Starting phenix.real_space_refine on Thu Sep 26 04:21:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyb_0089/09_2024/6gyb_0089.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyb_0089/09_2024/6gyb_0089.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyb_0089/09_2024/6gyb_0089.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyb_0089/09_2024/6gyb_0089.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyb_0089/09_2024/6gyb_0089.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyb_0089/09_2024/6gyb_0089.cif" } resolution = 3.28 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= 0.001 sd= 0.009 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 168 5.16 5 C 37758 2.51 5 N 10122 2.21 5 O 11270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 196 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 59318 Number of models: 1 Model: "" Number of chains: 42 Chain: "a" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 842 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 9, 'TRANS': 101} Chain: "b" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1840 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain breaks: 1 Chain: "c" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1555 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 13, 'TRANS': 191} Chain breaks: 2 Chain: "d" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 842 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 9, 'TRANS': 101} Chain: "e" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1840 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain breaks: 1 Chain: "f" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1555 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 13, 'TRANS': 191} Chain breaks: 2 Chain: "g" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 842 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 9, 'TRANS': 101} Chain: "h" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1840 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain breaks: 1 Chain: "i" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1555 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 13, 'TRANS': 191} Chain breaks: 2 Chain: "j" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 842 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 9, 'TRANS': 101} Chain: "k" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1840 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain breaks: 1 Chain: "l" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1555 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 13, 'TRANS': 191} Chain breaks: 2 Chain: "m" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 842 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 9, 'TRANS': 101} Chain: "n" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1840 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain breaks: 1 Chain: "o" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1555 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 13, 'TRANS': 191} Chain breaks: 2 Chain: "p" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 842 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 9, 'TRANS': 101} Chain: "q" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1840 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain breaks: 1 Chain: "r" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1555 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 13, 'TRANS': 191} Chain breaks: 2 Chain: "s" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 842 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 9, 'TRANS': 101} Chain: "t" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1840 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain breaks: 1 Chain: "u" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1555 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 13, 'TRANS': 191} Chain breaks: 2 Chain: "A" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 842 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 9, 'TRANS': 101} Chain: "B" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1840 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain breaks: 1 Chain: "C" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1555 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 13, 'TRANS': 191} Chain breaks: 2 Chain: "D" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 842 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 9, 'TRANS': 101} Chain: "E" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1840 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain breaks: 1 Chain: "F" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1555 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 13, 'TRANS': 191} Chain breaks: 2 Chain: "G" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 842 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 9, 'TRANS': 101} Chain: "H" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1840 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain breaks: 1 Chain: "I" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1555 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 13, 'TRANS': 191} Chain breaks: 2 Chain: "J" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 842 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 9, 'TRANS': 101} Chain: "K" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1840 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain breaks: 1 Chain: "L" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1555 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 13, 'TRANS': 191} Chain breaks: 2 Chain: "M" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 842 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 9, 'TRANS': 101} Chain: "N" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1840 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain breaks: 1 Chain: "O" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1555 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 13, 'TRANS': 191} Chain breaks: 2 Chain: "P" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 842 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 9, 'TRANS': 101} Chain: "Q" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1840 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain breaks: 1 Chain: "R" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1555 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 13, 'TRANS': 191} Chain breaks: 2 Chain: "S" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 842 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 9, 'TRANS': 101} Chain: "T" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1840 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain breaks: 1 Chain: "U" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1555 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 13, 'TRANS': 191} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 42 residue: pdb=" N SER a 122 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER a 122 " occ=0.50 residue: pdb=" N ALA a 123 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA a 123 " occ=0.50 residue: pdb=" N ASN a 124 " occ=0.50 ... (6 atoms not shown) pdb=" ND2 ASN a 124 " occ=0.50 residue: pdb=" N SER d 122 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER d 122 " occ=0.50 residue: pdb=" N ALA d 123 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA d 123 " occ=0.50 residue: pdb=" N ASN d 124 " occ=0.50 ... (6 atoms not shown) pdb=" ND2 ASN d 124 " occ=0.50 residue: pdb=" N SER g 122 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER g 122 " occ=0.50 residue: pdb=" N ALA g 123 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA g 123 " occ=0.50 residue: pdb=" N ASN g 124 " occ=0.50 ... (6 atoms not shown) pdb=" ND2 ASN g 124 " occ=0.50 residue: pdb=" N SER j 122 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER j 122 " occ=0.50 residue: pdb=" N ALA j 123 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA j 123 " occ=0.50 residue: pdb=" N ASN j 124 " occ=0.50 ... (6 atoms not shown) pdb=" ND2 ASN j 124 " occ=0.50 ... (remaining 30 not shown) Time building chain proxies: 25.09, per 1000 atoms: 0.42 Number of scatterers: 59318 At special positions: 0 Unit cell: (246.98, 242.74, 133.56, 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 168 16.00 O 11270 8.00 N 10122 7.00 C 37758 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS c 206 " - pdb=" SG CYS c 222 " distance=2.03 Simple disulfide: pdb=" SG CYS f 206 " - pdb=" SG CYS f 222 " distance=2.03 Simple disulfide: pdb=" SG CYS i 206 " - pdb=" SG CYS i 222 " distance=2.03 Simple disulfide: pdb=" SG CYS l 206 " - pdb=" SG CYS l 222 " distance=2.03 Simple disulfide: pdb=" SG CYS o 206 " - pdb=" SG CYS o 222 " distance=2.03 Simple disulfide: pdb=" SG CYS r 206 " - pdb=" SG CYS r 222 " distance=2.03 Simple disulfide: pdb=" SG CYS u 206 " - pdb=" SG CYS u 222 " distance=2.03 Simple disulfide: pdb=" SG CYS C 206 " - pdb=" SG CYS C 222 " distance=2.03 Simple disulfide: pdb=" SG CYS F 206 " - pdb=" SG CYS F 222 " distance=2.03 Simple disulfide: pdb=" SG CYS I 206 " - pdb=" SG CYS I 222 " distance=2.03 Simple disulfide: pdb=" SG CYS L 206 " - pdb=" SG CYS L 222 " distance=2.03 Simple disulfide: pdb=" SG CYS O 206 " - pdb=" SG CYS O 222 " distance=2.03 Simple disulfide: pdb=" SG CYS R 206 " - pdb=" SG CYS R 222 " distance=2.03 Simple disulfide: pdb=" SG CYS U 206 " - pdb=" SG CYS U 222 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 10.88 Conformation dependent library (CDL) restraints added in 5.8 seconds 14756 Ramachandran restraints generated. 7378 Oldfield, 0 Emsley, 7378 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14056 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 182 sheets defined 18.4% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.84 Creating SS restraints... Processing helix chain 'a' and resid 63 through 74 removed outlier: 3.628A pdb=" N ARG a 70 " --> pdb=" O THR a 66 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 94 Processing helix chain 'a' and resid 100 through 112 removed outlier: 3.599A pdb=" N VAL a 111 " --> pdb=" O GLU a 107 " (cutoff:3.500A) Processing helix chain 'b' and resid 67 through 69 No H-bonds generated for 'chain 'b' and resid 67 through 69' Processing helix chain 'b' and resid 116 through 123 removed outlier: 3.609A pdb=" N LYS b 120 " --> pdb=" O LEU b 116 " (cutoff:3.500A) Processing helix chain 'b' and resid 135 through 140 removed outlier: 3.533A pdb=" N ASN b 139 " --> pdb=" O ASP b 135 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN b 140 " --> pdb=" O THR b 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 135 through 140' Processing helix chain 'c' and resid 152 through 160 removed outlier: 3.515A pdb=" N LEU c 158 " --> pdb=" O GLU c 154 " (cutoff:3.500A) Processing helix chain 'c' and resid 295 through 319 removed outlier: 3.580A pdb=" N ILE c 300 " --> pdb=" O TRP c 296 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA c 301 " --> pdb=" O GLY c 297 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA c 303 " --> pdb=" O LYS c 299 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE c 305 " --> pdb=" O ALA c 301 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE c 306 " --> pdb=" O SER c 302 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER c 307 " --> pdb=" O ALA c 303 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE c 313 " --> pdb=" O LEU c 309 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU c 319 " --> pdb=" O TYR c 315 " (cutoff:3.500A) Processing helix chain 'c' and resid 342 through 359 removed outlier: 3.505A pdb=" N MET c 347 " --> pdb=" O THR c 343 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN c 348 " --> pdb=" O ALA c 344 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU c 350 " --> pdb=" O SER c 346 " (cutoff:3.500A) Processing helix chain 'd' and resid 63 through 74 removed outlier: 3.627A pdb=" N ARG d 70 " --> pdb=" O THR d 66 " (cutoff:3.500A) Processing helix chain 'd' and resid 90 through 94 Processing helix chain 'd' and resid 100 through 112 removed outlier: 3.598A pdb=" N VAL d 111 " --> pdb=" O GLU d 107 " (cutoff:3.500A) Processing helix chain 'e' and resid 67 through 69 No H-bonds generated for 'chain 'e' and resid 67 through 69' Processing helix chain 'e' and resid 116 through 123 removed outlier: 3.608A pdb=" N LYS e 120 " --> pdb=" O LEU e 116 " (cutoff:3.500A) Processing helix chain 'e' and resid 135 through 140 removed outlier: 3.534A pdb=" N ASN e 139 " --> pdb=" O ASP e 135 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN e 140 " --> pdb=" O THR e 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 135 through 140' Processing helix chain 'f' and resid 152 through 160 removed outlier: 3.514A pdb=" N LEU f 158 " --> pdb=" O GLU f 154 " (cutoff:3.500A) Processing helix chain 'f' and resid 295 through 319 removed outlier: 3.580A pdb=" N ILE f 300 " --> pdb=" O TRP f 296 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA f 301 " --> pdb=" O GLY f 297 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA f 303 " --> pdb=" O LYS f 299 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE f 305 " --> pdb=" O ALA f 301 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE f 306 " --> pdb=" O SER f 302 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER f 307 " --> pdb=" O ALA f 303 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE f 313 " --> pdb=" O LEU f 309 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU f 319 " --> pdb=" O TYR f 315 " (cutoff:3.500A) Processing helix chain 'f' and resid 342 through 359 removed outlier: 3.505A pdb=" N MET f 347 " --> pdb=" O THR f 343 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN f 348 " --> pdb=" O ALA f 344 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU f 350 " --> pdb=" O SER f 346 " (cutoff:3.500A) Processing helix chain 'g' and resid 63 through 74 removed outlier: 3.628A pdb=" N ARG g 70 " --> pdb=" O THR g 66 " (cutoff:3.500A) Processing helix chain 'g' and resid 90 through 94 Processing helix chain 'g' and resid 100 through 112 removed outlier: 3.598A pdb=" N VAL g 111 " --> pdb=" O GLU g 107 " (cutoff:3.500A) Processing helix chain 'h' and resid 67 through 69 No H-bonds generated for 'chain 'h' and resid 67 through 69' Processing helix chain 'h' and resid 116 through 123 removed outlier: 3.609A pdb=" N LYS h 120 " --> pdb=" O LEU h 116 " (cutoff:3.500A) Processing helix chain 'h' and resid 135 through 140 removed outlier: 3.534A pdb=" N ASN h 139 " --> pdb=" O ASP h 135 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN h 140 " --> pdb=" O THR h 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 135 through 140' Processing helix chain 'i' and resid 152 through 160 removed outlier: 3.514A pdb=" N LEU i 158 " --> pdb=" O GLU i 154 " (cutoff:3.500A) Processing helix chain 'i' and resid 295 through 319 removed outlier: 3.580A pdb=" N ILE i 300 " --> pdb=" O TRP i 296 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA i 301 " --> pdb=" O GLY i 297 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA i 303 " --> pdb=" O LYS i 299 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE i 305 " --> pdb=" O ALA i 301 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE i 306 " --> pdb=" O SER i 302 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER i 307 " --> pdb=" O ALA i 303 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE i 313 " --> pdb=" O LEU i 309 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU i 319 " --> pdb=" O TYR i 315 " (cutoff:3.500A) Processing helix chain 'i' and resid 342 through 359 removed outlier: 3.505A pdb=" N MET i 347 " --> pdb=" O THR i 343 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN i 348 " --> pdb=" O ALA i 344 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU i 350 " --> pdb=" O SER i 346 " (cutoff:3.500A) Processing helix chain 'j' and resid 63 through 74 removed outlier: 3.628A pdb=" N ARG j 70 " --> pdb=" O THR j 66 " (cutoff:3.500A) Processing helix chain 'j' and resid 90 through 94 Processing helix chain 'j' and resid 100 through 112 removed outlier: 3.599A pdb=" N VAL j 111 " --> pdb=" O GLU j 107 " (cutoff:3.500A) Processing helix chain 'k' and resid 67 through 69 No H-bonds generated for 'chain 'k' and resid 67 through 69' Processing helix chain 'k' and resid 116 through 123 removed outlier: 3.609A pdb=" N LYS k 120 " --> pdb=" O LEU k 116 " (cutoff:3.500A) Processing helix chain 'k' and resid 135 through 140 removed outlier: 3.534A pdb=" N ASN k 139 " --> pdb=" O ASP k 135 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN k 140 " --> pdb=" O THR k 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 135 through 140' Processing helix chain 'l' and resid 152 through 160 removed outlier: 3.514A pdb=" N LEU l 158 " --> pdb=" O GLU l 154 " (cutoff:3.500A) Processing helix chain 'l' and resid 295 through 319 removed outlier: 3.580A pdb=" N ILE l 300 " --> pdb=" O TRP l 296 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA l 301 " --> pdb=" O GLY l 297 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA l 303 " --> pdb=" O LYS l 299 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE l 305 " --> pdb=" O ALA l 301 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE l 306 " --> pdb=" O SER l 302 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER l 307 " --> pdb=" O ALA l 303 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE l 313 " --> pdb=" O LEU l 309 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU l 319 " --> pdb=" O TYR l 315 " (cutoff:3.500A) Processing helix chain 'l' and resid 342 through 359 removed outlier: 3.505A pdb=" N MET l 347 " --> pdb=" O THR l 343 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN l 348 " --> pdb=" O ALA l 344 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU l 350 " --> pdb=" O SER l 346 " (cutoff:3.500A) Processing helix chain 'm' and resid 63 through 74 removed outlier: 3.628A pdb=" N ARG m 70 " --> pdb=" O THR m 66 " (cutoff:3.500A) Processing helix chain 'm' and resid 90 through 94 Processing helix chain 'm' and resid 100 through 112 removed outlier: 3.599A pdb=" N VAL m 111 " --> pdb=" O GLU m 107 " (cutoff:3.500A) Processing helix chain 'n' and resid 67 through 69 No H-bonds generated for 'chain 'n' and resid 67 through 69' Processing helix chain 'n' and resid 116 through 123 removed outlier: 3.609A pdb=" N LYS n 120 " --> pdb=" O LEU n 116 " (cutoff:3.500A) Processing helix chain 'n' and resid 135 through 140 removed outlier: 3.533A pdb=" N ASN n 139 " --> pdb=" O ASP n 135 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN n 140 " --> pdb=" O THR n 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 135 through 140' Processing helix chain 'o' and resid 152 through 160 removed outlier: 3.514A pdb=" N LEU o 158 " --> pdb=" O GLU o 154 " (cutoff:3.500A) Processing helix chain 'o' and resid 295 through 319 removed outlier: 3.580A pdb=" N ILE o 300 " --> pdb=" O TRP o 296 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA o 301 " --> pdb=" O GLY o 297 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA o 303 " --> pdb=" O LYS o 299 