Starting phenix.real_space_refine on Mon Mar 18 12:42:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zqb_14869/03_2024/7zqb_14869.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zqb_14869/03_2024/7zqb_14869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zqb_14869/03_2024/7zqb_14869.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zqb_14869/03_2024/7zqb_14869.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zqb_14869/03_2024/7zqb_14869.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zqb_14869/03_2024/7zqb_14869.pdb" } resolution = 3.88 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= 0.000 sd= 0.002 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 219 5.16 5 C 54702 2.51 5 N 14469 2.21 5 O 17190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "i PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 230": "OE1" <-> "OE2" Residue "i GLU 250": "OE1" <-> "OE2" Residue "h PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 230": "OE1" <-> "OE2" Residue "h GLU 250": "OE1" <-> "OE2" Residue "j PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 230": "OE1" <-> "OE2" Residue "j GLU 250": "OE1" <-> "OE2" Residue "R GLU 4": "OE1" <-> "OE2" Residue "R GLU 95": "OE1" <-> "OE2" Residue "I GLU 87": "OE1" <-> "OE2" Residue "a GLU 32": "OE1" <-> "OE2" Residue "S GLU 4": "OE1" <-> "OE2" Residue "S GLU 95": "OE1" <-> "OE2" Residue "S GLU 129": "OE1" <-> "OE2" Residue "N GLU 4": "OE1" <-> "OE2" Residue "N GLU 95": "OE1" <-> "OE2" Residue "H GLU 87": "OE1" <-> "OE2" Residue "X GLU 40": "OE1" <-> "OE2" Residue "X GLU 61": "OE1" <-> "OE2" Residue "Y GLU 32": "OE1" <-> "OE2" Residue "O GLU 4": "OE1" <-> "OE2" Residue "O GLU 95": "OE1" <-> "OE2" Residue "O GLU 129": "OE1" <-> "OE2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C GLU 162": "OE1" <-> "OE2" Residue "C GLU 348": "OE1" <-> "OE2" Residue "C TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 4": "OE1" <-> "OE2" Residue "J GLU 95": "OE1" <-> "OE2" Residue "G GLU 87": "OE1" <-> "OE2" Residue "W GLU 32": "OE1" <-> "OE2" Residue "K GLU 4": "OE1" <-> "OE2" Residue "K GLU 95": "OE1" <-> "OE2" Residue "K GLU 129": "OE1" <-> "OE2" Residue "A GLU 49": "OE1" <-> "OE2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A GLU 348": "OE1" <-> "OE2" Residue "A TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B GLU 348": "OE1" <-> "OE2" Residue "B TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 1187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 1199": "NH1" <-> "NH2" Residue "g PHE 1187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 1199": "NH1" <-> "NH2" Residue "e PHE 1187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 1199": "NH1" <-> "NH2" Residue "V GLU 40": "OE1" <-> "OE2" Residue "V GLU 61": "OE1" <-> "OE2" Residue "Z GLU 40": "OE1" <-> "OE2" Residue "Z GLU 61": "OE1" <-> "OE2" Residue "b GLU 27": "OE1" <-> "OE2" Residue "b GLU 86": "OE1" <-> "OE2" Residue "b GLU 88": "OE1" <-> "OE2" Residue "b GLU 198": "OE1" <-> "OE2" Residue "b GLU 222": "OE1" <-> "OE2" Residue "b GLU 298": "OE1" <-> "OE2" Residue "b TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 429": "OE1" <-> "OE2" Residue "b GLU 535": "OE1" <-> "OE2" Residue "b GLU 621": "OE1" <-> "OE2" Residue "b TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 672": "OE1" <-> "OE2" Residue "b GLU 695": "OE1" <-> "OE2" Residue "b GLU 760": "OE1" <-> "OE2" Residue "b GLU 791": "OE1" <-> "OE2" Residue "b GLU 796": "OE1" <-> "OE2" Residue "b GLU 801": "OE1" <-> "OE2" Residue "d GLU 27": "OE1" <-> "OE2" Residue "d GLU 86": "OE1" <-> "OE2" Residue "d GLU 88": "OE1" <-> "OE2" Residue "d GLU 198": "OE1" <-> "OE2" Residue "d GLU 222": "OE1" <-> "OE2" Residue "d GLU 298": "OE1" <-> "OE2" Residue "d TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 429": "OE1" <-> "OE2" Residue "d GLU 535": "OE1" <-> "OE2" Residue "d GLU 621": "OE1" <-> "OE2" Residue "d TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 672": "OE1" <-> "OE2" Residue "d GLU 695": "OE1" <-> "OE2" Residue "d GLU 760": "OE1" <-> "OE2" Residue "d GLU 791": "OE1" <-> "OE2" Residue "d GLU 796": "OE1" <-> "OE2" Residue "d GLU 801": "OE1" <-> "OE2" Residue "c GLU 27": "OE1" <-> "OE2" Residue "c GLU 86": "OE1" <-> "OE2" Residue "c GLU 88": "OE1" <-> "OE2" Residue "c GLU 198": "OE1" <-> "OE2" Residue "c GLU 222": "OE1" <-> "OE2" Residue "c GLU 298": "OE1" <-> "OE2" Residue "c TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 429": "OE1" <-> "OE2" Residue "c GLU 535": "OE1" <-> "OE2" Residue "c GLU 621": "OE1" <-> "OE2" Residue "c TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 672": "OE1" <-> "OE2" Residue "c GLU 695": "OE1" <-> "OE2" Residue "c GLU 760": "OE1" <-> "OE2" Residue "c GLU 791": "OE1" <-> "OE2" Residue "c GLU 796": "OE1" <-> "OE2" Residue "c GLU 801": "OE1" <-> "OE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 86580 Number of models: 1 Model: "" Number of chains: 36 Chain: "i" Number of atoms: 4078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4078 Classifications: {'peptide': 527} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 505} Chain breaks: 1 Chain: "h" Number of atoms: 4078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4078 Classifications: {'peptide': 527} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 505} Chain breaks: 1 Chain: "j" Number of atoms: 4078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4078 Classifications: {'peptide': 527} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 505} Chain breaks: 1 Chain: "R" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1048 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "I" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2423 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 14, 'TRANS': 283} Chain: "a" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1610 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 189} Chain: "Q" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1056 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "S" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1048 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "F" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Chain: "N" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1048 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "H" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2423 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 14, 'TRANS': 283} Chain: "X" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1610 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 189} Chain: "Y" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1610 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 189} Chain: "M" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1056 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "O" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1048 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "E" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Chain: "C" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Chain: "J" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1048 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "L" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1056 