Starting phenix.real_space_refine on Fri Mar 15 11:11:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyl_0545/03_2024/6nyl_0545.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyl_0545/03_2024/6nyl_0545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyl_0545/03_2024/6nyl_0545.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyl_0545/03_2024/6nyl_0545.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyl_0545/03_2024/6nyl_0545.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyl_0545/03_2024/6nyl_0545.pdb" } resolution = 3.7 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= 0.009 sd= 0.067 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 42948 2.51 5 N 12060 2.21 5 O 13512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-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: 27.16, per 1000 atoms: 0.40 Number of scatterers: 68664 At special positions: 0 Unit cell: (302.1, 287.26, 117.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 13512 8.00 N 12060 7.00 C 42948 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 749 " distance=2.03 Simple disulfide: pdb=" SG CYS G 738 " - pdb=" SG CYS G 749 " distance=2.03 Simple disulfide: pdb=" SG CYS H 738 " - pdb=" SG CYS H 749 " distance=2.03 Simple disulfide: pdb=" SG CYS I 738 " - pdb=" SG CYS I 749 " distance=2.03 Simple disulfide: pdb=" SG CYS J 738 " - pdb=" SG CYS J 749 " distance=2.03 Simple disulfide: pdb=" SG CYS K 738 " - pdb=" SG CYS K 749 " distance=2.03 Simple disulfide: pdb=" SG CYS L 738 " - pdb=" SG CYS L 749 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 19.51 Conformation dependent library (CDL) restraints added in 9.5 seconds 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16080 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 216 sheets defined 5.6% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.24 Creating SS restraints... Processing helix chain 'A' and resid 29 through 38 removed outlier: 3.799A pdb=" N ALA A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 removed outlier: 3.894A pdb=" N GLU A 59 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE A 60 " --> pdb=" O PHE A 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 56 through 60' Processing helix chain 'A' and resid 71 through 75 removed outlier: 4.236A pdb=" N SER A 74 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 726 removed outlier: 3.952A pdb=" N LEU A 726 " --> pdb=" O PHE A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 754 removed outlier: 4.468A pdb=" N ALA A 748 " --> pdb=" O ASP A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 765 removed outlier: 3.518A pdb=" N ASN A 764 " --> pdb=" O ASN A 761 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR A 765 " --> pdb=" O PRO A 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 761 through 765' Processing helix chain 'B' and resid 29 through 38 removed outlier: 3.798A pdb=" N ALA B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 removed outlier: 3.894A pdb=" N GLU B 59 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE B 60 " --> pdb=" O PHE B 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 56 through 60' Processing helix chain 'B' and resid 71 through 75 removed outlier: 4.237A pdb=" N SER B 74 " --> pdb=" O LEU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 726 removed outlier: 3.952A pdb=" N LEU B 726 " --> pdb=" O PHE B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 754 removed outlier: 4.467A pdb=" N ALA B 748 " --> pdb=" O ASP B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 removed outlier: 3.519A pdb=" N ASN B 764 " --> pdb=" O ASN B 761 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR B 765 " --> pdb=" O PRO B 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 761 through 765' Processing helix chain 'C' and resid 29 through 38 removed outlier: 3.799A pdb=" N ALA C 35 " --> pdb=" O GLY C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 removed outlier: 3.894A pdb=" N GLU C 59 " --> pdb=" O GLY C 56 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE C 60 " --> pdb=" O PHE C 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 56 through 60' Processing helix chain 'C' and resid 71 through 75 removed outlier: 4.237A pdb=" N SER C 74 " --> pdb=" O LEU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 726 removed outlier: 3.951A pdb=" N LEU C 726 " --> pdb=" O PHE C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 754 removed outlier: 4.468A pdb=" N ALA C 748 " --> pdb=" O ASP C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 765 removed outlier: 3.518A pdb=" N ASN C 764 " --> pdb=" O ASN C 761 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR C 765 " --> pdb=" O PRO C 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 761 through 765' Processing helix chain 'D' and resid 29 through 38 removed outlier: 3.799A pdb=" N ALA D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 removed outlier: 3.894A pdb=" N GLU D 59 " --> pdb=" O GLY D 56 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE D 60 " --> pdb=" O PHE D 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 56 through 60' Processing helix chain 'D' and resid 71 through 75 removed outlier: 4.236A pdb=" N SER D 74 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 726 removed outlier: 3.952A pdb=" N LEU D 726 " --> pdb=" O PHE D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 744 through 754 removed outlier: 4.468A pdb=" N ALA D 748 " --> pdb=" O ASP D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 765 removed outlier: 3.518A pdb=" N ASN D 764 " --> pdb=" O ASN D 761 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR D 765 " --> pdb=" O PRO D 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 761 through 765' Processing helix chain 'E' and resid 29 through 38 removed outlier: 3.799A pdb=" N ALA E 35 " --> pdb=" O GLY E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 60 removed outlier: 3.894A pdb=" N GLU E 59 " --> pdb=" O GLY E 56 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE E 60 " --> pdb=" O PHE E 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 56 through 60' Processing helix chain 'E' and resid 71 through 75 removed outlier: 4.236A pdb=" N SER E 74 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 721 through 726 removed outlier: 3.952A pdb=" N LEU E 726 " --> pdb=" O PHE E 722 " (cutoff:3.500A) Processing helix chain 'E' and resid 744 through 754 removed outlier: 4.467A pdb=" N ALA E 748 " --> pdb=" O ASP E 744 " (cutoff:3.500A) Processing helix chain 'E' and resid 761 through 765 removed outlier: 3.518A pdb=" N ASN E 764 " --> pdb=" O ASN E 761 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR E 765 " --> pdb=" O PRO E 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 761 through 765' Processing helix chain 'F' and resid 29 through 38 removed outlier: 3.799A pdb=" N ALA F 35 " --> pdb=" O GLY F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 60 removed outlier: 3.893A pdb=" N GLU F 59 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE F 60 " --> pdb=" O PHE F 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 56 through 60' Processing helix chain 'F' and resid 71 through 75 removed outlier: 4.237A pdb=" N SER F 74 " --> pdb=" O LEU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 721 through 726 removed outlier: 3.952A pdb=" N LEU F 726 " --> pdb=" O PHE F 722 " (cutoff:3.500A) Processing helix chain 'F' and resid 744 through 754 removed outlier: 4.467A pdb=" N ALA F 748 " --> pdb=" O ASP F 744 " (cutoff:3.500A) Processing helix chain 'F' and resid 761 through 765 removed outlier: 3.519A pdb=" N ASN F 764 " --> pdb=" O ASN F 761 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR F 765 " --> pdb=" O PRO F 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 761 through 765' Processing helix chain 'G' and resid 29 through 38 removed outlier: 3.799A pdb=" N ALA G 35 " --> pdb=" O GLY G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 60 removed outlier: 3.894A pdb=" N GLU G 59 " --> pdb=" O GLY G 56 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE G 60 " --> pdb=" O PHE G 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 56 through 60' Processing helix chain 'G' and resid 71 through 75 removed outlier: 4.235A pdb=" N SER G 74 " --> pdb=" O LEU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 721 through 726 removed outlier: 3.952A pdb=" N LEU G 726 " --> pdb=" O PHE G 722 " (cutoff:3.500A) Processing helix chain 'G' and resid 744 through 754 removed outlier: 4.467A pdb=" N ALA G 748 " --> pdb=" O ASP G 744 " (cutoff:3.500A) Processing helix chain 'G' and resid 761 through 765 removed outlier: 3.518A pdb=" N ASN G 764 " --> pdb=" O ASN G 761 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TYR G 765 " --> pdb=" O PRO G 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 761 through 765' Processing helix chain 'H' and resid 29 through 38 removed outlier: 3.798A pdb=" N ALA H 35 " --> pdb=" O GLY H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 60 removed outlier: 3.894A pdb=" N GLU H 59 " --> pdb=" O GLY H 56 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE H 60 " --> pdb=" O PHE H 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 56 through 60' Processing helix chain 'H' and resid 71 through 75 removed outlier: 4.236A pdb=" N SER H 74 " --> pdb=" O LEU H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 721 through 726 removed outlier: 3.952A pdb=" N LEU H 726 " --> pdb=" O PHE H 722 " (cutoff:3.500A) Processing helix chain 'H' and resid 744 through 754 removed outlier: 4.467A pdb=" N ALA H 748 " --> pdb=" O ASP H 744 " (cutoff:3.500A) Processing helix chain 'H' and resid 761 through 765 removed outlier: 3.519A pdb=" N ASN H 764 " --> pdb=" O ASN H 761 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR H 765 " --> pdb=" O PRO H 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 761 through 765' Processing helix chain 'I' and resid 29 through 38 removed outlier: 3.798A pdb=" N ALA I 35 " --> pdb=" O GLY I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 60 removed outlier: 3.894A pdb=" N GLU I 59 " --> pdb=" O GLY I 56 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE I 60 " --> pdb=" O PHE I 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 56 through 60' Processing helix chain 'I' and resid 71 through 75 removed outlier: 4.237A pdb=" N SER I 74 " --> pdb=" O LEU I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 721 through 726 removed outlier: 3.952A pdb=" N LEU I 726 " --> pdb=" O PHE I 722 " (cutoff:3.500A) Processing helix chain 'I' and resid 744 through 754 removed outlier: 4.467A pdb=" N ALA I 748 " --> pdb=" O ASP I 744 " (cutoff:3.500A) Processing helix chain 'I' and resid 761 through 765 removed outlier: 3.519A pdb=" N ASN I 764 " --> pdb=" O ASN I 761 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TYR I 765 " --> pdb=" O PRO I 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 761 through 765' Processing helix chain 'J' and resid 29 through 38 removed outlier: 3.799A pdb=" N ALA J 35 " --> pdb=" O GLY J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 60 removed outlier: 3.894A pdb=" N GLU J 59 " --> pdb=" O GLY J 56 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE J 60 " --> pdb=" O PHE J 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 56 through 60' Processing helix chain 'J' and resid 71 through 75 removed outlier: 4.236A pdb=" N SER J 74 " --> pdb=" O LEU J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 721 through 726 removed outlier: 3.952A pdb=" N LEU J 726 " --> pdb=" O PHE J 722 " (cutoff:3.500A) Processing helix chain 'J' and resid 744 through 754 removed outlier: 4.466A pdb=" N ALA J 748 " --> pdb=" O ASP J 744 " (cutoff:3.500A) Processing helix chain 'J' and resid 761 through 765 removed outlier: 3.518A pdb=" N ASN J 764 " --> pdb=" O ASN J 761 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR J 765 " --> pdb=" O PRO J 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 761 through 765' Processing helix chain 'K' and resid 29 through 38 removed outlier: 3.799A pdb=" N ALA K 35 " --> pdb=" O GLY K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 60 removed outlier: 3.894A pdb=" N GLU K 59 " --> pdb=" O GLY K 56 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE K 60 " --> pdb=" O PHE K 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 56 through 60' Processing helix chain 'K' and resid 71 through 75 removed outlier: 4.237A pdb=" N SER K 74 " --> pdb=" O LEU K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 721 through 726 removed outlier: 3.952A pdb=" N LEU K 726 " --> pdb=" O PHE K 722 " (cutoff:3.500A) Processing helix chain 'K' and resid 744 through 754 removed outlier: 4.467A pdb=" N ALA K 748 " --> pdb=" O ASP K 744 " (cutoff:3.500A) Processing helix chain 'K' and resid 761 through 765 removed outlier: 3.518A pdb=" N ASN K 764 " --> pdb=" O ASN K 761 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TYR K 765 " --> pdb=" O PRO K 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 761 through 765' Processing helix chain 'L' and resid 29 through 38 removed outlier: 3.798A pdb=" N ALA L 35 " --> pdb=" O GLY L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 60 removed outlier: 3.894A pdb=" N GLU L 59 " --> pdb=" O GLY L 56 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE L 60 " --> pdb=" O PHE L 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 56 through 60' Processing helix chain 'L' and resid 71 through 75 removed outlier: 4.236A pdb=" N SER L 74 " --> pdb=" O LEU L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 721 through 726 removed outlier: 3.951A pdb=" N LEU L 726 " --> pdb=" O PHE L 722 " (cutoff:3.500A) Processing helix chain 'L' and resid 744 through 754 removed outlier: 4.468A pdb=" N ALA L 748 " --> pdb=" O ASP L 744 " (cutoff:3.500A) Processing helix chain 'L' and resid 761 through 765 removed outlier: 3.519A pdb=" N ASN L 764 " --> pdb=" O ASN L 761 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR L 765 " --> pdb=" O PRO L 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 761 through 765' Processing sheet with id=AA1, first strand: chain 'A' and resid 156 through 157 removed outlier: 3.658A pdb=" N VAL A 125 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N ASP A 124 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N LEU A 99 " --> pdb=" O ASP A 124 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ASN A 126 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL A 101 " --> pdb=" O ASN A 126 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS A 98 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TRP A 49 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA A 53 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 10.437A pdb=" N ASP A 46 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N VAL A 48 " --> pdb=" O PRO F 341 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLN F 343 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG A 50 " --> pdb=" O GLN F 343 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ILE F 345 " --> pdb=" O ARG A 50 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLN A 52 " --> pdb=" O ILE F 345 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 109 through 111 Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 142 Processing sheet with id=AA4, first strand: chain 'A' and resid 203 through 205 removed outlier: 6.593A pdb=" N ILE A 203 " --> pdb=" O TRP A 225 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL A 252 " --> pdb=" O HIS A 276 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N GLY A 278 " --> pdb=" O VAL A 252 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 203 through 205 removed outlier: 6.593A pdb=" N ILE A 203 " --> pdb=" O TRP A 225 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N LYS A 274 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N ILE A 359 " --> pdb=" O LYS A 274 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N HIS A 276 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N ARG A 361 " --> pdb=" O HIS A 276 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY A 278 " --> pdb=" O ARG A 361 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ASN A 363 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU A 280 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 210 through 212 removed outlier: 6.732A pdb=" N LEU A 211 " --> pdb=" O ASN A 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 269 through 270 removed outlier: 6.662A pdb=" N ILE A 269 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 339 through 345 removed outlier: 7.373A pdb=" N VAL A 339 " --> pdb=" O ASP B 46 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL B 48 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ARG B 50 " --> pdb=" O PRO A 341 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS B 98 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TRP B 49 " --> pdb=" O LYS B 98 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA B 53 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N ASP B 124 " --> pdb=" O ASN B 97 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N LEU B 99 " --> pdb=" O ASP B 124 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ASN B 126 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B 101 " --> pdb=" O ASN B 126 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B 125 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 377 through 378 removed outlier: 6.545A pdb=" N ALA A 377 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLU A 407 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA A 435 " --> pdb=" O ASN A 463 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N LYS A 465 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N PHE A 437 " --> pdb=" O LYS A 465 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 387 through 388 removed outlier: 6.164A pdb=" N ILE A 413 " --> pdb=" O THR A 451 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 476 through 477 removed outlier: 6.714A pdb=" N ILE A 476 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR A 502 " --> pdb=" O ILE A 518 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 530 through 531 Processing sheet with id=AB4, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AB5, first strand: chain 'A' and resid 588 through 590 removed outlier: 5.579A pdb=" N VAL A 588 " --> pdb=" O THR A 614 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 608 through 609 removed outlier: 3.590A pdb=" N THR A 630 " --> pdb=" O LEU A 608 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 621 through 623 removed outlier: 5.561A pdb=" N MET A 621 " --> pdb=" O ASN A 643 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE A 642 " --> pdb=" O LYS A 680 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 691 through 696 removed outlier: 7.856A pdb=" N ILE A 787 " --> pdb=" O LEU A 695 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER A 788 " --> pdb=" O THR A 781 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 729 through 730 Processing sheet with id=AC1, first strand: chain 'A' and resid 771 through 773 Processing sheet with id=AC2, first strand: chain 'B' and resid 109 through 111 Processing sheet with id=AC3, first strand: chain 'B' and resid 140 through 142 Processing sheet with id=AC4, first strand: chain 'B' and resid 203 through 205 removed outlier: 6.591A pdb=" N ILE B 203 " --> pdb=" O TRP B 225 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL B 252 " --> pdb=" O HIS B 276 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLY B 278 " --> pdb=" O VAL B 252 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 203 through 205 removed outlier: 6.591A pdb=" N ILE B 203 " --> pdb=" O TRP B 225 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N LYS B 274 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N ILE B 359 " --> pdb=" O LYS B 274 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N HIS B 276 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 9.366A pdb=" N ARG B 361 " --> pdb=" O HIS B 276 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY B 278 " --> pdb=" O