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE o 305 " --> pdb=" O ALA o 301 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE o 306 " --> pdb=" O SER o 302 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER o 307 " --> pdb=" O ALA o 303 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE o 313 " --> pdb=" O LEU o 309 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU o 319 " --> pdb=" O TYR o 315 " (cutoff:3.500A) Processing helix chain 'o' and resid 342 through 359 removed outlier: 3.505A pdb=" N MET o 347 " --> pdb=" O THR o 343 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN o 348 " --> pdb=" O ALA o 344 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU o 350 " --> pdb=" O SER o 346 " (cutoff:3.500A) Processing helix chain 'p' and resid 63 through 74 removed outlier: 3.628A pdb=" N ARG p 70 " --> pdb=" O THR p 66 " (cutoff:3.500A) Processing helix chain 'p' and resid 90 through 94 Processing helix chain 'p' and resid 100 through 112 removed outlier: 3.598A pdb=" N VAL p 111 " --> pdb=" O GLU p 107 " (cutoff:3.500A) Processing helix chain 'q' and resid 67 through 69 No H-bonds generated for 'chain 'q' and resid 67 through 69' Processing helix chain 'q' and resid 116 through 123 removed outlier: 3.609A pdb=" N LYS q 120 " --> pdb=" O LEU q 116 " (cutoff:3.500A) Processing helix chain 'q' and resid 135 through 140 removed outlier: 3.534A pdb=" N ASN q 139 " --> pdb=" O ASP q 135 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN q 140 " --> pdb=" O THR q 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 135 through 140' Processing helix chain 'r' and resid 152 through 160 removed outlier: 3.514A pdb=" N LEU r 158 " --> pdb=" O GLU r 154 " (cutoff:3.500A) Processing helix chain 'r' and resid 295 through 319 removed outlier: 3.581A pdb=" N ILE r 300 " --> pdb=" O TRP r 296 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA r 301 " --> pdb=" O GLY r 297 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA r 303 " --> pdb=" O LYS r 299 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE r 305 " --> pdb=" O ALA r 301 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE r 306 " --> pdb=" O SER r 302 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER r 307 " --> pdb=" O ALA r 303 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE r 313 " --> pdb=" O LEU r 309 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU r 319 " --> pdb=" O TYR r 315 " (cutoff:3.500A) Processing helix chain 'r' and resid 342 through 359 removed outlier: 3.506A pdb=" N MET r 347 " --> pdb=" O THR r 343 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN r 348 " --> pdb=" O ALA r 344 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU r 350 " --> pdb=" O SER r 346 " (cutoff:3.500A) Processing helix chain 's' and resid 63 through 74 removed outlier: 3.627A pdb=" N ARG s 70 " --> pdb=" O THR s 66 " (cutoff:3.500A) Processing helix chain 's' and resid 90 through 94 Processing helix chain 's' and resid 100 through 112 removed outlier: 3.598A pdb=" N VAL s 111 " --> pdb=" O GLU s 107 " (cutoff:3.500A) Processing helix chain 't' and resid 67 through 69 No H-bonds generated for 'chain 't' and resid 67 through 69' Processing helix chain 't' and resid 116 through 123 removed outlier: 3.609A pdb=" N LYS t 120 " --> pdb=" O LEU t 116 " (cutoff:3.500A) Processing helix chain 't' and resid 135 through 140 removed outlier: 3.534A pdb=" N ASN t 139 " --> pdb=" O ASP t 135 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN t 140 " --> pdb=" O THR t 136 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 135 through 140' Processing helix chain 'u' and resid 152 through 160 removed outlier: 3.514A pdb=" N LEU u 158 " --> pdb=" O GLU u 154 " (cutoff:3.500A) Processing helix chain 'u' and resid 295 through 319 removed outlier: 3.581A pdb=" N ILE u 300 " --> pdb=" O TRP u 296 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA u 301 " --> pdb=" O GLY u 297 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA u 303 " --> pdb=" O LYS u 299 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE u 305 " --> pdb=" O ALA u 301 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE u 306 " --> pdb=" O SER u 302 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER u 307 " --> pdb=" O ALA u 303 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE u 313 " --> pdb=" O LEU u 309 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU u 319 " --> pdb=" O TYR u 315 " (cutoff:3.500A) Processing helix chain 'u' and resid 342 through 359 removed outlier: 3.505A pdb=" N MET u 347 " --> pdb=" O THR u 343 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN u 348 " --> pdb=" O ALA u 344 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU u 350 " --> pdb=" O SER u 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 74 removed outlier: 3.628A pdb=" N ARG A 70 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 94 Processing helix chain 'A' and resid 100 through 112 removed outlier: 3.599A pdb=" N VAL A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 69 No H-bonds generated for 'chain 'B' and resid 67 through 69' Processing helix chain 'B' and resid 116 through 123 removed outlier: 3.608A pdb=" N LYS B 120 " --> pdb=" O LEU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 removed outlier: 3.533A pdb=" N ASN B 139 " --> pdb=" O ASP B 135 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN B 140 " --> pdb=" O THR B 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 135 through 140' Processing helix chain 'C' and resid 152 through 160 removed outlier: 3.515A pdb=" N LEU C 158 " --> pdb=" O GLU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 319 removed outlier: 3.580A pdb=" N ILE C 300 " --> pdb=" O TRP C 296 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA C 301 " --> pdb=" O GLY C 297 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA C 303 " --> pdb=" O LYS C 299 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE C 305 " --> pdb=" O ALA C 301 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE C 306 " --> pdb=" O SER C 302 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER C 307 " --> pdb=" O ALA C 303 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE C 313 " --> pdb=" O LEU C 309 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU C 319 " --> pdb=" O TYR C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 359 removed outlier: 3.505A pdb=" N MET C 347 " --> pdb=" O THR C 343 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN C 348 " --> pdb=" O ALA C 344 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 74 removed outlier: 3.627A pdb=" N ARG D 70 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 100 through 112 removed outlier: 3.598A pdb=" N VAL D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 69 No H-bonds generated for 'chain 'E' and resid 67 through 69' Processing helix chain 'E' and resid 116 through 123 removed outlier: 3.608A pdb=" N LYS E 120 " --> pdb=" O LEU E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 140 removed outlier: 3.534A pdb=" N ASN E 139 " --> pdb=" O ASP E 135 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN E 140 " --> pdb=" O THR E 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 135 through 140' Processing helix chain 'F' and resid 152 through 160 removed outlier: 3.515A pdb=" N LEU F 158 " --> pdb=" O GLU F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 319 removed outlier: 3.580A pdb=" N ILE F 300 " --> pdb=" O TRP F 296 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA F 301 " --> pdb=" O GLY F 297 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA F 303 " --> pdb=" O LYS F 299 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE F 305 " --> pdb=" O ALA F 301 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE F 306 " --> pdb=" O SER F 302 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER F 307 " --> pdb=" O ALA F 303 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE F 313 " --> pdb=" O LEU F 309 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU F 319 " --> pdb=" O TYR F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 359 removed outlier: 3.504A pdb=" N MET F 347 " --> pdb=" O THR F 343 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN F 348 " --> pdb=" O ALA F 344 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU F 350 " --> pdb=" O SER F 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 74 removed outlier: 3.628A pdb=" N ARG G 70 " --> pdb=" O THR G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 94 Processing helix chain 'G' and resid 100 through 112 removed outlier: 3.599A pdb=" N VAL G 111 " --> pdb=" O GLU G 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 69 No H-bonds generated for 'chain 'H' and resid 67 through 69' Processing helix chain 'H' and resid 116 through 123 removed outlier: 3.609A pdb=" N LYS H 120 " --> pdb=" O LEU H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 140 removed outlier: 3.534A pdb=" N ASN H 139 " --> pdb=" O ASP H 135 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN H 140 " --> pdb=" O THR H 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 135 through 140' Processing helix chain 'I' and resid 152 through 160 removed outlier: 3.514A pdb=" N LEU I 158 " --> pdb=" O GLU I 154 " (cutoff:3.500A) Processing helix chain 'I' and resid 295 through 319 removed outlier: 3.580A pdb=" N ILE I 300 " --> pdb=" O TRP I 296 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA I 301 " --> pdb=" O GLY I 297 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA I 303 " --> pdb=" O LYS I 299 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE I 305 " --> pdb=" O ALA I 301 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE I 306 " --> pdb=" O SER I 302 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER I 307 " --> pdb=" O ALA I 303 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE I 313 " --> pdb=" O LEU I 309 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU I 319 " --> pdb=" O TYR I 315 " (cutoff:3.500A) Processing helix chain 'I' and resid 342 through 359 removed outlier: 3.506A pdb=" N MET I 347 " --> pdb=" O THR I 343 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN I 348 " --> pdb=" O ALA I 344 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU I 350 " --> pdb=" O SER I 346 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 74 removed outlier: 3.628A pdb=" N ARG J 70 " --> pdb=" O THR J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 94 Processing helix chain 'J' and resid 100 through 112 removed outlier: 3.599A pdb=" N VAL J 111 " --> pdb=" O GLU J 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 69 No H-bonds generated for 'chain 'K' and resid 67 through 69' Processing helix chain 'K' and resid 116 through 123 removed outlier: 3.609A pdb=" N LYS K 120 " --> pdb=" O LEU K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 140 removed outlier: 3.534A pdb=" N ASN K 139 " --> pdb=" O ASP K 135 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN K 140 " --> pdb=" O THR K 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 135 through 140' Processing helix chain 'L' and resid 152 through 160 removed outlier: 3.514A pdb=" N LEU L 158 " --> pdb=" O GLU L 154 " (cutoff:3.500A) Processing helix chain 'L' and resid 295 through 319 removed outlier: 3.580A pdb=" N ILE L 300 " --> pdb=" O TRP L 296 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA L 301 " --> pdb=" O GLY L 297 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA L 303 " --> pdb=" O LYS L 299 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE L 305 " --> pdb=" O ALA L 301 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE L 306 " --> pdb=" O SER L 302 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER L 307 " --> pdb=" O ALA L 303 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE L 313 " --> pdb=" O LEU L 309 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU L 319 " --> pdb=" O TYR L 315 " (cutoff:3.500A) Processing helix chain 'L' and resid 342 through 359 removed outlier: 3.505A pdb=" N MET L 347 " --> pdb=" O THR L 343 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN L 348 " --> pdb=" O ALA L 344 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU L 350 " --> pdb=" O SER L 346 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 74 removed outlier: 3.628A pdb=" N ARG M 70 " --> pdb=" O THR M 66 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 94 Processing helix chain 'M' and resid 100 through 112 removed outlier: 3.599A pdb=" N VAL M 111 " --> pdb=" O GLU M 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 69 No H-bonds generated for 'chain 'N' and resid 67 through 69' Processing helix chain 'N' and resid 116 through 123 removed outlier: 3.609A pdb=" N LYS N 120 " --> pdb=" O LEU N 116 " (cutoff:3.500A) Processing helix chain 'N' and resid 135 through 140 removed outlier: 3.533A pdb=" N ASN N 139 " --> pdb=" O ASP N 135 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN N 140 " --> pdb=" O THR N 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 135 through 140' Processing helix chain 'O' and resid 152 through 160 removed outlier: 3.514A pdb=" N LEU O 158 " --> pdb=" O GLU O 154 " (cutoff:3.500A) Processing helix chain 'O' and resid 295 through 319 removed outlier: 3.580A pdb=" N ILE O 300 " --> pdb=" O TRP O 296 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA O 301 " --> pdb=" O GLY O 297 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA O 303 " --> pdb=" O LYS O 299 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE O 305 " --> pdb=" O ALA O 301 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE O 306 " --> pdb=" O SER O 302 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER O 307 " --> pdb=" O ALA O 303 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE O 313 " --> pdb=" O LEU O 309 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU O 319 " --> pdb=" O TYR O 315 " (cutoff:3.500A) Processing helix chain 'O' and resid 342 through 359 removed outlier: 3.505A pdb=" N MET O 347 " --> pdb=" O THR O 343 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN O 348 " --> pdb=" O ALA O 344 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU O 350 " --> pdb=" O SER O 346 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 74 removed outlier: 3.628A pdb=" N ARG P 70 " --> pdb=" O THR P 66 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 94 Processing helix chain 'P' and resid 100 through 112 removed outlier: 3.598A pdb=" N VAL P 111 " --> pdb=" O GLU P 107 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 69 No H-bonds generated for 'chain 'Q' and resid 67 through 69' Processing helix chain 'Q' and resid 116 through 123 removed outlier: 3.609A pdb=" N LYS Q 120 " --> pdb=" O LEU Q 116 " (cutoff:3.500A) Processing helix chain 'Q' and resid 135 through 140 removed outlier: 3.534A pdb=" N ASN Q 139 " --> pdb=" O ASP Q 135 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN Q 140 " --> pdb=" O THR Q 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 135 through 140' Processing helix chain 'R' and resid 152 through 160 removed outlier: 3.514A pdb=" N LEU R 158 " --> pdb=" O GLU R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 319 removed outlier: 3.581A pdb=" N ILE R 300 " --> pdb=" O TRP R 296 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA R 301 " --> pdb=" O GLY R 297 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA R 303 " --> pdb=" O LYS R 299 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE R 305 " --> pdb=" O ALA R 301 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE R 306 " --> pdb=" O SER R 302 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER R 307 " --> pdb=" O ALA R 303 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE R 313 " --> pdb=" O LEU R 309 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU R 319 " --> pdb=" O TYR R 315 " (cutoff:3.500A) Processing helix chain 'R' and resid 342 through 359 removed outlier: 3.506A pdb=" N MET R 347 " --> pdb=" O THR R 343 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN R 348 " --> pdb=" O ALA R 344 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU R 350 " --> pdb=" O SER R 346 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 74 removed outlier: 3.627A pdb=" N ARG S 70 " --> pdb=" O THR S 66 " (cutoff:3.500A) Processing helix chain 'S' and resid 90 through 94 Processing helix chain 'S' and resid 100 through 112 removed outlier: 3.599A pdb=" N VAL S 111 " --> pdb=" O GLU S 107 " (cutoff:3.500A) Processing helix chain 'T' and resid 67 through 69 No H-bonds generated for 'chain 'T' and resid 67 through 69' Processing helix chain 'T' and resid 116 through 123 removed outlier: 3.609A pdb=" N LYS T 120 " --> pdb=" O LEU T 116 " (cutoff:3.500A) Processing helix chain 'T' and resid 135 through 140 removed outlier: 3.534A pdb=" N ASN T 139 " --> pdb=" O ASP T 135 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN T 140 " --> pdb=" O THR T 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 135 through 140' Processing helix chain 'U' and resid 152 through 160 removed outlier: 3.514A pdb=" N LEU U 158 " --> pdb=" O GLU U 154 " (cutoff:3.500A) Processing helix chain 'U' and resid 295 through 319 removed outlier: 3.581A pdb=" N ILE U 300 " --> pdb=" O TRP U 296 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA U 301 " --> pdb=" O GLY U 297 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA U 303 " --> pdb=" O LYS U 299 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE U 305 " --> pdb=" O ALA U 301 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE U 306 " --> pdb=" O SER U 302 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER U 307 " --> pdb=" O ALA U 303 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE U 313 " --> pdb=" O LEU U 309 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU U 319 " --> pdb=" O TYR U 315 " (cutoff:3.500A) Processing helix chain 'U' and resid 342 through 359 removed outlier: 3.505A pdb=" N MET U 347 " --> pdb=" O THR U 343 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN U 348 " --> pdb=" O ALA U 344 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU U 350 " --> pdb=" O SER U 346 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 35 through 36 Processing sheet with id=AA2, first strand: chain 'a' and resid 46 through 48 Processing sheet with id=AA3, first strand: chain 'a' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'a' and resid 78 through 81 removed outlier: 6.388A pdb=" N GLN a 78 " --> pdb=" O LEU a 126 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL a 128 " --> pdb=" O GLN a 78 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N SER a 80 " --> pdb=" O VAL a 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 85 through 87 Processing sheet with id=AA6, first strand: chain 'b' and resid 29 through 33 removed outlier: 6.434A pdb=" N GLN b 30 " --> pdb=" O VAL b 129 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N THR b 131 " --> pdb=" O GLN b 30 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TYR b 32 " --> pdb=" O THR b 131 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE b 130 " --> pdb=" O GLU b 53 