F 758 MET cc_start: 0.7301 (mpt) cc_final: 0.6884 (mpt) REVERT: F 768 LEU cc_start: 0.3245 (OUTLIER) cc_final: 0.2871 (mt) REVERT: G 658 ASN cc_start: 0.8306 (t0) cc_final: 0.8005 (t0) REVERT: G 662 MET cc_start: 0.6613 (mtm) cc_final: 0.5800 (mpp) REVERT: G 663 MET cc_start: 0.8165 (ttt) cc_final: 0.7688 (tmm) REVERT: G 768 LEU cc_start: 0.3444 (OUTLIER) cc_final: 0.3209 (mt) REVERT: H 574 TYR cc_start: 0.6408 (m-80) cc_final: 0.6157 (m-80) REVERT: H 594 PHE cc_start: 0.7045 (t80) cc_final: 0.5812 (t80) REVERT: H 621 MET cc_start: 0.6854 (mtp) cc_final: 0.6417 (tpt) REVERT: H 662 MET cc_start: 0.6508 (mtm) cc_final: 0.5641 (mpp) REVERT: I 103 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.7918 (mtt) REVERT: I 168 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8602 (tp) REVERT: I 658 ASN cc_start: 0.8339 (t0) cc_final: 0.7952 (t0) REVERT: I 663 MET cc_start: 0.7955 (ttt) cc_final: 0.7452 (tmm) REVERT: J 168 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8681 (tp) REVERT: J 580 PHE cc_start: 0.6434 (t80) cc_final: 0.6195 (t80) REVERT: J 662 MET cc_start: 0.6767 (mtm) cc_final: 0.5909 (mpp) REVERT: J 663 MET cc_start: 0.8177 (ttt) cc_final: 0.7657 (tmm) REVERT: J 768 LEU cc_start: 0.3451 (OUTLIER) cc_final: 0.3200 (mt) REVERT: K 621 MET cc_start: 0.6753 (mtp) cc_final: 0.6475 (ttp) REVERT: K 658 ASN cc_start: 0.8312 (t0) cc_final: 0.7972 (t0) REVERT: K 662 MET cc_start: 0.6585 (mtm) cc_final: 0.5784 (mpp) REVERT: L 148 SER cc_start: 0.9147 (p) cc_final: 0.8942 (t) REVERT: L 168 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8627 (tp) REVERT: L 658 ASN cc_start: 0.8370 (t0) cc_final: 0.8156 (t0) REVERT: L 663 MET cc_start: 0.8039 (ttt) cc_final: 0.7454 (tmm) REVERT: L 768 LEU cc_start: 0.3328 (OUTLIER) cc_final: 0.2955 (mt) outliers start: 162 outliers final: 79 residues processed: 398 average time/residue: 0.6055 time to fit residues: 438.2365 Evaluate side-chains 329 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 237 time to evaluate : 5.788 ------------------------------------------------------------------------------- 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 205 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 455 ASP Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 452 PHE Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 768 LEU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 353 LYS Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain E residue 768 LEU Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 455 ASP Chi-restraints excluded: chain F residue 654 LEU Chi-restraints excluded: chain F residue 768 LEU Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 452 PHE Chi-restraints excluded: chain G residue 455 ASP Chi-restraints excluded: chain G residue 768 LEU Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 486 LEU Chi-restraints excluded: chain H residue 768 LEU Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain I residue 229 LEU Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 620 VAL Chi-restraints excluded: chain I residue 654 LEU Chi-restraints excluded: chain J residue 43 ASP Chi-restraints excluded: chain J residue 127 MET Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 452 PHE Chi-restraints excluded: chain J residue 455 ASP Chi-restraints excluded: chain J residue 613 LEU Chi-restraints excluded: chain J residue 768 LEU Chi-restraints excluded: chain K residue 100 GLU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 486 LEU Chi-restraints excluded: chain K residue 654 LEU Chi-restraints excluded: chain K residue 768 LEU Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 168 LEU Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 229 LEU Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain L residue 455 ASP Chi-restraints excluded: chain L residue 654 LEU Chi-restraints excluded: chain L residue 768 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 808 optimal weight: 0.7980 chunk 615 optimal weight: 6.9990 chunk 424 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 390 optimal weight: 7.9990 chunk 549 optimal weight: 3.9990 chunk 821 optimal weight: 30.0000 chunk 869 optimal weight: 9.9990 chunk 429 optimal weight: 7.9990 chunk 778 optimal weight: 2.9990 chunk 234 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 ASN A 685 GLN A 731 ASN B 117 ASN ** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 ASN C 543 ASN C 685 GLN C 731 ASN D 117 ASN D 543 ASN D 685 GLN D 731 ASN E 117 ASN E 543 ASN E 685 GLN E 731 ASN F 543 ASN F 685 GLN F 731 ASN ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 ASN G 498 ASN G 543 ASN G 685 GLN G 731 ASN H 117 ASN H 543 ASN H 685 GLN H 731 ASN I 117 ASN ** I 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 685 GLN I 731 ASN J 117 ASN J 543 ASN J 685 GLN J 731 ASN K 117 ASN K 543 ASN K 685 GLN K 731 ASN ** L 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 685 GLN L 731 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 69840 Z= 0.296 Angle : 0.619 10.820 94584 Z= 0.330 Chirality : 0.048 0.162 10620 Planarity : 0.003 0.039 12396 Dihedral : 5.980 46.979 9529 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.05 % Favored : 86.95 % Rotamer: Outliers : 2.36 % Allowed : 7.83 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.54 (0.08), residues: 8952 helix: -1.85 (0.25), residues: 384 sheet: -3.47 (0.09), residues: 2484 loop : -3.07 (0.07), residues: 6084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 773 HIS 0.002 0.001 HIS A 693 PHE 0.019 0.002 PHE L 580 TYR 0.011 0.001 TYR H 574 ARG 0.003 0.000 ARG D 546 *********************** 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 429 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 254 time to evaluate : 5.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 580 PHE cc_start: 0.6315 (t80) cc_final: 0.6079 (t80) REVERT: A 658 ASN cc_start: 0.8335 (t0) cc_final: 0.8044 (t0) REVERT: A 662 MET cc_start: 0.6718 (mtm) cc_final: 0.5897 (mpp) REVERT: A 663 MET cc_start: 0.8037 (ttt) cc_final: 0.7479 (tmm) REVERT: A 768 LEU cc_start: 0.3406 (OUTLIER) cc_final: 0.3071 (mt) REVERT: B 621 MET cc_start: 0.6689 (mtp) cc_final: 0.5878 (tmm) REVERT: B 658 ASN cc_start: 0.8351 (t0) cc_final: 0.8041 (t0) REVERT: B 662 MET cc_start: 0.6346 (mtm) cc_final: 0.5623 (mpp) REVERT: B 768 LEU cc_start: 0.4177 (OUTLIER) cc_final: 0.3670 (mt) REVERT: C 103 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8159 (mtt) REVERT: C 658 ASN cc_start: 0.8339 (t0) cc_final: 0.8070 (t0) REVERT: C 663 MET cc_start: 0.7954 (ttt) cc_final: 0.7345 (tmm) REVERT: C 758 MET cc_start: 0.7051 (mpt) cc_final: 0.6643 (mpt) REVERT: D 407 GLU cc_start: 0.7367 (tt0) cc_final: 0.7045 (mt-10) REVERT: D 621 MET cc_start: 0.6871 (mtp) cc_final: 0.6562 (ttm) REVERT: D 662 MET cc_start: 0.6506 (mtm) cc_final: 0.5665 (mpp) REVERT: D 663 MET cc_start: 0.8047 (tmm) cc_final: 0.7405 (tmm) REVERT: D 768 LEU cc_start: 0.3349 (OUTLIER) cc_final: 0.3059 (mt) REVERT: E 