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "G" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2423 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 14, 'TRANS': 283} Chain: "W" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1610 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 189} Chain: "U" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1056 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "K" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1048 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "D" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Chain: "A" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Chain: "B" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Chain: "P" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1056 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "T" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1056 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "f" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 262 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'TRANS': 34} Chain: "g" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 262 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'TRANS': 34} Chain: "e" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 262 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'TRANS': 34} Chain: "V" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1610 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 189} Chain: "Z" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1610 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 189} Chain: "b" Number of atoms: 7577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7577 Classifications: {'peptide': 949} Link IDs: {'PTRANS': 36, 'TRANS': 912} Chain: "d" Number of atoms: 7577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7577 Classifications: {'peptide': 949} Link IDs: {'PTRANS': 36, 'TRANS': 912} Chain: "c" Number of atoms: 7577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7577 Classifications: {'peptide': 949} Link IDs: {'PTRANS': 36, 'TRANS': 912} Time building chain proxies: 33.95, per 1000 atoms: 0.39 Number of scatterers: 86580 At special positions: 0 Unit cell: (171.577, 183.736, 575.526, 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 219 16.00 O 17190 8.00 N 14469 7.00 C 54702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS b 316 " - pdb=" SG CYS b 327 " distance=2.03 Simple disulfide: pdb=" SG CYS d 316 " - pdb=" SG CYS d 327 " distance=2.03 Simple disulfide: pdb=" SG CYS c 316 " - pdb=" SG CYS c 327 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 25.34 Conformation dependent library (CDL) restraints added in 11.9 seconds 22062 Ramachandran restraints generated. 11031 Oldfield, 0 Emsley, 11031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 20652 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 167 sheets defined 12.5% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.90 Creating SS restraints... Processing helix chain 'i' and resid 83 through 90 Processing helix chain 'i' and resid 258 through 264 removed outlier: 3.864A pdb=" N VAL i 262 " --> pdb=" O SER i 258 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ARG i 263 " --> pdb=" O ALA i 259 " (cutoff:3.500A) Processing helix chain 'h' and resid 83 through 90 Processing helix chain 'h' and resid 258 through 264 removed outlier: 3.863A pdb=" N VAL h 262 " --> pdb=" O SER h 258 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ARG h 263 " --> pdb=" O ALA h 259 " (cutoff:3.500A) Processing helix chain 'j' and resid 83 through 90 Processing helix chain 'j' and resid 258 through 264 removed outlier: 3.862A pdb=" N VAL j 262 " --> pdb=" O SER j 258 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ARG j 263 " --> pdb=" O ALA j 259 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 7 removed outlier: 3.973A pdb=" N VAL R 7 " --> pdb=" O GLU R 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 92 Processing helix chain 'I' and resid 73 through 75 No H-bonds generated for 'chain 'I' and resid 73 through 75' Processing helix chain 'I' and resid 76 through 83 Processing helix chain 'I' and resid 200 through 204 removed outlier: 3.596A pdb=" N ILE I 204 " --> pdb=" O ILE I 201 " (cutoff:3.500A) Processing helix chain 'a' and resid 12 through 16 Processing helix chain 'a' and resid 58 through 76 Processing helix chain 'a' and resid 83 through 87 Processing helix chain 'Q' and resid 81 through 91 Processing helix chain 'S' and resid 81 through 92 removed outlier: 3.654A pdb=" N LYS S 91 " --> pdb=" O THR S 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 7 No H-bonds generated for 'chain 'F' and resid 5 through 7' Processing helix chain 'F' and resid 91 through 100 Processing helix chain 'F' and resid 185 through 190 Processing helix chain 'F' and resid 192 through 201 Processing helix chain 'F' and resid 275 through 287 removed outlier: 3.522A pdb=" N LEU F 287 " --> pdb=" O LEU F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 346 removed outlier: 4.255A pdb=" N GLY F 346 " --> pdb=" O LEU F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 369 Processing helix chain 'N' and resid 3 through 7 removed outlier: 3.974A pdb=" N VAL N 7 " --> pdb=" O GLU N 4 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 92 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 76 through 83 Processing helix chain 'H' and resid 200 through 204 removed outlier: 3.595A pdb=" N ILE H 204 " --> pdb=" O ILE H 201 " (cutoff:3.500A) Processing helix chain 'X' and resid 58 through 76 Processing helix chain 'Y' and resid 12 through 16 Processing helix chain 'Y' and resid 58 through 76 Processing helix chain 'Y' and resid 83 through 87 Processing helix chain 'M' and resid 81 through 91 Processing helix chain 'O' and resid 81 through 92 removed outlier: 3.654A pdb=" N LYS O 91 " --> pdb=" O THR O 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 7 No H-bonds generated for 'chain 'E' and resid 5 through 7' Processing helix chain 'E' and resid 91 through 100 Processing helix chain 'E' and resid 185 through 190 Processing helix chain 'E' and resid 192 through 201 Processing helix chain 'E' and resid 275 through 287 removed outlier: 3.520A pdb=" N LEU E 287 " --> pdb=" O LEU E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 346 removed outlier: 4.255A pdb=" N GLY E 346 " --> pdb=" O LEU E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 369 Processing helix chain 'C' and resid 91 through 100 removed outlier: 3.685A pdb=" N TRP C 95 " --> pdb=" O ASP C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 190 removed outlier: 3.829A pdb=" N ILE C 189 " --> pdb=" O ASP C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 201 Processing helix chain 'C' and resid 275 through 286 Processing helix chain 'C' and resid 358 through 369 Processing helix chain 'J' and resid 3 through 7 removed outlier: 3.973A pdb=" N VAL J 7 " --> pdb=" O GLU J 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 92 Processing helix chain 'L' and resid 81 through 91 Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 76 through 83 Processing helix chain 'G' and resid 200 through 204 removed outlier: 3.595A pdb=" N ILE G 204 " --> pdb=" O ILE G 201 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 16 Processing