ARG B 361 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ASN B 363 " --> pdb=" O GLY B 278 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU B 280 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 210 through 212 removed outlier: 6.732A pdb=" N LEU B 211 " --> pdb=" O ASN B 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 269 through 270 removed outlier: 6.663A pdb=" N ILE B 269 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 339 through 345 removed outlier: 7.409A pdb=" N VAL B 339 " --> pdb=" O ASP C 46 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL C 48 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ARG C 50 " --> pdb=" O PRO B 341 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS C 98 " --> pdb=" O LYS C 47 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TRP C 49 " --> pdb=" O LYS C 98 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA C 53 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N ASP C 124 " --> pdb=" O ASN C 97 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N LEU C 99 " --> pdb=" O ASP C 124 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ASN C 126 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL C 101 " --> pdb=" O ASN C 126 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL C 125 " --> pdb=" O ASP C 156 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 377 through 378 removed outlier: 6.544A pdb=" N ALA B 377 " --> pdb=" O LEU B 405 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLU B 407 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA B 435 " --> pdb=" O ASN B 463 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LYS B 465 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N PHE B 437 " --> pdb=" O LYS B 465 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 387 through 388 removed outlier: 6.163A pdb=" N ILE B 413 " --> pdb=" O THR B 451 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 476 through 477 removed outlier: 6.714A pdb=" N ILE B 476 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 502 " --> pdb=" O ILE B 518 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 530 through 531 Processing sheet with id=AD4, first strand: chain 'B' and resid 541 through 542 Processing sheet with id=AD5, first strand: chain 'B' and resid 588 through 590 removed outlier: 5.579A pdb=" N VAL B 588 " --> pdb=" O THR B 614 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 608 through 609 removed outlier: 3.590A pdb=" N THR B 630 " --> pdb=" O LEU B 608 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 621 through 623 removed outlier: 5.561A pdb=" N MET B 621 " --> pdb=" O ASN B 643 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE B 642 " --> pdb=" O LYS B 680 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 691 through 696 removed outlier: 7.856A pdb=" N ILE B 787 " --> pdb=" O LEU B 695 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER B 788 " --> pdb=" O THR B 781 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 729 through 730 Processing sheet with id=AE1, first strand: chain 'B' and resid 771 through 773 Processing sheet with id=AE2, first strand: chain 'C' and resid 109 through 111 Processing sheet with id=AE3, first strand: chain 'C' and resid 140 through 142 Processing sheet with id=AE4, first strand: chain 'C' and resid 203 through 205 removed outlier: 6.592A pdb=" N ILE C 203 " --> pdb=" O TRP C 225 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL C 252 " --> pdb=" O HIS C 276 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLY C 278 " --> pdb=" O VAL C 252 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 203 through 205 removed outlier: 6.592A pdb=" N ILE C 203 " --> pdb=" O TRP C 225 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N LYS C 274 " --> pdb=" O VAL C 357 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N ILE C 359 " --> pdb=" O LYS C 274 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N HIS C 276 " --> pdb=" O ILE C 359 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N ARG C 361 " --> pdb=" O HIS C 276 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY C 278 " --> pdb=" O ARG C 361 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ASN C 363 " --> pdb=" O GLY C 278 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU C 280 " --> pdb=" O ASN C 363 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 210 through 212 removed outlier: 6.731A pdb=" N LEU C 211 " --> pdb=" O ASN C 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 269 through 270 removed outlier: 6.663A pdb=" N ILE C 269 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 339 through 345 removed outlier: 7.410A pdb=" N VAL C 339 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL D 48 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ARG D 50 " --> pdb=" O PRO C 341 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS D 98 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TRP D 49 " --> pdb=" O LYS D 98 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA D 53 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N ASP D 124 " --> pdb=" O ASN D 97 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N LEU D 99 " --> pdb=" O ASP D 124 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ASN D 126 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL D 101 " --> pdb=" O ASN D 126 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL D 125 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 377 through 378 removed outlier: 6.544A pdb=" N ALA C 377 " --> pdb=" O LEU C 405 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLU C 407 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA C 435 " --> pdb=" O ASN C 463 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LYS C 465 " --> pdb=" O ALA C 435 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N PHE C 437 " --> pdb=" O LYS C 465 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 387 through 388 removed outlier: 6.163A pdb=" N ILE C 413 " --> pdb=" O THR C 451 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 476 through 477 removed outlier: 6.713A pdb=" N ILE C 476 " --> pdb=" O ILE C 501 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR C 502 " --> pdb=" O ILE C 518 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 530 through 531 Processing sheet with id=AF4, first strand: chain 'C' and resid 541 through 542 Processing sheet with id=AF5, first strand: chain 'C' and resid 588 through 590 removed outlier: 5.579A pdb=" N VAL C 588 " --> pdb=" O THR C 614 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 608 through 609 removed outlier: 3.590A pdb=" N THR C 630 " --> pdb=" O LEU C 608 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'C' and resid 621 through 623 removed outlier: 5.561A pdb=" N MET C 621 " --> pdb=" O ASN C 643 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE C 642 " --> pdb=" O LYS C 680 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'C' and resid 691 through 696 removed outlier: 7.856A pdb=" N ILE C 787 " --> pdb=" O LEU C 695 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER C 788 " --> pdb=" O THR C 781 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR C 781 " --> pdb=" O SER C 788 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 729 through 730 Processing sheet with id=AG1, first strand: chain 'C' and resid 771 through 773 Processing sheet with id=AG2, first strand: chain 'D' and resid 109 through 111 Processing sheet with id=AG3, first strand: chain 'D' and resid 140 through 142 Processing sheet with id=AG4, first strand: chain 'D' and resid 203 through 205 removed outlier: 6.592A pdb=" N ILE D 203 " --> pdb=" O TRP D 225 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL D 252 " --> pdb=" O HIS D 276 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N GLY D 278 " --> pdb=" O VAL D 252 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 203 through 205 removed outlier: 6.592A pdb=" N ILE D 203 " --> pdb=" O TRP D 225 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N LYS D 274 " --> pdb=" O VAL D 357 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N ILE D 359 " --> pdb=" O LYS D 274 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N HIS D 276 " --> pdb=" O ILE D 359 " (cutoff:3.500A) removed outlier: 9.366A pdb=" N ARG D 361 " --> pdb=" O HIS D 276 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY D 278 " --> pdb=" O ARG D 361 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ASN D 363 " --> pdb=" O GLY D 278 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU D 280 " --> pdb=" O ASN D 363 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 210 through 212 removed outlier: 6.731A pdb=" N LEU D 211 " --> pdb=" O ASN D 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'D' and resid 269 through 270 removed outlier: 6.663A pdb=" N ILE D 269 " --> pdb=" O ILE D 291 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'D' and resid 339 through 345 removed outlier: 7.347A pdb=" N VAL D 339 " --> pdb=" O ASP E 46 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL E 48 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ARG E 50 " --> pdb=" O PRO D 341 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS E 98 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TRP E 49 " --> pdb=" O LYS E 98 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA E 53 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N ASP E 124 " --> pdb=" O ASN E 97 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N LEU E 99 " --> pdb=" O ASP E 124 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ASN E 126 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL E 101 " --> pdb=" O ASN E 126 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL E 125 " --> pdb=" O ASP E 156 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 377 through 378 removed outlier: 6.545A pdb=" N ALA D 377 " --> pdb=" O LEU D 405 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLU D 407 " --> pdb=" O ALA D 377 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA D 435 " --> pdb=" O ASN D 463 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LYS D 465 " --> pdb=" O ALA D 435 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE D 437 " --> pdb=" O LYS D 465 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 387 through 388 removed outlier: 6.164A pdb=" N ILE D 413 " --> pdb=" O THR D 451 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'D' and resid 476 through 477 removed outlier: 6.713A pdb=" N ILE D 476 " --> pdb=" O ILE D 501 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR D 502 " --> pdb=" O ILE D 518 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'D' and resid 530 through 531 Processing sheet with id=AH4, first strand: chain 'D' and resid 541 through 542 Processing sheet with id=AH5, first strand: chain 'D' and resid 588 through 590 removed outlier: 5.579A pdb=" N VAL D 588 " --> pdb=" O THR D 614 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'D' and resid 608 through 609 removed outlier: 3.590A pdb=" N THR D 630 " --> pdb=" O LEU D 608 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH6 Processing sheet with id=AH7, first strand: chain 'D' and resid 621 through 623 removed outlier: 5.561A pdb=" N MET D 621 " --> pdb=" O ASN D 643 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE D 642 " --> pdb=" O LYS D 680 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'D' and resid 691 through 696 removed outlier: 7.856A pdb=" N ILE D 787 " --> pdb=" O LEU D 695 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER D 788 " --> pdb=" O THR D 781 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'D' and resid 729 through 730 Processing sheet with id=AI1, first strand: chain 'D' and resid 771 through 773 Processing sheet with id=AI2, first strand: chain 'E' and resid 109 through 111 Processing sheet with id=AI3, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AI4, first strand: chain 'E' and resid 203 through 205 removed outlier: 6.592A pdb=" N ILE E 203 " --> pdb=" O TRP E 225 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL E 252 " --> pdb=" O HIS E 276 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLY E 278 " --> pdb=" O VAL E 252 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'E' and resid 203 through 205 removed outlier: 6.592A pdb=" N ILE E 203 " --> pdb=" O TRP E 225 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N LYS E 274 " --> pdb=" O VAL E 357 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N ILE E 359 " --> pdb=" O LYS E 274 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N HIS E 276 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N ARG E 361 " --> pdb=" O HIS E 276 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY E 278 " --> pdb=" O ARG E 361 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ASN E 363 " --> pdb=" O GLY E 278 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU E 280 " --> pdb=" O ASN E 363 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'E' and resid 210 through 212 removed outlier: 6.731A pdb=" N LEU E 211 " --> pdb=" O ASN E 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'E' and resid 269 through 270 removed outlier: 6.663A pdb=" N ILE E 269 " --> pdb=" O ILE E 291 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'E' and resid 339 through 345 removed outlier: 7.553A pdb=" N VAL E 339 " --> pdb=" O ASP F 46 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL F 48 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ARG F 50 " --> pdb=" O PRO E 341 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS F 98 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TRP F 49 " --> pdb=" O LYS F 98 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA F 53 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 9.300A pdb=" N ASP F 124 " --> pdb=" O ASN F 97 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N LEU F 99 " --> pdb=" O ASP F 124 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ASN F 126 " --> pdb=" O LEU F 99 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL F 101 " --> pdb=" O ASN F 126 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL F 125 " --> pdb=" O ASP F 156 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'E' and resid 377 through 378 removed outlier: 6.545A pdb=" N ALA E 377 " --> pdb=" O LEU E 405 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLU E 407 " --> pdb=" O ALA E 377 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA E 435 " --> pdb=" O ASN E 463 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LYS E 465 " --> pdb=" O ALA E 435 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N PHE E 437 " --> pdb=" O LYS E 465 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'E' and resid 387 through 388 removed outlier: 6.164A pdb=" N ILE E 413 " --> pdb=" O THR E 451 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'E' and resid 476 through 477 removed outlier: 6.714A pdb=" N ILE E 476 " --> pdb=" O ILE E 501 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR E 502 " --> pdb=" O ILE E 518 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'E' and resid 530 through 531 Processing sheet with id=AJ4, first strand: chain 'E' and resid 541 through 542 Processing sheet with id=AJ5, first strand: chain 'E' and resid 588 through 590 removed outlier: 5.579A pdb=" N VAL E 588 " --> pdb=" O THR E 614 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'E' and resid 608 through 609 removed outlier: 3.590A pdb=" N THR E 630 " --> pdb=" O LEU E 608 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ6 Processing sheet with id=AJ7, first strand: chain 'E' and resid 621 through 623 removed outlier: 5.561A pdb=" N MET E 621 " --> pdb=" O ASN E 643 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE E 642 " --> pdb=" O LYS E 680 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ7 Processing sheet with id=AJ8, first strand: chain 'E' and resid 691 through 696 removed outlier: 7.856A pdb=" N ILE E 787 " --> pdb=" O LEU E 695 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER E 788 " --> pdb=" O THR E 781 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'E' and resid 729 through 730 Processing sheet with id=AK1, first strand: chain 'E' and resid 771 through 773 Processing sheet with id=AK2, first strand: chain 'F' and resid 109 through 111 Processing sheet with id=AK3, first strand: chain 'F' and resid 140 through 142 Processing sheet with id=AK4, first strand: chain 'F' and resid 203 through 205 removed outlier: 6.592A pdb=" N ILE F 203 " --> pdb=" O TRP F 225 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL F 252 " --> pdb=" O HIS F 276 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N GLY F 278 " --> pdb=" O VAL F 252 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'F' and resid 203 through 205 removed outlier: 6.592A pdb=" N ILE F 203 " --> pdb=" O TRP F 225 " (cutoff:3.500A) removed outlier: 8.932A pdb=" N LYS F 274 " --> pdb=" O VAL F 357 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N ILE F 359 " --> pdb=" O LYS F 274 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N HIS F 276 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N ARG F 361 " --> pdb=" O HIS F 276 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY F 278 " --> pdb=" O ARG F 361 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ASN F 363 " --> pdb=" O GLY F 278 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU F 280 " --> pdb=" O ASN F 363 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'F' and resid 210 through 212 removed outlier: 6.731A pdb=" N LEU F 211 " --> pdb=" O ASN F 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK6 Processing sheet with id=AK7, first strand: chain 'F' and resid 269 through 270 removed outlier: 6.663A pdb=" N ILE F 269 " --> pdb=" O ILE F 291 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'F' and resid 377 through 378 removed outlier: 6.545A pdb=" N ALA F 377 " --> pdb=" O LEU F 405 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLU F 407 " --> pdb=" O ALA F 377 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA F 435 " --> pdb=" O ASN F 463 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LYS F 465 " --> pdb=" O ALA F 435 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N PHE F 437 " --> pdb=" O LYS F 465 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'F' and resid 387 through 388 removed outlier: 6.163A pdb=" N ILE F 413 " --> pdb=" O THR F 451 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'F' and resid 476 through 477 removed outlier: 6.714A pdb=" N ILE F 476 " --> pdb=" O ILE F 501 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR F 502 " --> pdb=" O ILE F 518 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'F' and resid 530 through 531 Processing sheet with id=AL3, first strand: chain 'F' and resid 541 through 542 Processing sheet with id=AL4, first strand: chain 'F' and resid 588 through 590 removed outlier: 5.579A pdb=" N VAL F 588 " --> pdb=" O THR F 614 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'F' and resid 608 through 609 removed outlier: 3.590A pdb=" N THR F 630 " --> pdb=" O LEU F 608 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL5 Processing sheet with id=AL6, first strand: chain 'F' and resid 621 through 623 removed outlier: 5.561A pdb=" N MET F 621 " --> pdb=" O ASN F 643 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE F 642 " --> pdb=" O LYS F 680 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL6 Processing sheet with id=AL7, first strand: chain 'F' and resid 691 through 696 removed outlier: 7.857A pdb=" N ILE F 787 " --> pdb=" O LEU F 695 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER F 788 " --> pdb=" O THR F 781 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR F 781 " --> pdb=" O SER F 788 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'F' and resid 729 through 730 Processing sheet with id=AL9, first strand: chain 'F' and resid 771 through 773 Processing sheet with id=AM1, first strand: chain 'G' and resid 156 through 157 removed outlier: 3.657A pdb=" N VAL G 125 " --> pdb=" O ASP G 156 