574 TYR cc_start: 0.6549 (m-80) cc_final: 0.6145 (m-80) REVERT: E 621 MET cc_start: 0.6567 (mtp) cc_final: 0.6208 (tpt) REVERT: E 658 ASN cc_start: 0.8319 (t0) cc_final: 0.7970 (t0) REVERT: E 662 MET cc_start: 0.6640 (mtm) cc_final: 0.5603 (mpp) REVERT: E 768 LEU cc_start: 0.4180 (OUTLIER) cc_final: 0.3705 (mt) REVERT: F 103 MET cc_start: 0.8302 (mtt) cc_final: 0.7834 (mtt) REVERT: F 658 ASN cc_start: 0.8361 (t0) cc_final: 0.7981 (t0) REVERT: F 663 MET cc_start: 0.7937 (ttt) cc_final: 0.7705 (tmm) REVERT: F 758 MET cc_start: 0.6891 (mpt) cc_final: 0.6461 (mpt) REVERT: F 768 LEU cc_start: 0.3084 (OUTLIER) cc_final: 0.2747 (mt) REVERT: G 407 GLU cc_start: 0.7345 (tt0) cc_final: 0.7067 (mt-10) REVERT: G 658 ASN cc_start: 0.8346 (t0) cc_final: 0.7998 (t0) REVERT: G 662 MET cc_start: 0.6691 (mtm) cc_final: 0.5835 (mpp) REVERT: G 663 MET cc_start: 0.8151 (ttt) cc_final: 0.7636 (tmm) REVERT: G 768 LEU cc_start: 0.3538 (OUTLIER) cc_final: 0.3290 (mt) REVERT: H 555 PHE cc_start: 0.5071 (m-80) cc_final: 0.4726 (m-80) REVERT: H 574 TYR cc_start: 0.6442 (m-80) cc_final: 0.6127 (m-80) REVERT: H 594 PHE cc_start: 0.6961 (t80) cc_final: 0.5715 (t80) REVERT: H 621 MET cc_start: 0.6923 (mtp) cc_final: 0.6380 (tpt) REVERT: H 662 MET cc_start: 0.6492 (mtm) cc_final: 0.5783 (mpp) REVERT: I 103 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.7823 (mtt) REVERT: I 658 ASN cc_start: 0.8361 (t0) cc_final: 0.7986 (t0) REVERT: I 663 MET cc_start: 0.7935 (ttt) cc_final: 0.7640 (tmm) REVERT: I 758 MET cc_start: 0.7050 (mpt) cc_final: 0.6740 (mpt) REVERT: J 168 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8642 (tp) REVERT: J 662 MET cc_start: 0.6764 (mtm) cc_final: 0.5914 (mpp) REVERT: J 663 MET cc_start: 0.8128 (ttt) cc_final: 0.7592 (tmm) REVERT: J 768 LEU cc_start: 0.3438 (OUTLIER) cc_final: 0.3218 (mt) REVERT: K 574 TYR cc_start: 0.6556 (m-80) cc_final: 0.6134 (m-80) REVERT: K 621 MET cc_start: 0.6741 (mtp) cc_final: 0.6366 (tpt) REVERT: K 658 ASN cc_start: 0.8413 (t0) cc_final: 0.8063 (t0) REVERT: K 662 MET cc_start: 0.6543 (mtm) cc_final: 0.5836 (mpp) REVERT: L 103 MET cc_start: 0.8318 (mtt) cc_final: 0.7846 (mtt) REVERT: L 148 SER cc_start: 0.9079 (p) cc_final: 0.8879 (t) REVERT: L 658 ASN cc_start: 0.8355 (t0) cc_final: 0.8071 (t0) REVERT: L 663 MET cc_start: 0.8018 (ttt) cc_final: 0.7393 (tmm) REVERT: L 768 LEU cc_start: 0.3399 (OUTLIER) cc_final: 0.2942 (mt) outliers start: 175 outliers final: 107 residues processed: 403 average time/residue: 0.5950 time to fit residues: 426.8613 Evaluate side-chains 352 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 234 time to evaluate : 5.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 412 ASN Chi-restraints excluded: chain C residue 455 ASP Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 412 ASN Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 768 LEU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 353 LYS Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 412 ASN Chi-restraints excluded: chain E residue 654 LEU Chi-restraints excluded: chain E residue 726 LEU Chi-restraints excluded: chain E residue 768 LEU Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 412 ASN Chi-restraints excluded: chain F residue 455 ASP Chi-restraints excluded: chain F residue 654 LEU Chi-restraints excluded: chain F residue 768 LEU Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain G residue 455 ASP Chi-restraints excluded: chain G residue 768 LEU Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 277 ILE Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain H residue 412 ASN Chi-restraints excluded: chain H residue 654 LEU Chi-restraints excluded: chain H residue 726 LEU Chi-restraints excluded: chain H residue 768 LEU Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain I residue 229 LEU Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 379 LEU Chi-restraints excluded: chain I residue 412 ASN Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain J residue 43 ASP Chi-restraints excluded: chain J residue 103 MET Chi-restraints excluded: chain J residue 127 MET Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 277 ILE Chi-restraints excluded: chain J residue 345 ILE Chi-restraints excluded: chain J residue 379 LEU Chi-restraints excluded: chain J residue 412 ASN Chi-restraints excluded: chain J residue 455 ASP Chi-restraints excluded: chain J residue 613 LEU Chi-restraints excluded: chain J residue 768 LEU Chi-restraints excluded: chain K residue 100 GLU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 277 ILE Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 379 LEU Chi-restraints excluded: chain K residue 726 LEU Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain L residue 345 ILE Chi-restraints excluded: chain L residue 379 LEU Chi-restraints excluded: chain L residue 412 ASN Chi-restraints excluded: chain L residue 455 ASP Chi-restraints excluded: chain L residue 654 LEU Chi-restraints excluded: chain L residue 768 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 724 optimal weight: 0.9980 chunk 493 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 647 optimal weight: 10.0000 chunk 358 optimal weight: 20.0000 chunk 742 optimal weight: 3.9990 chunk 601 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 444 optimal weight: 40.0000 chunk 780 optimal weight: 10.0000 chunk 219 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 469 HIS E 628 ASN F 117 ASN ** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 469 HIS ** H 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 543 ASN K 469 HIS K 628 ASN L 117 ASN ** L 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 543 ASN ** L 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 69840 Z= 0.341 Angle : 0.646 10.147 94584 Z= 0.344 Chirality : 0.049 0.164 10620 Planarity : 0.003 0.034 12396 Dihedral : 5.923 43.057 9521 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.72 % Favored : 83.28 % Rotamer: Outliers : 2.24 % Allowed : 9.35 % Favored : 88.41 % 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: -4.47 (0.08), residues: 8952 helix: -1.52 (0.26), residues: 384 sheet: -3.50 (0.10), residues: 2424 loop : -3.02 (0.07), residues: 6144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 225 HIS 0.002 0.001 HIS E 693 PHE 0.024 0.002 PHE G 580 TYR 0.011 0.001 TYR C 574 ARG 0.003 0.001 ARG A 402 *********************** 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 416 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 250 time to evaluate : 6.