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR b 74 " --> pdb=" O TYR b 81 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 39 through 45 removed outlier: 6.693A pdb=" N TYR b 40 " --> pdb=" O GLU b 105 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N LYS b 107 " --> pdb=" O TYR b 40 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL b 42 " --> pdb=" O LYS b 107 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL b 109 " --> pdb=" O VAL b 42 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N THR b 44 " --> pdb=" O VAL b 109 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 182 through 185 removed outlier: 3.576A pdb=" N TYR b 184 " --> pdb=" O TYR b 191 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 206 through 210 Processing sheet with id=AB1, first strand: chain 'c' and resid 188 through 190 removed outlier: 3.599A pdb=" N LYS c 189 " --> pdb=" O ASP U 272 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN U 374 " --> pdb=" O ILE U 280 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS U 206 " --> pdb=" O LEU U 373 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLN U 247 " --> pdb=" O TRP U 262 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N TRP U 262 " --> pdb=" O GLN U 247 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'c' and resid 197 through 198 Processing sheet with id=AB3, first strand: chain 'f' and resid 188 through 190 removed outlier: 3.606A pdb=" N LYS f 189 " --> pdb=" O ASP c 272 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN c 374 " --> pdb=" O ILE c 280 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS c 206 " --> pdb=" O LEU c 373 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLN c 247 " --> pdb=" O TRP c 262 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N TRP c 262 " --> pdb=" O GLN c 247 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'c' and resid 212 through 213 Processing sheet with id=AB5, first strand: chain 'c' and resid 228 through 229 Processing sheet with id=AB6, first strand: chain 'c' and resid 257 through 258 Processing sheet with id=AB7, first strand: chain 'd' and resid 35 through 36 Processing sheet with id=AB8, first strand: chain 'd' and resid 46 through 48 Processing sheet with id=AB9, first strand: chain 'd' and resid 55 through 56 Processing sheet with id=AC1, first strand: chain 'd' and resid 78 through 81 removed outlier: 6.388A pdb=" N GLN d 78 " --> pdb=" O LEU d 126 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL d 128 " --> pdb=" O GLN d 78 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N SER d 80 " --> pdb=" O VAL d 128 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'e' and resid 29 through 33 removed outlier: 6.433A pdb=" N GLN e 30 " --> pdb=" O VAL e 129 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N THR e 131 " --> pdb=" O GLN e 30 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TYR e 32 " --> pdb=" O THR e 131 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE e 130 " --> pdb=" O GLU e 53 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR e 74 " --> pdb=" O TYR e 81 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'e' and resid 39 through 45 removed outlier: 6.692A pdb=" N TYR e 40 " --> pdb=" O GLU e 105 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N LYS e 107 " --> pdb=" O TYR e 40 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL e 42 " --> pdb=" O LYS e 107 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL e 109 " --> pdb=" O VAL e 42 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N THR e 44 " --> pdb=" O VAL e 109 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'e' and resid 182 through 185 removed outlier: 3.576A pdb=" N TYR e 184 " --> pdb=" O TYR e 191 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'e' and resid 206 through 210 Processing sheet with id=AC6, first strand: chain 'f' and resid 197 through 198 Processing sheet with id=AC7, first strand: chain 'i' and resid 188 through 190 removed outlier: 3.607A pdb=" N LYS i 189 " --> pdb=" O ASP f 272 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN f 374 " --> pdb=" O ILE f 280 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS f 206 " --> pdb=" O LEU f 373 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLN f 247 " --> pdb=" O TRP f 262 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N TRP f 262 " --> pdb=" O GLN f 247 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'f' and resid 212 through 213 Processing sheet with id=AC9, first strand: chain 'f' and resid 228 through 229 Processing sheet with id=AD1, first strand: chain 'f' and resid 257 through 258 Processing sheet with id=AD2, first strand: chain 'g' and resid 35 through 36 Processing sheet with id=AD3, first strand: chain 'g' and resid 46 through 48 Processing sheet with id=AD4, first strand: chain 'g' and resid 55 through 56 Processing sheet with id=AD5, first strand: chain 'g' and resid 78 through 81 removed outlier: 6.389A pdb=" N GLN g 78 " --> pdb=" O LEU g 126 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL g 128 " --> pdb=" O GLN g 78 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N SER g 80 " --> pdb=" O VAL g 128 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'h' and resid 29 through 33 removed outlier: 6.434A pdb=" N GLN h 30 " --> pdb=" O VAL h 129 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR h 131 " --> pdb=" O GLN h 30 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TYR h 32 " --> pdb=" O THR h 131 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE h 130 " --> pdb=" O GLU h 53 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR h 74 " --> pdb=" O TYR h 81 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'h' and resid 39 through 45 removed outlier: 6.693A pdb=" N TYR h 40 " --> pdb=" O GLU h 105 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LYS h 107 " --> pdb=" O TYR h 40 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL h 42 " --> pdb=" O LYS h 107 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL h 109 " --> pdb=" O VAL h 42 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N THR h 44 " --> pdb=" O VAL h 109 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'h' and resid 182 through 185 removed outlier: 3.577A pdb=" N TYR h 184 " --> pdb=" O TYR h 191 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'h' and resid 206 through 210 Processing sheet with id=AE1, first strand: chain 'i' and resid 197 through 198 Processing sheet with id=AE2, first strand: chain 'l' and resid 188 through 190 removed outlier: 3.603A pdb=" N LYS l 189 " --> pdb=" O ASP i 272 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN i 374 " --> pdb=" O ILE i 280 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS i 206 " --> pdb=" O LEU i 373 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLN i 247 " --> pdb=" O TRP i 262 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N TRP i 262 " --> pdb=" O GLN i 247 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'i' and resid 212 through 213 Processing sheet with id=AE4, first strand: chain 'i' and resid 228 through 229 Processing sheet with id=AE5, first strand: chain 'i' and resid 257 through 258 Processing sheet with id=AE6, first strand: chain 'j' and resid 35 through 36 Processing sheet with id=AE7, first strand: chain 'j' and resid 46 through 48 Processing sheet with id=AE8, first strand: chain 'j' and resid 55 through 56 Processing sheet with id=AE9, first strand: chain 'j' and resid 78 through 81 removed outlier: 6.388A pdb=" N GLN j 78 " --> pdb=" O LEU j 126 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL j 128 " --> pdb=" O GLN j 78 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N SER j 80 " --> pdb=" O VAL j 128 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'k' and resid 29 through 33 removed outlier: 6.435A pdb=" N GLN k 30 " --> pdb=" O VAL k 129 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N THR k 131 " --> pdb=" O GLN k 30 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TYR k 32 " --> pdb=" O THR k 131 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE k 130 " --> pdb=" O GLU k 53 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR k 74 " --> pdb=" O TYR k 81 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'k' and resid 39 through 45 removed outlier: 6.693A pdb=" N TYR k 40 " --> pdb=" O GLU k 105 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N LYS k 107 " --> pdb=" O TYR k 40 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL k 42 " --> pdb=" O LYS k 107 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL k 109 " --> pdb=" O VAL k 42 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N THR k 44 " --> pdb=" O VAL k 109 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'k' and resid 182 through 185 removed outlier: 3.577A pdb=" N TYR k 184 " --> pdb=" O TYR k 191 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'k' and resid 206 through 210 Processing sheet with id=AF5, first strand: chain 'l' and resid 197 through 198 Processing sheet with id=AF6, first strand: chain 'o' and resid 188 through 190 removed outlier: 3.599A pdb=" N LYS o 189 " --> pdb=" O ASP l 272 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN l 374 " --> pdb=" O ILE l 280 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS l 206 " --> pdb=" O LEU l 373 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLN l 247 " --> pdb=" O TRP l 262 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N TRP l 262 " --> pdb=" O GLN l 247 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'l' and resid 212 through 213 Processing sheet with id=AF8, first strand: chain 'l' and resid 228 through 229 Processing sheet with id=AF9, first strand: chain 'l' and resid 257 through 258 Processing sheet with id=AG1, first strand: chain 'm' and resid 35 through 36 Processing sheet with id=AG2, first strand: chain 'm' and resid 46 through 48 Processing sheet with id=AG3, first strand: chain 'm' and resid 55 through 56 Processing sheet with id=AG4, first strand: chain 'm' and resid 78 through 81 removed outlier: 6.388A pdb=" N GLN m 78 " --> pdb=" O LEU m 126 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL m 128 " --> pdb=" O GLN m 78 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N SER m 80 " --> pdb=" O VAL m 128 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'n' and resid 29 through 33 removed outlier: 6.434A pdb=" N GLN n 30 " --> pdb=" O VAL n 129 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR n 131 " --> pdb=" O GLN n 30 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TYR n 32 " --> pdb=" O THR n 131 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE n 130 " --> pdb=" O GLU n 53 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR n 74 " --> pdb=" O TYR n 81 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'n' and resid 39 through 45 removed outlier: 6.693A pdb=" N TYR n 40 " --> pdb=" O GLU n 105 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N LYS n 107 " --> pdb=" O TYR n 40 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL n 42 " --> pdb=" O LYS n 107 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL n 109 " --> pdb=" O VAL n 42 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N THR n 44 " --> pdb=" O VAL n 109 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'n' and resid 182 through 185 removed outlier: 3.577A pdb=" N TYR n 184 " --> pdb=" O TYR n 191 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'n' and resid 206 through 210 Processing sheet with id=AG9, first strand: chain 'o' and resid 197 through 198 Processing sheet with id=AH1, first strand: chain 'r' and resid 188 through 190 removed outlier: 3.607A pdb=" N LYS r 189 " --> pdb=" O ASP o 272 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN o 374 " --> pdb=" O ILE o 280 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS o 206 " --> pdb=" O LEU o 373 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLN o 247 " --> pdb=" O TRP o 262 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N TRP o 262 " --> pdb=" O GLN o 247 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'o' and resid 212 through 213 Processing sheet with id=AH3, first strand: chain 'o' and resid 228 through 229 Processing sheet with id=AH4, first strand: chain 'o' and resid 257 through 258 Processing sheet with id=AH5, first strand: chain 'p' and resid 35 through 36 Processing sheet with id=AH6, first strand: chain 'p' and resid 46 through 48 Processing sheet with id=AH7, first strand: chain 'p' and resid 55 through 56 Processing sheet with id=AH8, first strand: chain 'p' and resid 78 through 81 removed outlier: 6.388A pdb=" N GLN p 78 " --> pdb=" O LEU p 126 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL p 128 " --> pdb=" O GLN p 78 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N SER p 80 " --> pdb=" O VAL p 128 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'q' and resid 29 through 33 removed outlier: 6.434A pdb=" N GLN q 30 " --> pdb=" O VAL q 129 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N THR q 131 " --> pdb=" O GLN q 30 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TYR q 32 " --> pdb=" O THR q 131 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE q 130 " --> pdb=" O GLU q 53 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR q 74 " --> pdb=" O TYR q 81 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'q' and resid 39 through 45 removed outlier: 6.693A pdb=" N TYR q 40 " --> pdb=" O GLU q 105 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LYS q 107 " --> pdb=" O TYR q 40 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL q 42 " --> pdb=" O LYS q 107 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL q 109 " --> pdb=" O VAL q 42 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N THR q 44 " --> pdb=" O VAL q 109 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'q' and resid 182 through 185 removed outlier: 3.576A pdb=" N TYR q 184 " --> pdb=" O TYR q 191 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'q' and resid 206 through 210 Processing sheet with id=AI4, first strand: chain 'r' and resid 197 through 198 Processing sheet with id=AI5, first strand: chain 'u' and resid 188 through 190 removed outlier: 3.600A pdb=" N LYS u 189 " --> pdb=" O ASP r 272 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN r 374 " --> pdb=" O ILE r 280 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS r 206 " --> pdb=" O LEU r 373 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLN r 247 " --> pdb=" O TRP r 262 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N TRP r 262 " --> pdb=" O GLN r 247 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'r' and resid 212 through 213 Processing sheet with id=AI7, first strand: chain 'r' and resid 228 through 229 Processing sheet with id=AI8, first strand: chain 'r' and resid 257 through 258 Processing sheet with id=AI9, first strand: chain 's' and resid 35 through 36 Processing sheet with id=AJ1, first strand: chain 's' and resid 46 through 48 Processing sheet with id=AJ2, first strand: chain 's' and resid 55 through 56 Processing sheet with id=AJ3, first strand: chain 's' and resid 78 through 81 removed outlier: 6.388A pdb=" N GLN s 78 " --> pdb=" O LEU s 126 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL s 128 " --> pdb=" O GLN s 78 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N SER s 80 " --> pdb=" O VAL s 128 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 't' and resid 29 through 33 removed outlier: 6.434A pdb=" N GLN t 30 " --> pdb=" O VAL t 129 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N THR t 131 " --> pdb=" O GLN t 30 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N TYR t 32 " --> pdb=" O THR t 131 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE t 130 " --> pdb=" O GLU t 53 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR t 74 " --> pdb=" O TYR t 81 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 't' and resid 39 through 45 removed outlier: 6.693A pdb=" N TYR t 40 " --> pdb=" O GLU t 105 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N LYS t 107 " --> pdb=" O TYR t 40 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL t 42 " --> pdb=" O LYS t 107 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL t 109 " --> pdb=" O VAL t 42 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N THR t 44 " --> pdb=" O VAL t 109 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 't' and resid 182 through 185 removed outlier: 3.577A pdb=" N TYR t 184 " --> pdb=" O TYR t 191 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 't' and resid 206 through 210 Processing sheet with id=AJ8, first strand: chain 'u' and resid 197 through 198 Processing sheet with id=AJ9, first strand: chain 'C' and resid 188 through 190 removed outlier: 3.599A pdb=" N LYS C 189 " --> pdb=" O ASP u 272 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN u 374 " --> pdb=" O ILE u 280 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS u 206 " --> pdb=" O LEU u 373 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLN u 247 " --> pdb=" O TRP u 262 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N TRP u 262 " --> pdb=" O GLN u 247 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'u' and resid 212 through 213 Processing sheet with id=AK2, first strand: chain 'u' and resid 228 through 229 Processing sheet with id=AK3, first strand: chain 'u' and resid 257 through 258 Processing sheet with id=AK4, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AK5, first strand: chain 'A' and resid 46 through 48 Processing sheet with id=AK6, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AK7, first strand: chain 'A' and resid 78 through 81 removed outlier: 6.388A pdb=" N GLN A 78 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL A 128 " --> pdb=" O GLN A 78 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N SER A 80 " --> pdb=" O VAL A 128 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'B' and resid 29 through 33 removed outlier: 6.434A pdb=" N GLN B 30 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N THR B 131 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TYR B 32 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE B 130 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR B 74 " --> pdb=" O TYR B 81 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'B' and resid 39 through 45 removed outlier: 6.693A pdb=" N TYR B 40 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N LYS B 107 " --> pdb=" O TYR B 40 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL B 42 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL B 109 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N THR B 44 " --> pdb=" O VAL B 109 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'B' and resid 182 through 185 removed outlier: 3.577A pdb=" N TYR B 184 " --> pdb=" O TYR B 191 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'B' and resid 206 through 210 Processing sheet with id=AL3, first strand: chain 'C' and resid 197 through 198 Processing sheet with id=AL4, first strand: chain 'F' and resid 188 through 190 removed outlier: 3.606A pdb=" N LYS F 189 