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N ASP G 124 " --> pdb=" O ASN G 97 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N LEU G 99 " --> pdb=" O ASP G 124 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ASN G 126 " --> pdb=" O LEU G 99 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL G 101 " --> pdb=" O ASN G 126 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS G 98 " --> pdb=" O LYS G 47 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TRP G 49 " --> pdb=" O LYS G 98 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA G 53 " --> pdb=" O ASP G 102 " (cutoff:3.500A) removed outlier: 10.441A pdb=" N ASP G 46 " --> pdb=" O VAL L 339 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N VAL G 48 " --> pdb=" O PRO L 341 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N GLN L 343 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ARG G 50 " --> pdb=" O GLN L 343 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ILE L 345 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLN G 52 " --> pdb=" O ILE L 345 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'G' and resid 109 through 111 Processing sheet with id=AM3, first strand: chain 'G' and resid 140 through 142 Processing sheet with id=AM4, first strand: chain 'G' and resid 203 through 205 removed outlier: 6.593A pdb=" N ILE G 203 " --> pdb=" O TRP G 225 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL G 252 " --> pdb=" O HIS G 276 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLY G 278 " --> pdb=" O VAL G 252 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'G' and resid 203 through 205 removed outlier: 6.593A pdb=" N ILE G 203 " --> pdb=" O TRP G 225 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N LYS G 274 " --> pdb=" O VAL G 357 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N ILE G 359 " --> pdb=" O LYS G 274 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N HIS G 276 " --> pdb=" O ILE G 359 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N ARG G 361 " --> pdb=" O HIS G 276 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY G 278 " --> pdb=" O ARG G 361 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ASN G 363 " --> pdb=" O GLY G 278 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU G 280 " --> pdb=" O ASN G 363 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'G' and resid 210 through 212 removed outlier: 6.731A pdb=" N LEU G 211 " --> pdb=" O ASN G 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM6 Processing sheet with id=AM7, first strand: chain 'G' and resid 269 through 270 removed outlier: 6.663A pdb=" N ILE G 269 " --> pdb=" O ILE G 291 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'G' and resid 339 through 345 removed outlier: 7.410A pdb=" N VAL G 339 " --> pdb=" O ASP H 46 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL H 48 " --> pdb=" O VAL G 339 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG H 50 " --> pdb=" O PRO G 341 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS H 98 " --> pdb=" O LYS H 47 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TRP H 49 " --> pdb=" O LYS H 98 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA H 53 " --> pdb=" O ASP H 102 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N ASP H 124 " --> pdb=" O ASN H 97 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N LEU H 99 " --> pdb=" O ASP H 124 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ASN H 126 " --> pdb=" O LEU H 99 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL H 101 " --> pdb=" O ASN H 126 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL H 125 " --> pdb=" O ASP H 156 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'G' and resid 377 through 378 removed outlier: 6.545A pdb=" N ALA G 377 " --> pdb=" O LEU G 405 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLU G 407 " --> pdb=" O ALA G 377 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA G 435 " --> pdb=" O ASN G 463 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LYS G 465 " --> pdb=" O ALA G 435 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N PHE G 437 " --> pdb=" O LYS G 465 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'G' and resid 387 through 388 removed outlier: 6.163A pdb=" N ILE G 413 " --> pdb=" O THR G 451 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'G' and resid 476 through 477 removed outlier: 6.713A pdb=" N ILE G 476 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR G 502 " --> pdb=" O ILE G 518 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'G' and resid 530 through 531 Processing sheet with id=AN4, first strand: chain 'G' and resid 541 through 542 Processing sheet with id=AN5, first strand: chain 'G' and resid 588 through 590 removed outlier: 5.579A pdb=" N VAL G 588 " --> pdb=" O THR G 614 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain 'G' and resid 608 through 609 removed outlier: 3.590A pdb=" N THR G 630 " --> pdb=" O LEU G 608 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN6 Processing sheet with id=AN7, first strand: chain 'G' and resid 621 through 623 removed outlier: 5.561A pdb=" N MET G 621 " --> pdb=" O ASN G 643 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE G 642 " --> pdb=" O LYS G 680 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN7 Processing sheet with id=AN8, first strand: chain 'G' and resid 691 through 696 removed outlier: 7.857A pdb=" N ILE G 787 " --> pdb=" O LEU G 695 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER G 788 " --> pdb=" O THR G 781 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain 'G' and resid 729 through 730 Processing sheet with id=AO1, first strand: chain 'G' and resid 771 through 773 Processing sheet with id=AO2, first strand: chain 'H' and resid 109 through 111 Processing sheet with id=AO3, first strand: chain 'H' and resid 140 through 142 Processing sheet with id=AO4, first strand: chain 'H' and resid 203 through 205 removed outlier: 6.592A pdb=" N ILE H 203 " --> pdb=" O TRP H 225 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL H 252 " --> pdb=" O HIS H 276 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLY H 278 " --> pdb=" O VAL H 252 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'H' and resid 203 through 205 removed outlier: 6.592A pdb=" N ILE H 203 " --> pdb=" O TRP H 225 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N LYS H 274 " --> pdb=" O VAL H 357 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N ILE H 359 " --> pdb=" O LYS H 274 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N HIS H 276 " --> pdb=" O ILE H 359 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N ARG H 361 " --> pdb=" O HIS H 276 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY H 278 " --> pdb=" O ARG H 361 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ASN H 363 " --> pdb=" O GLY H 278 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU H 280 " --> pdb=" O ASN H 363 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'H' and resid 210 through 212 removed outlier: 6.732A pdb=" N LEU H 211 " --> pdb=" O ASN H 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AO6 Processing sheet with id=AO7, first strand: chain 'H' and resid 269 through 270 removed outlier: 6.663A pdb=" N ILE H 269 " --> pdb=" O ILE H 291 " (cutoff:3.500A) Processing sheet with id=AO8, first strand: chain 'H' and resid 339 through 345 removed outlier: 7.409A pdb=" N VAL H 339 " --> pdb=" O ASP I 46 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL I 48 " --> pdb=" O VAL H 339 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG I 50 " --> pdb=" O PRO H 341 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS I 98 " --> pdb=" O LYS I 47 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TRP I 49 " --> pdb=" O LYS I 98 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA I 53 " --> pdb=" O ASP I 102 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N ASP I 124 " --> pdb=" O ASN I 97 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N LEU I 99 " --> pdb=" O ASP I 124 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N ASN I 126 " --> pdb=" O LEU I 99 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL I 101 " --> pdb=" O ASN I 126 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL I 125 " --> pdb=" O ASP I 156 " (cutoff:3.500A) Processing sheet with id=AO9, first strand: chain 'H' and resid 377 through 378 removed outlier: 6.545A pdb=" N ALA H 377 " --> pdb=" O LEU H 405 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLU H 407 " --> pdb=" O ALA H 377 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA H 435 " --> pdb=" O ASN H 463 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LYS H 465 " --> pdb=" O ALA H 435 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N PHE H 437 " --> pdb=" O LYS H 465 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'H' and resid 387 through 388 removed outlier: 6.163A pdb=" N ILE H 413 " --> pdb=" O THR H 451 " (cutoff:3.500A) Processing sheet with id=AP2, first strand: chain 'H' and resid 476 through 477 removed outlier: 6.713A pdb=" N ILE H 476 " --> pdb=" O ILE H 501 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR H 502 " --> pdb=" O ILE H 518 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'H' and resid 530 through 531 Processing sheet with id=AP4, first strand: chain 'H' and resid 541 through 542 Processing sheet with id=AP5, first strand: chain 'H' and resid 588 through 590 removed outlier: 5.579A pdb=" N VAL H 588 " --> pdb=" O THR H 614 " (cutoff:3.500A) Processing sheet with id=AP6, first strand: chain 'H' and resid 608 through 609 removed outlier: 3.590A pdb=" N THR H 630 " --> pdb=" O LEU H 608 " (cutoff:3.500A) No H-bonds generated for sheet with id=AP6 Processing sheet with id=AP7, first strand: chain 'H' and resid 621 through 623 removed outlier: 5.562A pdb=" N MET H 621 " --> pdb=" O ASN H 643 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE H 642 " --> pdb=" O LYS H 680 " (cutoff:3.500A) No H-bonds generated for sheet with id=AP7 Processing sheet with id=AP8, first strand: chain 'H' and resid 691 through 696 removed outlier: 7.857A pdb=" N ILE H 787 " --> pdb=" O LEU H 695 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER H 788 " --> pdb=" O THR H 781 " (cutoff:3.500A) Processing sheet with id=AP9, first strand: chain 'H' and resid 729 through 730 Processing sheet with id=AQ1, first strand: chain 'H' and resid 771 through 773 Processing sheet with id=AQ2, first strand: chain 'I' and resid 109 through 111 Processing sheet with id=AQ3, first strand: chain 'I' and resid 140 through 142 Processing sheet with id=AQ4, first strand: chain 'I' and resid 203 through 205 removed outlier: 6.593A pdb=" N ILE I 203 " --> pdb=" O TRP I 225 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL I 252 " --> pdb=" O HIS I 276 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLY I 278 " --> pdb=" O VAL I 252 " (cutoff:3.500A) Processing sheet with id=AQ5, first strand: chain 'I' and resid 203 through 205 removed outlier: 6.593A pdb=" N ILE I 203 " --> pdb=" O TRP I 225 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N LYS I 274 " --> pdb=" O VAL I 357 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N ILE I 359 " --> pdb=" O LYS I 274 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N HIS I 276 " --> pdb=" O ILE I 359 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N ARG I 361 " --> pdb=" O HIS I 276 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY I 278 " --> pdb=" O ARG I 361 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ASN I 363 " --> pdb=" O GLY I 278 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU I 280 " --> pdb=" O ASN I 363 " (cutoff:3.500A) Processing sheet with id=AQ6, first strand: chain 'I' and resid 210 through 212 removed outlier: 6.732A pdb=" N LEU I 211 " --> pdb=" O ASN I 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AQ6 Processing sheet with id=AQ7, first strand: chain 'I' and resid 269 through 270 removed outlier: 6.662A pdb=" N ILE I 269 " --> pdb=" O ILE I 291 " (cutoff:3.500A) Processing sheet with id=AQ8, first strand: chain 'I' and resid 339 through 345 removed outlier: 7.316A pdb=" N VAL I 339 " --> pdb=" O ASP J 46 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL J 48 " --> pdb=" O VAL I 339 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ARG J 50 " --> pdb=" O PRO I 341 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN J 52 " --> pdb=" O GLN I 343 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS J 98 " --> pdb=" O LYS J 47 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TRP J 49 " --> pdb=" O LYS J 98 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA J 53 " --> pdb=" O ASP J 102 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N ASP J 124 " --> pdb=" O ASN J 97 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N LEU J 99 " --> pdb=" O ASP J 124 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ASN J 126 " --> pdb=" O LEU J 99 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL J 101 " --> pdb=" O ASN J 126 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL J 125 " --> pdb=" O ASP J 156 " (cutoff:3.500A) Processing sheet with id=AQ9, first strand: chain 'I' and resid 377 through 378 removed outlier: 6.545A pdb=" N ALA I 377 " --> pdb=" O LEU I 405 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLU I 407 " --> pdb=" O ALA I 377 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA I 435 " --> pdb=" O ASN I 463 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LYS I 465 " --> pdb=" O ALA I 435 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N PHE I 437 " --> pdb=" O LYS I 465 " (cutoff:3.500A) Processing sheet with id=AR1, first strand: chain 'I' and resid 387 through 388 removed outlier: 6.163A pdb=" N ILE I 413 " --> pdb=" O THR I 451 " (cutoff:3.500A) Processing sheet with id=AR2, first strand: chain 'I' and resid 476 through 477 removed outlier: 6.713A pdb=" N ILE I 476 " --> pdb=" O ILE I 501 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR I 502 " --> pdb=" O ILE I 518 " (cutoff:3.500A) Processing sheet with id=AR3, first strand: chain 'I' and resid 530 through 531 Processing sheet with id=AR4, first strand: chain 'I' and resid 541 through 542 Processing sheet with id=AR5, first strand: chain 'I' and resid 588 through 590 removed outlier: 5.579A pdb=" N VAL I 588 " --> pdb=" O THR I 614 " (cutoff:3.500A) Processing sheet with id=AR6, first strand: chain 'I' and resid 608 through 609 removed outlier: 3.591A pdb=" N THR I 630 " --> pdb=" O LEU I 608 " (cutoff:3.500A) No H-bonds generated for sheet with id=AR6 Processing sheet with id=AR7, first strand: chain 'I' and resid 621 through 623 removed outlier: 5.561A pdb=" N MET I 621 " --> pdb=" O ASN I 643 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE I 642 " --> pdb=" O LYS I 680 " (cutoff:3.500A) No H-bonds generated for sheet with id=AR7 Processing sheet with id=AR8, first strand: chain 'I' and resid 691 through 696 removed outlier: 7.857A pdb=" N ILE I 787 " --> pdb=" O LEU I 695 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER I 788 " --> pdb=" O THR I 781 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR I 781 " --> pdb=" O SER I 788 " (cutoff:3.500A) Processing sheet with id=AR9, first strand: chain 'I' and resid 729 through 730 Processing sheet with id=AS1, first strand: chain 'I' and resid 771 through 773 Processing sheet with id=AS2, first strand: chain 'J' and resid 109 through 111 Processing sheet with id=AS3, first strand: chain 'J' and resid 140 through 142 Processing sheet with id=AS4, first strand: chain 'J' and resid 203 through 205 removed outlier: 6.592A pdb=" N ILE J 203 " --> pdb=" O TRP J 225 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL J 252 " --> pdb=" O HIS J 276 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLY J 278 " --> pdb=" O VAL J 252 " (cutoff:3.500A) Processing sheet with id=AS5, first strand: chain 'J' and resid 203 through 205 removed outlier: 6.592A pdb=" N ILE J 203 " --> pdb=" O TRP J 225 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N LYS J 274 " --> pdb=" O VAL J 357 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N ILE J 359 " --> pdb=" O LYS J 274 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N HIS J 276 " --> pdb=" O ILE J 359 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N ARG J 361 " --> pdb=" O HIS J 276 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY J 278 " --> pdb=" O ARG J 361 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ASN J 363 " --> pdb=" O GLY J 278 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU J 280 " --> pdb=" O ASN J 363 " (cutoff:3.500A) Processing sheet with id=AS6, first strand: chain 'J' and resid 210 through 212 removed outlier: 6.732A pdb=" N LEU J 211 " --> pdb=" O ASN J 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AS6 Processing sheet with id=AS7, first strand: chain 'J' and resid 269 through 270 removed outlier: 6.662A pdb=" N ILE J 269 " --> pdb=" O ILE J 291 " (cutoff:3.500A) Processing sheet with id=AS8, first strand: chain 'J' and resid 339 through 345 removed outlier: 7.430A pdb=" N VAL J 339 " --> pdb=" O ASP K 46 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL K 48 " --> pdb=" O VAL J 339 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ARG K 50 " --> pdb=" O PRO J 341 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS K 98 " --> pdb=" O LYS K 47 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TRP K 49 " --> pdb=" O LYS K 98 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA K 53 " --> pdb=" O ASP K 102 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N ASP K 124 " --> pdb=" O ASN K 97 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N LEU K 99 " --> pdb=" O ASP K 124 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ASN K 126 " --> pdb=" O LEU K 99 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL K 101 " --> pdb=" O ASN K 126 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL K 125 " --> pdb=" O ASP K 156 " (cutoff:3.500A) Processing sheet with id=AS9, first strand: chain 'J' and resid 377 through 378 removed outlier: 6.545A pdb=" N ALA J 377 " --> pdb=" O LEU J 405 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLU J 407 " --> pdb=" O ALA J 377 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA J 435 " --> pdb=" O ASN J 463 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LYS J 465 " --> pdb=" O ALA J 435 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N PHE J 437 " --> pdb=" O LYS J 465 " (cutoff:3.500A) Processing sheet with id=AT1, first strand: chain 'J' and resid 387 through 388 removed outlier: 6.163A pdb=" N ILE J 413 " --> pdb=" O THR J 451 " (cutoff:3.500A) Processing sheet with id=AT2, first strand: chain 'J' and resid 476 through 477 removed outlier: 6.713A pdb=" N ILE J 476 " --> pdb=" O ILE J 501 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR J 502 " --> pdb=" O ILE J 518 " (cutoff:3.500A) Processing sheet with id=AT3, first strand: chain 'J' and resid 530 through 531 Processing sheet with id=AT4, first strand: chain 'J' and resid 541 through 542 Processing sheet with id=AT5, first strand: chain 'J' and resid 588 through 590 removed outlier: 5.579A pdb=" N VAL J 588 " --> pdb=" O THR J 614 " (cutoff:3.500A) Processing sheet with id=AT6, first strand: chain 'J' and resid 608 through 609 removed outlier: 3.590A pdb=" N THR J 630 " --> pdb=" O LEU J 608 " (cutoff:3.500A) No H-bonds generated for sheet with id=AT6 Processing sheet with id=AT7, first strand: chain 'J' and resid 621 through 623 removed outlier: 5.561A pdb=" N MET J 621 " --> pdb=" O ASN J 643 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE J 642 " --> pdb=" O LYS J 680 " (cutoff:3.500A) No H-bonds generated for sheet with id=AT7 Processing sheet with id=AT8, first strand: chain 'J' and resid 691 through 696 removed outlier: 7.856A pdb=" N ILE J 787 " --> pdb=" O LEU J 695 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER J 788 " --> pdb=" O THR J 781 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR J 781 " --> pdb=" O SER J 788 " (cutoff:3.500A) Processing sheet with id=AT9, first