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 658 ASN cc_start: 0.8335 (t0) cc_final: 0.8030 (t0) REVERT: A 662 MET cc_start: 0.6623 (mtm) cc_final: 0.5739 (mpp) REVERT: A 663 MET cc_start: 0.7963 (ttt) cc_final: 0.7454 (tmm) REVERT: A 768 LEU cc_start: 0.3337 (OUTLIER) cc_final: 0.3060 (mt) REVERT: B 621 MET cc_start: 0.6606 (mtp) cc_final: 0.5785 (tmm) REVERT: B 658 ASN cc_start: 0.8356 (t0) cc_final: 0.8042 (t0) REVERT: B 662 MET cc_start: 0.6478 (mtm) cc_final: 0.5653 (mpp) REVERT: B 768 LEU cc_start: 0.4176 (OUTLIER) cc_final: 0.3708 (mt) REVERT: C 103 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8230 (mtt) REVERT: C 658 ASN cc_start: 0.8354 (t0) cc_final: 0.8063 (t0) REVERT: C 663 MET cc_start: 0.7889 (ttt) cc_final: 0.7660 (tmm) REVERT: C 758 MET cc_start: 0.7140 (mpt) cc_final: 0.6588 (mpt) REVERT: D 407 GLU cc_start: 0.7418 (tt0) cc_final: 0.7042 (mt-10) REVERT: D 621 MET cc_start: 0.6943 (mtp) cc_final: 0.6662 (ttm) REVERT: D 662 MET cc_start: 0.6558 (mtm) cc_final: 0.5528 (mpp) REVERT: D 663 MET cc_start: 0.8029 (tmm) cc_final: 0.7323 (tmm) REVERT: E 574 TYR cc_start: 0.6663 (m-80) cc_final: 0.6116 (m-80) REVERT: E 609 MET cc_start: 0.4584 (ttt) cc_final: 0.4214 (mtp) REVERT: E 621 MET cc_start: 0.6699 (mtp) cc_final: 0.6277 (tpt) REVERT: E 658 ASN cc_start: 0.8316 (t0) cc_final: 0.7977 (t0) REVERT: E 662 MET cc_start: 0.6586 (mtm) cc_final: 0.5530 (mpp) REVERT: E 768 LEU cc_start: 0.4081 (OUTLIER) cc_final: 0.3704 (mt) REVERT: F 103 MET cc_start: 0.8377 (mtt) cc_final: 0.7961 (mtt) REVERT: F 658 ASN cc_start: 0.8373 (t0) cc_final: 0.8131 (t0) REVERT: F 758 MET cc_start: 0.7059 (mpt) cc_final: 0.6454 (mpt) REVERT: F 768 LEU cc_start: 0.3226 (OUTLIER) cc_final: 0.2899 (mt) REVERT: G 407 GLU cc_start: 0.7344 (tt0) cc_final: 0.7074 (mt-10) REVERT: G 658 ASN cc_start: 0.8364 (t0) cc_final: 0.8013 (t0) REVERT: G 662 MET cc_start: 0.6655 (mtm) cc_final: 0.5705 (mpp) REVERT: G 663 MET cc_start: 0.7937 (ttt) cc_final: 0.7404 (tmm) REVERT: H 555 PHE cc_start: 0.4973 (m-80) cc_final: 0.4706 (m-80) REVERT: H 594 PHE cc_start: 0.7016 (t80) cc_final: 0.6458 (t80) REVERT: H 621 MET cc_start: 0.6819 (mtp) cc_final: 0.5781 (tmm) REVERT: H 662 MET cc_start: 0.6588 (mtm) cc_final: 0.5772 (mpp) REVERT: I 103 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.7895 (mtt) REVERT: I 658 ASN cc_start: 0.8366 (t0) cc_final: 0.8105 (t0) REVERT: I 663 MET cc_start: 0.7862 (ttt) cc_final: 0.7586 (tmm) REVERT: I 758 MET cc_start: 0.7170 (mpt) cc_final: 0.6849 (mpt) REVERT: J 168 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8687 (tp) REVERT: J 662 MET cc_start: 0.6806 (mtm) cc_final: 0.5851 (mpp) REVERT: J 663 MET cc_start: 0.7995 (ttt) cc_final: 0.7595 (tmm) REVERT: K 88 HIS cc_start: 0.7205 (OUTLIER) cc_final: 0.6981 (t70) REVERT: K 621 MET cc_start: 0.6841 (mtp) cc_final: 0.5988 (tmm) REVERT: K 658 ASN cc_start: 0.8428 (t0) cc_final: 0.8054 (t0) REVERT: K 662 MET cc_start: 0.6649 (mtm) cc_final: 0.5886 (mpp) REVERT: L 103 MET cc_start: 0.8405 (mtt) cc_final: 0.7971 (mtt) REVERT: L 658 ASN cc_start: 0.8362 (t0) cc_final: 0.8059 (t0) REVERT: L 663 MET cc_start: 0.7923 (ttt) cc_final: 0.7703 (tmm) REVERT: L 768 LEU cc_start: 0.3413 (OUTLIER) cc_final: 0.2975 (mt) outliers start: 166 outliers final: 132 residues processed: 387 average time/residue: 0.5918 time to fit residues: 410.9925 Evaluate side-chains 367 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 226 time to evaluate : 5.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 412 ASN Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 412 ASN Chi-restraints excluded: chain D residue 452 PHE Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 353 LYS Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 412 ASN Chi-restraints excluded: chain E residue 654 LEU Chi-restraints excluded: chain E residue 726 LEU Chi-restraints excluded: chain E residue 768 LEU Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 412 ASN Chi-restraints excluded: chain F residue 455 ASP Chi-restraints excluded: chain F residue 654 LEU Chi-restraints excluded: chain F residue 768 LEU Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain G residue 452 PHE Chi-restraints excluded: chain G residue 455 ASP Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 277 ILE Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 412 ASN Chi-restraints excluded: chain H residue 654 LEU Chi-restraints excluded: chain H residue 726 LEU Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain I residue 229 LEU Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 277 ILE Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 379 LEU Chi-restraints excluded: chain I residue 412 ASN Chi-restraints excluded: chain I residue 456 ILE Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 620 VAL Chi-restraints excluded: chain I residue 654 LEU Chi-restraints excluded: chain J residue 43 ASP Chi-restraints excluded: chain J residue 103 MET Chi-restraints excluded: chain J residue 127 MET Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 196 THR Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 277 ILE Chi-restraints excluded: chain J residue 345 ILE Chi-restraints excluded: chain J residue 379 LEU Chi-restraints excluded: chain J residue 412 ASN Chi-restraints excluded: chain J residue 452 PHE Chi-restraints excluded: chain J residue 455 ASP Chi-restraints excluded: chain J residue 613 LEU Chi-restraints excluded: chain K residue 88 HIS Chi-restraints excluded: chain K residue 100 GLU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 277 ILE Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 379 LEU Chi-restraints excluded: chain K residue 412 ASN Chi-restraints excluded: chain K residue 654 LEU Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 229 LEU Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain L residue 277 ILE Chi-restraints excluded: chain L residue 345 ILE Chi-restraints excluded: chain L residue 379 LEU Chi-restraints excluded: chain L residue 455 ASP Chi-restraints excluded: chain L residue 654 LEU Chi-restraints excluded: chain L residue 768 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 292 optimal weight: 10.0000 chunk 783 optimal weight: 9.9990 chunk 171 optimal weight: 1.9990 chunk 510 optimal weight: 0.0570 chunk 214 optimal weight: 5.9990 chunk 870 optimal weight: 10.0000 chunk 722 optimal weight: 9.9990 chunk 403 optimal weight: 4.9990 chunk 72 optimal weight: 20.0000 chunk 288 optimal weight: 30.0000 chunk 457 optimal weight: 2.9990 overall best weight: 3.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 HIS ** C 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 469 HIS ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 628 ASN ** I 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 469 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2703 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= 0.339 Angle : 0.642 9.966 94584 Z= 0.343 Chirality : 0.049 0.165 10620 Planarity : 0.003 0.038 12396 Dihedral : 5.884 45.700 9521 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.82 % Favored : 85.18 % Rotamer: Outliers : 2.47 % Allowed : 10.31 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.40 (0.08), residues: 8952 helix: -1.39 (0.26), residues: 384 sheet: -3.36 (0.09), residues: 2532 loop : -2.98 (0.07), residues: 6036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 773 HIS 0.002 0.001 HIS H 469 PHE 0.025 0.002 PHE A 580 TYR 0.011 0.001 TYR B 65 ARG 0.004 0.001 ARG A 402 *********************** 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 431 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 248 time to evaluate : 5.