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN C 374 " --> pdb=" O ILE C 280 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS C 206 " --> pdb=" O LEU C 373 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLN C 247 " --> pdb=" O TRP C 262 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N TRP C 262 " --> pdb=" O GLN C 247 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'C' and resid 212 through 213 Processing sheet with id=AL6, first strand: chain 'C' and resid 228 through 229 Processing sheet with id=AL7, first strand: chain 'C' and resid 257 through 258 Processing sheet with id=AL8, first strand: chain 'D' and resid 35 through 36 Processing sheet with id=AL9, first strand: chain 'D' and resid 46 through 48 Processing sheet with id=AM1, first strand: chain 'D' and resid 55 through 56 Processing sheet with id=AM2, first strand: chain 'D' and resid 78 through 81 removed outlier: 6.389A pdb=" N GLN D 78 " --> pdb=" O LEU D 126 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL D 128 " --> pdb=" O GLN D 78 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N SER D 80 " --> pdb=" O VAL D 128 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'E' and resid 29 through 33 removed outlier: 6.433A pdb=" N GLN E 30 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N THR E 131 " --> pdb=" O GLN E 30 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TYR E 32 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE E 130 " --> pdb=" O GLU E 53 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR E 74 " --> pdb=" O TYR E 81 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'E' and resid 39 through 45 removed outlier: 6.692A pdb=" N TYR E 40 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N LYS E 107 " --> pdb=" O TYR E 40 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL E 42 " --> pdb=" O LYS E 107 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL E 109 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N THR E 44 " --> pdb=" O VAL E 109 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'E' and resid 182 through 185 removed outlier: 3.576A pdb=" N TYR E 184 " --> pdb=" O TYR E 191 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'E' and resid 206 through 210 Processing sheet with id=AM7, first strand: chain 'F' and resid 197 through 198 Processing sheet with id=AM8, first strand: chain 'I' and resid 188 through 190 removed outlier: 3.607A pdb=" N LYS I 189 " --> pdb=" O ASP F 272 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN F 374 " --> pdb=" O ILE F 280 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS F 206 " --> pdb=" O LEU F 373 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLN F 247 " --> pdb=" O TRP F 262 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N TRP F 262 " --> pdb=" O GLN F 247 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'F' and resid 212 through 213 Processing sheet with id=AN1, first strand: chain 'F' and resid 228 through 229 Processing sheet with id=AN2, first strand: chain 'F' and resid 257 through 258 Processing sheet with id=AN3, first strand: chain 'G' and resid 35 through 36 Processing sheet with id=AN4, first strand: chain 'G' and resid 46 through 48 Processing sheet with id=AN5, first strand: chain 'G' and resid 55 through 56 Processing sheet with id=AN6, first strand: chain 'G' and resid 78 through 81 removed outlier: 6.388A pdb=" N GLN G 78 " --> pdb=" O LEU G 126 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL G 128 " --> pdb=" O GLN G 78 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N SER G 80 " --> pdb=" O VAL G 128 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'H' and resid 29 through 33 removed outlier: 6.434A pdb=" N GLN H 30 " --> pdb=" O VAL H 129 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR H 131 " --> pdb=" O GLN H 30 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TYR H 32 " --> pdb=" O THR H 131 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE H 130 " --> pdb=" O GLU H 53 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR H 74 " --> pdb=" O TYR H 81 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'H' and resid 39 through 45 removed outlier: 6.693A pdb=" N TYR H 40 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LYS H 107 " --> pdb=" O TYR H 40 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL H 42 " --> pdb=" O LYS H 107 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL H 109 " --> pdb=" O VAL H 42 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N THR H 44 " --> pdb=" O VAL H 109 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain 'H' and resid 182 through 185 removed outlier: 3.577A pdb=" N TYR H 184 " --> pdb=" O TYR H 191 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain 'H' and resid 206 through 210 Processing sheet with id=AO2, first strand: chain 'I' and resid 197 through 198 Processing sheet with id=AO3, first strand: chain 'L' and resid 188 through 190 removed outlier: 3.603A pdb=" N LYS L 189 " --> pdb=" O ASP I 272 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN I 374 " --> pdb=" O ILE I 280 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS I 206 " --> pdb=" O LEU I 373 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLN I 247 " --> pdb=" O TRP I 262 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N TRP I 262 " --> pdb=" O GLN I 247 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'I' and resid 212 through 213 Processing sheet with id=AO5, first strand: chain 'I' and resid 228 through 229 Processing sheet with id=AO6, first strand: chain 'I' and resid 257 through 258 Processing sheet with id=AO7, first strand: chain 'J' and resid 35 through 36 Processing sheet with id=AO8, first strand: chain 'J' and resid 46 through 48 Processing sheet with id=AO9, first strand: chain 'J' and resid 55 through 56 Processing sheet with id=AP1, first strand: chain 'J' and resid 78 through 81 removed outlier: 6.388A pdb=" N GLN J 78 " --> pdb=" O LEU J 126 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL J 128 " --> pdb=" O GLN J 78 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N SER J 80 " --> pdb=" O VAL J 128 " (cutoff:3.500A) Processing sheet with id=AP2, first strand: chain 'K' and resid 29 through 33 removed outlier: 6.435A pdb=" N GLN K 30 " --> pdb=" O VAL K 129 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N THR K 131 " --> pdb=" O GLN K 30 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TYR K 32 " --> pdb=" O THR K 131 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE K 130 " --> pdb=" O GLU K 53 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR K 74 " --> pdb=" O TYR K 81 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'K' and resid 39 through 45 removed outlier: 6.693A pdb=" N TYR K 40 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N LYS K 107 " --> pdb=" O TYR K 40 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL K 42 " --> pdb=" O LYS K 107 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL K 109 " --> pdb=" O VAL K 42 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N THR K 44 " --> pdb=" O VAL K 109 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'K' and resid 182 through 185 removed outlier: 3.577A pdb=" N TYR K 184 " --> pdb=" O TYR K 191 " (cutoff:3.500A) Processing sheet with id=AP5, first strand: chain 'K' and resid 206 through 210 Processing sheet with id=AP6, first strand: chain 'L' and resid 197 through 198 Processing sheet with id=AP7, first strand: chain 'O' and resid 188 through 190 removed outlier: 3.587A pdb=" N LYS O 189 " --> pdb=" O ASP L 272 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN L 374 " --> pdb=" O ILE L 280 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS L 206 " --> pdb=" O LEU L 373 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLN L 247 " --> pdb=" O TRP L 262 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N TRP L 262 " --> pdb=" O GLN L 247 " (cutoff:3.500A) Processing sheet with id=AP8, first strand: chain 'L' and resid 212 through 213 Processing sheet with id=AP9, first strand: chain 'L' and resid 228 through 229 Processing sheet with id=AQ1, first strand: chain 'L' and resid 257 through 258 Processing sheet with id=AQ2, first strand: chain 'M' and resid 35 through 36 Processing sheet with id=AQ3, first strand: chain 'M' and resid 46 through 48 Processing sheet with id=AQ4, first strand: chain 'M' and resid 55 through 56 Processing sheet with id=AQ5, first strand: chain 'M' and resid 78 through 81 removed outlier: 6.388A pdb=" N GLN M 78 " --> pdb=" O LEU M 126 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL M 128 " --> pdb=" O GLN M 78 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N SER M 80 " --> pdb=" O VAL M 128 " (cutoff:3.500A) Processing sheet with id=AQ6, first strand: chain 'N' and resid 29 through 33 removed outlier: 6.434A pdb=" N GLN N 30 " --> pdb=" O VAL N 129 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR N 131 " --> pdb=" O GLN N 30 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TYR N 32 " --> pdb=" O THR N 131 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE N 130 " --> pdb=" O GLU N 53 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR N 74 " --> pdb=" O TYR N 81 " (cutoff:3.500A) Processing sheet with id=AQ7, first strand: chain 'N' and resid 39 through 45 removed outlier: 6.693A pdb=" N TYR N 40 " --> pdb=" O GLU N 105 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N LYS N 107 " --> pdb=" O TYR N 40 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL N 42 " --> pdb=" O LYS N 107 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL N 109 " --> pdb=" O VAL N 42 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N THR N 44 " --> pdb=" O VAL N 109 " (cutoff:3.500A) Processing sheet with id=AQ8, first strand: chain 'N' and resid 182 through 185 removed outlier: 3.576A pdb=" N TYR N 184 " --> pdb=" O TYR N 191 " (cutoff:3.500A) Processing sheet with id=AQ9, first strand: chain 'N' and resid 206 through 210 Processing sheet with id=AR1, first strand: chain 'O' and resid 197 through 198 Processing sheet with id=AR2, first strand: chain 'R' and resid 188 through 190 removed outlier: 3.596A pdb=" N LYS R 189 " --> pdb=" O ASP O 272 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN O 374 " --> pdb=" O ILE O 280 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS O 206 " --> pdb=" O LEU O 373 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLN O 247 " --> pdb=" O TRP O 262 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N TRP O 262 " --> pdb=" O GLN O 247 " (cutoff:3.500A) Processing sheet with id=AR3, first strand: chain 'O' and resid 212 through 213 Processing sheet with id=AR4, first strand: chain 'O' and resid 228 through 229 Processing sheet with id=AR5, first strand: chain 'O' and resid 257 through 258 Processing sheet with id=AR6, first strand: chain 'P' and resid 35 through 36 Processing sheet with id=AR7, first strand: chain 'P' and resid 46 through 48 Processing sheet with id=AR8, first strand: chain 'P' and resid 55 through 56 Processing sheet with id=AR9, first strand: chain 'P' and resid 78 through 81 removed outlier: 6.388A pdb=" N GLN P 78 " --> pdb=" O LEU P 126 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL P 128 " --> pdb=" O GLN P 78 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N SER P 80 " --> pdb=" O VAL P 128 " (cutoff:3.500A) Processing sheet with id=AS1, first strand: chain 'Q' and resid 29 through 33 removed outlier: 6.434A pdb=" N GLN Q 30 " --> pdb=" O VAL Q 129 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N THR Q 131 " --> pdb=" O GLN Q 30 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TYR Q 32 " --> pdb=" O THR Q 131 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE Q 130 " --> pdb=" O GLU Q 53 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR Q 74 " --> pdb=" O TYR Q 81 " (cutoff:3.500A) Processing sheet with id=AS2, first strand: chain 'Q' and resid 39 through 45 removed outlier: 6.693A pdb=" N TYR Q 40 " --> pdb=" O GLU Q 105 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LYS Q 107 " --> pdb=" O TYR Q 40 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL Q 42 " --> pdb=" O LYS Q 107 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL Q 109 " --> pdb=" O VAL Q 42 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N THR Q 44 " --> pdb=" O VAL Q 109 " (cutoff:3.500A) Processing sheet with id=AS3, first strand: chain 'Q' and resid 182 through 185 removed outlier: 3.576A pdb=" N TYR Q 184 " --> pdb=" O TYR Q 191 " (cutoff:3.500A) Processing sheet with id=AS4, first strand: chain 'Q' and resid 206 through 210 Processing sheet with id=AS5, first strand: chain 'R' and resid 197 through 198 Processing sheet with id=AS6, first strand: chain 'U' and resid 188 through 190 removed outlier: 3.600A pdb=" N LYS U 189 " --> pdb=" O ASP R 272 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN R 374 " --> pdb=" O ILE R 280 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS R 206 " --> pdb=" O LEU R 373 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLN R 247 " --> pdb=" O TRP R 262 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N TRP R 262 " --> pdb=" O GLN R 247 " (cutoff:3.500A) Processing sheet with id=AS7, first strand: chain 'R' and resid 212 through 213 Processing sheet with id=AS8, first strand: chain 'R' and resid 228 through 229 Processing sheet with id=AS9, first strand: chain 'R' and resid 257 through 258 Processing sheet with id=AT1, first strand: chain 'S' and resid 35 through 36 Processing sheet with id=AT2, first strand: chain 'S' and resid 55 through 56 Processing sheet with id=AT3, first strand: chain 'S' and resid 78 through 81 removed outlier: 6.388A pdb=" N GLN S 78 " --> pdb=" O LEU S 126 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL S 128 " --> pdb=" O GLN S 78 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N SER S 80 " --> pdb=" O VAL S 128 " (cutoff:3.500A) Processing sheet with id=AT4, first strand: chain 'T' and resid 29 through 33 removed outlier: 6.434A pdb=" N GLN T 30 " --> pdb=" O VAL T 129 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N THR T 131 " --> pdb=" O GLN T 30 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N TYR T 32 " --> pdb=" O THR T 131 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE T 130 " --> pdb=" O GLU T 53 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR T 74 " --> pdb=" O TYR T 81 " (cutoff:3.500A) Processing sheet with id=AT5, first strand: chain 'T' and resid 39 through 45 removed outlier: 6.694A pdb=" N TYR T 40 " --> pdb=" O GLU T 105 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N LYS T 107 " --> pdb=" O TYR T 40 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL T 42 " --> pdb=" O LYS T 107 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL T 109 " --> pdb=" O VAL T 42 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N THR T 44 " --> pdb=" O VAL T 109 " (cutoff:3.500A) Processing sheet with id=AT6, first strand: chain 'T' and resid 182 through 185 removed outlier: 3.576A pdb=" N TYR T 184 " --> pdb=" O TYR T 191 " (cutoff:3.500A) Processing sheet with id=AT7, first strand: chain 'T' and resid 206 through 210 Processing sheet with id=AT8, first strand: chain 'U' and resid 197 through 198 Processing sheet with id=AT9, first strand: chain 'U' and resid 212 through 213 Processing sheet with id=AU1, first strand: chain 'U' and resid 228 through 229 Processing sheet with id=AU2, first strand: chain 'U' and resid 257 through 258 1820 hydrogen bonds defined for protein. 4662 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: 30.90 Time building geometry restraints manager: 13.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 18997 1.34 - 1.45: 9482 1.45 - 1.57: 31903 1.57 - 1.69: 0 1.69 - 1.80: 294 Bond restraints: 60676 Sorted by residual: bond pdb=" CG ARG b 251 " pdb=" CD ARG b 251 " ideal model delta sigma weight residual 1.520 1.460 0.060 3.00e-02 1.11e+03 3.96e+00 bond pdb=" CG ARG H 251 " pdb=" CD ARG H 251 " ideal model delta sigma weight residual 1.520 1.460 0.060 3.00e-02 1.11e+03 3.95e+00 bond pdb=" CG ARG h 251 " pdb=" CD ARG h 251 " ideal model delta sigma weight residual 1.520 1.460 0.060 3.00e-02 1.11e+03 3.95e+00 bond pdb=" CG ARG B 251 " pdb=" CD ARG B 251 " ideal model delta sigma weight residual 1.520 1.461 0.059 3.00e-02 1.11e+03 3.90e+00 bond pdb=" CG ARG e 251 " pdb=" CD ARG e 251 " ideal model delta sigma weight residual 1.520 1.461 0.059 3.00e-02 1.11e+03 3.90e+00 ... (remaining 60671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 80756 2.55 - 5.11: 1463 5.11 - 7.66: 288 7.66 - 10.22: 37 10.22 - 12.77: 14 Bond angle restraints: 82558 Sorted by residual: angle pdb=" C ARG t 76 " pdb=" N GLU t 77 " pdb=" CA GLU t 77 " ideal model delta sigma weight residual 121.54 129.24 -7.70 1.91e+00 2.74e-01 1.62e+01 angle pdb=" C ARG N 76 " pdb=" N GLU N 77 " pdb=" CA GLU N 77 " ideal model delta sigma weight residual 121.54 129.24 -7.70 1.91e+00 2.74e-01 1.62e+01 angle pdb=" C ARG n 76 " pdb=" N GLU n 77 " pdb=" CA GLU n 77 " ideal model delta sigma weight residual 121.54 129.24 -7.70 1.91e+00 2.74e-01 1.62e+01 angle pdb=" C ARG h 76 " pdb=" N GLU h 77 " pdb=" CA GLU h 77 " ideal model delta sigma weight residual 121.54 129.22 -7.68 1.91e+00 2.74e-01 1.62e+01 angle pdb=" C ARG Q 76 " pdb=" N GLU Q 77 " pdb=" CA GLU Q 77 " ideal model delta sigma weight residual 121.54 129.22 -7.68 1.91e+00 2.74e-01 1.62e+01 ... (remaining 82553 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.15: 34282 15.15 - 30.30: 1646 30.30 - 45.45: 318 45.45 - 60.60: 0 60.60 - 75.75: 28 Dihedral angle restraints: 36274 sinusoidal: 14336 harmonic: 21938 Sorted by residual: dihedral pdb=" CA ALA I 318 " pdb=" C ALA I 318 " pdb=" N GLU I 319 " pdb=" CA GLU I 319 " ideal model delta harmonic sigma weight residual 180.00 160.66 19.34 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA ALA i 318 " pdb=" C ALA i 318 " pdb=" N GLU i 319 " pdb=" CA GLU i 319 " ideal model delta harmonic sigma weight residual 180.00 160.69 19.31 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ALA L 318 " pdb=" C ALA L 318 " pdb=" N GLU L 319 " pdb=" CA GLU L 319 " ideal model delta harmonic sigma weight residual 180.00 160.69 19.31 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 36271 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 6168 0.053 - 0.105: 2408 0.105 - 0.158: 615 0.158 - 0.211: 133 0.211 - 0.263: 14 Chirality restraints: 9338 Sorted by residual: chirality pdb=" CA PHE H 199 " pdb=" N PHE H 199 " pdb=" C PHE H 199 " pdb=" CB PHE H 199 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA PHE B 199 " pdb=" N PHE B 199 " pdb=" C PHE B 199 " pdb=" CB PHE B 199 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA PHE b 199 " pdb=" N PHE b 199 " pdb=" C PHE b 199 " pdb=" CB PHE b 199 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 9335 not shown) Planarity restraints: 10570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR s 58 " 0.047 5.00e-02 4.00e+02 7.10e-02 8.07e+00 pdb=" N PRO s 59 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO s 59 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO s 59 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR S 58 " -0.047 5.00e-02 4.00e+02 7.10e-02 8.07e+00 pdb=" N PRO S 59 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO S 59 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO S 59 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 58 " 0.047 5.00e-02 4.00e+02 7.09e-02 8.03e+00 pdb=" N PRO A 59 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 59 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 59 " 0.039 5.00e-02 4.00e+02 ... (remaining 10567 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 17773 2.82 - 3.34: 47201 3.34 - 3.86: 95385 3.86 - 4.38: 107492 4.38 - 4.90: 194200 Nonbonded interactions: 462051 Sorted by model distance: nonbonded pdb=" NZ LYS L 379 " pdb=" O PRO O 184 " model vdw 2.304 3.120 nonbonded pdb=" NZ LYS f 379 " pdb=" O PRO i 184 " model vdw 2.340 3.120 nonbonded pdb=" NZ LYS F 379 " pdb=" O PRO I 184 " model vdw 2.340 3.120 nonbonded pdb=" NH1 ARG C 205 " pdb=" OE1 GLU C 226 " model vdw 2.341 3.120 nonbonded pdb=" NH1 ARG c 205 " pdb=" OE1 GLU c 226 " model vdw 2.341 3.120 ... (remaining 462046 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'a' selection = chain 'd' selection = chain 'g' selection = chain 'j' selection = chain 'm' selection = chain 'p' selection = chain 's' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'T' selection = chain 'b' selection = chain 'e' selection = chain 'h' selection = chain 'k' selection = chain 'n' selection = chain 'q' selection = chain 't' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'c' selection = chain 'f' selection = chain 'i' selection = chain 'l' selection = chain 'o' selection = chain 'r' selection = chain 'u' } 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.380 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: 1.830 Check model and map are aligned: 0.350 Set scattering table: 0.440 Process input model: 115.440 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.570 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 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 0.060 60676 Z= 0.538 Angle : 0.918 12.773 82558 Z= 0.477 Chirality : 0.060 0.263 9338 Planarity : 0.007 0.071 10570 Dihedral : 9.515 75.749 22176 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.22 % Allowed : 1.94 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.49 (0.08), residues: 7378 helix: -5.00 (0.04), residues: 1344 sheet: -1.68 (0.10), residues: 2226 loop : -3.04 (0.07), residues: 3808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP f 296 HIS 0.016 0.003 HIS L 234 PHE 0.030 0.003 PHE N 199 TYR 0.023 0.003 TYR h 126 ARG 0.017 0.002 ARG C 200 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14756 Ramachandran restraints generated. 