strand: chain 'J' and resid 729 through 730 Processing sheet with id=AU1, first strand: chain 'J' and resid 771 through 773 Processing sheet with id=AU2, first strand: chain 'K' and resid 109 through 111 Processing sheet with id=AU3, first strand: chain 'K' and resid 140 through 142 Processing sheet with id=AU4, first strand: chain 'K' and resid 203 through 205 removed outlier: 6.592A pdb=" N ILE K 203 " --> pdb=" O TRP K 225 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL K 252 " --> pdb=" O HIS K 276 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLY K 278 " --> pdb=" O VAL K 252 " (cutoff:3.500A) Processing sheet with id=AU5, first strand: chain 'K' and resid 203 through 205 removed outlier: 6.592A pdb=" N ILE K 203 " --> pdb=" O TRP K 225 " (cutoff:3.500A) removed outlier: 8.932A pdb=" N LYS K 274 " --> pdb=" O VAL K 357 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N ILE K 359 " --> pdb=" O LYS K 274 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N HIS K 276 " --> pdb=" O ILE K 359 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N ARG K 361 " --> pdb=" O HIS K 276 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY K 278 " --> pdb=" O ARG K 361 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ASN K 363 " --> pdb=" O GLY K 278 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU K 280 " --> pdb=" O ASN K 363 " (cutoff:3.500A) Processing sheet with id=AU6, first strand: chain 'K' and resid 210 through 212 removed outlier: 6.732A pdb=" N LEU K 211 " --> pdb=" O ASN K 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AU6 Processing sheet with id=AU7, first strand: chain 'K' and resid 269 through 270 removed outlier: 6.663A pdb=" N ILE K 269 " --> pdb=" O ILE K 291 " (cutoff:3.500A) Processing sheet with id=AU8, first strand: chain 'K' and resid 339 through 345 removed outlier: 7.518A pdb=" N VAL K 339 " --> pdb=" O ASP L 46 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL L 48 " --> pdb=" O VAL K 339 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ARG L 50 " --> pdb=" O PRO K 341 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS L 98 " --> pdb=" O LYS L 47 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TRP L 49 " --> pdb=" O LYS L 98 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA L 53 " --> pdb=" O ASP L 102 " (cutoff:3.500A) removed outlier: 9.300A pdb=" N ASP L 124 " --> pdb=" O ASN L 97 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N LEU L 99 " --> pdb=" O ASP L 124 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ASN L 126 " --> pdb=" O LEU L 99 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL L 101 " --> pdb=" O ASN L 126 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL L 125 " --> pdb=" O ASP L 156 " (cutoff:3.500A) Processing sheet with id=AU9, first strand: chain 'K' and resid 377 through 378 removed outlier: 6.545A pdb=" N ALA K 377 " --> pdb=" O LEU K 405 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLU K 407 " --> pdb=" O ALA K 377 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA K 435 " --> pdb=" O ASN K 463 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LYS K 465 " --> pdb=" O ALA K 435 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N PHE K 437 " --> pdb=" O LYS K 465 " (cutoff:3.500A) Processing sheet with id=AV1, first strand: chain 'K' and resid 387 through 388 removed outlier: 6.163A pdb=" N ILE K 413 " --> pdb=" O THR K 451 " (cutoff:3.500A) Processing sheet with id=AV2, first strand: chain 'K' and resid 476 through 477 removed outlier: 6.713A pdb=" N ILE K 476 " --> pdb=" O ILE K 501 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR K 502 " --> pdb=" O ILE K 518 " (cutoff:3.500A) Processing sheet with id=AV3, first strand: chain 'K' and resid 530 through 531 Processing sheet with id=AV4, first strand: chain 'K' and resid 541 through 542 Processing sheet with id=AV5, first strand: chain 'K' and resid 588 through 590 removed outlier: 5.579A pdb=" N VAL K 588 " --> pdb=" O THR K 614 " (cutoff:3.500A) Processing sheet with id=AV6, first strand: chain 'K' and resid 608 through 609 removed outlier: 3.590A pdb=" N THR K 630 " --> pdb=" O LEU K 608 " (cutoff:3.500A) No H-bonds generated for sheet with id=AV6 Processing sheet with id=AV7, first strand: chain 'K' and resid 621 through 623 removed outlier: 5.561A pdb=" N MET K 621 " --> pdb=" O ASN K 643 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE K 642 " --> pdb=" O LYS K 680 " (cutoff:3.500A) No H-bonds generated for sheet with id=AV7 Processing sheet with id=AV8, first strand: chain 'K' and resid 691 through 696 removed outlier: 7.856A pdb=" N ILE K 787 " --> pdb=" O LEU K 695 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER K 788 " --> pdb=" O THR K 781 " (cutoff:3.500A) Processing sheet with id=AV9, first strand: chain 'K' and resid 729 through 730 Processing sheet with id=AW1, first strand: chain 'K' and resid 771 through 773 Processing sheet with id=AW2, first strand: chain 'L' and resid 109 through 111 Processing sheet with id=AW3, first strand: chain 'L' and resid 140 through 142 Processing sheet with id=AW4, first strand: chain 'L' and resid 203 through 205 removed outlier: 6.592A pdb=" N ILE L 203 " --> pdb=" O TRP L 225 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL L 252 " --> pdb=" O HIS L 276 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N GLY L 278 " --> pdb=" O VAL L 252 " (cutoff:3.500A) Processing sheet with id=AW5, first strand: chain 'L' and resid 203 through 205 removed outlier: 6.592A pdb=" N ILE L 203 " --> pdb=" O TRP L 225 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N LYS L 274 " --> pdb=" O VAL L 357 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N ILE L 359 " --> pdb=" O LYS L 274 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N HIS L 276 " --> pdb=" O ILE L 359 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N ARG L 361 " --> pdb=" O HIS L 276 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY L 278 " --> pdb=" O ARG L 361 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ASN L 363 " --> pdb=" O GLY L 278 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU L 280 " --> pdb=" O ASN L 363 " (cutoff:3.500A) Processing sheet with id=AW6, first strand: chain 'L' and resid 210 through 212 removed outlier: 6.732A pdb=" N LEU L 211 " --> pdb=" O ASN L 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AW6 Processing sheet with id=AW7, first strand: chain 'L' and resid 269 through 270 removed outlier: 6.663A pdb=" N ILE L 269 " --> pdb=" O ILE L 291 " (cutoff:3.500A) Processing sheet with id=AW8, first strand: chain 'L' and resid 377 through 378 removed outlier: 6.545A pdb=" N ALA L 377 " --> pdb=" O LEU L 405 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLU L 407 " --> pdb=" O ALA L 377 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA L 435 " --> pdb=" O ASN L 463 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N LYS L 465 " --> pdb=" O ALA L 435 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N PHE L 437 " --> pdb=" O LYS L 465 " (cutoff:3.500A) Processing sheet with id=AW9, first strand: chain 'L' and resid 387 through 388 removed outlier: 6.163A pdb=" N ILE L 413 " --> pdb=" O THR L 451 " (cutoff:3.500A) Processing sheet with id=AX1, first strand: chain 'L' and resid 476 through 477 removed outlier: 6.713A pdb=" N ILE L 476 " --> pdb=" O ILE L 501 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR L 502 " --> pdb=" O ILE L 518 " (cutoff:3.500A) Processing sheet with id=AX2, first strand: chain 'L' and resid 530 through 531 Processing sheet with id=AX3, first strand: chain 'L' and resid 541 through 542 Processing sheet with id=AX4, first strand: chain 'L' and resid 588 through 590 removed outlier: 5.579A pdb=" N VAL L 588 " --> pdb=" O THR L 614 " (cutoff:3.500A) Processing sheet with id=AX5, first strand: chain 'L' and resid 608 through 609 removed outlier: 3.590A pdb=" N THR L 630 " --> pdb=" O LEU L 608 " (cutoff:3.500A) No H-bonds generated for sheet with id=AX5 Processing sheet with id=AX6, first strand: chain 'L' and resid 621 through 623 removed outlier: 5.561A pdb=" N MET L 621 " --> pdb=" O ASN L 643 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE L 642 " --> pdb=" O LYS L 680 " (cutoff:3.500A) No H-bonds generated for sheet with id=AX6 Processing sheet with id=AX7, first strand: chain 'L' and resid 691 through 696 removed outlier: 7.856A pdb=" N ILE L 787 " --> pdb=" O LEU L 695 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER L 788 " --> pdb=" O THR L 781 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR L 781 " --> pdb=" O SER L 788 " (cutoff:3.500A) Processing sheet with id=AX8, first strand: chain 'L' and resid 729 through 730 Processing sheet with id=AX9, first strand: chain 'L' and resid 771 through 773 672 hydrogen bonds defined for protein. 1872 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 30.25 Time building geometry restraints manager: 21.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 21734 1.33 - 1.45: 10210 1.45 - 1.57: 37632 1.57 - 1.69: 0 1.69 - 1.80: 264 Bond restraints: 69840 Sorted by residual: bond pdb=" C ASP H 124 " pdb=" N VAL H 125 " ideal model delta sigma weight residual 1.332 1.302 0.030 1.36e-02 5.41e+03 4.75e+00 bond pdb=" C ASP I 124 " pdb=" N VAL I 125 " ideal model delta sigma weight residual 1.332 1.302 0.030 1.36e-02 5.41e+03 4.73e+00 bond pdb=" C ASP C 124 " pdb=" N VAL C 125 " ideal model delta sigma weight residual 1.332 1.302 0.030 1.36e-02 5.41e+03 4.73e+00 bond pdb=" C ASP F 124 " pdb=" N VAL F 125 " ideal model delta sigma weight residual 1.332 1.302 0.030 1.36e-02 5.41e+03 4.73e+00 bond pdb=" C ASP B 124 " pdb=" N VAL B 125 " ideal model delta sigma weight residual 1.332 1.302 0.030 1.36e-02 5.41e+03 4.72e+00 ... (remaining 69835 not shown) Histogram of bond angle deviations from ideal: 98.44 - 105.59: 915 105.59 - 112.73: 35907 112.73 - 119.88: 23751 119.88 - 127.03: 33342 127.03 - 134.17: 669 Bond angle restraints: 94584 Sorted by residual: angle pdb=" C GLY L 83 " pdb=" N ASN L 84 " pdb=" CA ASN L 84 " ideal model delta sigma weight residual 121.54 130.91 -9.37 1.91e+00 2.74e-01 2.41e+01 angle pdb=" C GLY I 83 " pdb=" N ASN I 84 " pdb=" CA ASN I 84 " ideal model delta sigma weight residual 121.54 130.91 -9.37 1.91e+00 2.74e-01 2.41e+01 angle pdb=" C GLY H 83 " pdb=" N ASN H 84 " pdb=" CA ASN H 84 " ideal model delta sigma weight residual 121.54 130.91 -9.37 1.91e+00 2.74e-01 2.40e+01 angle pdb=" C GLY F 83 " pdb=" N ASN F 84 " pdb=" CA ASN F 84 " ideal model delta sigma weight residual 121.54 130.90 -9.36 1.91e+00 2.74e-01 2.40e+01 angle pdb=" C GLY B 83 " pdb=" N ASN B 84 " pdb=" CA ASN B 84 " ideal model delta sigma weight residual 121.54 130.88 -9.34 1.91e+00 2.74e-01 2.39e+01 ... (remaining 94579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.49: 37675 15.49 - 30.97: 2946 30.97 - 46.46: 479 46.46 - 61.95: 36 61.95 - 77.43: 36 Dihedral angle restraints: 41172 sinusoidal: 15828 harmonic: 25344 Sorted by residual: dihedral pdb=" CB CYS E 738 " pdb=" SG CYS E 738 " pdb=" SG CYS E 749 " pdb=" CB CYS E 749 " ideal model delta sinusoidal sigma weight residual -86.00 -163.43 77.43 1 1.00e+01 1.00e-02 7.51e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 749 " pdb=" CB CYS A 749 " ideal model delta sinusoidal sigma weight residual -86.00 -163.43 77.43 1 1.00e+01 1.00e-02 7.51e+01 dihedral pdb=" CB CYS G 738 " pdb=" SG CYS G 738 " pdb=" SG CYS G 749 " pdb=" CB CYS G 749 " ideal model delta sinusoidal sigma weight residual -86.00 -163.42 77.42 1 1.00e+01 1.00e-02 7.51e+01 ... (remaining 41169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 6694 0.053 - 0.107: 2902 0.107 - 0.160: 834 0.160 - 0.214: 154 0.214 - 0.267: 36 Chirality restraints: 10620 Sorted by residual: chirality pdb=" CB ILE C 345 " pdb=" CA ILE C 345 " pdb=" CG1 ILE C 345 " pdb=" CG2 ILE C 345 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB ILE A 345 " pdb=" CA ILE A 345 " pdb=" CG1 ILE A 345 " pdb=" CG2 ILE A 345 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB ILE K 345 " pdb=" CA ILE K 345 " pdb=" CG1 ILE K 345 " pdb=" CG2 ILE K 345 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 10617 not shown) Planarity restraints: 12396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER L 272 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.75e+00 pdb=" C SER L 272 " -0.033 2.00e-02 2.50e+03 pdb=" O SER L 272 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN L 273 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 272 " -0.010 2.00e-02 2.50e+03 1.94e-02 3.75e+00 pdb=" C SER C 272 " 0.033 2.00e-02 2.50e+03 pdb=" O SER C 272 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN C 273 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 272 " -0.010 2.00e-02 2.50e+03 1.93e-02 3.73e+00 pdb=" C SER B 272 " 0.033 2.00e-02 2.50e+03 pdb=" O SER B 272 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN B 273 " -0.011 2.00e-02 2.50e+03 ... (remaining 12393 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 13279 2.77 - 3.30: 66671 3.30 - 3.83: 122422 3.83 - 4.37: 138368 4.37 - 4.90: 242391 Nonbonded interactions: 583131 Sorted by model distance: nonbonded pdb=" O SER E 575 " pdb=" OG SER E 606 " model vdw 2.233 2.440 nonbonded pdb=" O SER I 575 " pdb=" OG SER I 606 " model vdw 2.233 2.440 nonbonded pdb=" O SER D 575 " pdb=" OG SER D 606 " model vdw 2.234 2.440 nonbonded pdb=" O SER K 575 " pdb=" OG SER K 606 " model vdw 2.234 2.440 nonbonded pdb=" O SER G 575 " pdb=" OG SER G 606 " model vdw 2.234 2.440 ... (remaining 583126 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.950 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: 0.080 Extract box with map and model: 13.650 Check model and map are aligned: 0.740 Set scattering table: 0.480 Process input model: 142.020 Find NCS groups from input model: 3.790 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 166.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 69840 Z= 0.517 Angle : 1.139 14.227 94584 Z= 0.645 Chirality : 0.064 0.267 10620 Planarity : 0.005 0.044 12396 Dihedral : 11.102 70.590 25056 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.05 % Favored : 83.95 % Rotamer: Outliers : 0.97 % Allowed : 3.43 % Favored : 95.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.60 (0.07), residues: 8952 helix: -4.67 (0.08), residues: 300 sheet: -4.06 (0.09), residues: 2160 loop : -3.83 (0.06), residues: 6492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP A 225 HIS 0.011 0.003 HIS J 385 PHE 0.025 0.004 PHE F 452 TYR 0.025 0.003 TYR C 206 ARG 0.012 0.001 ARG H 725 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 254 time to evaluate : 5.842 Fit side-chains REVERT: A 609 MET cc_start: 0.8770 (ttt) cc_final: 0.8506 (mtm) REVERT: A 621 MET cc_start: 0.8829 (mtp) cc_final: 0.8285 (tmm) REVERT: A 658 ASN cc_start: 0.8568 (t0) cc_final: 0.8286 (t0) REVERT: A 663 MET cc_start: 0.8526 (ttt) cc_final: 0.8023 (tmm) REVERT: B 226 MET cc_start: 0.7828 (mtm) cc_final: 0.7564 (mtp) REVERT: B 609 MET cc_start: 0.8573 (ttt) cc_final: 0.8311 (mtm) REVERT: B 658 ASN cc_start: 0.8478 (t0) cc_final: 0.8218 (m110) REVERT: B 663 MET cc_start: 0.8585 (ttt) cc_final: 0.8320 (tmm) REVERT: C 609 MET cc_start: 0.8691 (ttt) cc_final: 0.8329 (mtm) REVERT: C 658 ASN cc_start: 0.8604 (t0) cc_final: 0.8265 (t0) REVERT: C 663 MET cc_start: 0.8728 (ttt) cc_final: 0.8293 (tmm) REVERT: D 609 MET cc_start: 0.8767 (ttt) cc_final: 0.8500 (mtm) REVERT: D 621 MET cc_start: 0.8838 (mtp) cc_final: 0.8273 (tmm) REVERT: D 658 ASN cc_start: 0.8663 (t0) cc_final: 0.8394 (t0) REVERT: D 663 MET cc_start: 0.8527 (ttt) cc_final: 0.8021 (tmm) REVERT: E 226 MET cc_start: 0.7800 (mtm) cc_final: 0.7572 (mtp) REVERT: E 609 MET cc_start: 0.8619 (ttt) cc_final: 0.8308 (mtm) REVERT: E 621 MET cc_start: 0.8814 (mtp) cc_final: 0.8095 (tmm) REVERT: E 658 ASN cc_start: 0.8557 (t0) cc_final: 0.8308 (t0) REVERT: E 663 MET cc_start: 0.8707 (ttt) cc_final: 0.8417 (tmm) REVERT: F 609 MET cc_start: 0.8688 (ttt) cc_final: 0.8327 (mtm) REVERT: F 658 ASN cc_start: 0.8593 (t0) cc_final: 0.8258 (t0) REVERT: F 663 MET cc_start: 0.8714 (ttt) cc_final: 0.8290 (tmm) REVERT: G 609 MET cc_start: 0.8743 (ttt) cc_final: 0.8473 (mtm) REVERT: G 621 MET cc_start: 0.8842 (mtp) cc_final: 0.8278 (tmm) REVERT: G 658 ASN cc_start: 0.8655 (t0) cc_final: 0.8390 (t0) REVERT: G 663 MET cc_start: 0.8488 (ttt) cc_final: 0.8002 (tmm) REVERT: H 226 MET cc_start: 0.7828 (mtm) cc_final: 0.7589 (mtp) REVERT: H 609 MET cc_start: 0.8571 (ttt) cc_final: 0.8309 (mtm) REVERT: H 658 ASN cc_start: 0.8470 (t0) cc_final: 0.8149 (t0) REVERT: H 663 MET cc_start: 0.8615 (ttt) cc_final: 0.8348 (tmm) REVERT: I 609 MET cc_start: 0.8642 (ttt) cc_final: 0.8281 (mtm) REVERT: I 658 ASN cc_start: 0.8607 (t0) cc_final: 0.8270 (t0) REVERT: I 663 MET cc_start: 0.8729 (ttt) cc_final: 0.8293 (tmm) REVERT: J 609 MET cc_start: 0.8728 (ttt) cc_final: 0.8485 (mtm) REVERT: J 621 MET cc_start: 0.8836 (mtp) cc_final: 0.8318 (tmm) REVERT: J 658 ASN cc_start: 0.8622 (t0) cc_final: 0.8333 (t0) REVERT: J 663 MET cc_start: 0.8501 (ttt) cc_final: 0.8010 (tmm) REVERT: K 609 MET cc_start: 0.8577 (ttt) cc_final: 0.8312 (mtm) REVERT: K 621 MET cc_start: 0.8791 (mtp) cc_final: 0.8071 (tmm) REVERT: K 663 MET cc_start: 0.8642 (ttt) cc_final: 0.8311 (tmm) REVERT: L 609 MET cc_start: 0.8646 (ttt) cc_final: 0.8286 (mtm) REVERT: L 658 ASN cc_start: 0.8596 (t0) cc_final: 0.8260 (t0) REVERT: L 663 MET cc_start: 0.8721 (ttt) cc_final: 0.8290 (tmm) outliers start: 72 outliers final: 12 residues processed: 326 average time/residue: 0.6183 time to fit residues: 371.4417 Evaluate side-chains 162 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 150 time to evaluate : 5.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain L residue 421 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 759 optimal weight: 0.9990 chunk 682 optimal weight: 1.9990 chunk 378 optimal weight: 6.9990 chunk 233 optimal weight: 6.9990 chunk 460 optimal weight: 0.9990 chunk 364 optimal weight: 7.9990 chunk 705 optimal weight: 7.9990 chunk 272 optimal weight: 9.9990 chunk 428 optimal weight: 0.9990 chunk 525 optimal weight: 10.0000 chunk 817 optimal weight: 50.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 284 GLN A 289 ASN A 387 ASN A 453 ASN A 484 ASN ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN A 655 ASN A 665 ASN ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 ASN A 755 ASN A 803 ASN B 190 GLN B 284 GLN B 289 ASN B 387 ASN B 453 ASN B 484 ASN ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 ASN B 655 ASN B 665 ASN ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 ASN B 755 ASN B 803 ASN C 190 GLN C 284 GLN C 289 ASN C 387 ASN C 453 ASN C 484 ASN C 584 ASN C 655 ASN C 665 ASN ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 ASN C 755 ASN C 803 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 GLN D 284 GLN D 289 ASN D 387 ASN D 453 ASN D 484 ASN ** D 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 584 ASN D 655 ASN D 665 ASN ** D 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 690 ASN D 755 ASN D 803 ASN E 190 GLN E 284 GLN E 289 ASN E 387 ASN E 453 ASN E 484 ASN ** E 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 584 ASN E 655 ASN E 665 ASN ** E 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 690 ASN E 755 ASN E 803 ASN F 190 GLN F 284 GLN F 289 ASN F 387 ASN F 453 ASN F 484 ASN ** F 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 584 ASN F 655 ASN F 665 ASN ** F 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 690 ASN F 755 ASN F 803 ASN G 190 GLN G 284 GLN G 289 ASN G 387 ASN G 453 ASN G 484 ASN ** G 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 584 ASN G 655 ASN G 665 ASN ** G 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 690 ASN G 755 ASN G 803 ASN H 190 GLN H 284 GLN H 289 ASN H 387 ASN H 453 ASN H 484 ASN ** H 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 584 ASN H 655 ASN H 665 ASN ** H 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 690 ASN H 755 ASN H 803 ASN I 190 GLN I 284 GLN I 289 ASN I 387 ASN I 453 ASN I 484 ASN ** I 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 584 ASN I 655 ASN I 665 ASN ** I 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 690 ASN I 755 ASN I 803 ASN ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 190 GLN J 284 GLN J 289 ASN J 387 ASN J 453 ASN J 484 ASN ** J 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 584 ASN J 655 ASN J 665 ASN ** J 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 690 ASN J 755 ASN J 803 ASN ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 190 GLN K 284 GLN K 289 ASN K 387 ASN K 453 ASN K 484 ASN ** K 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 584 ASN K 655 ASN K 665 ASN ** K 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 690 ASN K 755 ASN K 803 ASN L 190 GLN L 284 GLN L 289 ASN L 387 ASN L 453 ASN L 484 ASN ** L 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 584 ASN L 655 ASN L 665 ASN ** L 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 690 ASN L 755 ASN L 803 ASN Total number of N/Q/H flips: 144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 69840 Z= 0.194 Angle : 0.608 8.300 94584 Z= 0.324 Chirality : 0.047 0.161 10620 Planarity : 0.003 0.035 12396 Dihedral : 6.738 29.337 9528 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.10 % Favored : 86.90 % Rotamer: Outliers : 1.08 % Allowed : 5.70 % Favored : 93.22 % 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: -5.25 (0.07), residues: 8952 helix: -3.90 (0.16), residues: 360 sheet: -3.74 (0.08), residues: 2508 loop : -3.56 (0.06), residues: 6084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 30 HIS 0.003 0.001 HIS C 385 PHE 0.010 0.001 PHE E 57 TYR 0.010 0.001 TYR L 765 ARG 0.003 0.000 ARG G 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 192 time to evaluate : 5.