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8631 (tp) REVERT: A 543 ASN cc_start: 0.8112 (m-40) cc_final: 0.7636 (t0) REVERT: A 658 ASN cc_start: 0.8340 (t0) cc_final: 0.8033 (t0) REVERT: A 662 MET cc_start: 0.6759 (mtm) cc_final: 0.5806 (mpp) REVERT: A 663 MET cc_start: 0.7907 (ttt) cc_final: 0.7520 (tmm) REVERT: A 768 LEU cc_start: 0.3478 (OUTLIER) cc_final: 0.3186 (mt) REVERT: B 621 MET cc_start: 0.6768 (mtp) cc_final: 0.5905 (tmm) REVERT: B 658 ASN cc_start: 0.8351 (t0) cc_final: 0.8044 (t0) REVERT: B 662 MET cc_start: 0.6623 (mtm) cc_final: 0.5772 (mpp) REVERT: B 768 LEU cc_start: 0.3993 (OUTLIER) cc_final: 0.3650 (mt) REVERT: C 103 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8286 (mtt) REVERT: C 658 ASN cc_start: 0.8345 (t0) cc_final: 0.8054 (t0) REVERT: C 663 MET cc_start: 0.7868 (ttt) cc_final: 0.7626 (tmm) REVERT: C 758 MET cc_start: 0.7134 (mpt) cc_final: 0.6565 (mpt) REVERT: D 407 GLU cc_start: 0.7410 (tt0) cc_final: 0.7044 (mt-10) REVERT: D 543 ASN cc_start: 0.8105 (m-40) cc_final: 0.7642 (t0) REVERT: D 621 MET cc_start: 0.7000 (mtp) cc_final: 0.6738 (ttm) REVERT: D 662 MET cc_start: 0.6833 (mtm) cc_final: 0.5847 (mpp) REVERT: E 574 TYR cc_start: 0.6641 (m-80) cc_final: 0.6062 (m-80) REVERT: E 621 MET cc_start: 0.6708 (mtp) cc_final: 0.6290 (tpt) REVERT: E 658 ASN cc_start: 0.8419 (t0) cc_final: 0.8073 (t0) REVERT: E 662 MET cc_start: 0.6525 (mtm) cc_final: 0.5617 (mpp) REVERT: F 103 MET cc_start: 0.8419 (mtt) cc_final: 0.8007 (mtt) REVERT: F 658 ASN cc_start: 0.8362 (t0) cc_final: 0.8101 (t0) REVERT: F 735 MET cc_start: 0.2921 (ptp) cc_final: 0.2535 (ptp) REVERT: F 758 MET cc_start: 0.7205 (mpt) cc_final: 0.6654 (mpt) REVERT: F 768 LEU cc_start: 0.3209 (OUTLIER) cc_final: 0.2934 (mt) REVERT: G 407 GLU cc_start: 0.7387 (tt0) cc_final: 0.7057 (mt-10) REVERT: G 543 ASN cc_start: 0.7961 (m-40) cc_final: 0.7441 (t0) REVERT: G 658 ASN cc_start: 0.8426 (t0) cc_final: 0.8122 (t0) REVERT: G 662 MET cc_start: 0.6848 (mtm) cc_final: 0.5871 (mpp) REVERT: G 663 MET cc_start: 0.7888 (ttt) cc_final: 0.7392 (tmm) REVERT: H 555 PHE cc_start: 0.5029 (m-80) cc_final: 0.4756 (m-80) REVERT: H 621 MET cc_start: 0.6695 (mtp) cc_final: 0.5708 (tmm) REVERT: H 662 MET cc_start: 0.6644 (mtm) cc_final: 0.5801 (mpp) REVERT: I 103 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.7991 (mtt) REVERT: I 354 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.8007 (p0) REVERT: I 658 ASN cc_start: 0.8346 (t0) cc_final: 0.8095 (t0) REVERT: I 663 MET cc_start: 0.7829 (ttt) cc_final: 0.7619 (tmm) REVERT: I 758 MET cc_start: 0.7108 (mpt) cc_final: 0.6784 (mpt) REVERT: J 168 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8679 (tp) REVERT: J 662 MET cc_start: 0.7078 (mtm) cc_final: 0.6120 (mpp) REVERT: J 663 MET cc_start: 0.7927 (ttt) cc_final: 0.7546 (tmm) REVERT: K 37 GLU cc_start: 0.8079 (tp30) cc_final: 0.7856 (mt-10) REVERT: K 658 ASN cc_start: 0.8422 (t0) cc_final: 0.8052 (t0) REVERT: K 662 MET cc_start: 0.6670 (mtm) cc_final: 0.5830 (mpp) REVERT: L 37 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6986 (mt-10) REVERT: L 103 MET cc_start: 0.8441 (mtt) cc_final: 0.8039 (mtt) REVERT: L 658 ASN cc_start: 0.8336 (t0) cc_final: 0.8021 (t0) REVERT: L 663 MET cc_start: 0.7860 (ttt) cc_final: 0.7658 (tmm) REVERT: L 735 MET cc_start: 0.2919 (OUTLIER) cc_final: 0.2457 (ptp) REVERT: L 768 LEU cc_start: 0.3436 (OUTLIER) cc_final: 0.3021 (mt) outliers start: 183 outliers final: 143 residues processed: 405 average time/residue: 0.5820 time to fit residues: 423.7967 Evaluate side-chains 379 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 226 time to evaluate : 5.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 412 ASN Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 496 ASN Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 412 ASN Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 353 LYS Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 412 ASN Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 654 LEU Chi-restraints excluded: chain E residue 726 LEU Chi-restraints excluded: chain E residue 768 LEU Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 455 ASP Chi-restraints excluded: chain F residue 496 ASN Chi-restraints excluded: chain F residue 654 LEU Chi-restraints excluded: chain F residue 768 LEU Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain G residue 455 ASP Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 277 ILE Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 412 ASN Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 654 LEU Chi-restraints excluded: chain H residue 726 LEU Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 148 SER Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain I residue 229 LEU Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 277 ILE Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 354 ASP Chi-restraints excluded: chain I residue 379 LEU Chi-restraints excluded: chain I residue 412 ASN Chi-restraints excluded: chain I residue 449 THR Chi-restraints excluded: chain I residue 456 ILE Chi-restraints excluded: chain I residue 496 ASN Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 620 VAL Chi-restraints excluded: chain I residue 654 LEU Chi-restraints excluded: chain J residue 43 ASP Chi-restraints excluded: chain J residue 103 MET Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 127 MET Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 196 THR Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 277 ILE Chi-restraints excluded: chain J residue 345 ILE Chi-restraints excluded: chain J residue 354 ASP Chi-restraints excluded: chain J residue 379 LEU Chi-restraints excluded: chain J residue 412 ASN Chi-restraints excluded: chain J residue 455 ASP Chi-restraints excluded: chain J residue 613 LEU Chi-restraints excluded: chain K residue 100 GLU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 277 ILE Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 379 LEU Chi-restraints excluded: chain K residue 412 ASN Chi-restraints excluded: chain K residue 449 THR Chi-restraints excluded: chain K residue 654 LEU Chi-restraints excluded: chain K residue 726 LEU Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 229 LEU Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain L residue 277 ILE Chi-restraints excluded: chain L residue 345 ILE Chi-restraints excluded: chain L residue 379 LEU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 455 ASP Chi-restraints excluded: chain L residue 496 ASN Chi-restraints excluded: chain L residue 654 LEU Chi-restraints excluded: chain L residue 735 MET Chi-restraints excluded: chain L residue 768 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 839 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 