7378 Oldfield, 0 Emsley, 7378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14756 Ramachandran restraints generated. 7378 Oldfield, 0 Emsley, 7378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1603 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1589 time to evaluate : 5.187 Fit side-chains REVERT: a 60 MET cc_start: 0.8287 (tpt) cc_final: 0.8033 (tpt) REVERT: b 64 SER cc_start: 0.9271 (t) cc_final: 0.9066 (t) REVERT: c 272 ASP cc_start: 0.7922 (t0) cc_final: 0.7717 (t0) REVERT: c 274 THR cc_start: 0.9384 (t) cc_final: 0.9052 (m) REVERT: d 56 GLN cc_start: 0.8882 (pt0) cc_final: 0.8638 (pt0) REVERT: d 60 MET cc_start: 0.8375 (tpt) cc_final: 0.8135 (tpt) REVERT: e 33 GLU cc_start: 0.7795 (tt0) cc_final: 0.7589 (tt0) REVERT: e 38 ARG cc_start: 0.7588 (ttm-80) cc_final: 0.7257 (ttp80) REVERT: e 93 MET cc_start: 0.8750 (ttp) cc_final: 0.8514 (ttt) REVERT: e 195 ASP cc_start: 0.8763 (p0) cc_final: 0.8545 (p0) REVERT: f 189 LYS cc_start: 0.9161 (pttm) cc_final: 0.8714 (pttp) REVERT: f 274 THR cc_start: 0.9419 (t) cc_final: 0.9111 (m) REVERT: g 60 MET cc_start: 0.8428 (tpt) cc_final: 0.8212 (tpt) REVERT: h 40 TYR cc_start: 0.9013 (m-80) cc_final: 0.8469 (m-80) REVERT: i 274 THR cc_start: 0.9364 (t) cc_final: 0.9046 (m) REVERT: j 60 MET cc_start: 0.8423 (tpt) cc_final: 0.8175 (tpt) REVERT: k 112 ASP cc_start: 0.7564 (t0) cc_final: 0.7337 (t0) REVERT: l 189 LYS cc_start: 0.9209 (pttm) cc_final: 0.8727 (pttp) REVERT: l 274 THR cc_start: 0.9470 (t) cc_final: 0.9135 (m) REVERT: m 60 MET cc_start: 0.8324 (tpt) cc_final: 0.7969 (tpp) REVERT: o 189 LYS cc_start: 0.9197 (pttm) cc_final: 0.8925 (pttp) REVERT: o 274 THR cc_start: 0.9412 (t) cc_final: 0.9160 (m) REVERT: p 46 GLU cc_start: 0.7870 (tt0) cc_final: 0.7580 (tt0) REVERT: p 60 MET cc_start: 0.8379 (tpt) cc_final: 0.7897 (tpp) REVERT: p 98 THR cc_start: 0.8000 (m) cc_final: 0.7764 (p) REVERT: q 195 ASP cc_start: 0.8719 (p0) cc_final: 0.8511 (p0) REVERT: r 189 LYS cc_start: 0.9144 (pttm) cc_final: 0.8890 (pttp) REVERT: r 225 THR cc_start: 0.9417 (t) cc_final: 0.9111 (p) REVERT: r 352 GLU cc_start: 0.8237 (mt-10) cc_final: 0.8017 (mt-10) REVERT: s 46 GLU cc_start: 0.7816 (tt0) cc_final: 0.7310 (tt0) REVERT: t 112 ASP cc_start: 0.7384 (t0) cc_final: 0.7137 (t0) REVERT: u 189 LYS cc_start: 0.9228 (pttm) cc_final: 0.8964 (pttp) REVERT: u 274 THR cc_start: 0.9360 (t) cc_final: 0.9083 (m) REVERT: A 60 MET cc_start: 0.8295 (tpt) cc_final: 0.8039 (tpt) REVERT: A 85 SER cc_start: 0.8201 (m) cc_final: 0.7996 (p) REVERT: B 64 SER cc_start: 0.9271 (t) cc_final: 0.9066 (t) REVERT: C 272 ASP cc_start: 0.7920 (t0) cc_final: 0.7713 (t0) REVERT: C 274 THR cc_start: 0.9383 (t) cc_final: 0.9053 (m) REVERT: D 56 GLN cc_start: 0.8879 (pt0) cc_final: 0.8634 (pt0) REVERT: D 60 MET cc_start: 0.8373 (tpt) cc_final: 0.8132 (tpt) REVERT: E 33 GLU cc_start: 0.7794 (tt0) cc_final: 0.7590 (tt0) REVERT: E 38 ARG cc_start: 0.7585 (ttm-80) cc_final: 0.7255 (ttp80) REVERT: E 93 MET cc_start: 0.8750 (ttp) cc_final: 0.8516 (ttt) REVERT: E 195 ASP cc_start: 0.8763 (p0) cc_final: 0.8544 (p0) REVERT: F 189 LYS cc_start: 0.9163 (pttm) cc_final: 0.8716 (pttp) REVERT: F 274 THR cc_start: 0.9420 (t) cc_final: 0.9112 (m) REVERT: G 60 MET cc_start: 0.8424 (tpt) cc_final: 0.8208 (tpt) REVERT: H 40 TYR cc_start: 0.9008 (m-80) cc_final: 0.8465 (m-80) REVERT: I 274 THR cc_start: 0.9365 (t) cc_final: 0.9046 (m) REVERT: J 60 MET cc_start: 0.8428 (tpt) cc_final: 0.8182 (tpt) REVERT: K 112 ASP cc_start: 0.7562 (t0) cc_final: 0.7336 (t0) REVERT: L 189 LYS cc_start: 0.9211 (pttm) cc_final: 0.8730 (pttp) REVERT: L 274 THR cc_start: 0.9470 (t) cc_final: 0.9135 (m) REVERT: M 60 MET cc_start: 0.8322 (tpt) cc_final: 0.7966 (tpp) REVERT: O 189 LYS cc_start: 0.9157 (pttm) cc_final: 0.8896 (pttp) REVERT: O 274 THR cc_start: 0.9473 (t) cc_final: 0.9205 (m) REVERT: P 46 GLU cc_start: 0.7877 (tt0) cc_final: 0.7585 (tt0) REVERT: P 60 MET cc_start: 0.8383 (tpt) cc_final: 0.7905 (tpp) REVERT: P 98 THR cc_start: 0.8001 (m) cc_final: 0.7760 (p) REVERT: Q 195 ASP cc_start: 0.8723 (p0) cc_final: 0.8513 (p0) REVERT: R 189 LYS cc_start: 0.9145 (pttm) cc_final: 0.8886 (pttp) REVERT: R 225 THR cc_start: 0.9416 (t) cc_final: 0.9111 (p) REVERT: R 352 GLU cc_start: 0.8236 (mt-10) cc_final: 0.8010 (mt-10) REVERT: S 46 GLU cc_start: 0.7817 (tt0) cc_final: 0.7297 (tt0) REVERT: T 112 ASP cc_start: 0.7384 (t0) cc_final: 0.7136 (t0) REVERT: U 189 LYS cc_start: 0.9230 (pttm) cc_final: 0.8966 (pttp) REVERT: U 274 THR cc_start: 0.9361 (t) cc_final: 0.9085 (m) outliers start: 14 outliers final: 14 residues processed: 1603 average time/residue: 0.5557 time to fit residues: 1493.0620 Evaluate side-chains 910 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 896 time to evaluate : 5.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 273 VAL Chi-restraints excluded: chain f residue 273 VAL Chi-restraints excluded: chain i residue 273 VAL Chi-restraints excluded: chain l residue 273 VAL Chi-restraints excluded: chain o residue 273 VAL Chi-restraints excluded: chain r residue 273 VAL Chi-restraints excluded: chain u residue 273 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain O residue 273 VAL Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain U residue 273 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 626 optimal weight: 0.6980 chunk 562 optimal weight: 0.9980 chunk 312 optimal weight: 3.9990 chunk 192 optimal weight: 0.3980 chunk 379 optimal weight: 6.9990 chunk 300 optimal weight: 0.0670 chunk 581 optimal weight: 0.7980 chunk 225 optimal weight: 0.9990 chunk 353 optimal weight: 0.9980 chunk 432 optimal weight: 3.9990 chunk 673 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 82 ASN b 51 GLN c 298 ASN e 51 GLN f 234 HIS f 298 ASN f 374 ASN g 129 GLN h 51 GLN h 139 ASN i 234 HIS i 298 ASN k 51 GLN m 39 HIS m 129 GLN o 234 HIS o 298 ASN p 129 GLN r 298 ASN s 129 GLN t 51 GLN u 374 ASN A 82 ASN B 51 GLN E 51 GLN F 234 HIS F 298 ASN F 374 ASN G 129 GLN H 51 GLN H 139 ASN I 234 HIS I 298 ASN K 51 GLN M 39 HIS M 129 GLN O 234 HIS P 129 GLN Q 51 GLN S 129 GLN T 51 GLN U 298 ASN U 374 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 60676 Z= 0.147 Angle : 0.545 7.006 82558 Z= 0.280 Chirality : 0.043 0.144 9338 Planarity : 0.005 0.058 10570 Dihedral : 5.131 32.598 8274 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.53 % Allowed : 9.10 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.08), residues: 7378 helix: -3.00 (0.10), residues: 1288 sheet: -1.28 (0.10), residues: 2212 loop : -2.35 (0.08), residues: 3878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 71 HIS 0.007 0.001 HIS P 36 PHE 0.009 0.001 PHE o 383 TYR 0.010 0.001 TYR Q 34 ARG 0.004 0.000 ARG t 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14756 Ramachandran restraints generated. 7378 Oldfield, 0 Emsley, 7378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14756 Ramachandran restraints generated. 7378 Oldfield, 0 Emsley, 7378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1128 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 1029 time to evaluate : 5.221 Fit side-chains REVERT: a 60 MET cc_start: 0.8439 (tpt) cc_final: 0.8156 (tpt) REVERT: c 272 ASP cc_start: 0.7823 (t0) cc_final: 0.7601 (t0) REVERT: c 323 GLU cc_start: 0.6117 (tt0) cc_final: 0.5794 (tt0) REVERT: d 60 MET cc_start: 0.8443 (tpt) cc_final: 0.8080 (tpp) REVERT: e 38 ARG cc_start: 0.7466 (ttm-80) cc_final: 0.7123 (ttp80) REVERT: e 195 ASP cc_start: 0.8649 (p0) cc_final: 0.8287 (p0) REVERT: f 189 LYS cc_start: 0.9164 (pttm) cc_final: 0.8745 (pttp) REVERT: i 225 THR cc_start: 0.9319 (t) cc_final: 0.9048 (p) REVERT: j 60 MET cc_start: 0.8509 (tpt) cc_final: 0.8180 (tpp) REVERT: l 189 LYS cc_start: 0.9178 (pttm) cc_final: 0.8731 (pttp) REVERT: l 357 LYS cc_start: 0.8859 (ttmt) cc_final: 0.8645 (ttmm) REVERT: m 60 MET cc_start: 0.8532 (tpt) cc_final: 0.8132 (tpp) REVERT: o 189 LYS cc_start: 0.9203 (pttm) cc_final: 0.8897 (pttp) REVERT: p 60 MET cc_start: 0.8483 (tpt) cc_final: 0.8038 (tpp) REVERT: r 189 LYS cc_start: 0.9096 (pttm) cc_final: 0.8778 (pttp) REVERT: r 215 ASP cc_start: 0.8886 (m-30) cc_final: 0.8647 (t0) REVERT: r 225 THR cc_start: 0.9389 (t) cc_final: 0.9137 (p) REVERT: u 189 LYS cc_start: 0.9147 (pttm) cc_final: 0.8916 (pttp) REVERT: A 60 MET cc_start: 0.8445 (tpt) cc_final: 0.8161 (tpt) REVERT: C 272 ASP cc_start: 0.7819 (t0) cc_final: 0.7603 (t0) REVERT: C 323 GLU cc_start: 0.6118 (tt0) cc_final: 0.5796 (tt0) REVERT: D 60 MET cc_start: 0.8446 (tpt) cc_final: 0.8081 (tpp) REVERT: E 38 ARG cc_start: 0.7465 (ttm-80) cc_final: 0.7122 (ttp80) REVERT: E 195 ASP cc_start: 0.8648 (p0) cc_final: 0.8283 (p0) REVERT: F 189 LYS cc_start: 0.9165 (pttm) cc_final: 0.8747 (pttp) REVERT: I 225 THR cc_start: 0.9318 (t) cc_final: 0.9044 (p) REVERT: J 60 MET cc_start: 0.8489 (tpt) cc_final: 0.8159 (tpp) REVERT: L 189 LYS cc_start: 0.9178 (pttm) cc_final: 0.8734 (pttp) REVERT: L 357 LYS cc_start: 0.8860 (ttmt) cc_final: 0.8640 (ttmm) REVERT: M 60 MET cc_start: 0.8536 (tpt) cc_final: 0.8135 (tpp) REVERT: O 189 LYS cc_start: 0.9200 (pttm) cc_final: 0.8913 (pttp) REVERT: O 357 LYS cc_start: 0.8797 (ttmt) cc_final: 0.8597 (ttmm) REVERT: P 60 MET cc_start: 0.8487 (tpt) cc_final: 0.8037 (tpp) REVERT: R 189 LYS cc_start: 0.9105 (pttm) cc_final: 0.8876 (pttp) REVERT: R 215 ASP cc_start: 0.8886 (m-30) cc_final: 0.8645 (t0) REVERT: R 225 THR cc_start: 0.9391 (t) cc_final: 0.9137 (p) REVERT: U 189 LYS cc_start: 0.9149 (pttm) cc_final: 0.8916 (pttp) outliers start: 99 outliers final: 42 residues processed: 1091 average time/residue: 0.6412 time to fit residues: 1152.5266 Evaluate side-chains 945 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 903 time to evaluate : 5.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 122 SER Chi-restraints excluded: chain c residue 273 VAL Chi-restraints excluded: chain d residue 122 SER Chi-restraints excluded: chain f residue 273 VAL Chi-restraints excluded: chain g residue 122 SER Chi-restraints excluded: chain h residue 129 VAL Chi-restraints excluded: chain h residue 149 ASN Chi-restraints excluded: chain h residue 194 MET Chi-restraints excluded: chain i residue 273 VAL Chi-restraints excluded: chain j residue 122 SER Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain l residue 273 VAL Chi-restraints excluded: chain l residue 276 MET Chi-restraints excluded: chain m residue 127 LEU Chi-restraints excluded: chain n residue 64 SER Chi-restraints excluded: chain n residue 129 VAL Chi-restraints excluded: chain n residue 194 MET Chi-restraints excluded: chain o residue 273 VAL Chi-restraints excluded: chain q residue 129 VAL Chi-restraints excluded: chain r residue 273 VAL Chi-restraints excluded: chain u residue 273 VAL Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 194 MET Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 276 MET Chi-restraints excluded: chain M residue 127 LEU Chi-restraints excluded: chain N residue 64 SER Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 194 MET Chi-restraints excluded: chain O residue 273 VAL Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain U residue 273 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 374 optimal weight: 0.6980 chunk 209 optimal weight: 6.9990 chunk 560 optimal weight: 2.9990 chunk 458 optimal weight: 0.0670 chunk 185 optimal weight: 1.9990 chunk 675 optimal weight: 2.9990 chunk 729 optimal weight: 2.9990 chunk 601 optimal weight: 1.9990 chunk 669 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 chunk 541 optimal weight: 7.9990 overall best weight: 1.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 82 ASN b 30 GLN g 129 GLN h 30 GLN h 118 GLN h 121 GLN h 139 ASN k 121 GLN m 129 GLN n 51 GLN o 342 ASN p 129 GLN q 51 GLN q 125 GLN r 342 ASN s 102 GLN B 30 GLN E 121 GLN F 342 ASN G 129 GLN H 30 GLN H 118 GLN H 121 GLN H 139 ASN L 342 ASN M 129 GLN O 342 ASN P 129 GLN Q 121 GLN Q 125 GLN R 342 ASN S 102 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 60676 Z= 0.227 Angle : 0.542 7.679 82558 Z= 0.275 Chirality : 0.044 0.140 9338 Planarity : 0.005 0.050 10570 Dihedral : 4.999 37.547 8274 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.94 % Allowed : 11.59 % Favored : 86.47 % 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: -2.34 (0.09), residues: 7378 helix: -1.58 (0.13), residues: 1302 sheet: -0.79 (0.11), residues: 2184 loop : -2.01 (0.09), residues: 3892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 71 HIS 0.008 0.002 HIS D 36 PHE 0.011 0.001 PHE L 383 TYR 0.013 0.001 TYR L 320 ARG 0.005 0.000 ARG k 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14756 Ramachandran restraints generated. 7378 Oldfield, 0 Emsley, 7378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14756 Ramachandran restraints generated. 7378 Oldfield, 0 Emsley, 7378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1030 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 904 time to evaluate : 5.208 Fit side-chains REVERT: a 60 MET cc_start: 0.8437 (tpt) cc_final: 0.8158 (tpt) REVERT: d 60 MET cc_start: 0.8578 (tpt) cc_final: 0.8230 (tpp) REVERT: e 38 ARG cc_start: 0.7498 (ttm-80) cc_final: 0.7149 (ttp80) REVERT: e 195 ASP cc_start: 0.8668 (p0) cc_final: 0.8273 (p0) REVERT: f 189 LYS cc_start: 0.9185 (pttm) cc_final: 0.8789 (pttp) REVERT: f 306 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8402 (mt) REVERT: h 139 ASN cc_start: 0.7823 (m-40) cc_final: 0.7583 (m-40) REVERT: j 60 MET cc_start: 0.8476 (tpt) cc_final: 0.8163 (tpp) REVERT: l 189 LYS cc_start: 0.9140 (pttm) cc_final: 0.8750 (pttp) REVERT: l 357 LYS cc_start: 0.8889 (ttmt) cc_final: 0.8625 (ttmm) REVERT: m 60 MET cc_start: 0.8639 (tpt) cc_final: 0.8241 (tpp) REVERT: o 189 LYS cc_start: 0.9110 (pttm) cc_final: 0.8820 (pttp) REVERT: o 308 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8249 (mp) REVERT: p 60 MET cc_start: 0.8570 (tpt) cc_final: 0.8189 (tpp) REVERT: p 128 VAL cc_start: 0.8731 (t) cc_final: 0.8440 (p) REVERT: r 225 THR cc_start: 0.9441 (t) cc_final: 0.9182 (p) REVERT: u 189 LYS cc_start: 0.9195 (pttm) cc_final: 0.8830 (pttp) REVERT: A 60 MET cc_start: 0.8447 (tpt) cc_final: 0.8143 (tpt) REVERT: D 60 MET cc_start: 0.8579 (tpt) cc_final: 0.8228 (tpp) REVERT: E 38 ARG cc_start: 0.7497 (ttm-80) cc_final: 0.7153 (ttp80) REVERT: E 195 ASP cc_start: 0.8669 (p0) cc_final: 0.8286 (p0) REVERT: F 189 LYS cc_start: 0.9183 (pttm) cc_final: 0.8786 (pttp) REVERT: F 306 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8402 (mt) REVERT: H 139 ASN cc_start: 0.7828 (m-40) cc_final: 0.7605 (m110) REVERT: J 60 MET cc_start: 0.8476 (tpt) cc_final: 0.8166 (tpp) REVERT: L 189 LYS cc_start: 0.9141 (pttm) cc_final: 0.8757 (pttp) REVERT: L 226 GLU cc_start: 0.8698 (tt0) cc_final: 0.8438 (tt0) REVERT: L 276 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7856 (ptm) REVERT: L 357 LYS cc_start: 0.8893 (ttmt) cc_final: 0.8624 (ttmm) REVERT: M 60 MET cc_start: 0.8643 (tpt) cc_final: 0.8239 (tpp) REVERT: O 189 LYS cc_start: 0.9199 (pttm) cc_final: 0.8906 (pttp) REVERT: P 60 MET cc_start: 0.8571 (tpt) cc_final: 0.8192 (tpp) REVERT: P 128 VAL cc_start: 0.8728 (t) cc_final: 0.8433 (p) REVERT: R 225 THR cc_start: 0.9440 (t) cc_final: 0.9157 (p) REVERT: U 189 LYS cc_start: 0.9196 (pttm) cc_final: 0.8831 (pttp) outliers start: 126 outliers final: 77 residues processed: 991 average time/residue: 0.6210 time to fit residues: 1013.8065 Evaluate side-chains 937 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 856 time to evaluate : 5.