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 MET cc_start: 0.7551 (mtm) cc_final: 0.7186 (mtp) REVERT: A 404 LEU cc_start: 0.9160 (tp) cc_final: 0.8841 (tp) REVERT: A 609 MET cc_start: 0.8789 (ttt) cc_final: 0.8555 (mtm) REVERT: A 621 MET cc_start: 0.8854 (mtp) cc_final: 0.8306 (tmm) REVERT: A 658 ASN cc_start: 0.8665 (t0) cc_final: 0.8387 (t0) REVERT: A 663 MET cc_start: 0.8573 (ttt) cc_final: 0.8085 (tmm) REVERT: B 609 MET cc_start: 0.8722 (ttt) cc_final: 0.8460 (mtm) REVERT: B 621 MET cc_start: 0.8737 (mtt) cc_final: 0.8462 (mmm) REVERT: B 658 ASN cc_start: 0.8397 (t0) cc_final: 0.8054 (m-40) REVERT: B 663 MET cc_start: 0.8594 (ttt) cc_final: 0.8297 (tmm) REVERT: C 609 MET cc_start: 0.8696 (ttt) cc_final: 0.8420 (mtm) REVERT: C 621 MET cc_start: 0.8728 (mtt) cc_final: 0.8502 (mmm) REVERT: C 658 ASN cc_start: 0.8549 (t0) cc_final: 0.8170 (t0) REVERT: C 663 MET cc_start: 0.8755 (ttt) cc_final: 0.8304 (tmm) REVERT: D 226 MET cc_start: 0.7570 (mtm) cc_final: 0.7216 (mtp) REVERT: D 404 LEU cc_start: 0.9153 (tp) cc_final: 0.8848 (tp) REVERT: D 609 MET cc_start: 0.8806 (ttt) cc_final: 0.8514 (mtm) REVERT: D 621 MET cc_start: 0.8867 (mtp) cc_final: 0.8317 (tmm) REVERT: D 658 ASN cc_start: 0.8691 (t0) cc_final: 0.8402 (t0) REVERT: D 663 MET cc_start: 0.8540 (ttt) cc_final: 0.7996 (tmm) REVERT: E 609 MET cc_start: 0.8653 (ttt) cc_final: 0.8400 (mtm) REVERT: E 658 ASN cc_start: 0.8483 (t0) cc_final: 0.8236 (m-40) REVERT: E 663 MET cc_start: 0.8692 (ttt) cc_final: 0.8370 (tmm) REVERT: F 609 MET cc_start: 0.8692 (ttt) cc_final: 0.8418 (mtm) REVERT: F 621 MET cc_start: 0.8725 (mtt) cc_final: 0.8497 (mmm) REVERT: F 658 ASN cc_start: 0.8560 (t0) cc_final: 0.8201 (t0) REVERT: F 663 MET cc_start: 0.8741 (ttt) cc_final: 0.8301 (tmm) REVERT: G 226 MET cc_start: 0.7625 (mtm) cc_final: 0.7316 (mtp) REVERT: G 404 LEU cc_start: 0.9155 (tp) cc_final: 0.8848 (tp) REVERT: G 609 MET cc_start: 0.8735 (ttt) cc_final: 0.8521 (mtm) REVERT: G 621 MET cc_start: 0.8871 (mtp) cc_final: 0.8314 (tmm) REVERT: G 658 ASN cc_start: 0.8685 (t0) cc_final: 0.8398 (t0) REVERT: G 663 MET cc_start: 0.8501 (ttt) cc_final: 0.7978 (tmm) REVERT: H 609 MET cc_start: 0.8718 (ttt) cc_final: 0.8457 (mtm) REVERT: H 658 ASN cc_start: 0.8384 (t0) cc_final: 0.8045 (m-40) REVERT: H 663 MET cc_start: 0.8588 (ttt) cc_final: 0.8295 (tmm) REVERT: I 609 MET cc_start: 0.8690 (ttt) cc_final: 0.8413 (mtm) REVERT: I 621 MET cc_start: 0.8725 (mtt) cc_final: 0.8501 (mmm) REVERT: I 658 ASN cc_start: 0.8557 (t0) cc_final: 0.8182 (t0) REVERT: I 663 MET cc_start: 0.8757 (ttt) cc_final: 0.8304 (tmm) REVERT: J 226 MET cc_start: 0.7509 (mtm) cc_final: 0.7209 (mtp) REVERT: J 609 MET cc_start: 0.8846 (ttt) cc_final: 0.8559 (mtm) REVERT: J 621 MET cc_start: 0.8907 (mtp) cc_final: 0.8360 (tmm) REVERT: J 658 ASN cc_start: 0.8714 (t0) cc_final: 0.8419 (t0) REVERT: J 663 MET cc_start: 0.8545 (ttt) cc_final: 0.8104 (tmm) REVERT: K 609 MET cc_start: 0.8655 (ttt) cc_final: 0.8370 (mtm) REVERT: K 621 MET cc_start: 0.8852 (mtp) cc_final: 0.8166 (tmm) REVERT: K 658 ASN cc_start: 0.8428 (t0) cc_final: 0.8189 (m-40) REVERT: K 663 MET cc_start: 0.8694 (ttt) cc_final: 0.8382 (tmm) REVERT: L 609 MET cc_start: 0.8691 (ttt) cc_final: 0.8416 (mtm) REVERT: L 621 MET cc_start: 0.8729 (mtt) cc_final: 0.8505 (mmm) REVERT: L 658 ASN cc_start: 0.8545 (t0) cc_final: 0.8174 (t0) REVERT: L 663 MET cc_start: 0.8748 (ttt) cc_final: 0.8303 (tmm) outliers start: 80 outliers final: 56 residues processed: 268 average time/residue: 0.5525 time to fit residues: 275.6093 Evaluate side-chains 211 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 155 time to evaluate : 5.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 613 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 613 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 613 LEU Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 345 ILE Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 613 LEU Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 613 LEU Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 345 ILE Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 613 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 454 optimal weight: 1.9990 chunk 253 optimal weight: 5.9990 chunk 680 optimal weight: 20.0000 chunk 556 optimal weight: 9.9990 chunk 225 optimal weight: 10.0000 chunk 818 optimal weight: 6.9990 chunk 884 optimal weight: 0.3980 chunk 729 optimal weight: 20.0000 chunk 811 optimal weight: 20.0000 chunk 279 optimal weight: 20.0000 chunk 656 optimal weight: 8.9990 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 GLN ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 GLN ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 340 GLN ** I 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 69840 Z= 0.335 Angle : 0.695 13.912 94584 Z= 0.370 Chirality : 0.049 0.165 10620 Planarity : 0.003 0.026 12396 Dihedral : 6.918 38.907 9528 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.90 % Favored : 81.10 % Rotamer: Outliers : 2.26 % Allowed : 7.21 % Favored : 90.53 % 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: -5.12 (0.07), residues: 8952 helix: -2.92 (0.23), residues: 312 sheet: -3.67 (0.09), residues: 2244 loop : -3.58 (0.06), residues: 6396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 30 HIS 0.007 0.002 HIS H 385 PHE 0.024 0.002 PHE K 57 TYR 0.011 0.001 TYR K 68 ARG 0.005 0.001 ARG K 361 *********************** 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 338 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 171 time to evaluate : 5.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 THR cc_start: 0.6628 (OUTLIER) cc_final: 0.6340 (t) REVERT: A 404 LEU cc_start: 0.9197 (tp) cc_final: 0.8861 (tp) REVERT: A 452 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7846 (m-80) REVERT: A 621 MET cc_start: 0.8905 (mtp) cc_final: 0.8301 (tmm) REVERT: A 658 ASN cc_start: 0.8687 (t0) cc_final: 0.8411 (m-40) REVERT: A 663 MET cc_start: 0.8567 (ttt) cc_final: 0.8328 (tmm) REVERT: B 609 MET cc_start: 0.8706 (ttt) cc_final: 0.8420 (mpp) REVERT: B 621 MET cc_start: 0.8789 (mtt) cc_final: 0.8529 (mmm) REVERT: B 658 ASN cc_start: 0.8441 (t0) cc_final: 0.8194 (m-40) REVERT: B 663 MET cc_start: 0.8603 (ttt) cc_final: 0.8315 (tmm) REVERT: B 751 MET cc_start: 0.9416 (mmm) cc_final: 0.9146 (tpp) REVERT: C 67 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7749 (tm) REVERT: C 609 MET cc_start: 0.8727 (ttt) cc_final: 0.8475 (mpp) REVERT: C 658 ASN cc_start: 0.8612 (t0) cc_final: 0.8265 (t0) REVERT: C 663 MET cc_start: 0.8608 (ttt) cc_final: 0.8260 (tmm) REVERT: D 143 THR cc_start: 0.6506 (OUTLIER) cc_final: 0.6219 (t) REVERT: D 452 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7818 (m-80) REVERT: D 609 MET cc_start: 0.8716 (ttt) cc_final: 0.8475 (mpp) REVERT: D 621 MET cc_start: 0.8886 (mtp) cc_final: 0.8264 (tmm) REVERT: D 658 ASN cc_start: 0.8717 (t0) cc_final: 0.8428 (m-40) REVERT: D 663 MET cc_start: 0.8537 (ttt) cc_final: 0.8284 (tmm) REVERT: E 143 THR cc_start: 0.6425 (OUTLIER) cc_final: 0.6205 (t) REVERT: E 609 MET cc_start: 0.8680 (ttt) cc_final: 0.8353 (mpp) REVERT: E 621 MET cc_start: 0.8848 (mtt) cc_final: 0.8558 (mmm) REVERT: E 658 ASN cc_start: 0.8464 (t0) cc_final: 0.8205 (m-40) REVERT: E 663 MET cc_start: 0.8604 (ttt) cc_final: 0.8319 (tmm) REVERT: F 67 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7722 (tm) REVERT: F 609 MET cc_start: 0.8722 (ttt) cc_final: 0.8473 (mpp) REVERT: F 658 ASN cc_start: 0.8600 (t0) cc_final: 0.8255 (t0) REVERT: F 663 MET cc_start: 0.8596 (ttt) cc_final: 0.8207 (tmm) REVERT: G 143 THR cc_start: 0.6514 (OUTLIER) cc_final: 0.6227 (t) REVERT: G 452 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7817 (m-80) REVERT: G 609 MET cc_start: 0.8715 (ttt) cc_final: 0.8473 (mpp) REVERT: G 621 MET cc_start: 0.8885 (mtp) cc_final: 0.8266 (tmm) REVERT: G 658 ASN cc_start: 0.8710 (t0) cc_final: 0.8422 (m-40) REVERT: G 663 MET cc_start: 0.8493 (ttt) cc_final: 0.8247 (tmm) REVERT: H 609 MET cc_start: 0.8703 (ttt) cc_final: 0.8417 (mpp) REVERT: H 658 ASN cc_start: 0.8432 (t0) cc_final: 0.8187 (m-40) REVERT: H 663 MET cc_start: 0.8592 (ttt) cc_final: 0.8311 (tmm) REVERT: H 751 MET cc_start: 0.9419 (mmm) cc_final: 0.9153 (tpp) REVERT: I 67 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7741 (tm) REVERT: I 609 MET cc_start: 0.8720 (ttt) cc_final: 0.8470 (mpp) REVERT: I 658 ASN cc_start: 0.8611 (t0) cc_final: 0.8264 (t0) REVERT: I 663 MET cc_start: 0.8614 (ttt) cc_final: 0.8267 (tmm) REVERT: J 143 THR cc_start: 0.6548 (OUTLIER) cc_final: 0.6254 (t) REVERT: J 452 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.7861 (m-80) REVERT: J 609 MET cc_start: 0.8736 (ttt) cc_final: 0.8487 (mpp) REVERT: J 621 MET cc_start: 0.8968 (mtp) cc_final: 0.8354 (tmm) REVERT: J 658 ASN cc_start: 0.8735 (t0) cc_final: 0.8487 (m-40) REVERT: J 663 MET cc_start: 0.8537 (ttt) cc_final: 0.8305 (tmm) REVERT: K 143 THR cc_start: 0.6490 (OUTLIER) cc_final: 0.6151 (t) REVERT: K 609 MET cc_start: 0.8685 (ttt) cc_final: 0.8394 (mpp) REVERT: K 621 MET cc_start: 0.8973 (mtp) cc_final: 0.8226 (tmm) REVERT: K 658 ASN cc_start: 0.8493 (t0) cc_final: 0.8260 (m-40) REVERT: K 662 MET cc_start: 0.6486 (mtp) cc_final: 0.5784 (mpp) REVERT: K 663 MET cc_start: 0.8679 (ttt) cc_final: 0.8403 (tmm) REVERT: L 67 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7726 (tm) REVERT: L 609 MET cc_start: 0.8722 (ttt) cc_final: 0.8470 (mpp) REVERT: L 658 ASN cc_start: 0.8600 (t0) cc_final: 0.8255 (t0) REVERT: L 663 MET cc_start: 0.8603 (ttt) cc_final: 0.8261 (tmm) outliers start: 167 outliers final: 102 residues processed: 332 average time/residue: 0.5439 time to fit residues: 338.1262 Evaluate side-chains 274 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 158 time to evaluate : 5.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 452 PHE Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 628 ASN Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain E residue 628 ASN Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 613 LEU Chi-restraints excluded: chain F residue 628 ASN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 162 ILE Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 452 PHE Chi-restraints excluded: chain G residue 613 LEU Chi-restraints excluded: chain G residue 628 ASN Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 613 LEU Chi-restraints excluded: chain H residue 628 ASN Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 628 ASN Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 345 ILE Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 452 PHE Chi-restraints excluded: chain J residue 613 LEU Chi-restraints excluded: chain J residue 628 ASN Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 185 THR Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 613 LEU Chi-restraints excluded: chain K residue 628 ASN Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain L residue 345 ILE Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 613 LEU Chi-restraints excluded: chain L residue 628 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 808 optimal weight: 30.0000 chunk 615 optimal weight: 6.9990 chunk 424 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 390 optimal weight: 7.9990 chunk 549 optimal weight: 10.0000 chunk 821 optimal weight: 1.9990 chunk 869 optimal weight: 20.0000 chunk 429 optimal weight: 20.0000 chunk 778 optimal weight: 2.9990 chunk 234 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 GLN ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN ** D 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 GLN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 GLN ** E 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 GLN ** F 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 GLN ** G 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 340 GLN ** G 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 340 GLN ** H 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 GLN ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 340 GLN ** J 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 340 GLN ** K 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 340 GLN ** L 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 69840 Z= 0.362 Angle : 0.718 12.193 94584 Z= 0.383 Chirality : 0.050 0.169 10620 Planarity : 0.003 0.025 12396 Dihedral : 7.040 40.232 9528 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.26 % Favored : 81.74 % Rotamer: Outliers : 3.12 % Allowed : 9.05 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.05 (0.07), residues: 8952 helix: -2.77 (0.24), residues: 312 sheet: -3.72 (0.09), residues: 2076 loop : -3.52 (0.06), residues: 6564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 577 HIS 0.007 0.002 HIS K 385 PHE 0.025 0.002 PHE K 57 TYR 0.010 0.002 TYR K 68 ARG 0.006 0.001 ARG B 361 *********************** 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 389 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 158 time to evaluate : 5.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 THR cc_start: 0.6573 (OUTLIER) cc_final: 0.6297 (t) REVERT: A 354 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7265 (t0) REVERT: A 621 MET cc_start: 0.8899 (mtp) cc_final: 0.8281 (tmm) REVERT: A 658 ASN cc_start: 0.8704 (t0) cc_final: 0.8374 (m-40) REVERT: A 663 MET cc_start: 0.8576 (ttt) cc_final: 0.8369 (tmm) REVERT: B 452 PHE cc_start: 0.7780 (OUTLIER) cc_final: 0.6906 (m-80) REVERT: B 609 MET cc_start: 0.8731 (ttt) cc_final: 0.8523 (mtm) REVERT: B 621 MET cc_start: 0.8803 (mtt) cc_final: 0.8462 (mmm) REVERT: B 658 ASN cc_start: 0.8443 (t0) cc_final: 0.8191 (m-40) REVERT: B 663 MET cc_start: 0.8551 (ttt) cc_final: 0.8283 (tmm) REVERT: B 751 MET cc_start: 0.9404 (mmm) cc_final: 0.9117 (tpp) REVERT: C 67 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7802 (tm) REVERT: C 99 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7289 (pp) REVERT: C 219 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8064 (ptpp) REVERT: C 354 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7402 (t0) REVERT: C 609 MET cc_start: 0.8721 (ttt) cc_final: 0.8453 (mpp) REVERT: C 621 MET cc_start: 0.8928 (mtt) cc_final: 0.8557 (mmm) REVERT: C 658 ASN cc_start: 0.8604 (t0) cc_final: 0.8233 (t0) REVERT: C 663 MET cc_start: 0.8656 (ttt) cc_final: 0.8251 (tmm) REVERT: D 143 THR cc_start: 0.6425 (OUTLIER) cc_final: 0.6113 (t) REVERT: D 354 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7276 (t0) REVERT: D 609 MET cc_start: 0.8737 (ttt) cc_final: 0.8477 (mpp) REVERT: D 621 MET cc_start: 0.8899 (mtp) cc_final: 0.8279 (tmm) REVERT: D 658 ASN cc_start: 0.8701 (t0) cc_final: 0.8423 (m-40) REVERT: D 663 MET cc_start: 0.8564 (ttt) cc_final: 0.8326 (tmm) REVERT: E 143 THR cc_start: 0.6408 (OUTLIER) cc_final: 0.6118 (t) REVERT: E 452 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.6906 (m-80) REVERT: E 609 MET cc_start: 0.8690 (ttt) cc_final: 0.8470 (mtm) REVERT: E 621 MET cc_start: 0.8864 (mtt) cc_final: 0.8421 (mmm) REVERT: E 658 ASN cc_start: 0.8477 (t0) cc_final: 0.8229 (m-40) REVERT: E 663 MET cc_start: 0.8593 (ttt) cc_final: 0.8325 (tmm) REVERT: F 67 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7767 (tm) REVERT: F 99 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7308 (pp) REVERT: F 219 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8075 (ptpp) REVERT: F 354 ASP cc_start: 0.7623 (OUTLIER) cc_final: 0.7395 (t0) REVERT: F 609 MET cc_start: 0.8718 (ttt) cc_final: 0.8451 (mpp) REVERT: F 621 MET cc_start: 0.8929 (mtt) cc_final: 0.8560 (mmm) REVERT: F 658 ASN cc_start: 0.8593 (t0) cc_final: 0.8226 (t0) REVERT: F 663 MET cc_start: 0.8643 (ttt) cc_final: 0.8245 (tmm) REVERT: G 143 THR cc_start: 0.6593 (OUTLIER) cc_final: 0.6276 (t) REVERT: G 354 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.7269 (t0) REVERT: G 609 MET cc_start: 0.8734 (ttt) cc_final: 0.8475 (mpp) REVERT: G 621 MET cc_start: 0.8901 (mtp) cc_final: 0.8281 (tmm) REVERT: G 658 ASN cc_start: 0.8696 (t0) cc_final: 0.8421 (m-40) REVERT: G 663 MET cc_start: 0.8542 (ttt) cc_final: 0.8279 (tmm) REVERT: H 452 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.6938 (m-80) REVERT: H 609 MET cc_start: 0.8729 (ttt) cc_final: 0.8451 (mpp) REVERT: H 658 ASN cc_start: 0.8433 (t0) cc_final: 0.8185 (m-40) REVERT: H 663 MET cc_start: 0.8582 (ttt) cc_final: 0.8306 (tmm) REVERT: H 751 MET cc_start: 0.9407 (mmm) cc_final: 0.9125 (tpp) REVERT: I 67 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7789 (tm) REVERT: I 99 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7296 (pp) REVERT: I 219 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8070 (ptpp) REVERT: I 354 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.7404 (t0) REVERT: I 609 MET cc_start: 0.8670 (ttt) cc_final: 0.8412 (mpp) REVERT: I 621 MET cc_start: 0.8921 (mtt) cc_final: 0.8556 (mmm) REVERT: I 658 ASN cc_start: 0.8604 (t0) cc_final: 0.8234 (t0) REVERT: I 663 MET cc_start: 0.8659 (ttt) cc_final: 0.8253 (tmm) REVERT: J 143 THR cc_start: 0.6367 (OUTLIER) cc_final: 0.6068 (t) REVERT: J 354 ASP cc_start: 0.7605 (OUTLIER) cc_final: 0.7185 (t0) REVERT: J 404 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8819 (tp) REVERT: J 609 MET cc_start: 0.8761 (ttt) cc_final: 0.8491 (mpp) REVERT: J 658 ASN cc_start: 0.8751 (t0) cc_final: 0.8503 (m-40) REVERT: K 143 THR cc_start: 0.6419 (OUTLIER) cc_final: 0.6105 (t) REVERT: K 452 PHE cc_start: 0.7784 (OUTLIER) cc_final: 0.6901 (m-80) REVERT: K 609 MET cc_start: 0.8685 (ttt) cc_final: 0.8462 (mtm) REVERT: K 658 ASN cc_start: 0.8509 (t0) cc_final: 0.8270 (m-40) REVERT: K 662 MET cc_start: 0.6494 (mtp) cc_final: 0.5806 (mpp) REVERT: K 663 MET cc_start: 0.8639 (ttt) cc_final: 0.8392 (tmm) REVERT: L 67 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7772 (tm) REVERT: L 99 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7318 (pp) REVERT: L 219 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8072 (ptpp) REVERT: L 354 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7395 (t0) REVERT: L 609 MET cc_start: 0.8672 (ttt) cc_final: 0.8414 (mpp) REVERT: L 621 MET cc_start: 0.8925 (mtt) cc_final: 0.8559 (mmm) REVERT: L 658 ASN cc_start: 0.8584 (t0) cc_final: 0.8220 (t0) REVERT: L 663 MET cc_start: 0.8649 (ttt) cc_final: 0.8250 (tmm) outliers start: 231 outliers final: 157 residues processed: 381 average time/residue: 0.5505 time to fit residues: 387.5509 Evaluate side-chains 344 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 156 time to evaluate : 5.