496 optimal weight: 20.0000 chunk 635 optimal weight: 5.9990 chunk 492 optimal weight: 9.9990 chunk 733 optimal weight: 5.9990 chunk 486 optimal weight: 10.0000 chunk 867 optimal weight: 0.9980 chunk 542 optimal weight: 0.8980 chunk 528 optimal weight: 2.9990 chunk 400 optimal weight: 0.1980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 GLN B 731 ASN ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 ASN ** G 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 69840 Z= 0.162 Angle : 0.557 9.103 94584 Z= 0.289 Chirality : 0.046 0.151 10620 Planarity : 0.002 0.037 12396 Dihedral : 5.272 41.705 9521 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.17 % Favored : 88.83 % Rotamer: Outliers : 1.36 % Allowed : 11.97 % Favored : 86.67 % 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: -4.16 (0.08), residues: 8952 helix: -1.32 (0.25), residues: 384 sheet: -3.15 (0.09), residues: 2868 loop : -2.76 (0.07), residues: 5700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP H 773 HIS 0.002 0.001 HIS K 88 PHE 0.021 0.001 PHE A 580 TYR 0.015 0.001 TYR F 574 ARG 0.002 0.000 ARG A 402 *********************** 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 378 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 277 time to evaluate : 5.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.7994 (mt) REVERT: A 543 ASN cc_start: 0.7774 (m-40) cc_final: 0.7406 (t0) REVERT: A 658 ASN cc_start: 0.8389 (t0) cc_final: 0.8080 (t0) REVERT: A 662 MET cc_start: 0.6584 (mtm) cc_final: 0.5650 (mpp) REVERT: A 768 LEU cc_start: 0.3300 (OUTLIER) cc_final: 0.3003 (mt) REVERT: B 580 PHE cc_start: 0.6223 (t80) cc_final: 0.6004 (t80) REVERT: B 621 MET cc_start: 0.6790 (mtp) cc_final: 0.6148 (tmm) REVERT: B 658 ASN cc_start: 0.8316 (t0) cc_final: 0.8001 (t0) REVERT: B 662 MET cc_start: 0.6383 (mtm) cc_final: 0.5656 (mpp) REVERT: B 768 LEU cc_start: 0.3847 (OUTLIER) cc_final: 0.3503 (mt) REVERT: C 103 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.8122 (mtt) REVERT: C 621 MET cc_start: 0.6950 (mtp) cc_final: 0.6416 (ttp) REVERT: C 658 ASN cc_start: 0.8282 (t0) cc_final: 0.7918 (t0) REVERT: C 663 MET cc_start: 0.7942 (ttt) cc_final: 0.7349 (tmm) REVERT: C 735 MET cc_start: 0.2617 (ptp) cc_final: 0.2179 (ptp) REVERT: C 758 MET cc_start: 0.7135 (mpt) cc_final: 0.6584 (mpt) REVERT: D 407 GLU cc_start: 0.7088 (tt0) cc_final: 0.6841 (mt-10) REVERT: D 543 ASN cc_start: 0.7720 (m-40) cc_final: 0.7399 (t0) REVERT: D 621 MET cc_start: 0.7101 (mtp) cc_final: 0.6816 (ttm) REVERT: D 662 MET cc_start: 0.6750 (mtm) cc_final: 0.5728 (mpp) REVERT: E 543 ASN cc_start: 0.7724 (m-40) cc_final: 0.7485 (t0) REVERT: E 580 PHE cc_start: 0.6196 (t80) cc_final: 0.5958 (t80) REVERT: E 594 PHE cc_start: 0.6981 (t80) cc_final: 0.6258 (t80) REVERT: E 621 MET cc_start: 0.6792 (mtp) cc_final: 0.6096 (tmm) REVERT: E 658 ASN cc_start: 0.8310 (t0) cc_final: 0.7996 (t0) REVERT: E 662 MET cc_start: 0.6680 (mtm) cc_final: 0.5681 (mpp) REVERT: F 621 MET cc_start: 0.6777 (mtp) cc_final: 0.5990 (ttp) REVERT: F 658 ASN cc_start: 0.8304 (t0) cc_final: 0.7994 (t0) REVERT: F 758 MET cc_start: 0.7104 (mpt) cc_final: 0.6545 (mpt) REVERT: F 768 LEU cc_start: 0.3280 (OUTLIER) cc_final: 0.3035 (mt) REVERT: G 345 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.8068 (mt) REVERT: G 407 GLU cc_start: 0.7157 (tt0) cc_final: 0.6883 (mt-10) REVERT: G 543 ASN cc_start: 0.7747 (m-40) cc_final: 0.7399 (t0) REVERT: G 658 ASN cc_start: 0.8350 (t0) cc_final: 0.8049 (t0) REVERT: G 662 MET cc_start: 0.6644 (mtm) cc_final: 0.5691 (mpp) REVERT: H 555 PHE cc_start: 0.5159 (m-80) cc_final: 0.4886 (m-80) REVERT: H 621 MET cc_start: 0.6777 (mtp) cc_final: 0.5810 (tmm) REVERT: H 662 MET cc_start: 0.6624 (mtm) cc_final: 0.5906 (mpp) REVERT: I 103 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7746 (mtt) REVERT: I 658 ASN cc_start: 0.8280 (t0) cc_final: 0.7916 (t0) REVERT: I 663 MET cc_start: 0.7894 (ttt) cc_final: 0.7671 (tmm) REVERT: J 543 ASN cc_start: 0.7736 (m-40) cc_final: 0.7373 (t0) REVERT: J 662 MET cc_start: 0.6992 (mtm) cc_final: 0.6038 (mpp) REVERT: K 580 PHE cc_start: 0.6276 (t80) cc_final: 0.6050 (t80) REVERT: K 621 MET cc_start: 0.6994 (mtp) cc_final: 0.6446 (ttp) REVERT: K 658 ASN cc_start: 0.8371 (t0) cc_final: 0.8030 (t0) REVERT: K 662 MET cc_start: 0.6578 (mtm) cc_final: 0.5910 (mpp) REVERT: L 658 ASN cc_start: 0.8285 (t0) cc_final: 0.7915 (t0) REVERT: L 735 MET cc_start: 0.2752 (OUTLIER) cc_final: 0.2331 (ptp) REVERT: L 768 LEU cc_start: 0.3352 (OUTLIER) cc_final: 0.3049 (mt) outliers start: 101 outliers final: 72 residues processed: 352 average time/residue: 0.6057 time to fit residues: 378.9401 Evaluate side-chains 323 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 242 time to evaluate : 5.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain C residue 706 VAL Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 353 LYS Chi-restraints excluded: chain E residue 654 LEU Chi-restraints excluded: chain E residue 726 LEU Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 412 ASN Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 654 LEU Chi-restraints excluded: chain F residue 726 LEU Chi-restraints excluded: chain F residue 768 LEU Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 449 THR Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 726 LEU Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 148 SER Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 449 THR Chi-restraints excluded: chain I residue 654 LEU Chi-restraints excluded: chain J residue 43 ASP Chi-restraints excluded: chain J residue 103 MET Chi-restraints excluded: chain J residue 127 MET Chi-restraints excluded: chain J residue 196 THR Chi-restraints excluded: chain J residue 345 ILE Chi-restraints excluded: chain J residue 449 THR Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 412 ASN Chi-restraints excluded: chain K residue 449 THR Chi-restraints excluded: chain K residue 654 LEU Chi-restraints excluded: chain K residue 726 LEU Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain L residue 345 ILE Chi-restraints excluded: chain L residue 412 ASN Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 735 MET Chi-restraints excluded: chain L residue 768 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 536 optimal weight: 0.8980 chunk 346 optimal weight: 20.0000 chunk 518 optimal weight: 30.0000 chunk 261 optimal weight: 7.9990 chunk 170 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 551 optimal weight: 0.6980 chunk 590 optimal weight: 0.0770 chunk 428 optimal weight: 7.9990 chunk 80 optimal weight: 8.9990 chunk 681 optimal weight: 7.9990 overall best weight: 3.