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 122 SER Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain b residue 89 VAL Chi-restraints excluded: chain c residue 273 VAL Chi-restraints excluded: chain c residue 386 VAL Chi-restraints excluded: chain d residue 122 SER Chi-restraints excluded: chain e residue 74 THR Chi-restraints excluded: chain f residue 273 VAL Chi-restraints excluded: chain f residue 306 ILE Chi-restraints excluded: chain h residue 74 THR Chi-restraints excluded: chain h residue 83 LYS Chi-restraints excluded: chain h residue 129 VAL Chi-restraints excluded: chain h residue 149 ASN Chi-restraints excluded: chain h residue 194 MET Chi-restraints excluded: chain i residue 273 VAL Chi-restraints excluded: chain j residue 122 SER Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain k residue 74 THR Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain l residue 273 VAL Chi-restraints excluded: chain l residue 276 MET Chi-restraints excluded: chain m residue 122 SER Chi-restraints excluded: chain m residue 127 LEU Chi-restraints excluded: chain n residue 74 THR Chi-restraints excluded: chain n residue 89 VAL Chi-restraints excluded: chain n residue 129 VAL Chi-restraints excluded: chain n residue 194 MET Chi-restraints excluded: chain o residue 273 VAL Chi-restraints excluded: chain o residue 308 LEU Chi-restraints excluded: chain p residue 122 SER Chi-restraints excluded: chain q residue 74 THR Chi-restraints excluded: chain q residue 89 VAL Chi-restraints excluded: chain q residue 129 VAL Chi-restraints excluded: chain r residue 273 VAL Chi-restraints excluded: chain s residue 47 ILE Chi-restraints excluded: chain s residue 122 SER Chi-restraints excluded: chain t residue 44 THR Chi-restraints excluded: chain t residue 74 THR Chi-restraints excluded: chain t residue 89 VAL Chi-restraints excluded: chain t residue 194 MET Chi-restraints excluded: chain u residue 273 VAL Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 194 MET Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 276 MET Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain M residue 127 LEU Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 194 MET Chi-restraints excluded: chain O residue 273 VAL Chi-restraints excluded: chain P residue 122 SER Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 122 SER Chi-restraints excluded: chain T residue 44 THR Chi-restraints excluded: chain T residue 74 THR Chi-restraints excluded: chain T residue 89 VAL Chi-restraints excluded: chain T residue 194 MET Chi-restraints excluded: chain U residue 273 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 666 optimal weight: 0.9980 chunk 507 optimal weight: 0.0870 chunk 350 optimal weight: 4.9990 chunk 74 optimal weight: 0.0870 chunk 322 optimal weight: 0.7980 chunk 453 optimal weight: 0.7980 chunk 677 optimal weight: 4.9990 chunk 717 optimal weight: 1.9990 chunk 353 optimal weight: 0.5980 chunk 642 optimal weight: 2.9990 chunk 193 optimal weight: 8.9990 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 232 HIS e 121 GLN g 129 GLN h 118 GLN k 125 GLN m 129 GLN n 121 GLN p 129 GLN q 121 GLN q 232 HIS t 125 GLN A 82 ASN B 232 HIS G 129 GLN H 118 GLN K 125 GLN M 129 GLN P 129 GLN Q 232 HIS T 125 GLN T 232 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 60676 Z= 0.127 Angle : 0.476 6.849 82558 Z= 0.241 Chirality : 0.042 0.127 9338 Planarity : 0.004 0.047 10570 Dihedral : 4.532 35.977 8274 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.64 % Allowed : 13.33 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.09), residues: 7378 helix: -0.81 (0.14), residues: 1302 sheet: -0.44 (0.11), residues: 2170 loop : -1.77 (0.09), residues: 3906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP m 71 HIS 0.006 0.001 HIS D 36 PHE 0.007 0.001 PHE o 383 TYR 0.011 0.001 TYR l 320 ARG 0.004 0.000 ARG k 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14756 Ramachandran restraints generated. 7378 Oldfield, 0 Emsley, 7378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14756 Ramachandran restraints generated. 7378 Oldfield, 0 Emsley, 7378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1083 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 977 time to evaluate : 5.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 60 MET cc_start: 0.8474 (tpt) cc_final: 0.8240 (tpt) REVERT: c 187 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8836 (pp) REVERT: c 272 ASP cc_start: 0.7853 (t0) cc_final: 0.7482 (t0) REVERT: d 60 MET cc_start: 0.8597 (tpt) cc_final: 0.8352 (tpp) REVERT: e 38 ARG cc_start: 0.7506 (ttm-80) cc_final: 0.7152 (ttp80) REVERT: e 195 ASP cc_start: 0.8536 (p0) cc_final: 0.8069 (p0) REVERT: f 189 LYS cc_start: 0.9203 (pttm) cc_final: 0.8847 (pttp) REVERT: g 128 VAL cc_start: 0.8648 (t) cc_final: 0.8380 (p) REVERT: h 83 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8450 (mttp) REVERT: h 139 ASN cc_start: 0.7828 (m-40) cc_final: 0.7599 (m-40) REVERT: i 347 MET cc_start: 0.7782 (mtm) cc_final: 0.7529 (ttm) REVERT: j 60 MET cc_start: 0.8515 (tpt) cc_final: 0.8234 (tpp) REVERT: k 112 ASP cc_start: 0.7514 (t0) cc_final: 0.7253 (p0) REVERT: l 189 LYS cc_start: 0.9122 (pttm) cc_final: 0.8780 (pttp) REVERT: l 226 GLU cc_start: 0.8649 (tt0) cc_final: 0.8381 (tt0) REVERT: l 244 MET cc_start: 0.8374 (mtp) cc_final: 0.8074 (tpp) REVERT: l 357 LYS cc_start: 0.8857 (ttmt) cc_final: 0.8612 (ttmm) REVERT: m 60 MET cc_start: 0.8648 (tpt) cc_final: 0.8256 (tpp) REVERT: m 107 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8198 (mt-10) REVERT: m 128 VAL cc_start: 0.8428 (t) cc_final: 0.8105 (p) REVERT: o 226 GLU cc_start: 0.8597 (tt0) cc_final: 0.8368 (tt0) REVERT: p 60 MET cc_start: 0.8606 (tpt) cc_final: 0.8319 (tpp) REVERT: p 128 VAL cc_start: 0.8606 (t) cc_final: 0.8282 (p) REVERT: r 154 GLU cc_start: 0.7947 (mp0) cc_final: 0.7609 (mp0) REVERT: r 215 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8388 (t0) REVERT: t 112 ASP cc_start: 0.7297 (t0) cc_final: 0.7025 (p0) REVERT: u 189 LYS cc_start: 0.9113 (pttm) cc_final: 0.8754 (pttp) REVERT: A 60 MET cc_start: 0.8457 (tpt) cc_final: 0.8216 (tpt) REVERT: C 187 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8840 (pp) REVERT: C 272 ASP cc_start: 0.7832 (t0) cc_final: 0.7469 (t0) REVERT: D 60 MET cc_start: 0.8600 (tpt) cc_final: 0.8351 (tpp) REVERT: E 38 ARG cc_start: 0.7502 (ttm-80) cc_final: 0.7149 (ttp80) REVERT: E 195 ASP cc_start: 0.8534 (p0) cc_final: 0.8066 (p0) REVERT: F 189 LYS cc_start: 0.9204 (pttm) cc_final: 0.8850 (pttp) REVERT: G 128 VAL cc_start: 0.8649 (t) cc_final: 0.8379 (p) REVERT: H 83 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8448 (mttp) REVERT: H 139 ASN cc_start: 0.7817 (m-40) cc_final: 0.7589 (m-40) REVERT: I 347 MET cc_start: 0.7793 (mtm) cc_final: 0.7532 (ttm) REVERT: J 60 MET cc_start: 0.8515 (tpt) cc_final: 0.8236 (tpp) REVERT: K 112 ASP cc_start: 0.7515 (t0) cc_final: 0.7252 (p0) REVERT: L 189 LYS cc_start: 0.9123 (pttm) cc_final: 0.8784 (pttp) REVERT: L 226 GLU cc_start: 0.8640 (tt0) cc_final: 0.8370 (tt0) REVERT: L 244 MET cc_start: 0.8374 (mtp) cc_final: 0.8072 (tpp) REVERT: L 357 LYS cc_start: 0.8860 (ttmt) cc_final: 0.8615 (ttmm) REVERT: M 60 MET cc_start: 0.8647 (tpt) cc_final: 0.8253 (tpp) REVERT: M 107 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8195 (mt-10) REVERT: M 128 VAL cc_start: 0.8422 (t) cc_final: 0.8097 (p) REVERT: P 60 MET cc_start: 0.8600 (tpt) cc_final: 0.8324 (tpp) REVERT: P 128 VAL cc_start: 0.8603 (t) cc_final: 0.8276 (p) REVERT: Q 112 ASP cc_start: 0.7327 (t0) cc_final: 0.7056 (p0) REVERT: R 154 GLU cc_start: 0.7948 (mp0) cc_final: 0.7611 (mp0) REVERT: R 215 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.8390 (t0) REVERT: T 112 ASP cc_start: 0.7295 (t0) cc_final: 0.7030 (p0) REVERT: U 189 LYS cc_start: 0.9118 (pttm) cc_final: 0.8758 (pttp) outliers start: 106 outliers final: 63 residues processed: 1030 average time/residue: 0.5992 time to fit residues: 1015.5579 Evaluate side-chains 977 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 908 time to evaluate : 5.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 89 VAL Chi-restraints excluded: chain b residue 101 SER Chi-restraints excluded: chain c residue 187 LEU Chi-restraints excluded: chain c residue 207 ILE Chi-restraints excluded: chain c residue 273 VAL Chi-restraints excluded: chain c residue 300 ILE Chi-restraints excluded: chain c residue 386 VAL Chi-restraints excluded: chain d residue 129 GLN Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain f residue 273 VAL Chi-restraints excluded: chain f residue 323 GLU Chi-restraints excluded: chain h residue 83 LYS Chi-restraints excluded: chain h residue 101 SER Chi-restraints excluded: chain h residue 129 VAL Chi-restraints excluded: chain h residue 194 MET Chi-restraints excluded: chain i residue 273 VAL Chi-restraints excluded: chain l residue 273 VAL Chi-restraints excluded: chain l residue 323 GLU Chi-restraints excluded: chain m residue 127 LEU Chi-restraints excluded: chain n residue 76 ARG Chi-restraints excluded: chain n residue 89 VAL Chi-restraints excluded: chain n residue 129 VAL Chi-restraints excluded: chain n residue 194 MET Chi-restraints excluded: chain o residue 207 ILE Chi-restraints excluded: chain o residue 273 VAL Chi-restraints excluded: chain p residue 122 SER Chi-restraints excluded: chain q residue 101 SER Chi-restraints excluded: chain q residue 129 VAL Chi-restraints excluded: chain r residue 215 ASP Chi-restraints excluded: chain r residue 273 VAL Chi-restraints excluded: chain s residue 47 ILE Chi-restraints excluded: chain s residue 122 SER Chi-restraints excluded: chain t residue 194 MET Chi-restraints excluded: chain u residue 273 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain D residue 129 GLN Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 323 GLU Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 194 MET Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 323 GLU Chi-restraints excluded: chain M residue 127 LEU Chi-restraints excluded: chain N residue 76 ARG Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 194 MET Chi-restraints excluded: chain O residue 207 ILE Chi-restraints excluded: chain O residue 273 VAL Chi-restraints excluded: chain P residue 122 SER Chi-restraints excluded: chain Q residue 101 SER Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain R residue 215 ASP Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 122 SER Chi-restraints excluded: chain T residue 194 MET Chi-restraints excluded: chain U residue 273 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 597 optimal weight: 7.9990 chunk 407 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 534 optimal weight: 5.9990 chunk 295 optimal weight: 0.8980 chunk 612 optimal weight: 4.9990 chunk 495 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 366 optimal weight: 3.9990 chunk 643 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 30 GLN b 125 GLN e 51 GLN g 129 GLN h 51 GLN h 118 GLN k 51 GLN l 298 ASN l 353 GLN m 129 GLN n 51 GLN o 353 GLN p 129 GLN q 51 GLN q 125 GLN t 30 GLN t 51 GLN t 232 HIS B 30 GLN B 125 GLN E 51 GLN G 129 GLN H 51 GLN H 118 GLN K 51 GLN L 298 ASN L 353 GLN M 129 GLN N 121 GLN O 353 GLN P 129 GLN Q 51 GLN Q 125 GLN T 30 GLN T 51 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 60676 Z= 0.494 Angle : 0.649 9.577 82558 Z= 0.331 Chirality : 0.048 0.157 9338 Planarity : 0.005 0.046 10570 Dihedral : 5.317 41.749 8274 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.33 % Allowed : 12.68 % 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: -1.84 (0.09), residues: 7378 helix: -0.59 (0.14), residues: 1330 sheet: -0.66 (0.11), residues: 2240 loop : -1.80 (0.09), residues: 3808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP o 296 HIS 0.011 0.002 HIS H 232 PHE 0.019 0.002 PHE l 383 TYR 0.023 0.002 TYR b 126 ARG 0.011 0.001 ARG i 200 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14756 Ramachandran restraints generated. 7378 Oldfield, 0 Emsley, 7378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14756 Ramachandran restraints generated. 7378 Oldfield, 0 Emsley, 7378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1038 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 887 time to evaluate : 5.270 Fit side-chains REVERT: a 60 MET cc_start: 0.8526 (tpt) cc_final: 0.8286 (tpt) REVERT: c 187 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8877 (pp) REVERT: c 226 GLU cc_start: 0.8541 (tt0) cc_final: 0.8336 (tt0) REVERT: d 60 MET cc_start: 0.8658 (tpt) cc_final: 0.8295 (tpt) REVERT: d 128 VAL cc_start: 0.8736 (t) cc_final: 0.8267 (p) REVERT: e 195 ASP cc_start: 0.8751 (p0) cc_final: 0.8399 (p0) REVERT: f 189 LYS cc_start: 0.9129 (pttm) cc_final: 0.8771 (pttp) REVERT: g 128 VAL cc_start: 0.8820 (t) cc_final: 0.8486 (p) REVERT: h 139 ASN cc_start: 0.7826 (m-40) cc_final: 0.7565 (m-40) REVERT: i 350 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8290 (mt) REVERT: j 128 VAL cc_start: 0.8743 (t) cc_final: 0.8371 (p) REVERT: k 112 ASP cc_start: 0.7756 (t0) cc_final: 0.7466 (p0) REVERT: l 189 LYS cc_start: 0.9126 (pttm) cc_final: 0.8707 (pttp) REVERT: l 350 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8158 (mt) REVERT: m 60 MET cc_start: 0.8662 (tpt) cc_final: 0.8280 (tpp) REVERT: m 128 VAL cc_start: 0.8492 (t) cc_final: 0.8196 (p) REVERT: o 308 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8254 (mp) REVERT: p 60 MET cc_start: 0.8601 (tpt) cc_final: 0.8278 (tpp) REVERT: p 128 VAL cc_start: 0.8716 (t) cc_final: 0.8321 (p) REVERT: r 215 ASP cc_start: 0.8923 (OUTLIER) cc_final: 0.8603 (t0) REVERT: t 79 VAL cc_start: 0.9390 (OUTLIER) cc_final: 0.9185 (m) REVERT: u 189 LYS cc_start: 0.9165 (pttm) cc_final: 0.8867 (pttp) REVERT: A 60 MET cc_start: 0.8516 (tpt) cc_final: 0.8265 (tpt) REVERT: C 187 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8885 (pp) REVERT: C 226 GLU cc_start: 0.8543 (tt0) cc_final: 0.8338 (tt0) REVERT: D 60 MET cc_start: 0.8660 (tpt) cc_final: 0.8302 (tpt) REVERT: D 128 VAL cc_start: 0.8730 (t) cc_final: 0.8253 (p) REVERT: E 195 ASP cc_start: 0.8749 (p0) cc_final: 0.8398 (p0) REVERT: F 189 LYS cc_start: 0.9128 (pttm) cc_final: 0.8770 (pttp) REVERT: F 357 LYS cc_start: 0.8694 (ttmm) cc_final: 0.8418 (ttmt) REVERT: G 128 VAL cc_start: 0.8821 (t) cc_final: 0.8485 (p) REVERT: H 139 ASN cc_start: 0.7834 (m-40) cc_final: 0.7576 (m-40) REVERT: I 350 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8287 (mt) REVERT: J 128 VAL cc_start: 0.8727 (t) cc_final: 0.8388 (p) REVERT: K 112 ASP cc_start: 0.7752 (t0) cc_final: 0.7463 (p0) REVERT: L 189 LYS cc_start: 0.9126 (pttm) cc_final: 0.8713 (pttp) REVERT: L 350 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8181 (mt) REVERT: M 60 MET cc_start: 0.8662 (tpt) cc_final: 0.8277 (tpp) REVERT: M 128 VAL cc_start: 0.8484 (t) cc_final: 0.8184 (p) REVERT: O 189 LYS cc_start: 0.9116 (pttm) cc_final: 0.8857 (pttp) REVERT: P 60 MET cc_start: 0.8604 (tpt) cc_final: 0.8282 (tpp) REVERT: P 128 VAL cc_start: 0.8708 (t) cc_final: 0.8310 (p) REVERT: R 215 ASP cc_start: 0.8923 (OUTLIER) cc_final: 0.8604 (t0) REVERT: T 79 VAL cc_start: 0.9386 (OUTLIER) cc_final: 0.9180 (m) REVERT: U 189 LYS cc_start: 0.9169 (pttm) cc_final: 0.8869 (pttp) outliers start: 151 outliers final: 104 residues processed: 979 average time/residue: 0.6889 time to fit residues: 1121.4235 Evaluate side-chains 964 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 849 time to evaluate : 5.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 47 ILE Chi-restraints excluded: chain a residue 122 SER Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain b residue 89 VAL Chi-restraints excluded: chain b residue 101 SER Chi-restraints excluded: chain c residue 187 LEU Chi-restraints excluded: chain c residue 215 ASP Chi-restraints excluded: chain c residue 223 ILE Chi-restraints excluded: chain c residue 273 VAL Chi-restraints excluded: chain c residue 300 ILE Chi-restraints excluded: chain c residue 386 VAL Chi-restraints excluded: chain d residue 47 ILE Chi-restraints excluded: chain e residue 74 THR Chi-restraints excluded: chain e residue 86 ASN Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain f residue 215 ASP Chi-restraints excluded: chain f residue 223 ILE Chi-restraints excluded: chain f residue 273 VAL Chi-restraints excluded: chain g residue 47 ILE Chi-restraints excluded: chain h residue 74 THR Chi-restraints excluded: chain h residue 83 LYS Chi-restraints excluded: chain h residue 101 SER Chi-restraints excluded: chain h residue 129 VAL Chi-restraints excluded: chain h residue 149 ASN Chi-restraints excluded: chain h residue 194 MET Chi-restraints excluded: chain i residue 223 ILE Chi-restraints excluded: chain i residue 273 VAL Chi-restraints excluded: chain i residue 350 LEU Chi-restraints excluded: chain j residue 122 SER Chi-restraints excluded: chain k residue 74 THR Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain l residue 273 VAL Chi-restraints excluded: chain l residue 350 LEU Chi-restraints excluded: chain m residue 122 SER Chi-restraints excluded: chain m residue 127 LEU Chi-restraints excluded: chain n residue 74 THR Chi-restraints excluded: chain n residue 101 SER Chi-restraints excluded: chain n residue 129 VAL Chi-restraints excluded: chain n residue 194 MET Chi-restraints excluded: chain o residue 273 VAL Chi-restraints excluded: chain o residue 308 LEU Chi-restraints excluded: chain p residue 122 SER Chi-restraints excluded: chain p residue 127 LEU Chi-restraints excluded: chain q residue 74 THR Chi-restraints excluded: chain q residue 101 SER Chi-restraints excluded: chain q residue 129 VAL Chi-restraints excluded: chain r residue 215 ASP Chi-restraints excluded: chain r residue 273 VAL Chi-restraints excluded: chain s residue 47 ILE Chi-restraints excluded: chain s residue 122 SER Chi-restraints excluded: chain t residue 74 THR Chi-restraints excluded: chain t residue 79 VAL Chi-restraints excluded: chain t residue 89 VAL Chi-restraints excluded: chain t residue 101 SER Chi-restraints excluded: chain t residue 194 MET Chi-restraints excluded: chain u residue 187 LEU Chi-restraints excluded: chain u residue 273 VAL Chi-restraints excluded: chain u residue 347 MET Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 194 MET Chi-restraints excluded: chain I residue 223 ILE Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 350 LEU Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain L residue 223 ILE Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 350 LEU Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain M residue 127 LEU Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 101 SER Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 194 MET Chi-restraints excluded: chain O residue 273 VAL Chi-restraints excluded: chain P residue 122 SER Chi-restraints excluded: chain P residue 127 LEU Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 101 SER Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain R residue 215 ASP Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 122 SER Chi-restraints excluded: chain T residue 74 THR Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 89 VAL Chi-restraints excluded: chain T residue 101 SER Chi-restraints excluded: chain T residue 194 MET Chi-restraints excluded: chain U residue 187 LEU Chi-restraints excluded: chain U residue 273 VAL Chi-restraints excluded: chain U residue 347 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 241 optimal weight: 0.9990 chunk 645 optimal weight: 0.4980 chunk 141 optimal weight: 0.0980 chunk 421 optimal weight: 0.0470 chunk 177 optimal weight: 1.9990 chunk 717 optimal weight: 0.7980 chunk 595 optimal weight: 2.9990 chunk 332 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 237 optimal weight: 6.9990 chunk 376 optimal weight: 0.6980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 30 GLN b 125 GLN ** e 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 232 HIS g 129 GLN h 118 GLN h 232 HIS k 232 HIS m 129 GLN n 232 HIS p 39 HIS p 129 GLN r 342 ASN A 82 ASN B 30 GLN B 125 GLN ** E 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 HIS G 129 GLN H 118 GLN H 232 HIS K 232 HIS M 129 GLN N 118 GLN N 232 HIS O 374 ASN P 39 HIS P 129 GLN R 342 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 60676 Z= 0.132 Angle : 0.487 7.136 82558 Z= 0.248 Chirality : 0.042 0.139 9338 Planarity : 0.004 0.044 10570 Dihedral : 4.629 37.802 8274 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.93 % Allowed : 13.22 % Favored : 84.85 % 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: -1.38 (0.10), residues: 7378 helix: -0.13 (0.14), residues: 1302 sheet: -0.47 (0.11), residues: 2352 loop : -1.48 (0.10), residues: 3724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 34 HIS 0.005 0.001 HIS s 36 PHE 0.006 0.001 PHE l 383 TYR 0.015 0.001 TYR L 320 ARG 0.003 0.000 ARG O 205 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14756 Ramachandran restraints generated. 