helix chain 'W' and resid 58 through 76 Processing helix chain 'W' and resid 83 through 87 Processing helix chain 'U' and resid 81 through 91 Processing helix chain 'K' and resid 81 through 92 removed outlier: 3.654A pdb=" N LYS K 91 " --> pdb=" O THR K 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 7 No H-bonds generated for 'chain 'D' and resid 5 through 7' Processing helix chain 'D' and resid 91 through 100 Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 192 through 201 Processing helix chain 'D' and resid 275 through 287 removed outlier: 3.520A pdb=" N LEU D 287 " --> pdb=" O LEU D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 346 removed outlier: 4.256A pdb=" N GLY D 346 " --> pdb=" O LEU D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 369 Processing helix chain 'A' and resid 91 through 100 removed outlier: 3.686A pdb=" N TRP A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 removed outlier: 3.830A pdb=" N ILE A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 201 Processing helix chain 'A' and resid 275 through 286 Processing helix chain 'A' and resid 358 through 369 Processing helix chain 'B' and resid 91 through 100 removed outlier: 3.684A pdb=" N TRP B 95 " --> pdb=" O ASP B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 190 removed outlier: 3.829A pdb=" N ILE B 189 " --> pdb=" O ASP B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 201 Processing helix chain 'B' and resid 275 through 286 Processing helix chain 'B' and resid 358 through 369 Processing helix chain 'P' and resid 81 through 91 Processing helix chain 'T' and resid 81 through 91 Processing helix chain 'f' and resid 1186 through 1193 removed outlier: 3.900A pdb=" N PHE f1190 " --> pdb=" O SER f1186 " (cutoff:3.500A) Processing helix chain 'f' and resid 1194 through 1207 removed outlier: 3.719A pdb=" N ALA f1205 " --> pdb=" O ALA f1201 " (cutoff:3.500A) Processing helix chain 'f' and resid 1212 through 1216 removed outlier: 3.647A pdb=" N SER f1215 " --> pdb=" O THR f1212 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU f1216 " --> pdb=" O LEU f1213 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 1212 through 1216' Processing helix chain 'g' and resid 1186 through 1193 removed outlier: 3.901A pdb=" N PHE g1190 " --> pdb=" O SER g1186 " (cutoff:3.500A) Processing helix chain 'g' and resid 1194 through 1207 removed outlier: 3.719A pdb=" N ALA g1205 " --> pdb=" O ALA g1201 " (cutoff:3.500A) Processing helix chain 'g' and resid 1212 through 1216 removed outlier: 3.647A pdb=" N SER g1215 " --> pdb=" O THR g1212 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU g1216 " --> pdb=" O LEU g1213 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 1212 through 1216' Processing helix chain 'e' and resid 1186 through 1193 removed outlier: 3.903A pdb=" N PHE e1190 " --> pdb=" O SER e1186 " (cutoff:3.500A) Processing helix chain 'e' and resid 1194 through 1207 removed outlier: 3.718A pdb=" N ALA e1205 " --> pdb=" O ALA e1201 " (cutoff:3.500A) Processing helix chain 'e' and resid 1212 through 1216 removed outlier: 3.644A pdb=" N SER e1215 " --> pdb=" O THR e1212 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU e1216 " --> pdb=" O LEU e1213 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 1212 through 1216' Processing helix chain 'V' and resid 58 through 76 Processing helix chain 'Z' and resid 58 through 76 Processing helix chain 'b' and resid 5 through 15 removed outlier: 3.655A pdb=" N ASN b 13 " --> pdb=" O LYS b 9 " (cutoff:3.500A) Processing helix chain 'b' and resid 87 through 94 removed outlier: 3.988A pdb=" N LYS b 91 " --> pdb=" O ASP b 87 " (cutoff:3.500A) Processing helix chain 'b' and resid 174 through 179 Processing helix chain 'b' and resid 196 through 202 removed outlier: 3.671A pdb=" N GLN b 200 " --> pdb=" O PRO b 197 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU b 201 " --> pdb=" O GLU b 198 " (cutoff:3.500A) Processing helix chain 'b' and resid 207 through 217 removed outlier: 4.664A pdb=" N THR b 212 " --> pdb=" O SER b 208 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N THR b 213 " --> pdb=" O ASN b 209 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS b 217 " --> pdb=" O THR b 213 " (cutoff:3.500A) Processing helix chain 'b' and resid 241 through 249 removed outlier: 3.607A pdb=" N VAL b 249 " --> pdb=" O TYR b 245 " (cutoff:3.500A) Processing helix chain 'b' and resid 258 through 263 removed outlier: 3.631A pdb=" N LYS b 262 " --> pdb=" O LEU b 259 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE b 263 " --> pdb=" O ALA b 260 " (cutoff:3.500A) Processing helix chain 'b' and resid 318 through 323 removed outlier: 3.543A pdb=" N ASP b 323 " --> pdb=" O GLU b 319 " (cutoff:3.500A) Processing helix chain 'b' and resid 339 through 344 Processing helix chain 'b' and resid 380 through 389 removed outlier: 3.610A pdb=" N LYS b 389 " --> pdb=" O ASP b 385 " (cutoff:3.500A) Processing helix chain 'b' and resid 392 through 398 Processing helix chain 'b' and resid 401 through 405 removed outlier: 3.531A pdb=" N TRP b 405 " --> pdb=" O PRO b 402 " (cutoff:3.500A) Processing helix chain 'b' and resid 459 through 469 Processing helix chain 'b' and resid 478 through 482 removed outlier: 3.552A pdb=" N PHE b 482 " --> pdb=" O LEU b 479 " (cutoff:3.500A) Processing helix chain 'b' and resid 483 through 495 removed outlier: 3.695A pdb=" N ILE b 493 " --> pdb=" O SER b 489 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU b 494 " --> pdb=" O GLU b 490 " (cutoff:3.500A) Processing helix chain 'b' and resid 502 through 506 Processing helix chain 'b' and resid 509 through 513 removed outlier: 3.531A pdb=" N VAL b 512 " --> pdb=" O TRP b 509 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY b 513 " --> pdb=" O ARG b 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 509 through 513' Processing helix chain 'b' and resid 536 through 545 Processing helix chain 'b' and resid 576 through 578 No H-bonds generated for 'chain 'b' and resid 576 through 578' Processing helix chain 'b' and resid 616 through 622 Processing helix chain 'b' and resid 623 through 626 Processing helix chain 'b' and resid 639 through 655 removed outlier: 3.759A pdb=" N ARG b 655 " --> pdb=" O LEU b 651 " (cutoff:3.500A) Processing helix chain 'b' and resid 713 through 717 Processing helix chain 'b' and resid 870 through 874 removed outlier: 3.984A pdb=" N GLU b 874 " --> pdb=" O PRO b 871 " (cutoff:3.500A) Processing helix chain 'b' and resid 907 through 921 removed outlier: 3.539A pdb=" N ASN b 911 " --> pdb=" O LEU b 907 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE b 915 " --> pdb=" O ASN b 911 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ALA b 916 " --> pdb=" O LYS b 912 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN b 919 " --> pdb=" O PHE b 915 " (cutoff:3.500A) Processing helix chain 'd' and resid 5 through 15 removed outlier: 3.656A pdb=" N ASN d 13 " --> pdb=" O LYS d 9 " (cutoff:3.500A) Processing helix chain 'd' and resid 87 through 94 removed outlier: 3.989A pdb=" N LYS d 91 " --> pdb=" O ASP d 87 " (cutoff:3.500A) Processing helix chain 'd' and resid 174 through 179 Processing helix chain 'd' and resid 196 through 202 removed outlier: 3.671A pdb=" N GLN d 200 " --> pdb=" O PRO