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 354 ASP Chi-restraints excluded: chain C residue 412 ASN Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 496 ASN Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 496 ASN Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 628 ASN Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 452 PHE Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain E residue 628 ASN Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 219 LYS Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain F residue 412 ASN Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 496 ASN Chi-restraints excluded: chain F residue 613 LEU Chi-restraints excluded: chain F residue 628 ASN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 354 ASP Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 496 ASN Chi-restraints excluded: chain G residue 613 LEU Chi-restraints excluded: chain G residue 628 ASN Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 127 MET Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 219 LYS Chi-restraints excluded: chain H residue 277 ILE Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain H residue 404 LEU Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 452 PHE Chi-restraints excluded: chain H residue 613 LEU Chi-restraints excluded: chain H residue 628 ASN Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 219 LYS Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 354 ASP Chi-restraints excluded: chain I residue 412 ASN Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 496 ASN Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 628 ASN Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain J residue 196 THR Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 345 ILE Chi-restraints excluded: chain J residue 354 ASP Chi-restraints excluded: chain J residue 404 LEU Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 496 ASN Chi-restraints excluded: chain J residue 613 LEU Chi-restraints excluded: chain J residue 628 ASN Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 127 MET Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 185 THR Chi-restraints excluded: chain K residue 196 THR Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 219 LYS Chi-restraints excluded: chain K residue 277 ILE Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 452 PHE Chi-restraints excluded: chain K residue 613 LEU Chi-restraints excluded: chain K residue 628 ASN Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 99 LEU Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain L residue 219 LYS Chi-restraints excluded: chain L residue 345 ILE Chi-restraints excluded: chain L residue 354 ASP Chi-restraints excluded: chain L residue 412 ASN Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 496 ASN Chi-restraints excluded: chain L residue 613 LEU Chi-restraints excluded: chain L residue 628 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 724 optimal weight: 9.9990 chunk 493 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 647 optimal weight: 20.0000 chunk 358 optimal weight: 30.0000 chunk 742 optimal weight: 30.0000 chunk 601 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 444 optimal weight: 20.0000 chunk 780 optimal weight: 7.9990 chunk 219 optimal weight: 0.0770 overall best weight: 2.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 GLN ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN ** D 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN ** E 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 ASN G 128 GLN ** G 382 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 34 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 GLN ** H 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 GLN ** J 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 GLN ** K 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 69840 Z= 0.185 Angle : 0.592 10.339 94584 Z= 0.307 Chirality : 0.046 0.160 10620 Planarity : 0.002 0.029 12396 Dihedral : 6.099 37.526 9528 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 2.38 % Allowed : 10.26 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.85 (0.08), residues: 8952 helix: -2.65 (0.28), residues: 264 sheet: -3.68 (0.09), residues: 2604 loop : -3.21 (0.07), residues: 6084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 577 HIS 0.002 0.001 HIS H 385 PHE 0.009 0.001 PHE K 57 TYR 0.008 0.001 TYR B 765 ARG 0.002 0.000 ARG J 361 *********************** 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 337 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 161 time to evaluate : 5.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 THR cc_start: 0.6552 (OUTLIER) cc_final: 0.6340 (t) REVERT: A 404 LEU cc_start: 0.9159 (tp) cc_final: 0.8849 (tp) REVERT: A 658 ASN cc_start: 0.8720 (t0) cc_final: 0.8398 (t0) REVERT: A 663 MET cc_start: 0.8541 (ttt) cc_final: 0.8286 (tmm) REVERT: B 354 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7316 (t0) REVERT: B 609 MET cc_start: 0.8740 (ttt) cc_final: 0.8496 (mtm) REVERT: B 621 MET cc_start: 0.8772 (mtt) cc_final: 0.8460 (mmm) REVERT: B 658 ASN cc_start: 0.8445 (t0) cc_final: 0.8212 (m-40) REVERT: B 663 MET cc_start: 0.8566 (ttt) cc_final: 0.8261 (tmm) REVERT: B 751 MET cc_start: 0.9386 (mmm) cc_final: 0.9054 (tpt) REVERT: C 67 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7970 (tm) REVERT: C 99 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7189 (pp) REVERT: C 609 MET cc_start: 0.8782 (ttt) cc_final: 0.8496 (mpp) REVERT: C 621 MET cc_start: 0.8913 (mtt) cc_final: 0.8630 (mmm) REVERT: C 658 ASN cc_start: 0.8590 (t0) cc_final: 0.8219 (t0) REVERT: C 663 MET cc_start: 0.8689 (ttt) cc_final: 0.8283 (tmm) REVERT: D 99 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7221 (pp) REVERT: D 143 THR cc_start: 0.6555 (OUTLIER) cc_final: 0.6315 (t) REVERT: D 609 MET cc_start: 0.8753 (ttt) cc_final: 0.8477 (mpp) REVERT: D 621 MET cc_start: 0.8984 (mtp) cc_final: 0.8304 (tmm) REVERT: D 658 ASN cc_start: 0.8741 (t0) cc_final: 0.8499 (m-40) REVERT: D 663 MET cc_start: 0.8579 (ttt) cc_final: 0.8328 (tmm) REVERT: E 354 ASP cc_start: 0.7679 (OUTLIER) cc_final: 0.7296 (t0) REVERT: E 621 MET cc_start: 0.8825 (mtt) cc_final: 0.8444 (mmm) REVERT: E 658 ASN cc_start: 0.8501 (t0) cc_final: 0.8251 (m-40) REVERT: E 663 MET cc_start: 0.8573 (ttt) cc_final: 0.8296 (tmm) REVERT: F 67 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7909 (tm) REVERT: F 99 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7205 (pp) REVERT: F 609 MET cc_start: 0.8778 (ttt) cc_final: 0.8494 (mpp) REVERT: F 621 MET cc_start: 0.8915 (mtt) cc_final: 0.8632 (mmm) REVERT: F 658 ASN cc_start: 0.8580 (t0) cc_final: 0.8213 (t0) REVERT: F 663 MET cc_start: 0.8675 (ttt) cc_final: 0.8275 (tmm) REVERT: G 99 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7227 (pp) REVERT: G 143 THR cc_start: 0.6562 (OUTLIER) cc_final: 0.6323 (t) REVERT: G 609 MET cc_start: 0.8751 (ttt) cc_final: 0.8477 (mpp) REVERT: G 621 MET cc_start: 0.8986 (mtp) cc_final: 0.8304 (tmm) REVERT: G 658 ASN cc_start: 0.8708 (t0) cc_final: 0.8467 (m-40) REVERT: G 663 MET cc_start: 0.8541 (ttt) cc_final: 0.8271 (tmm) REVERT: H 354 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7307 (t0) REVERT: H 430 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7860 (pp) REVERT: H 609 MET cc_start: 0.8738 (ttt) cc_final: 0.8496 (mtm) REVERT: H 621 MET cc_start: 0.8276 (mmm) cc_final: 0.7823 (mmm) REVERT: H 658 ASN cc_start: 0.8435 (t0) cc_final: 0.8205 (m-40) REVERT: H 663 MET cc_start: 0.8558 (ttt) cc_final: 0.8259 (tmm) REVERT: H 751 MET cc_start: 0.9388 (mmm) cc_final: 0.9063 (tpt) REVERT: I 67 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7957 (tm) REVERT: I 99 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7191 (pp) REVERT: I 609 MET cc_start: 0.8776 (ttt) cc_final: 0.8491 (mpp) REVERT: I 621 MET cc_start: 0.8913 (mtt) cc_final: 0.8633 (mmm) REVERT: I 658 ASN cc_start: 0.8591 (t0) cc_final: 0.8219 (t0) REVERT: I 663 MET cc_start: 0.8690 (ttt) cc_final: 0.8283 (tmm) REVERT: J 143 THR cc_start: 0.6409 (OUTLIER) cc_final: 0.6185 (t) REVERT: J 609 MET cc_start: 0.8776 (ttt) cc_final: 0.8490 (mpp) REVERT: J 658 ASN cc_start: 0.8706 (t0) cc_final: 0.8457 (m-40) REVERT: J 663 MET cc_start: 0.8140 (tmm) cc_final: 0.7749 (tmm) REVERT: K 354 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7292 (t0) REVERT: K 609 MET cc_start: 0.8706 (ttt) cc_final: 0.8461 (mtm) REVERT: K 658 ASN cc_start: 0.8490 (t0) cc_final: 0.8253 (m-40) REVERT: K 662 MET cc_start: 0.6558 (mtp) cc_final: 0.5892 (mpp) REVERT: K 663 MET cc_start: 0.8595 (ttt) cc_final: 0.8357 (tmm) REVERT: L 67 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7919 (tm) REVERT: L 99 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7220 (pp) REVERT: L 609 MET cc_start: 0.8777 (ttt) cc_final: 0.8493 (mpp) REVERT: L 621 MET cc_start: 0.8915 (mtt) cc_final: 0.8636 (mmm) REVERT: L 658 ASN cc_start: 0.8580 (t0) cc_final: 0.8212 (t0) REVERT: L 663 MET cc_start: 0.8682 (ttt) cc_final: 0.8282 (tmm) outliers start: 176 outliers final: 98 residues processed: 332 average time/residue: 0.5642 time to fit residues: 349.4738 Evaluate side-chains 272 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 155 time to evaluate : 5.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 412 ASN Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 496 ASN Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 39 ASN Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 354 ASP Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 472 ASN Chi-restraints excluded: chain E residue 496 ASN Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain F residue 39 ASN Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 412 ASN Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 496 ASN Chi-restraints excluded: chain F residue 613 LEU Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 367 ASP Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 613 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 354 ASP Chi-restraints excluded: chain H residue 367 ASP Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain H residue 472 ASN Chi-restraints excluded: chain H residue 496 ASN Chi-restraints excluded: chain H residue 613 LEU Chi-restraints excluded: chain I residue 39 ASN Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 367 ASP Chi-restraints excluded: chain I residue 412 ASN Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 496 ASN Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain J residue 39 ASN Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 613 LEU Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 354 ASP Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 472 ASN Chi-restraints excluded: chain K residue 496 ASN Chi-restraints excluded: chain K residue 613 LEU Chi-restraints excluded: chain L residue 39 ASN Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 99 LEU Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 412 ASN Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 496 ASN Chi-restraints excluded: chain L residue 613 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 292 optimal weight: 8.9990 chunk 783 optimal weight: 6.9990 chunk 171 optimal weight: 8.9990 chunk 510 optimal weight: 20.0000 chunk 214 optimal weight: 40.0000 chunk 870 optimal weight: 10.0000 chunk 722 optimal weight: 20.0000 chunk 403 optimal weight: 9.9990 chunk 72 optimal weight: 40.0000 chunk 288 optimal weight: 7.9990 chunk 457 optimal weight: 7.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 ASN A 136 GLN ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN B 62 ASN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN C 62 ASN ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN C 128 GLN C 136 GLN ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN D 62 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN D 136 GLN ** D 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 GLN F 62 ASN ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 ASN F 128 GLN ** F 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 756 GLN G 62 ASN ** G 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 136 GLN ** G 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 GLN H 62 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 GLN I 62 ASN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 ASN I 128 GLN I 136 GLN ** I 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 756 GLN J 62 ASN ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 126 ASN J 136 GLN ** J 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 34 GLN K 62 ASN ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 GLN L 62 ASN ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 126 ASN L 128 GLN L 136 GLN ** L 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 756 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 69840 Z= 0.511 Angle : 0.821 11.868 94584 Z= 0.440 Chirality : 0.053 0.184 10620 Planarity : 0.004 0.031 12396 Dihedral : 7.470 43.911 9528 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 29.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.84 % Favored : 76.16 % Rotamer: Outliers : 4.27 % Allowed : 9.93 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.09 (0.07), residues: 8952 helix: -2.56 (0.25), residues: 300 sheet: -3.95 (0.09), residues: 2328 loop : -3.42 (0.07), residues: 6324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 577 HIS 0.010 0.002 HIS K 385 PHE 0.026 0.002 PHE H 57 TYR 0.017 0.002 TYR K 298 ARG 0.007 0.001 ARG A 361 *********************** 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 470 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 316 poor density : 154 time to evaluate : 7.026 Fit side-chains REVERT: A 143 THR cc_start: 0.6566 (OUTLIER) cc_final: 0.6196 (t) REVERT: A 168 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7123 (tp) REVERT: A 658 ASN cc_start: 0.8769 (t0) cc_final: 0.8496 (m-40) REVERT: A 663 MET cc_start: 0.8488 (ttt) cc_final: 0.8227 (tmm) REVERT: B 354 ASP cc_start: 0.7588 (OUTLIER) cc_final: 0.7285 (t0) REVERT: B 609 MET cc_start: 0.8702 (ttt) cc_final: 0.8492 (mtm) REVERT: B 621 MET cc_start: 0.8864 (mtt) cc_final: 0.8344 (mmm) REVERT: B 658 ASN cc_start: 0.8502 (t0) cc_final: 0.8283 (m-40) REVERT: B 663 MET cc_start: 0.8584 (ttt) cc_final: 0.8310 (tmm) REVERT: B 751 MET cc_start: 0.9417 (mmm) cc_final: 0.9098 (tpt) REVERT: C 67 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7908 (tm) REVERT: C 354 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7417 (t0) REVERT: C 609 MET cc_start: 0.8649 (ttt) cc_final: 0.8419 (mpp) REVERT: C 621 MET cc_start: 0.8969 (mtt) cc_final: 0.8521 (mmm) REVERT: C 658 ASN cc_start: 0.8564 (t0) cc_final: 0.8168 (t0) REVERT: C 663 MET cc_start: 0.8716 (ttt) cc_final: 0.8333 (tmm) REVERT: C 751 MET cc_start: 0.9375 (mmm) cc_final: 0.9163 (tpp) REVERT: D 143 THR cc_start: 0.6602 (OUTLIER) cc_final: 0.6190 (t) REVERT: D 168 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7144 (tp) REVERT: D 609 MET cc_start: 0.8725 (ttt) cc_final: 0.8459 (mpp) REVERT: D 658 ASN cc_start: 0.8762 (t0) cc_final: 0.8496 (m-40) REVERT: D 663 MET cc_start: 0.8503 (ttt) cc_final: 0.8233 (tmm) REVERT: E 354 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.7317 (t0) REVERT: E 609 MET cc_start: 0.8034 (mtm) cc_final: 0.7367 (mpp) REVERT: E 621 MET cc_start: 0.8904 (mtt) cc_final: 0.8459 (mmm) REVERT: E 658 ASN cc_start: 0.8518 (t0) cc_final: 0.8226 (m-40) REVERT: E 663 MET cc_start: 0.8634 (ttt) cc_final: 0.8354 (tmm) REVERT: F 67 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7891 (tm) REVERT: F 354 ASP cc_start: 0.7669 (OUTLIER) cc_final: 0.7412 (t0) REVERT: F 609 MET cc_start: 0.8646 (ttt) cc_final: 0.8419 (mpp) REVERT: F 621 MET cc_start: 0.8973 (mtt) cc_final: 0.8527 (mmm) REVERT: F 658 ASN cc_start: 0.8550 (t0) cc_final: 0.8157 (t0) REVERT: F 663 MET cc_start: 0.8645 (ttt) cc_final: 0.8274 (tmm) REVERT: G 143 THR cc_start: 0.6608 (OUTLIER) cc_final: 0.6199 (t) REVERT: G 168 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7084 (tp) REVERT: G 609 MET cc_start: 0.8723 (ttt) cc_final: 0.8458 (mpp) REVERT: G 658 ASN cc_start: 0.8758 (t0) cc_final: 0.8496 (m-40) REVERT: G 663 MET cc_start: 0.8491 (ttt) cc_final: 0.8225 (tmm) REVERT: H 354 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7324 (t0) REVERT: H 609 MET cc_start: 0.8698 (ttt) cc_final: 0.8490 (mtm) REVERT: H 663 MET cc_start: 0.8603 (ttt) cc_final: 0.8320 (tmm) REVERT: H 751 MET cc_start: 0.9410 (mmm) cc_final: 0.9082 (tpt) REVERT: I 67 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7898 (tm) REVERT: I 354 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7420 (t0) REVERT: I 609 MET cc_start: 0.8642 (ttt) cc_final: 0.8414 (mpp) REVERT: I 621 MET cc_start: 0.8969 (mtt) cc_final: 0.8524 (mmm) REVERT: I 658 ASN cc_start: 0.8562 (t0) cc_final: 0.8166 (t0) REVERT: I 663 MET cc_start: 0.8720 (ttt) cc_final: 0.8335 (tmm) REVERT: I 751 MET cc_start: 0.9375 (mmm) cc_final: 0.9164 (tpp) REVERT: J 143 THR cc_start: 0.6473 (OUTLIER) cc_final: 0.6092 (t) REVERT: J 168 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7173 (tp) REVERT: J 354 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.7321 (t0) REVERT: J 404 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8599 (tt) REVERT: J 609 MET cc_start: 0.8738 (ttt) cc_final: 0.8481 (mpp) REVERT: J 658 ASN cc_start: 0.8771 (t0) cc_final: 0.8486 (m-40) REVERT: J 663 MET cc_start: 0.8032 (tmm) cc_final: 0.7732 (tmm) REVERT: K 354 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.7284 (t0) REVERT: K 609 MET cc_start: 0.8667 (ttt) cc_final: 0.8433 (mtm) REVERT: K 663 MET cc_start: 0.8584 (ttt) cc_final: 0.8270 (tmm) REVERT: L 67 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7897 (tm) REVERT: L 354 ASP cc_start: 0.7671 (OUTLIER) cc_final: 0.7416 (t0) REVERT: L 609 MET cc_start: 0.8637 (ttt) cc_final: 0.8402 (mpp) REVERT: L 621 MET cc_start: 0.8970 (mtt) cc_final: 0.8528 (mmm) REVERT: L 658 ASN cc_start: 0.8553 (t0) cc_final: 0.8160 (t0) REVERT: L 663 MET cc_start: 0.8712 (ttt) cc_final: 0.8333 (tmm) outliers start: 316 outliers final: 211 residues processed: 459 average time/residue: 0.5501 time to fit residues: 465.1474 Evaluate side-chains 384 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 151 time to evaluate : 5.