7378 Oldfield, 0 Emsley, 7378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14756 Ramachandran restraints generated. 7378 Oldfield, 0 Emsley, 7378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1015 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 890 time to evaluate : 5.308 Fit side-chains REVERT: d 60 MET cc_start: 0.8605 (tpt) cc_final: 0.8338 (tpp) REVERT: d 128 VAL cc_start: 0.8610 (t) cc_final: 0.8153 (p) REVERT: e 195 ASP cc_start: 0.8627 (p0) cc_final: 0.8199 (p0) REVERT: g 128 VAL cc_start: 0.8714 (t) cc_final: 0.8386 (p) REVERT: h 139 ASN cc_start: 0.7830 (m-40) cc_final: 0.7621 (m110) REVERT: i 244 MET cc_start: 0.8580 (mtp) cc_final: 0.8369 (ttm) REVERT: j 60 MET cc_start: 0.8557 (tpt) cc_final: 0.8270 (tpp) REVERT: j 128 VAL cc_start: 0.8627 (t) cc_final: 0.8282 (p) REVERT: l 189 LYS cc_start: 0.9051 (pttm) cc_final: 0.8682 (pttp) REVERT: m 60 MET cc_start: 0.8592 (tpt) cc_final: 0.8216 (tpp) REVERT: m 128 VAL cc_start: 0.8422 (t) cc_final: 0.8117 (p) REVERT: o 226 GLU cc_start: 0.8555 (tt0) cc_final: 0.8348 (tt0) REVERT: o 306 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8255 (mt) REVERT: p 60 MET cc_start: 0.8588 (tpt) cc_final: 0.8349 (tpp) REVERT: p 128 VAL cc_start: 0.8665 (t) cc_final: 0.8296 (p) REVERT: r 215 ASP cc_start: 0.8830 (OUTLIER) cc_final: 0.8424 (t0) REVERT: u 189 LYS cc_start: 0.9055 (pttm) cc_final: 0.8767 (pttp) REVERT: D 60 MET cc_start: 0.8607 (tpt) cc_final: 0.8340 (tpp) REVERT: D 128 VAL cc_start: 0.8604 (t) cc_final: 0.8144 (p) REVERT: E 195 ASP cc_start: 0.8626 (p0) cc_final: 0.8198 (p0) REVERT: G 128 VAL cc_start: 0.8713 (t) cc_final: 0.8384 (p) REVERT: H 139 ASN cc_start: 0.7831 (m-40) cc_final: 0.7625 (m110) REVERT: I 244 MET cc_start: 0.8582 (mtp) cc_final: 0.8371 (ttm) REVERT: J 60 MET cc_start: 0.8534 (tpt) cc_final: 0.8251 (tpp) REVERT: J 128 VAL cc_start: 0.8625 (t) cc_final: 0.8278 (p) REVERT: L 189 LYS cc_start: 0.9060 (pttm) cc_final: 0.8686 (pttp) REVERT: M 60 MET cc_start: 0.8593 (tpt) cc_final: 0.8213 (tpp) REVERT: M 128 VAL cc_start: 0.8413 (t) cc_final: 0.8103 (p) REVERT: P 60 MET cc_start: 0.8587 (tpt) cc_final: 0.8350 (tpp) REVERT: P 128 VAL cc_start: 0.8653 (t) cc_final: 0.8282 (p) REVERT: R 215 ASP cc_start: 0.8832 (OUTLIER) cc_final: 0.8423 (t0) REVERT: U 189 LYS cc_start: 0.9062 (pttm) cc_final: 0.8771 (pttp) outliers start: 125 outliers final: 76 residues processed: 963 average time/residue: 0.6087 time to fit residues: 963.4435 Evaluate side-chains 923 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 844 time to evaluate : 5.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 101 SER Chi-restraints excluded: chain c residue 273 VAL Chi-restraints excluded: chain c residue 386 VAL Chi-restraints excluded: chain d residue 47 ILE Chi-restraints excluded: chain e residue 65 THR Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain e residue 194 MET Chi-restraints excluded: chain f residue 273 VAL Chi-restraints excluded: chain h residue 65 THR Chi-restraints excluded: chain h residue 83 LYS Chi-restraints excluded: chain h residue 101 SER Chi-restraints excluded: chain h residue 149 ASN Chi-restraints excluded: chain h residue 194 MET Chi-restraints excluded: chain i residue 273 VAL Chi-restraints excluded: chain j residue 122 SER Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain l residue 273 VAL Chi-restraints excluded: chain m residue 122 SER Chi-restraints excluded: chain m residue 129 GLN Chi-restraints excluded: chain n residue 64 SER Chi-restraints excluded: chain n residue 65 THR Chi-restraints excluded: chain n residue 129 VAL Chi-restraints excluded: chain n residue 194 MET Chi-restraints excluded: chain o residue 273 VAL Chi-restraints excluded: chain o residue 306 ILE Chi-restraints excluded: chain p residue 122 SER Chi-restraints excluded: chain q residue 65 THR Chi-restraints excluded: chain q residue 101 SER Chi-restraints excluded: chain q residue 129 VAL Chi-restraints excluded: chain r residue 215 ASP Chi-restraints excluded: chain r residue 273 VAL Chi-restraints excluded: chain r residue 343 THR Chi-restraints excluded: chain s residue 47 ILE Chi-restraints excluded: chain s residue 122 SER Chi-restraints excluded: chain t residue 44 THR Chi-restraints excluded: chain t residue 89 VAL Chi-restraints excluded: chain t residue 194 MET Chi-restraints excluded: chain u residue 273 VAL Chi-restraints excluded: chain u residue 350 LEU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 194 MET Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 194 MET Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain M residue 129 GLN Chi-restraints excluded: chain N residue 64 SER Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 194 MET Chi-restraints excluded: chain O residue 273 VAL Chi-restraints excluded: chain P residue 122 SER Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 101 SER Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain R residue 215 ASP Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 122 SER Chi-restraints excluded: chain T residue 44 THR Chi-restraints excluded: chain T residue 89 VAL Chi-restraints excluded: chain T residue 194 MET Chi-restraints excluded: chain U residue 273 VAL Chi-restraints excluded: chain U residue 350 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 692 optimal weight: 7.9990 chunk 80 optimal weight: 0.0470 chunk 409 optimal weight: 0.1980 chunk 524 optimal weight: 8.9990 chunk 406 optimal weight: 0.6980 chunk 604 optimal weight: 0.9980 chunk 400 optimal weight: 3.9990 chunk 715 optimal weight: 0.9990 chunk 447 optimal weight: 4.9990 chunk 436 optimal weight: 0.3980 chunk 330 optimal weight: 6.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 82 ASN b 30 GLN ** e 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 129 GLN m 129 GLN p 129 GLN A 82 ASN B 30 GLN ** E 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 GLN M 129 GLN P 129 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 60676 Z= 0.131 Angle : 0.478 7.564 82558 Z= 0.243 Chirality : 0.042 0.138 9338 Planarity : 0.004 0.044 10570 Dihedral : 4.376 36.718 8274 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.18 % Allowed : 13.22 % Favored : 84.60 % 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: -1.07 (0.10), residues: 7378 helix: 0.15 (0.14), residues: 1316 sheet: 0.02 (0.12), residues: 2100 loop : -1.43 (0.09), residues: 3962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 71 HIS 0.005 0.001 HIS G 36 PHE 0.005 0.001 PHE k 218 TYR 0.016 0.001 TYR l 320 ARG 0.003 0.000 ARG k 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14756 Ramachandran restraints generated. 7378 Oldfield, 0 Emsley, 7378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14756 Ramachandran restraints generated. 7378 Oldfield, 0 Emsley, 7378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1039 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 898 time to evaluate : 5.198 Fit side-chains revert: symmetry clash REVERT: a 56 GLN cc_start: 0.8675 (pt0) cc_final: 0.8448 (pt0) REVERT: d 60 MET cc_start: 0.8607 (tpt) cc_final: 0.8369 (tpp) REVERT: d 128 VAL cc_start: 0.8562 (t) cc_final: 0.8102 (p) REVERT: e 194 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8311 (mtm) REVERT: e 195 ASP cc_start: 0.8487 (p0) cc_final: 0.8045 (p0) REVERT: g 128 VAL cc_start: 0.8603 (t) cc_final: 0.8242 (p) REVERT: h 83 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8479 (mttp) REVERT: i 244 MET cc_start: 0.8568 (mtp) cc_final: 0.8273 (tpp) REVERT: i 350 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8156 (mt) REVERT: j 128 VAL cc_start: 0.8550 (t) cc_final: 0.8215 (p) REVERT: l 189 LYS cc_start: 0.9037 (pttm) cc_final: 0.8617 (pttp) REVERT: l 244 MET cc_start: 0.8356 (mtp) cc_final: 0.8083 (tpp) REVERT: l 319 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7606 (pp20) REVERT: l 350 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7878 (mt) REVERT: m 60 MET cc_start: 0.8591 (tpt) cc_final: 0.8216 (tpp) REVERT: m 128 VAL cc_start: 0.8283 (t) cc_final: 0.7966 (p) REVERT: o 226 GLU cc_start: 0.8543 (tt0) cc_final: 0.8309 (tt0) REVERT: o 347 MET cc_start: 0.7948 (mmm) cc_final: 0.7738 (ttm) REVERT: p 60 MET cc_start: 0.8647 (tpt) cc_final: 0.8421 (tpp) REVERT: p 128 VAL cc_start: 0.8552 (t) cc_final: 0.8138 (p) REVERT: r 215 ASP cc_start: 0.8819 (OUTLIER) cc_final: 0.8386 (t0) REVERT: r 314 LYS cc_start: 0.8392 (ttmt) cc_final: 0.7935 (tttm) REVERT: u 189 LYS cc_start: 0.9120 (pttm) cc_final: 0.8635 (pttp) REVERT: D 60 MET cc_start: 0.8610 (tpt) cc_final: 0.8370 (tpp) REVERT: D 128 VAL cc_start: 0.8556 (t) cc_final: 0.8095 (p) REVERT: E 195 ASP cc_start: 0.8483 (p0) cc_final: 0.8044 (p0) REVERT: G 128 VAL cc_start: 0.8603 (t) cc_final: 0.8242 (p) REVERT: H 83 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8501 (mttp) REVERT: I 244 MET cc_start: 0.8571 (mtp) cc_final: 0.8275 (tpp) REVERT: I 350 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8153 (mt) REVERT: J 128 VAL cc_start: 0.8547 (t) cc_final: 0.8212 (p) REVERT: L 189 LYS cc_start: 0.9043 (pttm) cc_final: 0.8627 (pttp) REVERT: L 319 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7612 (pp20) REVERT: L 347 MET cc_start: 0.7700 (mmm) cc_final: 0.7382 (mmm) REVERT: L 350 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7876 (mt) REVERT: M 60 MET cc_start: 0.8640 (tpt) cc_final: 0.8251 (tpp) REVERT: M 128 VAL cc_start: 0.8275 (t) cc_final: 0.7954 (p) REVERT: P 60 MET cc_start: 0.8645 (tpt) cc_final: 0.8423 (tpp) REVERT: P 128 VAL cc_start: 0.8544 (t) cc_final: 0.8129 (p) REVERT: R 215 ASP cc_start: 0.8819 (OUTLIER) cc_final: 0.8384 (t0) REVERT: R 314 LYS cc_start: 0.8394 (ttmt) cc_final: 0.7937 (tttm) REVERT: U 189 LYS cc_start: 0.9078 (pttm) cc_final: 0.8808 (pttp) outliers start: 141 outliers final: 89 residues processed: 988 average time/residue: 0.5923 time to fit residues: 962.5647 Evaluate side-chains 958 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 858 time to evaluate : 6.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 122 SER Chi-restraints excluded: chain b residue 64 SER Chi-restraints excluded: chain b residue 65 THR Chi-restraints excluded: chain b residue 89 VAL Chi-restraints excluded: chain b residue 101 SER Chi-restraints excluded: chain c residue 273 VAL Chi-restraints excluded: chain c residue 386 VAL Chi-restraints excluded: chain d residue 47 ILE Chi-restraints excluded: chain e residue 65 THR Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain e residue 194 MET Chi-restraints excluded: chain f residue 185 VAL Chi-restraints excluded: chain f residue 273 VAL Chi-restraints excluded: chain g residue 47 ILE Chi-restraints excluded: chain h residue 65 THR Chi-restraints excluded: chain h residue 83 LYS Chi-restraints excluded: chain h residue 101 SER Chi-restraints excluded: chain h residue 149 ASN Chi-restraints excluded: chain h residue 194 MET Chi-restraints excluded: chain i residue 273 VAL Chi-restraints excluded: chain i residue 350 LEU Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain l residue 185 VAL Chi-restraints excluded: chain l residue 273 VAL Chi-restraints excluded: chain l residue 319 GLU Chi-restraints excluded: chain l residue 350 LEU Chi-restraints excluded: chain m residue 122 SER Chi-restraints excluded: chain n residue 65 THR Chi-restraints excluded: chain n residue 129 VAL Chi-restraints excluded: chain o residue 273 VAL Chi-restraints excluded: chain p residue 122 SER Chi-restraints excluded: chain p residue 127 LEU Chi-restraints excluded: chain q residue 65 THR Chi-restraints excluded: chain q residue 89 VAL Chi-restraints excluded: chain q residue 101 SER Chi-restraints excluded: chain q residue 129 VAL Chi-restraints excluded: chain r residue 215 ASP Chi-restraints excluded: chain r residue 273 VAL Chi-restraints excluded: chain r residue 343 THR Chi-restraints excluded: chain s residue 47 ILE Chi-restraints excluded: chain s residue 122 SER Chi-restraints excluded: chain t residue 65 THR Chi-restraints excluded: chain t residue 89 VAL Chi-restraints excluded: chain t residue 101 SER Chi-restraints excluded: chain t residue 194 MET Chi-restraints excluded: chain u residue 273 VAL Chi-restraints excluded: chain u residue 347 MET Chi-restraints excluded: chain u residue 350 LEU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 194 MET Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 350 LEU Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 319 GLU Chi-restraints excluded: chain L residue 350 LEU Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain O residue 273 VAL Chi-restraints excluded: chain P residue 122 SER Chi-restraints excluded: chain P residue 127 LEU Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 101 SER Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain R residue 215 ASP Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 122 SER Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain T residue 89 VAL Chi-restraints excluded: chain T residue 101 SER Chi-restraints excluded: chain T residue 194 MET Chi-restraints excluded: chain U residue 273 VAL Chi-restraints excluded: chain U residue 347 MET Chi-restraints excluded: chain U residue 350 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 442 optimal weight: 3.9990 chunk 285 optimal weight: 4.9990 chunk 427 optimal weight: 0.0770 chunk 215 optimal weight: 7.9990 chunk 140 optimal weight: 10.0000 chunk 138 optimal weight: 6.9990 chunk 454 optimal weight: 0.5980 chunk 487 optimal weight: 2.9990 chunk 353 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 562 optimal weight: 2.9990 overall best weight: 1.7344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 82 ASN b 30 GLN ** e 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 39 HIS g 129 GLN h 118 GLN h 139 ASN l 353 GLN m 102 GLN m 129 GLN n 118 GLN p 129 GLN t 118 GLN A 82 ASN B 30 GLN ** E 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 HIS G 129 GLN H 139 ASN L 353 GLN M 102 GLN M 129 GLN P 129 GLN T 118 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 60676 Z= 0.269 Angle : 0.535 8.127 82558 Z= 0.273 Chirality : 0.044 0.143 9338 Planarity : 0.004 0.043 10570 Dihedral : 4.716 37.326 8274 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.05 % Allowed : 13.64 % Favored : 84.31 % 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: -1.10 (0.10), residues: 7378 helix: 0.28 (0.14), residues: 1302 sheet: -0.26 (0.11), residues: 2212 loop : -1.36 (0.09), residues: 3864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 296 HIS 0.005 0.001 HIS G 36 PHE 0.011 0.001 PHE l 383 TYR 0.032 0.001 TYR o 320 ARG 0.006 0.000 ARG i 200 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14756 Ramachandran restraints generated. 7378 Oldfield, 0 Emsley, 7378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14756 Ramachandran restraints generated. 7378 Oldfield, 0 Emsley, 7378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 984 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 851 time to evaluate : 5.283 Fit side-chains REVERT: c 315 TYR cc_start: 0.8747 (t80) cc_final: 0.8476 (t80) REVERT: d 60 MET cc_start: 0.8680 (tpt) cc_final: 0.8395 (tpp) REVERT: d 128 VAL cc_start: 0.8607 (t) cc_final: 0.8122 (p) REVERT: e 195 ASP cc_start: 0.8616 (p0) cc_final: 0.8186 (p0) REVERT: g 128 VAL cc_start: 0.8703 (t) cc_final: 0.8352 (p) REVERT: i 244 MET cc_start: 0.8662 (mtp) cc_final: 0.8366 (ttm) REVERT: j 128 VAL cc_start: 0.8559 (t) cc_final: 0.8289 (p) REVERT: l 189 LYS cc_start: 0.9073 (pttm) cc_final: 0.8673 (pttp) REVERT: l 350 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.7977 (mt) REVERT: m 60 MET cc_start: 0.8645 (tpt) cc_final: 0.8293 (tpp) REVERT: m 128 VAL cc_start: 0.8417 (t) cc_final: 0.8166 (p) REVERT: o 209 GLU cc_start: 0.8120 (tt0) cc_final: 0.7910 (tt0) REVERT: p 60 MET cc_start: 0.8636 (tpt) cc_final: 0.8418 (tpp) REVERT: r 215 ASP cc_start: 0.8875 (OUTLIER) cc_final: 0.8504 (t0) REVERT: u 189 LYS cc_start: 0.9154 (pttm) cc_final: 0.8919 (pttp) REVERT: C 315 TYR cc_start: 0.8747 (t80) cc_final: 0.8477 (t80) REVERT: D 60 MET cc_start: 0.8685 (tpt) cc_final: 0.8396 (tpp) REVERT: D 128 VAL cc_start: 0.8599 (t) cc_final: 0.8115 (p) REVERT: E 195 ASP cc_start: 0.8639 (p0) cc_final: 0.8213 (p0) REVERT: G 128 VAL cc_start: 0.8705 (t) cc_final: 0.8354 (p) REVERT: I 244 MET cc_start: 0.8662 (mtp) cc_final: 0.8368 (ttm) REVERT: J 128 VAL cc_start: 0.8553 (t) cc_final: 0.8282 (p) REVERT: L 189 LYS cc_start: 0.9079 (pttm) cc_final: 0.8685 (pttp) REVERT: L 347 MET cc_start: 0.7963 (mmm) cc_final: 0.7645 (mmm) REVERT: L 350 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7961 (mt) REVERT: M 60 MET cc_start: 0.8650 (tpt) cc_final: 0.8295 (tpp) REVERT: M 128 VAL cc_start: 0.8405 (t) cc_final: 0.8152 (p) REVERT: O 306 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8357 (mt) REVERT: P 60 MET cc_start: 0.8638 (tpt) cc_final: 0.8420 (tpp) REVERT: R 215 ASP cc_start: 0.8880 (OUTLIER) cc_final: 0.8504 (t0) REVERT: U 189 LYS cc_start: 0.9163 (pttm) cc_final: 0.8900 (pttp) outliers start: 133 outliers final: 103 residues processed: 937 average time/residue: 0.6083 time to fit residues: 931.9093 Evaluate side-chains 940 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 832 time to evaluate : 5.