d 197 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU d 201 " --> pdb=" O GLU d 198 " (cutoff:3.500A) Processing helix chain 'd' and resid 207 through 217 removed outlier: 4.663A pdb=" N THR d 212 " --> pdb=" O SER d 208 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N THR d 213 " --> pdb=" O ASN d 209 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS d 217 " --> pdb=" O THR d 213 " (cutoff:3.500A) Processing helix chain 'd' and resid 241 through 249 removed outlier: 3.607A pdb=" N VAL d 249 " --> pdb=" O TYR d 245 " (cutoff:3.500A) Processing helix chain 'd' and resid 258 through 263 removed outlier: 3.631A pdb=" N LYS d 262 " --> pdb=" O LEU d 259 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE d 263 " --> pdb=" O ALA d 260 " (cutoff:3.500A) Processing helix chain 'd' and resid 318 through 323 removed outlier: 3.542A pdb=" N ASP d 323 " --> pdb=" O GLU d 319 " (cutoff:3.500A) Processing helix chain 'd' and resid 339 through 344 Processing helix chain 'd' and resid 380 through 389 removed outlier: 3.611A pdb=" N LYS d 389 " --> pdb=" O ASP d 385 " (cutoff:3.500A) Processing helix chain 'd' and resid 392 through 398 Processing helix chain 'd' and resid 401 through 405 removed outlier: 3.531A pdb=" N TRP d 405 " --> pdb=" O PRO d 402 " (cutoff:3.500A) Processing helix chain 'd' and resid 459 through 469 Processing helix chain 'd' and resid 478 through 482 removed outlier: 3.552A pdb=" N PHE d 482 " --> pdb=" O LEU d 479 " (cutoff:3.500A) Processing helix chain 'd' and resid 483 through 495 removed outlier: 3.695A pdb=" N ILE d 493 " --> pdb=" O SER d 489 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU d 494 " --> pdb=" O GLU d 490 " (cutoff:3.500A) Processing helix chain 'd' and resid 502 through 506 Processing helix chain 'd' and resid 509 through 513 removed outlier: 3.532A pdb=" N VAL d 512 " --> pdb=" O TRP d 509 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY d 513 " --> pdb=" O ARG d 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 509 through 513' Processing helix chain 'd' and resid 536 through 545 Processing helix chain 'd' and resid 576 through 578 No H-bonds generated for 'chain 'd' and resid 576 through 578' Processing helix chain 'd' and resid 616 through 622 Processing helix chain 'd' and resid 623 through 626 Processing helix chain 'd' and resid 639 through 655 removed outlier: 3.759A pdb=" N ARG d 655 " --> pdb=" O LEU d 651 " (cutoff:3.500A) Processing helix chain 'd' and resid 713 through 717 Processing helix chain 'd' and resid 870 through 874 removed outlier: 3.984A pdb=" N GLU d 874 " --> pdb=" O PRO d 871 " (cutoff:3.500A) Processing helix chain 'd' and resid 907 through 921 removed outlier: 3.539A pdb=" N ASN d 911 " --> pdb=" O LEU d 907 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE d 915 " --> pdb=" O ASN d 911 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ALA d 916 " --> pdb=" O LYS d 912 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN d 919 " --> pdb=" O PHE d 915 " (cutoff:3.500A) Processing helix chain 'c' and resid 5 through 15 removed outlier: 3.656A pdb=" N ASN c 13 " --> pdb=" O LYS c 9 " (cutoff:3.500A) Processing helix chain 'c' and resid 87 through 94 removed outlier: 3.989A pdb=" N LYS c 91 " --> pdb=" O ASP c 87 " (cutoff:3.500A) Processing helix chain 'c' and resid 174 through 179 Processing helix chain 'c' and resid 196 through 202 removed outlier: 3.671A pdb=" N GLN c 200 " --> pdb=" O PRO c 197 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU c 201 " --> pdb=" O GLU c 198 " (cutoff:3.500A) Processing helix chain 'c' and resid 207 through 217 removed outlier: 4.664A pdb=" N THR c 212 " --> pdb=" O SER c 208 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N THR c 213 " --> pdb=" O ASN c 209 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS c 217 " --> pdb=" O THR c 213 " (cutoff:3.500A) Processing helix chain 'c' and resid 241 through 249 removed outlier: 3.608A pdb=" N VAL c 249 " --> pdb=" O TYR c 245 " (cutoff:3.500A) Processing helix chain 'c' and resid 258 through 263 removed outlier: 3.630A pdb=" N LYS c 262 " --> pdb=" O LEU c 259 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE c 263 " --> pdb=" O ALA c 260 " (cutoff:3.500A) Processing helix chain 'c' and resid 318 through 323 removed outlier: 3.544A pdb=" N ASP c 323 " --> pdb=" O GLU c 319 " (cutoff:3.500A) Processing helix chain 'c' and resid 339 through 344 Processing helix chain 'c' and resid 380 through 389 removed outlier: 3.612A pdb=" N LYS c 389 " --> pdb=" O ASP c 385 " (cutoff:3.500A) Processing helix chain 'c' and resid 392 through 398 Processing helix chain 'c' and resid 401 through 405 removed outlier: 3.532A pdb=" N TRP c 405 " --> pdb=" O PRO c 402 " (cutoff:3.500A) Processing helix chain 'c' and resid 459 through 469 Processing helix chain 'c' and resid 478 through 482 removed outlier: 3.553A pdb=" N PHE c 482 " --> pdb=" O LEU c 479 " (cutoff:3.500A) Processing helix chain 'c' and resid 483 through 495 removed outlier: 3.695A pdb=" N ILE c 493 " --> pdb=" O SER c 489 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU c 494 " --> pdb=" O GLU c 490 " (cutoff:3.500A) Processing helix chain 'c' and resid 502 through 506 Processing helix chain 'c' and resid 509 through 513 removed outlier: 3.531A pdb=" N VAL c 512 " --> pdb=" O TRP c 509 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY c 513 " --> pdb=" O ARG c 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 509 through 513' Processing helix chain 'c' and resid 536 through 545 Processing helix chain 'c' and resid 576 through 578 No H-bonds generated for 'chain 'c' and resid 576 through 578' Processing helix chain 'c' and resid 616 through 622 Processing helix chain 'c' and resid 623 through 626 Processing helix chain 'c' and resid 639 through 655 removed outlier: 3.759A pdb=" N ARG c 655 " --> pdb=" O LEU c 651 " (cutoff:3.500A) Processing helix chain 'c' and resid 713 through 717 Processing helix chain 'c' and resid 870 through 874 removed outlier: 3.984A pdb=" N GLU c 874 " --> pdb=" O PRO c 871 " (cutoff:3.500A) Processing helix chain 'c' and resid 907 through 921 removed outlier: 3.539A pdb=" N ASN c 911 " --> pdb=" O LEU c 907 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE c 915 " --> pdb=" O ASN c 911 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ALA c 916 " --> pdb=" O LYS c 912 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN c 919 " --> pdb=" O PHE c 915 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'i' and resid 12 through 17 Processing sheet with id=AA2, first strand: chain 'i' and resid 34 through 42 Processing sheet with id=AA3, first strand: chain 'i' and resid 109 through 115 removed outlier: 3.670A pdb=" N VAL i 128 " --> pdb=" O PHE i 167 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE i 167 " --> pdb=" O VAL i 128 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'i' and resid 139 through 144 removed outlier: 6.631A pdb=" N CYS i 139 " --> pdb=" O VAL i 158 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL i 158 " --> pdb=" O CYS i 139 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ILE i 141 " --> pdb=" O TYR i 156 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'i' and resid 154 through 159 current: chain 'i' and