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 ASN ** G 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 69840 Z= 0.332 Angle : 0.635 8.395 94584 Z= 0.335 Chirality : 0.048 0.165 10620 Planarity : 0.003 0.030 12396 Dihedral : 5.664 46.135 9521 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.77 % Favored : 84.23 % Rotamer: Outliers : 1.72 % Allowed : 12.03 % Favored : 86.25 % 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: -4.14 (0.08), residues: 8952 helix: -1.24 (0.26), residues: 384 sheet: -3.19 (0.09), residues: 2688 loop : -2.75 (0.07), residues: 5880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 773 HIS 0.002 0.001 HIS K 693 PHE 0.027 0.002 PHE C 580 TYR 0.021 0.001 TYR C 574 ARG 0.005 0.000 ARG E 741 *********************** 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 394 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 267 time to evaluate : 5.960 Fit side-chains revert: symmetry clash REVERT: A 168 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8570 (tp) REVERT: A 543 ASN cc_start: 0.7664 (m-40) cc_final: 0.7355 (t0) REVERT: A 574 TYR cc_start: 0.6407 (m-80) cc_final: 0.5454 (m-80) REVERT: A 658 ASN cc_start: 0.8440 (t0) cc_final: 0.8144 (t0) REVERT: A 662 MET cc_start: 0.6823 (mtm) cc_final: 0.5876 (mpp) REVERT: A 768 LEU cc_start: 0.3361 (OUTLIER) cc_final: 0.3067 (mt) REVERT: B 580 PHE cc_start: 0.6394 (t80) cc_final: 0.6173 (t80) REVERT: B 621 MET cc_start: 0.6827 (mtp) cc_final: 0.6163 (tmm) REVERT: B 658 ASN cc_start: 0.8406 (t0) cc_final: 0.8093 (t0) REVERT: B 662 MET cc_start: 0.6570 (mtm) cc_final: 0.5720 (mpp) REVERT: C 103 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8247 (mtt) REVERT: C 516 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7929 (tm-30) REVERT: C 543 ASN cc_start: 0.7764 (m-40) cc_final: 0.7547 (t0) REVERT: C 621 MET cc_start: 0.6825 (mtp) cc_final: 0.6293 (ttp) REVERT: C 658 ASN cc_start: 0.8306 (t0) cc_final: 0.7979 (t0) REVERT: C 663 MET cc_start: 0.7899 (ttt) cc_final: 0.7678 (tmm) REVERT: C 758 MET cc_start: 0.7210 (mpt) cc_final: 0.6653 (mpt) REVERT: D 407 GLU cc_start: 0.7304 (tt0) cc_final: 0.6974 (mt-10) REVERT: D 543 ASN cc_start: 0.7649 (m-40) cc_final: 0.7365 (t0) REVERT: D 621 MET cc_start: 0.7023 (mtp) cc_final: 0.6737 (ttm) REVERT: D 662 MET cc_start: 0.6986 (mtm) cc_final: 0.5627 (mpp) REVERT: E 580 PHE cc_start: 0.6300 (t80) cc_final: 0.6072 (t80) REVERT: E 621 MET cc_start: 0.6736 (mtp) cc_final: 0.5863 (tmm) REVERT: E 658 ASN cc_start: 0.8381 (t0) cc_final: 0.8057 (t0) REVERT: E 662 MET cc_start: 0.6625 (mtm) cc_final: 0.5756 (mpp) REVERT: F 103 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8265 (mtt) REVERT: F 516 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7910 (tm-30) REVERT: F 543 ASN cc_start: 0.7848 (m-40) cc_final: 0.7578 (t0) REVERT: F 658 ASN cc_start: 0.8357 (t0) cc_final: 0.8069 (t0) REVERT: F 735 MET cc_start: 0.3179 (ptp) cc_final: 0.2614 (ptp) REVERT: F 758 MET cc_start: 0.7195 (mpt) cc_final: 0.6641 (mpt) REVERT: F 768 LEU cc_start: 0.3315 (OUTLIER) cc_final: 0.3086 (mt) REVERT: G 407 GLU cc_start: 0.7267 (tt0) cc_final: 0.6987 (mt-10) REVERT: G 516 GLU cc_start: 0.8331 (tm-30) cc_final: 0.8045 (tm-30) REVERT: G 543 ASN cc_start: 0.7633 (m-40) cc_final: 0.7353 (t0) REVERT: G 658 ASN cc_start: 0.8391 (t0) cc_final: 0.8099 (t0) REVERT: G 662 MET cc_start: 0.6894 (mtm) cc_final: 0.5894 (mpp) REVERT: H 555 PHE cc_start: 0.4982 (m-80) cc_final: 0.4711 (m-80) REVERT: H 621 MET cc_start: 0.6823 (mtp) cc_final: 0.5825 (tmm) REVERT: H 662 MET cc_start: 0.6687 (mtm) cc_final: 0.5845 (mpp) REVERT: I 103 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7970 (mtt) REVERT: I 516 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7919 (tm-30) REVERT: I 543 ASN cc_start: 0.7892 (m-40) cc_final: 0.7467 (t0) REVERT: I 658 ASN cc_start: 0.8322 (t0) cc_final: 0.8004 (t0) REVERT: I 663 MET cc_start: 0.7935 (ttt) cc_final: 0.7734 (tmm) REVERT: J 543 ASN cc_start: 0.7599 (m-40) cc_final: 0.7308 (t0) REVERT: J 662 MET cc_start: 0.6984 (mtm) cc_final: 0.6030 (mpp) REVERT: K 580 PHE cc_start: 0.6296 (t80) cc_final: 0.6092 (t80) REVERT: K 621 MET cc_start: 0.6906 (mtp) cc_final: 0.6370 (ttp) REVERT: K 658 ASN cc_start: 0.8426 (t0) cc_final: 0.8047 (t0) REVERT: K 662 MET cc_start: 0.6693 (mtm) cc_final: 0.5866 (mpp) REVERT: L 103 MET cc_start: 0.8475 (mtt) cc_final: 0.8274 (mtt) REVERT: L 658 ASN cc_start: 0.8303 (t0) cc_final: 0.7943 (t0) REVERT: L 735 MET cc_start: 0.2854 (OUTLIER) cc_final: 0.2484 (ptp) REVERT: L 768 LEU cc_start: 0.3424 (OUTLIER) cc_final: 0.3139 (mt) outliers start: 127 outliers final: 95 residues processed: 368 average time/residue: 0.5946 time to fit residues: 391.8084 Evaluate side-chains 347 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 244 time to evaluate : 5.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 412 ASN Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 496 ASN Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain C residue 706 VAL Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 353 LYS Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 654 LEU Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 496 ASN Chi-restraints excluded: chain F residue 654 LEU Chi-restraints excluded: chain F residue 768 LEU Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 449 THR Chi-restraints excluded: chain G residue 620 VAL Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 654 LEU Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 148 SER Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 245 THR Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 379 LEU Chi-restraints excluded: chain I residue 449 THR Chi-restraints excluded: chain I residue 496 ASN Chi-restraints excluded: chain I residue 654 LEU Chi-restraints excluded: chain J residue 43 ASP Chi-restraints excluded: chain J residue 103 MET Chi-restraints excluded: chain J residue 127 MET Chi-restraints excluded: chain J residue 196 THR Chi-restraints excluded: chain J residue 345 ILE Chi-restraints excluded: chain J residue 354 ASP Chi-restraints excluded: chain J residue 449 THR Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 412 ASN Chi-restraints excluded: chain K residue 449 THR Chi-restraints excluded: chain K residue 654 LEU Chi-restraints excluded: chain K residue 726 LEU Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain L residue 245 THR Chi-restraints excluded: chain L residue 345 ILE Chi-restraints excluded: chain L residue 379 LEU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 496 ASN Chi-restraints excluded: chain L residue 654 LEU Chi-restraints excluded: chain L residue 735 MET Chi-restraints excluded: chain L residue 768 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 789 optimal weight: 2.9990 chunk 831 optimal weight: 0.9990 chunk 758 optimal weight: 5.9990 chunk 808 optimal weight: 8.9990 chunk 830 optimal weight: 20.0000 chunk 486 optimal weight: 6.9990 chunk 352 optimal weight: 8.9990 chunk 634 optimal weight: 7.9990 chunk 248 optimal weight: 0.9980 chunk 730 optimal weight: 20.0000 chunk 764 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3048 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= 0.356 Angle : 0.656 8.082 94584 Z= 0.347 Chirality : 0.049 0.167 10620 Planarity : 0.003 0.032 12396 Dihedral : 5.816 48.182 9521 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.26 % Favored : 84.74 % Rotamer: Outliers : 2.12 % Allowed : 11.74 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.24 (0.08), residues: 8952 helix: -1.25 (0.26), residues: 384 sheet: -3.31 (0.09), residues: 2808 loop : -2.76 (0.07), residues: 5760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 773 HIS 0.003 0.001 HIS H 693 PHE 0.026 0.002 PHE I 580 TYR 0.023 0.001 TYR C 574 ARG 0.004 0.001 ARG A 402 *********************** 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 420 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 263 time to evaluate : 5.