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 122 SER Chi-restraints excluded: chain b residue 64 SER Chi-restraints excluded: chain b residue 65 THR Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain b residue 89 VAL Chi-restraints excluded: chain b residue 101 SER Chi-restraints excluded: chain c residue 273 VAL Chi-restraints excluded: chain c residue 386 VAL Chi-restraints excluded: chain d residue 47 ILE Chi-restraints excluded: chain e residue 65 THR Chi-restraints excluded: chain e residue 86 ASN Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain e residue 194 MET Chi-restraints excluded: chain f residue 185 VAL Chi-restraints excluded: chain f residue 273 VAL Chi-restraints excluded: chain g residue 47 ILE Chi-restraints excluded: chain h residue 65 THR Chi-restraints excluded: chain h residue 83 LYS Chi-restraints excluded: chain h residue 101 SER Chi-restraints excluded: chain h residue 149 ASN Chi-restraints excluded: chain h residue 194 MET Chi-restraints excluded: chain i residue 273 VAL Chi-restraints excluded: chain j residue 122 SER Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain l residue 223 ILE Chi-restraints excluded: chain l residue 273 VAL Chi-restraints excluded: chain l residue 350 LEU Chi-restraints excluded: chain m residue 127 LEU Chi-restraints excluded: chain m residue 129 GLN Chi-restraints excluded: chain n residue 65 THR Chi-restraints excluded: chain n residue 129 VAL Chi-restraints excluded: chain n residue 194 MET Chi-restraints excluded: chain o residue 273 VAL Chi-restraints excluded: chain p residue 122 SER Chi-restraints excluded: chain p residue 127 LEU Chi-restraints excluded: chain q residue 65 THR Chi-restraints excluded: chain q residue 89 VAL Chi-restraints excluded: chain q residue 101 SER Chi-restraints excluded: chain q residue 129 VAL Chi-restraints excluded: chain r residue 215 ASP Chi-restraints excluded: chain r residue 273 VAL Chi-restraints excluded: chain r residue 343 THR Chi-restraints excluded: chain s residue 47 ILE Chi-restraints excluded: chain s residue 122 SER Chi-restraints excluded: chain t residue 65 THR Chi-restraints excluded: chain t residue 74 THR Chi-restraints excluded: chain t residue 89 VAL Chi-restraints excluded: chain t residue 101 SER Chi-restraints excluded: chain t residue 194 MET Chi-restraints excluded: chain u residue 273 VAL Chi-restraints excluded: chain u residue 347 MET Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 194 MET Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 350 LEU Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain M residue 127 LEU Chi-restraints excluded: chain M residue 129 GLN Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 194 MET Chi-restraints excluded: chain O residue 223 ILE Chi-restraints excluded: chain O residue 273 VAL Chi-restraints excluded: chain O residue 306 ILE Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 122 SER Chi-restraints excluded: chain P residue 127 LEU Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 101 SER Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain R residue 215 ASP Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 122 SER Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain T residue 74 THR Chi-restraints excluded: chain T residue 89 VAL Chi-restraints excluded: chain T residue 101 SER Chi-restraints excluded: chain T residue 194 MET Chi-restraints excluded: chain U residue 273 VAL Chi-restraints excluded: chain U residue 347 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 650 optimal weight: 2.9990 chunk 685 optimal weight: 6.9990 chunk 625 optimal weight: 0.8980 chunk 666 optimal weight: 0.9990 chunk 684 optimal weight: 0.7980 chunk 401 optimal weight: 0.9980 chunk 290 optimal weight: 6.9990 chunk 523 optimal weight: 4.9990 chunk 204 optimal weight: 8.9990 chunk 602 optimal weight: 1.9990 chunk 630 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 82 ASN b 30 GLN ** e 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 39 HIS g 129 GLN h 118 GLN k 118 GLN m 129 GLN p 129 GLN A 82 ASN B 30 GLN ** E 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 HIS G 129 GLN H 118 GLN K 118 GLN M 129 GLN P 129 GLN Q 118 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 60676 Z= 0.196 Angle : 0.511 7.980 82558 Z= 0.261 Chirality : 0.043 0.156 9338 Planarity : 0.004 0.044 10570 Dihedral : 4.616 36.717 8274 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.85 % Allowed : 14.01 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.10), residues: 7378 helix: 0.41 (0.14), residues: 1288 sheet: -0.22 (0.11), residues: 2212 loop : -1.33 (0.09), residues: 3878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP m 71 HIS 0.005 0.001 HIS g 36 PHE 0.008 0.001 PHE l 383 TYR 0.032 0.001 TYR o 320 ARG 0.003 0.000 ARG i 200 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14756 Ramachandran restraints generated. 7378 Oldfield, 0 Emsley, 7378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14756 Ramachandran restraints generated. 7378 Oldfield, 0 Emsley, 7378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 860 time to evaluate : 5.254 Fit side-chains REVERT: d 60 MET cc_start: 0.8677 (tpt) cc_final: 0.8401 (tpp) REVERT: d 128 VAL cc_start: 0.8590 (t) cc_final: 0.8092 (p) REVERT: e 195 ASP cc_start: 0.8608 (p0) cc_final: 0.8109 (p0) REVERT: g 128 VAL cc_start: 0.8683 (t) cc_final: 0.8327 (p) REVERT: i 244 MET cc_start: 0.8631 (mtp) cc_final: 0.8356 (ttm) REVERT: j 128 VAL cc_start: 0.8526 (t) cc_final: 0.8267 (p) REVERT: l 189 LYS cc_start: 0.9044 (pttm) cc_final: 0.8630 (pttp) REVERT: l 350 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7881 (mt) REVERT: m 60 MET cc_start: 0.8650 (tpt) cc_final: 0.8294 (tpp) REVERT: m 128 VAL cc_start: 0.8313 (t) cc_final: 0.8085 (p) REVERT: o 209 GLU cc_start: 0.8100 (tt0) cc_final: 0.7866 (tt0) REVERT: p 60 MET cc_start: 0.8632 (tpt) cc_final: 0.8425 (tpp) REVERT: r 154 GLU cc_start: 0.8019 (mp0) cc_final: 0.7746 (mp0) REVERT: r 215 ASP cc_start: 0.8861 (OUTLIER) cc_final: 0.8463 (t0) REVERT: t 30 GLN cc_start: 0.8622 (tp40) cc_final: 0.8375 (tp40) REVERT: u 189 LYS cc_start: 0.9110 (pttm) cc_final: 0.8831 (pttp) REVERT: D 60 MET cc_start: 0.8682 (tpt) cc_final: 0.8400 (tpp) REVERT: D 128 VAL cc_start: 0.8589 (t) cc_final: 0.8091 (p) REVERT: E 195 ASP cc_start: 0.8624 (p0) cc_final: 0.8132 (p0) REVERT: G 128 VAL cc_start: 0.8685 (t) cc_final: 0.8327 (p) REVERT: I 244 MET cc_start: 0.8634 (mtp) cc_final: 0.8361 (ttm) REVERT: J 128 VAL cc_start: 0.8525 (t) cc_final: 0.8264 (p) REVERT: L 189 LYS cc_start: 0.9044 (pttm) cc_final: 0.8632 (pttp) REVERT: L 347 MET cc_start: 0.7943 (mmm) cc_final: 0.7542 (mmm) REVERT: L 350 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7890 (mt) REVERT: M 60 MET cc_start: 0.8650 (tpt) cc_final: 0.8293 (tpp) REVERT: M 128 VAL cc_start: 0.8302 (t) cc_final: 0.8073 (p) REVERT: O 306 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8368 (mt) REVERT: P 60 MET cc_start: 0.8635 (tpt) cc_final: 0.8429 (tpp) REVERT: R 154 GLU cc_start: 0.8022 (mp0) cc_final: 0.7751 (mp0) REVERT: R 215 ASP cc_start: 0.8865 (OUTLIER) cc_final: 0.8462 (t0) REVERT: T 30 GLN cc_start: 0.8622 (tp40) cc_final: 0.8376 (tp40) REVERT: U 189 LYS cc_start: 0.9140 (pttm) cc_final: 0.8879 (pttp) outliers start: 120 outliers final: 100 residues processed: 935 average time/residue: 0.6076 time to fit residues: 929.0745 Evaluate side-chains 952 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 847 time to evaluate : 5.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 122 SER Chi-restraints excluded: chain b residue 64 SER Chi-restraints excluded: chain b residue 65 THR Chi-restraints excluded: chain b residue 89 VAL Chi-restraints excluded: chain b residue 101 SER Chi-restraints excluded: chain c residue 273 VAL Chi-restraints excluded: chain c residue 386 VAL Chi-restraints excluded: chain d residue 47 ILE Chi-restraints excluded: chain e residue 65 THR Chi-restraints excluded: chain e residue 86 ASN Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain e residue 194 MET Chi-restraints excluded: chain f residue 273 VAL Chi-restraints excluded: chain g residue 39 HIS Chi-restraints excluded: chain g residue 47 ILE Chi-restraints excluded: chain h residue 65 THR Chi-restraints excluded: chain h residue 74 THR Chi-restraints excluded: chain h residue 83 LYS Chi-restraints excluded: chain h residue 101 SER Chi-restraints excluded: chain h residue 149 ASN Chi-restraints excluded: chain h residue 194 MET Chi-restraints excluded: chain i residue 273 VAL Chi-restraints excluded: chain j residue 122 SER Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain l residue 223 ILE Chi-restraints excluded: chain l residue 273 VAL Chi-restraints excluded: chain l residue 350 LEU Chi-restraints excluded: chain m residue 122 SER Chi-restraints excluded: chain n residue 64 SER Chi-restraints excluded: chain n residue 65 THR Chi-restraints excluded: chain n residue 129 VAL Chi-restraints excluded: chain n residue 194 MET Chi-restraints excluded: chain o residue 223 ILE Chi-restraints excluded: chain o residue 273 VAL Chi-restraints excluded: chain p residue 101 VAL Chi-restraints excluded: chain p residue 122 SER Chi-restraints excluded: chain q residue 65 THR Chi-restraints excluded: chain q residue 89 VAL Chi-restraints excluded: chain q residue 101 SER Chi-restraints excluded: chain q residue 129 VAL Chi-restraints excluded: chain r residue 215 ASP Chi-restraints excluded: chain r residue 273 VAL Chi-restraints excluded: chain s residue 47 ILE Chi-restraints excluded: chain s residue 122 SER Chi-restraints excluded: chain t residue 65 THR Chi-restraints excluded: chain t residue 74 THR Chi-restraints excluded: chain t residue 89 VAL Chi-restraints excluded: chain t residue 101 SER Chi-restraints excluded: chain t residue 194 MET Chi-restraints excluded: chain u residue 273 VAL Chi-restraints excluded: chain u residue 347 MET Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain G residue 39 HIS Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 194 MET Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 308 LEU Chi-restraints excluded: chain L residue 350 LEU Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 194 MET Chi-restraints excluded: chain O residue 273 VAL Chi-restraints excluded: chain O residue 306 ILE Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 122 SER Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 101 SER Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain R residue 215 ASP Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 122 SER Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain T residue 74 THR Chi-restraints excluded: chain T residue 89 VAL Chi-restraints excluded: chain T residue 101 SER Chi-restraints excluded: chain T residue 194 MET Chi-restraints excluded: chain U residue 273 VAL Chi-restraints excluded: chain U residue 347 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 664 optimal weight: 3.9990 chunk 437 optimal weight: 3.9990 chunk 704 optimal weight: 0.8980 chunk 430 optimal weight: 10.0000 chunk 334 optimal weight: 0.6980 chunk 489 optimal weight: 0.9990 chunk 739 optimal weight: 7.9990 chunk 680 optimal weight: 5.9990 chunk 588 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 454 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 82 ASN b 30 GLN ** e 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 115 GLN g 129 GLN m 129 GLN p 115 GLN p 129 GLN q 118 GLN A 82 ASN B 30 GLN ** E 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 GLN G 129 GLN H 118 GLN K 100 HIS M 129 GLN P 115 GLN P 129 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 60676 Z= 0.163 Angle : 0.496 7.748 82558 Z= 0.253 Chirality : 0.043 0.154 9338 Planarity : 0.004 0.045 10570 Dihedral : 4.504 35.830 8274 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.82 % Allowed : 13.99 % Favored : 84.19 % 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: -0.87 (0.10), residues: 7378 helix: 0.51 (0.14), residues: 1288 sheet: 0.10 (0.12), residues: 2100 loop : -1.35 (0.09), residues: 3990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP g 34 HIS 0.006 0.001 HIS G 39 PHE 0.007 0.001 PHE L 383 TYR 0.035 0.001 TYR L 320 ARG 0.003 0.000 ARG K 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14756 Ramachandran restraints generated. 7378 Oldfield, 0 Emsley, 7378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14756 Ramachandran restraints generated. 7378 Oldfield, 0 Emsley, 7378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 977 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 859 time to evaluate : 5.240 Fit side-chains revert: symmetry clash REVERT: d 60 MET cc_start: 0.8621 (tpt) cc_final: 0.8356 (tpp) REVERT: d 128 VAL cc_start: 0.8600 (t) cc_final: 0.8122 (p) REVERT: e 195 ASP cc_start: 0.8513 (p0) cc_final: 0.8121 (p0) REVERT: g 128 VAL cc_start: 0.8608 (t) cc_final: 0.8277 (p) REVERT: h 83 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8517 (mttp) REVERT: i 244 MET cc_start: 0.8601 (mtp) cc_final: 0.8340 (ttm) REVERT: j 128 VAL cc_start: 0.8431 (t) cc_final: 0.8162 (p) REVERT: l 189 LYS cc_start: 0.9031 (pttm) cc_final: 0.8601 (pttp) REVERT: l 350 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7873 (mt) REVERT: m 60 MET cc_start: 0.8646 (tpt) cc_final: 0.8295 (tpp) REVERT: m 128 VAL cc_start: 0.8242 (t) cc_final: 0.8023 (p) REVERT: r 154 GLU cc_start: 0.8048 (mp0) cc_final: 0.7769 (mp0) REVERT: r 215 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8434 (t0) REVERT: t 30 GLN cc_start: 0.8654 (tp40) cc_final: 0.8397 (tp40) REVERT: u 189 LYS cc_start: 0.9084 (pttm) cc_final: 0.8799 (pttp) REVERT: D 60 MET cc_start: 0.8626 (tpt) cc_final: 0.8359 (tpp) REVERT: D 128 VAL cc_start: 0.8601 (t) cc_final: 0.8124 (p) REVERT: E 195 ASP cc_start: 0.8516 (p0) cc_final: 0.8119 (p0) REVERT: G 128 VAL cc_start: 0.8606 (t) cc_final: 0.8275 (p) REVERT: H 83 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8511 (mttp) REVERT: I 244 MET cc_start: 0.8601 (mtp) cc_final: 0.8342 (ttm) REVERT: J 128 VAL cc_start: 0.8423 (t) cc_final: 0.8157 (p) REVERT: L 154 GLU cc_start: 0.8017 (mp0) cc_final: 0.7718 (mp0) REVERT: L 189 LYS cc_start: 0.9029 (pttm) cc_final: 0.8602 (pttp) REVERT: L 347 MET cc_start: 0.7878 (mmm) cc_final: 0.7451 (mmm) REVERT: L 350 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7912 (mt) REVERT: M 60 MET cc_start: 0.8648 (tpt) cc_final: 0.8294 (tpp) REVERT: M 128 VAL cc_start: 0.8257 (t) cc_final: 0.8032 (p) REVERT: O 306 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8345 (mt) REVERT: R 154 GLU cc_start: 0.8052 (mp0) cc_final: 0.7771 (mp0) REVERT: R 215 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8437 (t0) REVERT: T 30 GLN cc_start: 0.8657 (tp40) cc_final: 0.8398 (tp40) REVERT: U 189 LYS cc_start: 0.9105 (pttm) cc_final: 0.8831 (pttp) outliers start: 118 outliers final: 101 residues processed: 942 average time/residue: 0.6070 time to fit residues: 937.1347 Evaluate side-chains 953 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 845 time to evaluate : 5.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 122 SER Chi-restraints excluded: chain b residue 64 SER Chi-restraints excluded: chain b residue 65 THR Chi-restraints excluded: chain b residue 89 VAL Chi-restraints excluded: chain b residue 101 SER Chi-restraints excluded: chain c residue 273 VAL Chi-restraints excluded: chain c residue 300 ILE Chi-restraints excluded: chain c residue 386 VAL Chi-restraints excluded: chain d residue 47 ILE Chi-restraints excluded: chain e residue 65 THR Chi-restraints excluded: chain e residue 86 ASN Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain e residue 194 MET Chi-restraints excluded: chain f residue 273 VAL Chi-restraints excluded: chain g residue 47 ILE Chi-restraints excluded: chain h residue 65 THR Chi-restraints excluded: chain h residue 74 THR Chi-restraints excluded: chain h residue 83 LYS Chi-restraints excluded: chain h residue 101 SER Chi-restraints excluded: chain h residue 149 ASN Chi-restraints excluded: chain h residue 194 MET Chi-restraints excluded: chain i residue 273 VAL Chi-restraints excluded: chain j residue 122 SER Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain l residue 273 VAL Chi-restraints excluded: chain l residue 350 LEU Chi-restraints excluded: chain m residue 122 SER Chi-restraints excluded: chain m residue 129 GLN Chi-restraints excluded: chain n residue 64 SER Chi-restraints excluded: chain n residue 65 THR Chi-restraints excluded: chain n residue 129 VAL Chi-restraints excluded: chain n residue 194 MET Chi-restraints excluded: chain o residue 273 VAL Chi-restraints excluded: chain p residue 101 VAL Chi-restraints excluded: chain q residue 65 THR Chi-restraints excluded: chain q residue 89 VAL Chi-restraints excluded: chain q residue 101 SER Chi-restraints excluded: chain q residue 129 VAL Chi-restraints excluded: chain r residue 215 ASP Chi-restraints excluded: chain r residue 273 VAL Chi-restraints excluded: chain s residue 47 ILE Chi-restraints excluded: chain s residue 122 SER Chi-restraints excluded: chain t residue 44 THR Chi-restraints excluded: chain t residue 65 THR Chi-restraints excluded: chain t residue 74 THR Chi-restraints excluded: chain t residue 89 VAL Chi-restraints excluded: chain t residue 101 SER Chi-restraints excluded: chain t residue 194 MET Chi-restraints excluded: chain u residue 273 VAL Chi-restraints excluded: chain u residue 347 MET Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 194 MET Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 308 LEU Chi-restraints excluded: chain L residue 350 LEU Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain M residue 129 GLN Chi-restraints excluded: chain N residue 64 SER Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 194 MET Chi-restraints excluded: chain O residue 273 VAL Chi-restraints excluded: chain O residue 306 ILE Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 101 SER Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain R residue 215 ASP Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 122 SER Chi-restraints excluded: chain T residue 44 THR Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain T residue 74 THR Chi-restraints excluded: chain T residue 89 VAL Chi-restraints excluded: chain T residue 101 SER Chi-restraints excluded: chain T residue 194 MET Chi-restraints excluded: chain U residue 273 VAL Chi-restraints excluded: chain U residue 347 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 360 optimal weight: 0.0870 chunk 467 optimal weight: 2.9990 chunk 627 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 542 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 163 optimal weight: 0.2980 chunk 589 optimal weight: 3.9990 chunk 246 optimal weight: 8.9990 chunk 605 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.8764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 82 ASN b 30 GLN ** e 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 39 HIS g 115 GLN g 129 GLN m 129 GLN p 129 GLN A 82 ASN B 30 GLN ** E 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 HIS G 115 GLN G 129 GLN H 118 GLN L 342 ASN M 129 GLN P 129 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.118636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.082807 restraints weight = 77642.975| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 2.07 r_work: 0.2628 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2491 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2513 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2513 r_free = 0.2513 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2508 r_free = 0.2508 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 60676 Z= 0.288 Angle : 0.558 7.930 82558 Z= 0.284 Chirality : 0.045 0.159 9338 Planarity : 0.004 0.044 10570 Dihedral : 4.821 38.407 8274 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.99 % Allowed : 13.88 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.10), residues: 7378 helix: 0.44 (0.14), residues: 1302 sheet: -0.28 (0.11), residues: 2212 loop : -1.30 (0.09), residues: 3864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP i 296 HIS 0.006 0.001 HIS g 36 PHE 0.011 0.001 PHE L 383 TYR 0.038 0.001 TYR l 320 ARG 0.006 0.000 ARG R 200 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16901.98 seconds wall clock time: 291 minutes 59.70 seconds (17519.70 seconds total)