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 354 ASP Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain C residue 496 ASN Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain D residue 39 ASN Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 382 ASN Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 496 ASN Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 628 ASN Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 221 ASN Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 354 ASP Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 472 ASN Chi-restraints excluded: chain E residue 496 ASN Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain E residue 628 ASN Chi-restraints excluded: chain F residue 39 ASN Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 219 LYS Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 472 ASN Chi-restraints excluded: chain F residue 496 ASN Chi-restraints excluded: chain F residue 613 LEU Chi-restraints excluded: chain F residue 628 ASN Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 219 LYS Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 367 ASP Chi-restraints excluded: chain G residue 382 ASN Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 496 ASN Chi-restraints excluded: chain G residue 613 LEU Chi-restraints excluded: chain G residue 628 ASN Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 127 MET Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 219 LYS Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain H residue 354 ASP Chi-restraints excluded: chain H residue 367 ASP Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 472 ASN Chi-restraints excluded: chain H residue 496 ASN Chi-restraints excluded: chain H residue 613 LEU Chi-restraints excluded: chain H residue 628 ASN Chi-restraints excluded: chain I residue 39 ASN Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 156 ASP Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 219 LYS Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 354 ASP Chi-restraints excluded: chain I residue 367 ASP Chi-restraints excluded: chain I residue 404 LEU Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 449 THR Chi-restraints excluded: chain I residue 472 ASN Chi-restraints excluded: chain I residue 496 ASN Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 628 ASN Chi-restraints excluded: chain J residue 39 ASN Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain J residue 196 THR Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 345 ILE Chi-restraints excluded: chain J residue 354 ASP Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 382 ASN Chi-restraints excluded: chain J residue 404 LEU Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 496 ASN Chi-restraints excluded: chain J residue 613 LEU Chi-restraints excluded: chain J residue 628 ASN Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 127 MET Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 185 THR Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 219 LYS Chi-restraints excluded: chain K residue 221 ASN Chi-restraints excluded: chain K residue 277 ILE Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 354 ASP Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 449 THR Chi-restraints excluded: chain K residue 472 ASN Chi-restraints excluded: chain K residue 496 ASN Chi-restraints excluded: chain K residue 613 LEU Chi-restraints excluded: chain K residue 628 ASN Chi-restraints excluded: chain L residue 39 ASN Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 156 ASP Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain L residue 219 LYS Chi-restraints excluded: chain L residue 345 ILE Chi-restraints excluded: chain L residue 354 ASP Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 404 LEU Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 472 ASN Chi-restraints excluded: chain L residue 496 ASN Chi-restraints excluded: chain L residue 613 LEU Chi-restraints excluded: chain L residue 628 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 839 optimal weight: 0.4980 chunk 98 optimal weight: 6.9990 chunk 496 optimal weight: 4.9990 chunk 635 optimal weight: 3.9990 chunk 492 optimal weight: 9.9990 chunk 733 optimal weight: 30.0000 chunk 486 optimal weight: 0.9980 chunk 867 optimal weight: 9.9990 chunk 542 optimal weight: 0.9990 chunk 528 optimal weight: 4.9990 chunk 400 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 513 ASN ** E 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 658 ASN ** H 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 GLN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 513 ASN ** K 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 69840 Z= 0.166 Angle : 0.598 9.869 94584 Z= 0.309 Chirality : 0.047 0.169 10620 Planarity : 0.002 0.031 12396 Dihedral : 6.158 39.043 9528 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.66 % Favored : 88.34 % Rotamer: Outliers : 2.57 % Allowed : 11.89 % Favored : 85.55 % 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: -4.75 (0.08), residues: 8952 helix: -2.43 (0.29), residues: 264 sheet: -3.86 (0.09), residues: 2472 loop : -3.06 (0.07), residues: 6216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 577 HIS 0.003 0.001 HIS A 469 PHE 0.010 0.001 PHE E 488 TYR 0.008 0.001 TYR H 110 ARG 0.002 0.000 ARG J 228 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 169 time to evaluate : 5.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 THR cc_start: 0.6450 (OUTLIER) cc_final: 0.6227 (t) REVERT: A 219 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7734 (mttp) REVERT: A 609 MET cc_start: 0.8101 (mpp) cc_final: 0.7619 (mpp) REVERT: A 658 ASN cc_start: 0.8755 (t0) cc_final: 0.8458 (m-40) REVERT: A 662 MET cc_start: 0.7073 (mtp) cc_final: 0.6420 (mpp) REVERT: A 663 MET cc_start: 0.8544 (ttt) cc_final: 0.8303 (tmm) REVERT: B 354 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7326 (t0) REVERT: B 609 MET cc_start: 0.8777 (ttt) cc_final: 0.8512 (mtm) REVERT: B 621 MET cc_start: 0.8751 (mtt) cc_final: 0.8429 (mmm) REVERT: B 663 MET cc_start: 0.8585 (ttt) cc_final: 0.8366 (tmm) REVERT: B 792 LEU cc_start: 0.9724 (OUTLIER) cc_final: 0.9504 (mp) REVERT: C 67 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8078 (tm) REVERT: C 609 MET cc_start: 0.8786 (ttt) cc_final: 0.8552 (mtm) REVERT: C 621 MET cc_start: 0.8866 (mtt) cc_final: 0.8462 (mmm) REVERT: C 658 ASN cc_start: 0.8579 (t0) cc_final: 0.8173 (t0) REVERT: C 663 MET cc_start: 0.8703 (ttt) cc_final: 0.8310 (tmm) REVERT: C 751 MET cc_start: 0.9434 (mmm) cc_final: 0.9168 (tpp) REVERT: D 99 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7126 (pp) REVERT: D 143 THR cc_start: 0.6462 (OUTLIER) cc_final: 0.6202 (t) REVERT: D 609 MET cc_start: 0.8789 (ttt) cc_final: 0.8495 (mpp) REVERT: D 658 ASN cc_start: 0.8720 (t0) cc_final: 0.8380 (t0) REVERT: D 663 MET cc_start: 0.8549 (ttt) cc_final: 0.8313 (tmm) REVERT: E 354 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7311 (t0) REVERT: E 609 MET cc_start: 0.8068 (mtm) cc_final: 0.7365 (mpp) REVERT: E 621 MET cc_start: 0.8830 (mtt) cc_final: 0.8474 (mmm) REVERT: E 663 MET cc_start: 0.8567 (ttt) cc_final: 0.8270 (tmm) REVERT: F 67 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8017 (tm) REVERT: F 609 MET cc_start: 0.8790 (ttt) cc_final: 0.8561 (mtm) REVERT: F 621 MET cc_start: 0.8870 (mtt) cc_final: 0.8465 (mmm) REVERT: F 658 ASN cc_start: 0.8564 (t0) cc_final: 0.8163 (t0) REVERT: F 662 MET cc_start: 0.6980 (mtp) cc_final: 0.6379 (mpp) REVERT: F 663 MET cc_start: 0.8689 (ttt) cc_final: 0.8302 (tmm) REVERT: G 99 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7133 (pp) REVERT: G 143 THR cc_start: 0.6468 (OUTLIER) cc_final: 0.6211 (t) REVERT: G 609 MET cc_start: 0.8728 (ttt) cc_final: 0.8494 (mpp) REVERT: G 658 ASN cc_start: 0.8715 (t0) cc_final: 0.8414 (m-40) REVERT: G 662 MET cc_start: 0.6847 (mtp) cc_final: 0.6200 (mpp) REVERT: G 663 MET cc_start: 0.8541 (ttt) cc_final: 0.8312 (tmm) REVERT: H 354 ASP cc_start: 0.7716 (OUTLIER) cc_final: 0.7320 (t0) REVERT: H 609 MET cc_start: 0.8773 (ttt) cc_final: 0.8567 (mtm) REVERT: H 621 MET cc_start: 0.8226 (mmm) cc_final: 0.7724 (mmm) REVERT: H 663 MET cc_start: 0.8576 (ttt) cc_final: 0.8346 (tmm) REVERT: H 792 LEU cc_start: 0.9719 (OUTLIER) cc_final: 0.9496 (mp) REVERT: I 67 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7993 (tm) REVERT: I 609 MET cc_start: 0.8779 (ttt) cc_final: 0.8545 (mtm) REVERT: I 621 MET cc_start: 0.8879 (mtt) cc_final: 0.8482 (mmm) REVERT: I 658 ASN cc_start: 0.8579 (t0) cc_final: 0.8173 (t0) REVERT: I 663 MET cc_start: 0.8704 (ttt) cc_final: 0.8310 (tmm) REVERT: I 751 MET cc_start: 0.9436 (mmm) cc_final: 0.9170 (tpp) REVERT: J 143 THR cc_start: 0.6378 (OUTLIER) cc_final: 0.6139 (t) REVERT: J 219 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7724 (mttp) REVERT: J 609 MET cc_start: 0.8728 (ttt) cc_final: 0.8487 (mpp) REVERT: J 658 ASN cc_start: 0.8724 (t0) cc_final: 0.8428 (m-40) REVERT: K 354 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7299 (t0) REVERT: K 609 MET cc_start: 0.8746 (ttt) cc_final: 0.8534 (mtm) REVERT: K 662 MET cc_start: 0.6644 (mtp) cc_final: 0.6014 (mpp) REVERT: K 663 MET cc_start: 0.8546 (ttt) cc_final: 0.8291 (tmm) REVERT: L 67 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8029 (tm) REVERT: L 609 MET cc_start: 0.8781 (ttt) cc_final: 0.8548 (mtm) REVERT: L 621 MET cc_start: 0.8849 (mtt) cc_final: 0.8445 (mmm) REVERT: L 658 ASN cc_start: 0.8571 (t0) cc_final: 0.8169 (t0) REVERT: L 663 MET cc_start: 0.8698 (ttt) cc_final: 0.8310 (tmm) outliers start: 190 outliers final: 132 residues processed: 351 average time/residue: 0.5521 time to fit residues: 361.1023 Evaluate side-chains 304 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 154 time to evaluate : 5.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 412 ASN Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain D residue 39 ASN Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 496 ASN Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 354 ASP Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 472 ASN Chi-restraints excluded: chain E residue 513 ASN Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain F residue 39 ASN Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 412 ASN Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 472 ASN Chi-restraints excluded: chain F residue 613 LEU Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 367 ASP Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 449 THR Chi-restraints excluded: chain G residue 496 ASN Chi-restraints excluded: chain G residue 613 LEU Chi-restraints excluded: chain G residue 628 ASN Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain H residue 354 ASP Chi-restraints excluded: chain H residue 367 ASP Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 472 ASN Chi-restraints excluded: chain H residue 613 LEU Chi-restraints excluded: chain H residue 792 LEU Chi-restraints excluded: chain I residue 39 ASN Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 367 ASP Chi-restraints excluded: chain I residue 412 ASN Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 449 THR Chi-restraints excluded: chain I residue 472 ASN Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain J residue 39 ASN Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 127 MET Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 219 LYS Chi-restraints excluded: chain J residue 345 ILE Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 449 THR Chi-restraints excluded: chain J residue 496 ASN Chi-restraints excluded: chain J residue 613 LEU Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 354 ASP Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 472 ASN Chi-restraints excluded: chain K residue 513 ASN Chi-restraints excluded: chain K residue 613 LEU Chi-restraints excluded: chain L residue 39 ASN Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 156 ASP Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain L residue 345 ILE Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 412 ASN Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 472 ASN Chi-restraints excluded: chain L residue 613 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 536 optimal weight: 6.9990 chunk 346 optimal weight: 9.9990 chunk 518 optimal weight: 7.9990 chunk 261 optimal weight: 20.0000 chunk 170 optimal weight: 20.0000 chunk 168 optimal weight: 1.9990 chunk 551 optimal weight: 1.9990 chunk 590 optimal weight: 30.0000 chunk 428 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 chunk 681 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 ASN ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 513 ASN ** H 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 69840 Z= 0.273 Angle : 0.647 10.442 94584 Z= 0.338 Chirality : 0.048 0.174 10620 Planarity : 0.003 0.030 12396 Dihedral : 6.378 40.563 9528 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 21.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.27 % Favored : 82.73 % Rotamer: Outliers : 3.40 % Allowed : 11.60 % Favored : 84.99 % 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: -4.67 (0.08), residues: 8952 helix: -2.26 (0.29), residues: 264 sheet: -3.78 (0.09), residues: 2388 loop : -3.05 (0.07), residues: 6300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 577 HIS 0.004 0.001 HIS K 385 PHE 0.016 0.001 PHE B 57 TYR 0.013 0.001 TYR D 529 ARG 0.004 0.000 ARG J 361 *********************** 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 421 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 169 time to evaluate : 6.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 THR cc_start: 0.6533 (OUTLIER) cc_final: 0.6252 (t) REVERT: A 168 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7175 (tp) REVERT: A 609 MET cc_start: 0.8101 (mpp) cc_final: 0.7633 (mpp) REVERT: A 658 ASN cc_start: 0.8720 (t0) cc_final: 0.8417 (m-40) REVERT: A 662 MET cc_start: 0.7121 (mtp) cc_final: 0.6464 (mpp) REVERT: A 663 MET cc_start: 0.8534 (ttt) cc_final: 0.8265 (tmm) REVERT: B 354 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.7225 (t0) REVERT: B 430 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7892 (pp) REVERT: B 609 MET cc_start: 0.8744 (ttt) cc_final: 0.8500 (mtm) REVERT: B 621 MET cc_start: 0.8786 (mtt) cc_final: 0.8453 (mmm) REVERT: B 663 MET cc_start: 0.8539 (ttt) cc_final: 0.8318 (tmm) REVERT: B 792 LEU cc_start: 0.9698 (OUTLIER) cc_final: 0.9445 (mp) REVERT: C 67 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7951 (tm) REVERT: C 609 MET cc_start: 0.8759 (ttt) cc_final: 0.8539 (mtm) REVERT: C 621 MET cc_start: 0.8891 (mtt) cc_final: 0.8492 (mmm) REVERT: C 658 ASN cc_start: 0.8554 (t0) cc_final: 0.8134 (t0) REVERT: C 663 MET cc_start: 0.8784 (ttt) cc_final: 0.8372 (tmm) REVERT: C 751 MET cc_start: 0.9430 (mmm) cc_final: 0.9166 (tpp) REVERT: D 143 THR cc_start: 0.6529 (OUTLIER) cc_final: 0.6227 (t) REVERT: D 168 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7191 (tp) REVERT: D 609 MET cc_start: 0.8741 (ttt) cc_final: 0.8466 (mpp) REVERT: D 658 ASN cc_start: 0.8720 (t0) cc_final: 0.8373 (t0) REVERT: D 663 MET cc_start: 0.8541 (ttt) cc_final: 0.8225 (tmm) REVERT: E 354 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7306 (t0) REVERT: E 609 MET cc_start: 0.7953 (mtm) cc_final: 0.7283 (mpp) REVERT: E 621 MET cc_start: 0.8827 (mtt) cc_final: 0.8429 (mmm) REVERT: E 658 ASN cc_start: 0.8520 (t0) cc_final: 0.8284 (m-40) REVERT: E 663 MET cc_start: 0.8635 (ttt) cc_final: 0.8414 (tmm) REVERT: F 67 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7938 (tm) REVERT: F 609 MET cc_start: 0.8754 (ttt) cc_final: 0.8537 (mtm) REVERT: F 621 MET cc_start: 0.8894 (mtt) cc_final: 0.8495 (mmm) REVERT: F 658 ASN cc_start: 0.8587 (t0) cc_final: 0.8170 (t0) REVERT: F 663 MET cc_start: 0.8763 (ttt) cc_final: 0.8371 (tmm) REVERT: G 143 THR cc_start: 0.6538 (OUTLIER) cc_final: 0.6246 (t) REVERT: G 168 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7130 (tp) REVERT: G 609 MET cc_start: 0.8741 (ttt) cc_final: 0.8467 (mpp) REVERT: G 658 ASN cc_start: 0.8714 (t0) cc_final: 0.8371 (t0) REVERT: G 663 MET cc_start: 0.8531 (ttt) cc_final: 0.8219 (tmm) REVERT: H 354 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.7229 (t0) REVERT: H 621 MET cc_start: 0.8198 (mmm) cc_final: 0.7715 (mmm) REVERT: H 663 MET cc_start: 0.8588 (ttt) cc_final: 0.8361 (tmm) REVERT: H 792 LEU cc_start: 0.9700 (OUTLIER) cc_final: 0.9448 (mp) REVERT: I 67 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7890 (tm) REVERT: I 609 MET cc_start: 0.8750 (ttt) cc_final: 0.8533 (mtm) REVERT: I 621 MET cc_start: 0.8896 (mtt) cc_final: 0.8479 (mmm) REVERT: I 658 ASN cc_start: 0.8557 (t0) cc_final: 0.8138 (t0) REVERT: I 663 MET cc_start: 0.8780 (ttt) cc_final: 0.8363 (tmm) REVERT: I 751 MET cc_start: 0.9431 (mmm) cc_final: 0.9166 (tpp) REVERT: J 143 THR cc_start: 0.6483 (OUTLIER) cc_final: 0.6173 (t) REVERT: J 609 MET cc_start: 0.8778 (ttt) cc_final: 0.8494 (mpp) REVERT: J 658 ASN cc_start: 0.8702 (t0) cc_final: 0.8393 (m-40) REVERT: J 663 MET cc_start: 0.7988 (tmm) cc_final: 0.7752 (tmm) REVERT: K 354 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7290 (t0) REVERT: K 662 MET cc_start: 0.6771 (mtp) cc_final: 0.6188 (mpp) REVERT: K 663 MET cc_start: 0.8554 (ttt) cc_final: 0.8231 (tmm) REVERT: L 67 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7939 (tm) REVERT: L 609 MET cc_start: 0.8755 (ttt) cc_final: 0.8537 (mtm) REVERT: L 621 MET cc_start: 0.8853 (mtt) cc_final: 0.8426 (mmm) REVERT: L 658 ASN cc_start: 0.8546 (t0) cc_final: 0.8130 (t0) REVERT: L 663 MET cc_start: 0.8771 (ttt) cc_final: 0.8361 (tmm) outliers start: 252 outliers final: 185 residues processed: 413 average time/residue: 0.5862 time to fit residues: 446.5612 Evaluate side-chains 359 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 156 time to evaluate : 5.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 513 ASN Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 412 ASN Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain C residue 496 ASN Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain D residue 39 ASN Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 358 ASN Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 382 ASN Chi-restraints excluded: chain D residue 412 ASN Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 496 ASN Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 628 ASN Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 354 ASP Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 472 ASN Chi-restraints excluded: chain E residue 496 ASN Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain E residue 628 ASN Chi-restraints excluded: chain F residue 39 ASN Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 412 ASN Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 472 ASN Chi-restraints excluded: chain F residue 496 ASN Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 613 LEU Chi-restraints excluded: chain F residue 628 ASN Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 367 ASP Chi-restraints excluded: chain G residue 382 ASN Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 449 THR Chi-restraints excluded: chain G residue 496 ASN Chi-restraints excluded: chain G residue 613 LEU Chi-restraints excluded: chain G residue 628 ASN Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain H residue 354 ASP Chi-restraints excluded: chain H residue 367 ASP Chi-restraints excluded: chain H residue 382 ASN Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 472 ASN Chi-restraints excluded: chain H residue 496 ASN Chi-restraints excluded: chain H residue 513 ASN Chi-restraints excluded: chain H residue 559 VAL Chi-restraints excluded: chain H residue 613 LEU Chi-restraints excluded: chain H residue 628 ASN Chi-restraints excluded: chain H residue 792 LEU Chi-restraints excluded: chain I residue 39 ASN Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 156 ASP Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 367 ASP Chi-restraints excluded: chain I residue 412 ASN Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 449 THR Chi-restraints excluded: chain I residue 472 ASN Chi-restraints excluded: chain I residue 496 ASN Chi-restraints excluded: chain I residue 559 VAL Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 628 ASN Chi-restraints excluded: chain J residue 39 ASN Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 127 MET Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 219 LYS Chi-restraints excluded: chain J residue 345 ILE Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 382 ASN Chi-restraints excluded: chain J residue 412 ASN Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 449 THR Chi-restraints excluded: chain J residue 496 ASN Chi-restraints excluded: chain J residue 613 LEU Chi-restraints excluded: chain J residue 628 ASN Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 185 THR Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 354 ASP Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 472 ASN Chi-restraints excluded: chain K residue 496 ASN Chi-restraints excluded: chain K residue 613 LEU Chi-restraints excluded: chain K residue 628 ASN Chi-restraints excluded: chain L residue 39 ASN Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain L residue 345 ILE Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 412 ASN Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 472 ASN Chi-restraints excluded: chain L residue 496 ASN Chi-restraints excluded: chain L residue 559 VAL Chi-restraints excluded: chain L residue 613 LEU Chi-restraints excluded: chain L residue 628 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 789 optimal weight: 9.9990 chunk 831 optimal weight: 7.9990 chunk 758 optimal weight: 9.9990 chunk 808 optimal weight: 20.0000 chunk 830 optimal weight: 5.9990 chunk 486 optimal weight: 8.9990 chunk 352 optimal weight: 7.9990 chunk 634 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 730 optimal weight: 30.0000 chunk 764 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 GLN ** E 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 GLN ** F 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 GLN ** H 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 GLN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 136 GLN ** K 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 69840 Z= 0.514 Angle : 0.841 14.929 94584 Z= 0.447 Chirality : 0.054 0.197 10620 Planarity : 0.005 0.030 12396 Dihedral : 7.624 44.249 9528 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 30.