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8632 (tp) REVERT: A 516 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8107 (tm-30) REVERT: A 543 ASN cc_start: 0.7625 (m-40) cc_final: 0.7344 (t0) REVERT: A 658 ASN cc_start: 0.8446 (t0) cc_final: 0.8156 (t0) REVERT: A 662 MET cc_start: 0.7001 (mtm) cc_final: 0.6039 (mpp) REVERT: A 768 LEU cc_start: 0.3374 (OUTLIER) cc_final: 0.3075 (mt) REVERT: B 580 PHE cc_start: 0.6367 (t80) cc_final: 0.6142 (t80) REVERT: B 621 MET cc_start: 0.6818 (mtp) cc_final: 0.6114 (tmm) REVERT: B 658 ASN cc_start: 0.8374 (t0) cc_final: 0.8062 (t0) REVERT: B 662 MET cc_start: 0.6690 (mtm) cc_final: 0.5743 (mpp) REVERT: C 103 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8257 (mtt) REVERT: C 516 GLU cc_start: 0.8243 (tm-30) cc_final: 0.8019 (tm-30) REVERT: C 621 MET cc_start: 0.6741 (mtp) cc_final: 0.6229 (ttp) REVERT: C 658 ASN cc_start: 0.8313 (t0) cc_final: 0.7973 (t0) REVERT: C 663 MET cc_start: 0.7890 (ttt) cc_final: 0.7679 (tmm) REVERT: C 758 MET cc_start: 0.7317 (mpt) cc_final: 0.6768 (mpt) REVERT: D 407 GLU cc_start: 0.7362 (tt0) cc_final: 0.7003 (mt-10) REVERT: D 543 ASN cc_start: 0.7605 (m-40) cc_final: 0.7369 (t0) REVERT: D 621 MET cc_start: 0.7031 (mtp) cc_final: 0.6315 (ttm) REVERT: D 662 MET cc_start: 0.7188 (mtm) cc_final: 0.5864 (mpp) REVERT: E 580 PHE cc_start: 0.6350 (t80) cc_final: 0.6082 (t80) REVERT: E 621 MET cc_start: 0.6721 (mtp) cc_final: 0.5876 (tmm) REVERT: E 658 ASN cc_start: 0.8389 (t0) cc_final: 0.8072 (t0) REVERT: E 662 MET cc_start: 0.6670 (mtm) cc_final: 0.5667 (mpp) REVERT: F 516 GLU cc_start: 0.8225 (tm-30) cc_final: 0.8025 (tm-30) REVERT: F 658 ASN cc_start: 0.8362 (t0) cc_final: 0.8094 (t0) REVERT: F 758 MET cc_start: 0.7262 (mpt) cc_final: 0.6708 (mpt) REVERT: G 407 GLU cc_start: 0.7250 (tt0) cc_final: 0.6961 (mt-10) REVERT: G 516 GLU cc_start: 0.8379 (tm-30) cc_final: 0.8099 (tm-30) REVERT: G 543 ASN cc_start: 0.7584 (m-40) cc_final: 0.7344 (t0) REVERT: G 658 ASN cc_start: 0.8375 (t0) cc_final: 0.8092 (t0) REVERT: G 662 MET cc_start: 0.7028 (mtm) cc_final: 0.6010 (mpp) REVERT: H 555 PHE cc_start: 0.5093 (m-80) cc_final: 0.4814 (m-80) REVERT: H 621 MET cc_start: 0.6813 (mtp) cc_final: 0.5847 (tmm) REVERT: H 662 MET cc_start: 0.6762 (mtm) cc_final: 0.5804 (mpp) REVERT: I 103 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8083 (mtt) REVERT: I 354 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7999 (p0) REVERT: I 658 ASN cc_start: 0.8348 (t0) cc_final: 0.8052 (t0) REVERT: I 735 MET cc_start: 0.2677 (ptp) cc_final: 0.2076 (ptp) REVERT: J 516 GLU cc_start: 0.8339 (tm-30) cc_final: 0.8074 (tm-30) REVERT: J 543 ASN cc_start: 0.7583 (m-40) cc_final: 0.7311 (t0) REVERT: J 662 MET cc_start: 0.7133 (mtm) cc_final: 0.6125 (mpp) REVERT: K 580 PHE cc_start: 0.6367 (t80) cc_final: 0.6139 (t80) REVERT: K 658 ASN cc_start: 0.8417 (t0) cc_final: 0.8058 (t0) REVERT: K 662 MET cc_start: 0.6771 (mtm) cc_final: 0.5856 (mpp) REVERT: L 103 MET cc_start: 0.8584 (mtt) cc_final: 0.8047 (mtt) REVERT: L 658 ASN cc_start: 0.8313 (t0) cc_final: 0.7961 (t0) REVERT: L 768 LEU cc_start: 0.3380 (OUTLIER) cc_final: 0.3097 (mt) outliers start: 157 outliers final: 135 residues processed: 395 average time/residue: 0.5797 time to fit residues: 414.2422 Evaluate side-chains 386 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 245 time to evaluate : 5.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 496 ASN Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 412 ASN Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 353 LYS Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 412 ASN Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 654 LEU Chi-restraints excluded: chain E residue 726 LEU Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 496 ASN Chi-restraints excluded: chain F residue 654 LEU Chi-restraints excluded: chain F residue 726 LEU Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 354 ASP Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain G residue 449 THR Chi-restraints excluded: chain G residue 620 VAL Chi-restraints excluded: chain G residue 706 VAL Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 654 LEU Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 148 SER Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 245 THR Chi-restraints excluded: chain I residue 277 ILE Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 354 ASP Chi-restraints excluded: chain I residue 379 LEU Chi-restraints excluded: chain I residue 449 THR Chi-restraints excluded: chain I residue 496 ASN Chi-restraints excluded: chain I residue 620 VAL Chi-restraints excluded: chain I residue 654 LEU Chi-restraints excluded: chain J residue 43 ASP Chi-restraints excluded: chain J residue 103 MET Chi-restraints excluded: chain J residue 127 MET Chi-restraints excluded: chain J residue 196 THR Chi-restraints excluded: chain J residue 245 THR Chi-restraints excluded: chain J residue 277 ILE Chi-restraints excluded: chain J residue 345 ILE Chi-restraints excluded: chain J residue 354 ASP Chi-restraints excluded: chain J residue 379 LEU Chi-restraints excluded: chain J residue 412 ASN Chi-restraints excluded: chain J residue 449 THR Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 277 ILE Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 379 LEU Chi-restraints excluded: chain K residue 412 ASN Chi-restraints excluded: chain K residue 449 THR Chi-restraints excluded: chain K residue 654 LEU Chi-restraints excluded: chain K residue 726 LEU Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain L residue 245 THR Chi-restraints excluded: chain L residue 345 ILE Chi-restraints excluded: chain L residue 379 LEU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 496 ASN Chi-restraints excluded: chain L residue 654 LEU Chi-restraints excluded: chain L residue 768 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 805 optimal weight: 3.9990 chunk 530 optimal weight: 7.9990 chunk 854 optimal weight: 1.9990 chunk 521 optimal weight: 20.0000 chunk 405 optimal weight: 6.9990 chunk 594 optimal weight: 20.0000 chunk 896 optimal weight: 6.9990 chunk 825 optimal weight: 0.9990 chunk 713 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 551 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 ASN ** G 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 543 ASN ** I 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 69840 Z= 0.160 Angle : 0.563 8.476 94584 Z= 0.292 Chirality : 0.046 0.151 10620 Planarity : 0.002 0.035 12396 Dihedral : 5.157 44.182 9521 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 1.50 % Allowed : 12.47 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.08), residues: 8952 helix: -0.35 (0.29), residues: 312 sheet: -2.95 (0.10), residues: 2628 loop : -2.63 (0.07), residues: 6012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP L 773 HIS 0.002 0.001 HIS B 88 PHE 0.024 0.001 PHE I 580 TYR 0.022 0.001 TYR E 574 ARG 0.003 0.000 ARG I 583 ********************** 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 375 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 264 time to evaluate : 5.