resid 197 through 198 Processing sheet with id=AA5, first strand: chain 'i' and resid 182 through 184 Processing sheet with id=AA6, first strand: chain 'i' and resid 216 through 223 removed outlier: 4.366A pdb=" N ASN i 217 " --> pdb=" O ASP i 239 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP i 239 " --> pdb=" O ASN i 217 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS i 221 " --> pdb=" O ARG i 235 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'i' and resid 251 through 257 removed outlier: 4.102A pdb=" N PHE i 251 " --> pdb=" O VAL i 274 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'i' and resid 270 through 274 current: chain 'i' and resid 307 through 309 Processing sheet with id=AA8, first strand: chain 'i' and resid 333 through 335 Processing sheet with id=AA9, first strand: chain 'i' and resid 413 through 415 removed outlier: 4.025A pdb=" N GLY i 431 " --> pdb=" O LYS i 440 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS i 440 " --> pdb=" O GLY i 431 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'i' and resid 676 through 679 removed outlier: 3.829A pdb=" N HIS i 686 " --> pdb=" O LYS i 677 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'h' and resid 12 through 17 Processing sheet with id=AB3, first strand: chain 'h' and resid 34 through 42 Processing sheet with id=AB4, first strand: chain 'h' and resid 109 through 115 removed outlier: 3.671A pdb=" N VAL h 128 " --> pdb=" O PHE h 167 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE h 167 " --> pdb=" O VAL h 128 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'h' and resid 139 through 144 removed outlier: 6.632A pdb=" N CYS h 139 " --> pdb=" O VAL h 158 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL h 158 " --> pdb=" O CYS h 139 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ILE h 141 " --> pdb=" O TYR h 156 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'h' and resid 154 through 159 current: chain 'h' and resid 197 through 198 Processing sheet with id=AB6, first strand: chain 'h' and resid 182 through 184 Processing sheet with id=AB7, first strand: chain 'h' and resid 216 through 223 removed outlier: 4.366A pdb=" N ASN h 217 " --> pdb=" O ASP h 239 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP h 239 " --> pdb=" O ASN h 217 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS h 221 " --> pdb=" O ARG h 235 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'h' and resid 251 through 257 removed outlier: 4.102A pdb=" N PHE h 251 " --> pdb=" O VAL h 274 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'h' and resid 270 through 274 current: chain 'h' and resid 307 through 309 Processing sheet with id=AB9, first strand: chain 'h' and resid 333 through 335 Processing sheet with id=AC1, first strand: chain 'h' and resid 413 through 415 removed outlier: 4.025A pdb=" N GLY h 431 " --> pdb=" O LYS h 440 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS h 440 " --> pdb=" O GLY h 431 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'h' and resid 676 through 679 removed outlier: 3.829A pdb=" N HIS h 686 " --> pdb=" O LYS h 677 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'j' and resid 12 through 17 Processing sheet with id=AC4, first strand: chain 'j' and resid 34 through 42 Processing sheet with id=AC5, first strand: chain 'j' and resid 109 through 115 removed outlier: 3.669A pdb=" N VAL j 128 " --> pdb=" O PHE j 167 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE j 167 " --> pdb=" O VAL j 128 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'j' and resid 139 through 144 removed outlier: 6.631A pdb=" N CYS j 139 " --> pdb=" O VAL j 158 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL j 158 " --> pdb=" O CYS j 139 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ILE j 141 " --> pdb=" O TYR j 156 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'j' and resid 154 through 159 current: chain 'j' and resid 197 through 198 Processing sheet with id=AC7, first strand: chain 'j' and resid 182 through 184 Processing sheet with id=AC8, first strand: chain 'j' and resid 216 through 223 removed outlier: 4.366A pdb=" N ASN j 217 " --> pdb=" O ASP j 239 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP j 239 " --> pdb=" O ASN j 217 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS j 221 " --> pdb=" O ARG j 235 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'j' and resid 251 through 257 removed outlier: 4.102A pdb=" N PHE j 251 " --> pdb=" O VAL j 274 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'j' and resid 270 through 274 current: chain 'j' and resid 307 through 309 Processing sheet with id=AD1, first strand: chain 'j' and resid 333 through 335 Processing sheet with id=AD2, first strand: chain 'j' and resid 413 through 415 removed outlier: 4.025A pdb=" N GLY j 431 " --> pdb=" O LYS j 440 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS j 440 " --> pdb=" O GLY j 431 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'j' and resid 676 through 679 removed outlier: 3.828A pdb=" N HIS j 686 " --> pdb=" O LYS j 677 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.338A pdb=" N LEU R 10 " --> pdb=" O TYR R 133 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N SER R 135 " --> pdb=" O LEU R 10 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL R 12 " --> pdb=" O SER R 135 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL R 111 " --> pdb=" O ILE R 127 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU R 129 " --> pdb=" O TYR R 109 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TYR R 109 " --> pdb=" O GLU R 129 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LYS R 131 " --> pdb=" O GLY R 107 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLY R 107 " --> pdb=" O LYS R 131 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR R 133 " --> pdb=" O LEU R 105 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU R 105 " --> pdb=" O TYR R 133 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N SER R 135 " --> pdb=" O GLN R 103 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLN R 103 " --> pdb=" O SER R 135 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP R 110 " --> pdb=" O SER R 49 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE R 50 " --> pdb=" O VAL R 61 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 18 through 23 removed outlier: 3.784A pdb=" N LEU R 80 " --> pdb=" O TYR R 18 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL R 75 " --> pdb=" O ASP R 70 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER R 77 " --> pdb=" O ILE R 68 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ILE R 68 " --> pdb=" O SER R 77 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 25 through 27 Processing sheet with id=AD7, first strand: chain 'I' and resid 2 through 3 removed outlier: 3.576A pdb=" N LYS H 230 " --> pdb=" O PHE I 2 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 9 through 15 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 18 through 21 current: chain 'I' and resid 62 through 68 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 62 through 68 current: chain 'I' and resid 90 through 92 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 90 through 92 current: chain 