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.54 % Favored : 76.46 % Rotamer: Outliers : 3.47 % Allowed : 12.34 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -5.01 (0.08), residues: 8952 helix: -2.14 (0.25), residues: 372 sheet: -4.14 (0.09), residues: 2388 loop : -3.25 (0.07), residues: 6192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 577 HIS 0.008 0.002 HIS B 385 PHE 0.023 0.002 PHE H 57 TYR 0.020 0.002 TYR H 298 ARG 0.007 0.001 ARG C 133 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 152 time to evaluate : 5.839 Fit side-chains REVERT: A 143 THR cc_start: 0.6497 (OUTLIER) cc_final: 0.6050 (t) REVERT: A 658 ASN cc_start: 0.8778 (t0) cc_final: 0.8525 (m-40) REVERT: A 662 MET cc_start: 0.7395 (mtp) cc_final: 0.6729 (mpp) REVERT: A 663 MET cc_start: 0.8475 (ttt) cc_final: 0.8194 (tmm) REVERT: B 354 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7247 (t0) REVERT: B 609 MET cc_start: 0.8726 (ttt) cc_final: 0.8515 (mtm) REVERT: B 621 MET cc_start: 0.8889 (mtt) cc_final: 0.8403 (mmm) REVERT: B 663 MET cc_start: 0.8447 (ttt) cc_final: 0.8148 (tmm) REVERT: B 751 MET cc_start: 0.8302 (tmm) cc_final: 0.8029 (ppp) REVERT: B 792 LEU cc_start: 0.9709 (OUTLIER) cc_final: 0.9465 (mp) REVERT: C 67 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8045 (tm) REVERT: C 609 MET cc_start: 0.8642 (ttt) cc_final: 0.8405 (mtm) REVERT: C 621 MET cc_start: 0.8983 (mtt) cc_final: 0.8490 (mmm) REVERT: C 658 ASN cc_start: 0.8571 (t0) cc_final: 0.8180 (t0) REVERT: C 663 MET cc_start: 0.8666 (ttt) cc_final: 0.8281 (tmm) REVERT: C 751 MET cc_start: 0.9341 (mmm) cc_final: 0.9069 (tpp) REVERT: D 143 THR cc_start: 0.6495 (OUTLIER) cc_final: 0.6084 (t) REVERT: D 609 MET cc_start: 0.8722 (ttt) cc_final: 0.8461 (mpp) REVERT: D 621 MET cc_start: 0.8933 (mtt) cc_final: 0.8282 (mpp) REVERT: D 658 ASN cc_start: 0.8779 (t0) cc_final: 0.8521 (m-40) REVERT: D 663 MET cc_start: 0.8504 (ttt) cc_final: 0.8229 (tmm) REVERT: E 354 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7221 (t0) REVERT: E 609 MET cc_start: 0.7998 (mtm) cc_final: 0.7325 (mpp) REVERT: E 621 MET cc_start: 0.8870 (mtt) cc_final: 0.8419 (mmm) REVERT: E 663 MET cc_start: 0.8661 (ttt) cc_final: 0.8375 (tmm) REVERT: F 67 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8024 (tm) REVERT: F 621 MET cc_start: 0.8987 (mtt) cc_final: 0.8495 (mmm) REVERT: F 658 ASN cc_start: 0.8562 (t0) cc_final: 0.8172 (t0) REVERT: F 663 MET cc_start: 0.8655 (ttt) cc_final: 0.8324 (tmm) REVERT: G 143 THR cc_start: 0.6491 (OUTLIER) cc_final: 0.6081 (t) REVERT: G 609 MET cc_start: 0.8659 (ttt) cc_final: 0.8456 (mpp) REVERT: G 621 MET cc_start: 0.8935 (mtt) cc_final: 0.8286 (mpp) REVERT: G 658 ASN cc_start: 0.8773 (t0) cc_final: 0.8515 (m-40) REVERT: G 663 MET cc_start: 0.8492 (ttt) cc_final: 0.8223 (tmm) REVERT: H 354 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.7184 (t0) REVERT: H 609 MET cc_start: 0.8160 (mtm) cc_final: 0.7165 (mpp) REVERT: H 621 MET cc_start: 0.8239 (mmm) cc_final: 0.7839 (mmm) REVERT: H 663 MET cc_start: 0.8441 (ttt) cc_final: 0.8147 (tmm) REVERT: H 751 MET cc_start: 0.8304 (tmm) cc_final: 0.8031 (ppp) REVERT: H 792 LEU cc_start: 0.9734 (OUTLIER) cc_final: 0.9498 (mp) REVERT: I 67 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8023 (tm) REVERT: I 609 MET cc_start: 0.8633 (ttt) cc_final: 0.8398 (mtm) REVERT: I 621 MET cc_start: 0.8984 (mtt) cc_final: 0.8495 (mmm) REVERT: I 658 ASN cc_start: 0.8573 (t0) cc_final: 0.8181 (t0) REVERT: I 663 MET cc_start: 0.8670 (ttt) cc_final: 0.8334 (tmm) REVERT: I 751 MET cc_start: 0.9341 (mmm) cc_final: 0.9069 (tpp) REVERT: J 143 THR cc_start: 0.6485 (OUTLIER) cc_final: 0.6047 (t) REVERT: J 658 ASN cc_start: 0.8776 (t0) cc_final: 0.8525 (m-40) REVERT: K 354 ASP cc_start: 0.7543 (OUTLIER) cc_final: 0.7232 (t0) REVERT: K 609 MET cc_start: 0.8078 (mtm) cc_final: 0.7048 (mpp) REVERT: K 663 MET cc_start: 0.8677 (ttt) cc_final: 0.8423 (tmm) REVERT: L 67 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8025 (tm) REVERT: L 609 MET cc_start: 0.8646 (ttt) cc_final: 0.8403 (mtm) REVERT: L 621 MET cc_start: 0.8988 (mtt) cc_final: 0.8509 (mmm) REVERT: L 658 ASN cc_start: 0.8564 (t0) cc_final: 0.8174 (t0) REVERT: L 663 MET cc_start: 0.8658 (ttt) cc_final: 0.8278 (tmm) outliers start: 257 outliers final: 210 residues processed: 400 average time/residue: 0.5464 time to fit residues: 407.6543 Evaluate side-chains 376 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 152 time to evaluate : 5.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain C residue 496 ASN Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain D residue 39 ASN Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 382 ASN Chi-restraints excluded: chain D residue 412 ASN Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 496 ASN Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 628 ASN Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 221 ASN Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 354 ASP Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 382 ASN Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 472 ASN Chi-restraints excluded: chain E residue 496 ASN Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain E residue 628 ASN Chi-restraints excluded: chain F residue 39 ASN Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 472 ASN Chi-restraints excluded: chain F residue 496 ASN Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 613 LEU Chi-restraints excluded: chain F residue 628 ASN Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 219 LYS Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 367 ASP Chi-restraints excluded: chain G residue 382 ASN Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain G residue 416 ASP Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 449 THR Chi-restraints excluded: chain G residue 496 ASN Chi-restraints excluded: chain G residue 613 LEU Chi-restraints excluded: chain G residue 628 ASN Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 221 ASN Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain H residue 354 ASP Chi-restraints excluded: chain H residue 367 ASP Chi-restraints excluded: chain H residue 382 ASN Chi-restraints excluded: chain H residue 412 ASN Chi-restraints excluded: chain H residue 416 ASP Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 472 ASN Chi-restraints excluded: chain H residue 496 ASN Chi-restraints excluded: chain H residue 559 VAL Chi-restraints excluded: chain H residue 613 LEU Chi-restraints excluded: chain H residue 628 ASN Chi-restraints excluded: chain H residue 792 LEU Chi-restraints excluded: chain I residue 39 ASN Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 102 ASP Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 156 ASP Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 367 ASP Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 449 THR Chi-restraints excluded: chain I residue 472 ASN Chi-restraints excluded: chain I residue 496 ASN Chi-restraints excluded: chain I residue 559 VAL Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 628 ASN Chi-restraints excluded: chain J residue 39 ASN Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 219 LYS Chi-restraints excluded: chain J residue 345 ILE Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 382 ASN Chi-restraints excluded: chain J residue 412 ASN Chi-restraints excluded: chain J residue 416 ASP Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 449 THR Chi-restraints excluded: chain J residue 496 ASN Chi-restraints excluded: chain J residue 613 LEU Chi-restraints excluded: chain J residue 628 ASN Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 185 THR Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 221 ASN Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 354 ASP Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 382 ASN Chi-restraints excluded: chain K residue 416 ASP Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 449 THR Chi-restraints excluded: chain K residue 472 ASN Chi-restraints excluded: chain K residue 496 ASN Chi-restraints excluded: chain K residue 613 LEU Chi-restraints excluded: chain K residue 628 ASN Chi-restraints excluded: chain L residue 39 ASN Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 99 LEU Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain L residue 345 ILE Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 472 ASN Chi-restraints excluded: chain L residue 496 ASN Chi-restraints excluded: chain L residue 559 VAL Chi-restraints excluded: chain L residue 613 LEU Chi-restraints excluded: chain L residue 628 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 805 optimal weight: 20.0000 chunk 530 optimal weight: 10.0000 chunk 854 optimal weight: 2.9990 chunk 521 optimal weight: 40.0000 chunk 405 optimal weight: 6.9990 chunk 594 optimal weight: 50.0000 chunk 896 optimal weight: 7.9990 chunk 825 optimal weight: 0.9990 chunk 713 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 551 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 69840 Z= 0.309 Angle : 0.695 12.112 94584 Z= 0.364 Chirality : 0.049 0.189 10620 Planarity : 0.003 0.033 12396 Dihedral : 6.845 41.547 9528 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 24.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.57 % Favored : 83.43 % Rotamer: Outliers : 3.15 % Allowed : 12.82 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.82 (0.08), residues: 8952 helix: -2.12 (0.28), residues: 336 sheet: -4.00 (0.09), residues: 2412 loop : -3.11 (0.07), residues: 6204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 577 HIS 0.004 0.001 HIS E 385 PHE 0.016 0.002 PHE B 57 TYR 0.012 0.002 TYR G 298 ARG 0.005 0.001 ARG F 361 ********************** 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 391 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 158 time to evaluate : 5.900 Fit side-chains REVERT: A 143 THR cc_start: 0.6360 (OUTLIER) cc_final: 0.5971 (t) REVERT: A 609 MET cc_start: 0.8162 (mpp) cc_final: 0.7758 (mpp) REVERT: A 658 ASN cc_start: 0.8777 (t0) cc_final: 0.8532 (m-40) REVERT: A 662 MET cc_start: 0.7357 (mtp) cc_final: 0.6676 (mpp) REVERT: A 663 MET cc_start: 0.8409 (ttt) cc_final: 0.8155 (tmm) REVERT: A 751 MET cc_start: 0.9427 (mmm) cc_final: 0.9154 (tpp) REVERT: B 354 ASP cc_start: 0.7693 (OUTLIER) cc_final: 0.7255 (t0) REVERT: B 609 MET cc_start: 0.8762 (ttt) cc_final: 0.8515 (mtm) REVERT: B 621 MET cc_start: 0.8774 (mtt) cc_final: 0.8397 (mmm) REVERT: B 751 MET cc_start: 0.8312 (tmm) cc_final: 0.8029 (ppp) REVERT: B 792 LEU cc_start: 0.9755 (OUTLIER) cc_final: 0.9551 (mp) REVERT: C 67 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7968 (tm) REVERT: C 609 MET cc_start: 0.8722 (ttt) cc_final: 0.8445 (mtm) REVERT: C 621 MET cc_start: 0.8884 (mtt) cc_final: 0.8429 (mmm) REVERT: C 658 ASN cc_start: 0.8560 (t0) cc_final: 0.8183 (t0) REVERT: C 663 MET cc_start: 0.8660 (ttt) cc_final: 0.8279 (tmm) REVERT: C 751 MET cc_start: 0.9341 (mmm) cc_final: 0.9066 (tpp) REVERT: D 143 THR cc_start: 0.6366 (OUTLIER) cc_final: 0.5959 (t) REVERT: D 609 MET cc_start: 0.8733 (ttt) cc_final: 0.8498 (mpp) REVERT: D 621 MET cc_start: 0.8887 (mtt) cc_final: 0.8261 (mpp) REVERT: D 658 ASN cc_start: 0.8749 (t0) cc_final: 0.8472 (m-40) REVERT: D 663 MET cc_start: 0.8501 (ttt) cc_final: 0.8230 (tmm) REVERT: E 354 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7170 (t0) REVERT: E 609 MET cc_start: 0.7988 (mtm) cc_final: 0.7305 (mpp) REVERT: E 621 MET cc_start: 0.8807 (mtt) cc_final: 0.8386 (mmm) REVERT: E 663 MET cc_start: 0.8592 (ttt) cc_final: 0.8269 (tmm) REVERT: F 67 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8021 (tm) REVERT: F 609 MET cc_start: 0.8043 (mtm) cc_final: 0.7521 (mpp) REVERT: F 621 MET cc_start: 0.8886 (mtt) cc_final: 0.8433 (mmm) REVERT: F 658 ASN cc_start: 0.8554 (t0) cc_final: 0.8163 (t0) REVERT: F 663 MET cc_start: 0.8696 (ttt) cc_final: 0.8312 (tmm) REVERT: G 143 THR cc_start: 0.6375 (OUTLIER) cc_final: 0.5975 (t) REVERT: G 226 MET cc_start: 0.7856 (ttp) cc_final: 0.7620 (ttt) REVERT: G 609 MET cc_start: 0.8731 (ttt) cc_final: 0.8498 (mpp) REVERT: G 621 MET cc_start: 0.8888 (mtt) cc_final: 0.8265 (mpp) REVERT: G 658 ASN cc_start: 0.8744 (t0) cc_final: 0.8467 (m-40) REVERT: G 663 MET cc_start: 0.8450 (ttt) cc_final: 0.8168 (tmm) REVERT: H 354 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7229 (t0) REVERT: H 609 MET cc_start: 0.8087 (mtm) cc_final: 0.7095 (mpp) REVERT: H 621 MET cc_start: 0.8264 (mmm) cc_final: 0.7872 (mmm) REVERT: H 751 MET cc_start: 0.8311 (tmm) cc_final: 0.8028 (ppp) REVERT: H 792 LEU cc_start: 0.9751 (OUTLIER) cc_final: 0.9541 (mp) REVERT: I 67 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7888 (tm) REVERT: I 609 MET cc_start: 0.8715 (ttt) cc_final: 0.8440 (mtm) REVERT: I 621 MET cc_start: 0.8865 (mtt) cc_final: 0.8406 (mmm) REVERT: I 658 ASN cc_start: 0.8559 (t0) cc_final: 0.8180 (t0) REVERT: I 663 MET cc_start: 0.8660 (ttt) cc_final: 0.8278 (tmm) REVERT: I 751 MET cc_start: 0.9342 (mmm) cc_final: 0.9067 (tpp) REVERT: J 143 THR cc_start: 0.6303 (OUTLIER) cc_final: 0.5853 (t) REVERT: J 358 ASN cc_start: 0.8297 (OUTLIER) cc_final: 0.8090 (m-40) REVERT: J 658 ASN cc_start: 0.8762 (t0) cc_final: 0.8514 (m-40) REVERT: J 662 MET cc_start: 0.7360 (mtp) cc_final: 0.6835 (mtt) REVERT: K 354 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7217 (t0) REVERT: K 609 MET cc_start: 0.7944 (mtm) cc_final: 0.6930 (mpp) REVERT: K 663 MET cc_start: 0.8672 (ttt) cc_final: 0.8422 (tmm) REVERT: L 67 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8023 (tm) REVERT: L 609 MET cc_start: 0.8718 (ttt) cc_final: 0.8443 (mtm) REVERT: L 621 MET cc_start: 0.8872 (mtt) cc_final: 0.8418 (mmm) REVERT: L 658 ASN cc_start: 0.8550 (t0) cc_final: 0.8174 (t0) REVERT: L 663 MET cc_start: 0.8651 (ttt) cc_final: 0.8275 (tmm) outliers start: 233 outliers final: 201 residues processed: 382 average time/residue: 0.5428 time to fit residues: 386.5835 Evaluate side-chains 371 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 155 time to evaluate : 5.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 412 ASN Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain C residue 496 ASN Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain D residue 39 ASN Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 382 ASN Chi-restraints excluded: chain D residue 412 ASN Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 496 ASN Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 628 ASN Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 354 ASP Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 412 ASN Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 472 ASN Chi-restraints excluded: chain E residue 496 ASN Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain E residue 628 ASN Chi-restraints excluded: chain F residue 39 ASN Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 412 ASN Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 472 ASN Chi-restraints excluded: chain F residue 496 ASN Chi-restraints excluded: chain F residue 613 LEU Chi-restraints excluded: chain F residue 628 ASN Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 219 LYS Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 367 ASP Chi-restraints excluded: chain G residue 382 ASN Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain G residue 416 ASP Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 449 THR Chi-restraints excluded: chain G residue 496 ASN Chi-restraints excluded: chain G residue 613 LEU Chi-restraints excluded: chain G residue 628 ASN Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain H residue 354 ASP Chi-restraints excluded: chain H residue 367 ASP Chi-restraints excluded: chain H residue 382 ASN Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 472 ASN Chi-restraints excluded: chain H residue 496 ASN Chi-restraints excluded: chain H residue 559 VAL Chi-restraints excluded: chain H residue 613 LEU Chi-restraints excluded: chain H residue 628 ASN Chi-restraints excluded: chain H residue 792 LEU Chi-restraints excluded: chain I residue 39 ASN Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 156 ASP Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 367 ASP Chi-restraints excluded: chain I residue 412 ASN Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 449 THR Chi-restraints excluded: chain I residue 472 ASN Chi-restraints excluded: chain I residue 496 ASN Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 628 ASN Chi-restraints excluded: chain J residue 39 ASN Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 219 LYS Chi-restraints excluded: chain J residue 345 ILE Chi-restraints excluded: chain J residue 358 ASN Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 382 ASN Chi-restraints excluded: chain J residue 412 ASN Chi-restraints excluded: chain J residue 416 ASP Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 449 THR Chi-restraints excluded: chain J residue 496 ASN Chi-restraints excluded: chain J residue 613 LEU Chi-restraints excluded: chain J residue 628 ASN Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 185 THR Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 354 ASP Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 382 ASN Chi-restraints excluded: chain K residue 416 ASP Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 449 THR Chi-restraints excluded: chain K residue 472 ASN Chi-restraints excluded: chain K residue 496 ASN Chi-restraints excluded: chain K residue 613 LEU Chi-restraints excluded: chain K residue 628 ASN Chi-restraints excluded: chain L residue 39 ASN Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 99 LEU Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain L residue 345 ILE Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 412 ASN Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 472 ASN Chi-restraints excluded: chain L residue 496 ASN Chi-restraints excluded: chain L residue 613 LEU Chi-restraints excluded: chain L residue 628 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 437 optimal weight: 0.0770 chunk 567 optimal weight: 9.9990 chunk 760 optimal weight: 10.0000 chunk 218 optimal weight: 0.5980 chunk 658 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 198 optimal weight: 9.9990 chunk 715 optimal weight: 9.9990 chunk 299 optimal weight: 30.0000 chunk 734 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 overall best weight: 3.7344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.080499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.044790 restraints weight = 218303.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.046251 restraints weight = 129148.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.047203 restraints weight = 95557.912| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 69840 Z= 0.261 Angle : 0.656 11.565 94584 Z= 0.340 Chirality : 0.048 0.176 10620 Planarity : 0.003 0.025 12396 Dihedral : 6.458 40.484 9528 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 22.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.44 % Favored : 82.56 % Rotamer: Outliers : 3.07 % Allowed : 13.10 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.67 (0.08), residues: 8952 helix: -2.04 (0.28), residues: 336 sheet: -3.81 (0.09), residues: 2292 loop : -3.07 (0.07), residues: 6324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 577 HIS 0.003 0.001 HIS B 385 PHE 0.014 0.001 PHE B 57 TYR 0.010 0.001 TYR F 298 ARG 0.004 0.000 ARG A 361 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9795.01 seconds wall clock time: 178 minutes 59.52 seconds (10739.52 seconds total)