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 658 ASN cc_start: 0.8342 (t0) cc_final: 0.8061 (t0) REVERT: A 662 MET cc_start: 0.7026 (mtm) cc_final: 0.5668 (mpp) REVERT: A 768 LEU cc_start: 0.3368 (OUTLIER) cc_final: 0.3046 (mt) REVERT: B 580 PHE cc_start: 0.6227 (t80) cc_final: 0.5951 (t80) REVERT: B 621 MET cc_start: 0.6774 (mtp) cc_final: 0.6108 (tmm) REVERT: B 658 ASN cc_start: 0.8364 (t0) cc_final: 0.8057 (t0) REVERT: B 662 MET cc_start: 0.6652 (mtm) cc_final: 0.5857 (mpp) REVERT: C 103 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.8091 (mtt) REVERT: C 621 MET cc_start: 0.6879 (mtp) cc_final: 0.6559 (ttm) REVERT: C 658 ASN cc_start: 0.8272 (t0) cc_final: 0.7840 (t0) REVERT: C 758 MET cc_start: 0.7112 (mpt) cc_final: 0.6557 (mpt) REVERT: D 662 MET cc_start: 0.7207 (mtm) cc_final: 0.6898 (mpp) REVERT: E 103 MET cc_start: 0.7469 (mtt) cc_final: 0.7122 (mtt) REVERT: E 580 PHE cc_start: 0.6129 (t80) cc_final: 0.5860 (t80) REVERT: E 621 MET cc_start: 0.6764 (mtp) cc_final: 0.6121 (tmm) REVERT: E 658 ASN cc_start: 0.8339 (t0) cc_final: 0.8027 (t0) REVERT: E 662 MET cc_start: 0.6735 (mtm) cc_final: 0.5869 (mpp) REVERT: F 621 MET cc_start: 0.6723 (mtp) cc_final: 0.6233 (ttm) REVERT: F 658 ASN cc_start: 0.8250 (t0) cc_final: 0.7900 (t0) REVERT: F 758 MET cc_start: 0.6908 (mpt) cc_final: 0.6336 (mpt) REVERT: G 345 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.8024 (mt) REVERT: G 658 ASN cc_start: 0.8327 (t0) cc_final: 0.8060 (t0) REVERT: G 662 MET cc_start: 0.7001 (mtm) cc_final: 0.5759 (mpp) REVERT: H 555 PHE cc_start: 0.5079 (m-80) cc_final: 0.4787 (m-80) REVERT: H 621 MET cc_start: 0.6740 (mtp) cc_final: 0.5924 (tmm) REVERT: H 662 MET cc_start: 0.6774 (mtm) cc_final: 0.5923 (mpp) REVERT: I 103 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7786 (mtt) REVERT: I 658 ASN cc_start: 0.8271 (t0) cc_final: 0.7910 (t0) REVERT: J 516 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7761 (tm-30) REVERT: J 662 MET cc_start: 0.7149 (mtm) cc_final: 0.5931 (mpp) REVERT: K 580 PHE cc_start: 0.6155 (t80) cc_final: 0.5926 (t80) REVERT: K 621 MET cc_start: 0.6924 (mtp) cc_final: 0.6374 (ttp) REVERT: K 658 ASN cc_start: 0.8344 (t0) cc_final: 0.8029 (t0) REVERT: K 662 MET cc_start: 0.6774 (mtm) cc_final: 0.5937 (mpp) REVERT: L 658 ASN cc_start: 0.8255 (t0) cc_final: 0.7829 (t0) REVERT: L 768 LEU cc_start: 0.3522 (OUTLIER) cc_final: 0.3242 (mt) outliers start: 111 outliers final: 98 residues processed: 355 average time/residue: 0.5938 time to fit residues: 378.0535 Evaluate side-chains 337 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 234 time to evaluate : 5.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 412 ASN Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 412 ASN Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 353 LYS Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 654 LEU Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 412 ASN Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 726 LEU Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 449 THR Chi-restraints excluded: chain G residue 620 VAL Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 412 ASN Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 726 LEU Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 245 THR Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 379 LEU Chi-restraints excluded: chain I residue 449 THR Chi-restraints excluded: chain I residue 654 LEU Chi-restraints excluded: chain J residue 43 ASP Chi-restraints excluded: chain J residue 103 MET Chi-restraints excluded: chain J residue 127 MET Chi-restraints excluded: chain J residue 196 THR Chi-restraints excluded: chain J residue 345 ILE Chi-restraints excluded: chain J residue 354 ASP Chi-restraints excluded: chain J residue 379 LEU Chi-restraints excluded: chain J residue 412 ASN Chi-restraints excluded: chain J residue 449 THR Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 379 LEU Chi-restraints excluded: chain K residue 412 ASN Chi-restraints excluded: chain K residue 449 THR Chi-restraints excluded: chain K residue 726 LEU Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain L residue 245 THR Chi-restraints excluded: chain L residue 345 ILE Chi-restraints excluded: chain L residue 412 ASN Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 768 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 437 optimal weight: 6.9990 chunk 567 optimal weight: 1.9990 chunk 760 optimal weight: 0.9990 chunk 218 optimal weight: 20.0000 chunk 658 optimal weight: 0.7980 chunk 105 optimal weight: 9.9990 chunk 198 optimal weight: 9.9990 chunk 715 optimal weight: 8.9990 chunk 299 optimal weight: 0.9980 chunk 734 optimal weight: 20.0000 chunk 90 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 ASN A 543 ASN ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN ** D 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 ASN ** E 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 ASN G 543 ASN ** G 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 543 ASN ** I 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 543 ASN ** J 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.137114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.081635 restraints weight = 114547.127| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 3.57 r_work: 0.3690 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 69840 Z= 0.261 Angle : 0.602 8.204 94584 Z= 0.314 Chirality : 0.047 0.159 10620 Planarity : 0.003 0.028 12396 Dihedral : 5.377 45.320 9521 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.43 % Favored : 85.57 % Rotamer: Outliers : 1.92 % Allowed : 12.25 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.08), residues: 8952 helix: -1.16 (0.26), residues: 384 sheet: -3.11 (0.09), residues: 2856 loop : -2.55 (0.07), residues: 5712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP L 773 HIS 0.002 0.000 HIS K 693 PHE 0.023 0.002 PHE L 580 TYR 0.024 0.001 TYR E 574 ARG 0.003 0.000 ARG A 402 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13411.89 seconds wall clock time: 239 minutes 49.78 seconds (14389.78 seconds total)