'I' and resid 115 through 131 removed outlier: 6.411A pdb=" N GLY I 141 " --> pdb=" O SER I 125 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL I 127 " --> pdb=" O ASN I 139 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ASN I 139 " --> pdb=" O VAL I 127 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N PHE I 129 " --> pdb=" O ILE I 137 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE I 137 " --> pdb=" O PHE I 129 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 137 through 143 current: chain 'I' and resid 177 through 178 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 177 through 178 current: chain 'I' and resid 213 through 227 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 213 through 227 current: chain 'I' and resid 255 through 269 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 275 through 282 current: chain 'G' and resid 52 through 59 Processing sheet with id=AD9, first strand: chain 'I' and resid 31 through 39 removed outlier: 4.644A pdb=" N SER I 33 " --> pdb=" O ASP I 59 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA I 57 " --> pdb=" O GLN I 35 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N PHE I 37 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE I 55 " --> pdb=" O PHE I 37 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N THR I 39 " --> pdb=" O SER I 53 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N SER I 53 " --> pdb=" O THR I 39 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 52 through 59 current: chain 'H' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 18 through 21 current: chain 'H' and resid 62 through 68 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 62 through 68 current: chain 'H' and resid 90 through 92 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 90 through 92 current: chain 'H' and resid 115 through 131 removed outlier: 6.408A pdb=" N GLY H 141 " --> pdb=" O SER H 125 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL H 127 " --> pdb=" O ASN H 139 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ASN H 139 " --> pdb=" O VAL H 127 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N PHE H 129 " --> pdb=" O ILE H 137 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE H 137 " --> pdb=" O PHE H 129 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 137 through 143 current: chain 'H' and resid 177 through 178 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 177 through 178 current: chain 'H' and resid 213 through 227 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 213 through 227 current: chain 'H' and resid 255 through 269 Processing sheet with id=AE1, first strand: chain 'a' and resid 79 through 81 removed outlier: 5.239A pdb=" N TRP a 48 " --> pdb=" O GLU a 202 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN a 25 " --> pdb=" O TYR a 47 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER a 19 " --> pdb=" O SER a 53 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL a 20 " --> pdb=" O LEU Z 187 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N THR Z 186 " --> pdb=" O SER Z 194 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER Z 194 " --> pdb=" O THR Z 186 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'a' and resid 29 through 32 WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 38 through 42 current: chain 'V' and resid 38 through 41 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 38 through 41 current: chain 'b' and resid 659 through 664 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 659 through 664 current: chain 'b' and resid 689 through 698 removed outlier: 6.451A pdb=" N VAL b 707 " --> pdb=" O ASP b 694 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL b 696 " --> pdb=" O ASN b 705 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN b 705 " --> pdb=" O VAL b 696 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 704 through 710 current: chain 'd' and resid 38 through 42 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 38 through 42 current: chain 'd' and resid 77 through 81 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 77 through 81 current: chain 'd' and resid 128 through 135 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 128 through 135 current: chain 'd' and resid 149 through 159 Processing sheet with id=AE3, first strand: chain 'a' and resid 92 through 93 Processing sheet with id=AE4, first strand: chain 'a' and resid 108 through 112 removed outlier: 7.158A pdb=" N VAL a 147 " --> pdb=" O SER a 143 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N SER a 143 " --> pdb=" O VAL a 147 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN a 149 " --> pdb=" O PHE a 141 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE a 141 " --> pdb=" O ASN a 149 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N SER a 151 " --> pdb=" O THR a 139 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'a' and resid 182 through 183 WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 182 through 183 current: chain 'a' and resid 193 through 194 WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 193 through 194 current: chain 'V' and resid 47 through 53 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 47 through 53 current: chain 'V' and resid 173 through 177 Processing sheet with id=AE6, first strand: chain 'Q' and resid 10 through 13 removed outlier: 6.530A pdb=" N LEU Q 10 " --> pdb=" O TYR Q 133 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N SER Q 135 " --> pdb=" O LEU Q 10 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL Q 12 " --> pdb=" O SER Q 135 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ARG Q 126 " --> pdb=" O ILE Q 113 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE Q 113 " --> pdb=" O ARG Q 126 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET Q 128 " --> pdb=" O VAL Q 111 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY Q 130 " --> pdb=" O TYR Q 109 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ILE Q 134 " --> pdb=" O LEU Q 105 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LEU Q 105 " --> pdb=" O ILE Q 134 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA Q 62 " --> pdb=" O ILE Q 50 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 18 through 23 removed outlier: 7.474A pdb=" N VAL Q 75 " --> pdb=" O VAL Q 69 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL Q 69 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 25 through 28 removed outlier: 3.816A pdb=" N THR Q 35 " --> pdb=" O ASP Q 28 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'S' and resid 10 through 13 removed outlier: 6.412A pdb=" N LEU S 10 " --> pdb=" O TYR S 133 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N SER S 135 " --> pdb=" O LEU S 10 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL S 12 " --> pdb=" O SER S 135 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL S 111 " --> pdb=" O ILE S 127 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLU S 129 " --> pdb=" O TYR S 109 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR S 109 " --> pdb=" O GLU S 129 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LYS S 131 " --> pdb=" O GLY S 107 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLY S 107 " --> pdb=" O LYS S 131 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TYR S 133 " --> pdb=" O LEU S 105 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU S 105 " --> pdb=" O TYR S 133 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER S 135 " --> pdb=" O GLN S 103 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLN S 103 " --> pdb=" O SER S 135 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP S 110 " --> pdb=" O SER S 49 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER S 49 " --> pdb=" O ASP S 110 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'S' and resid 18 through 23 removed outlier: 3.750A pdb=" N TYR S 18 " --> pdb=" O LEU S 80 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'S' and resid 26 through 28 removed outlier: 3.730A pdb=" N LYS S 37 " --> pdb=" O ASP S 26 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP S 28 " --> pdb=" O THR S 35 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 9 through 14 removed outlier: 4.239A pdb=" N ILE F 11 " --> pdb=" O ILE F 28 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 25 through 28 current: chain 'F' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 68 through 75 current: chain 'F' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 119 through 122 current: chain 'F' and resid 143 through 159 removed outlier: 5.644A pdb=" N ILE F 152 " --> pdb=" O ASN F 172 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN F 172 " --> pdb=" O ILE F 152 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN F 158 " --> pdb=" O ARG F 166 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ARG F 166 " --> pdb=" O ASN F 158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 166 through 173 current: chain 'F' and resid 221 through 222 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 221 through 222 current: chain 'F' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 260 through 268 current: chain 'F' and resid 309 through 319 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 309 through 319 current: chain 'F' and resid 331 through 338 Processing sheet with id=AF4, first strand: chain 'F' and resid 40 through 44 removed outlier: 3.918A pdb=" N SER F 64 " --> pdb=" O ASN F 41 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR F 43 " --> pdb=" O ASN F 62 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ASN F 62 " --> pdb=" O THR F 43 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 79 through 80 Processing sheet with id=AF6, first strand: chain 'F' and resid 238 through 239 Processing sheet with id=AF7, first strand: chain 'F' and resid 378 through 382 removed outlier: 3.558A pdb=" N ALA F 378 " --> pdb=" O THR F 403 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR F 380 " --> pdb=" O GLU F 401 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU F 401 " --> pdb=" O THR F 380 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 389 through 390 removed outlier: 3.917A pdb=" N LEU F 390 " --> pdb=" O THR F 459 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL F 440 " --> pdb=" O ILE F 458 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 396 through 397 Processing sheet with id=AG1, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.340A pdb=" N LEU N 10 " --> pdb=" O TYR N 133 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N SER N 135 " --> pdb=" O LEU N 10 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL N 12 " --> pdb=" O SER N 135 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL N 111 " --> pdb=" O ILE N 127 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU N 129 " --> pdb=" O TYR N 109 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N TYR N 109 " --> pdb=" O GLU N 129 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LYS N 131 " --> pdb=" O GLY N 107 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLY N 107 " --> pdb=" O LYS N 131 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR N 133 " --> pdb=" O LEU N 105 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU N 105 " --> pdb=" O TYR N 133 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N SER N 135 " --> pdb=" O GLN N 103 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLN N 103 " --> pdb=" O SER N 135 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP N 110 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE N 50 " --> pdb=" O VAL N 61 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'N' and resid 18 through 23 removed outlier: 3.785A pdb=" N LEU N 80 " --> pdb=" O TYR N 18 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL N 75 " --> pdb=" O ASP N 70 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER N 77 " --> pdb=" O ILE N 68 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ILE N 68 " --> pdb=" O SER N 77 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 25 through 27 Processing sheet with id=AG4, first strand: chain 'H' and resid 2 through 3 removed outlier: 3.515A pdb=" N PHE H 2 " --> pdb=" O LYS G 230 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS G 230 " --> pdb=" O PHE H 2 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'H' and resid 31 through 39 removed outlier: 4.642A pdb=" N SER H 33 " --> pdb=" O ASP H 59 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA H 57 " --> pdb=" O GLN H 35 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N PHE H 37 " --> pdb=" O ILE H 55 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE H 55 " --> pdb=" O PHE H 37 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N THR H 39 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N SER H 53 " --> pdb=" O THR H 39 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 52 through 59 current: chain 'G' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 18 through 21 current: chain 'G' and resid 62 through 68 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 62 through 68 current: chain 'G' and resid 90 through 92 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 90 through 92 current: chain 'G' and resid 115 through 131 removed outlier: 6.407A pdb=" N GLY G 141 " --> pdb=" O SER G 125 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL G 127 " --> pdb=" O ASN G 139 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN G 139 " --> pdb=" O VAL G 127 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N PHE G 129 " --> pdb=" O ILE G 137 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE G 137 " --> pdb=" O PHE G 129 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 137 through 143 current: chain 'G' and resid 177 through 178 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 177 through 178 current: chain 'G' and resid 213 through 227 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 213 through 227 current: chain 'G' and resid 255 through 269 Processing sheet with id=AG6, first strand: chain 'X' and resid 19 through 25 removed outlier: 3.530A pdb=" N ASN X 25 " --> pdb=" O TYR X 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 47 through 53 current: chain 'X' and resid 173 through 177 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 197 through 202 current: chain 'W' and resid 193 through 194 Processing sheet with id=AG7, first strand: chain 'X' and resid 28 through 32 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 38 through 41 current: chain 'W' and resid 38 through 42 removed outlier: 8.701A pdb=" N LEU b 18 " --> pdb=" O VAL W 38 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLU W 40 " --> pdb=" O LEU b 18 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N THR b 20 " --> pdb=" O GLU W 40 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LYS W 42 " --> pdb=" O THR b 20 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N CYS b 22 " --> pdb=" O LYS W 42 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 38 through 42 current: chain 'b' and resid 77 through 81 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 77 through 81 current: chain 'b' and resid 128 through 135 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 128 through 135 current: chain 'b' and resid 149 through 159 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 149 through 159 current: chain 'c' and resid 659 through 664 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 659 through 664 current: chain 'c' and resid 689 through 698 removed outlier: 6.452A pdb=" N VAL c 707 " --> pdb=" O ASP c 694 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL c 696 " --> pdb=" O ASN c 705 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASN c 705 " --> pdb=" O VAL c 696 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'X' and resid 108 through 112 removed outlier: 6.966A pdb=" N VAL X 147 " --> pdb=" O SER X 143 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N SER X 143 " --> pdb=" O VAL X 147 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASN X 149 " --> pdb=" O PHE X 141 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE X 141 " --> pdb=" O ASN X 149 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER X 151 " --> pdb=" O THR X 139 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS X 128 " --> pdb=" O VAL X 167 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'X' and resid 193 through 194 removed outlier: 3.506A pdb=" N SER X 194 " --> pdb=" O THR X 186 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N THR X 186 " --> pdb=" O SER X 194 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL Y 20 " --> pdb=" O LEU X 187 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER Y 19 " --> pdb=" O SER Y 53 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN Y 25 " --> pdb=" O TYR Y 47 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N TRP Y 48 " --> pdb=" O GLU Y 202 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Y' and resid 29 through 32 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 38 through 42 current: chain 'Z' and resid 38 through 41 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 38 through 41 current: chain 'd' and resid 659 through 664 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 659 through 664 current: chain 'd' and resid 689 through 698 removed outlier: 6.452A pdb=" N VAL d 707 " --> pdb=" O ASP d 694 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL d 696 " --> pdb=" O ASN d 705 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASN d 705 " --> pdb=" O VAL d 696 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 704 through 710 current: chain 'c' and resid 38 through 42 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 38 through 42 current: chain 'c' and resid 77 through 81 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 77 through 81 current: chain 'c' and resid 128 through 135 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 128 through 135 current: chain 'c' and resid 149 through 159 Processing sheet with id=AH2, first strand: chain 'Y' and resid 92 through 93 Processing sheet with id=AH3, first strand: chain 'Y' and resid 108 through 112 removed outlier: 7.157A pdb=" N VAL Y 147 " --> pdb=" O SER Y 143 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N SER Y 143 " --> pdb=" O VAL Y 147 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN Y 149 " --> pdb=" O PHE Y 141 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE Y 141 " --> pdb=" O ASN Y 149 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N SER Y 151 " --> pdb=" O THR Y 139 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Y' and resid 182 through 183 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 182 through 183 current: chain 'Y' and resid 193 through 194 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 193 through 194 current: chain 'Z' and resid 47 through 53 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 47 through 53 current: chain 'Z' and resid 173 through 177 Processing sheet with id=AH5, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.527A pdb=" N LEU M 10 " --> pdb=" O TYR M 133 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N SER M 135 " --> pdb=" O LEU M 10 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL M 12 " --> pdb=" O SER M 135 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ARG M 126 " --> pdb=" O ILE M 113 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE M 113 " --> pdb=" O ARG M 126 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET M 128 " --> pdb=" O VAL M 111 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY M 130 " --> pdb=" O TYR M 109 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ILE M 134 " --> pdb=" O LEU M 105 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LEU M 105 " --> pdb=" O ILE M 134 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA M 62 " --> pdb=" O ILE M 50 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'M' and resid 18 through 23 removed outlier: 7.473A pdb=" N VAL M 75 " --> pdb=" O VAL M 69 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL M 69 " --> pdb=" O VAL M 75 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'M' and resid 25 through 28 removed outlier: 3.812A pdb=" N THR M 35 " --> pdb=" O ASP M 28 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'O' and resid 10 through 13 removed outlier: 6.413A pdb=" N LEU O 10 " --> pdb=" O TYR O 133 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N SER O 135 " --> pdb=" O LEU O 10 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL O 12 " --> pdb=" O SER O 135 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL O 111 " --> pdb=" O ILE O 127 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLU O 129 " --> pdb=" O TYR O 109 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR O 109 " --> pdb=" O GLU O 129 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LYS O 131 " --> pdb=" O GLY O 107 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLY O 107 " --> pdb=" O LYS O 131 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TYR O 133 " --> pdb=" O LEU O 105 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU O 105 " --> pdb=" O TYR O 133 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N SER O 135 " --> pdb=" O GLN O 103 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN O 103 " --> pdb=" O SER O 135 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP O 110 " --> pdb=" O SER O 49 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER O 49 " --> pdb=" O ASP O 110 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'O' and resid 18 through 23 removed outlier: 3.751A pdb=" N TYR O 18 " --> pdb=" O LEU O 80 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'O' and resid 26 through 28 removed outlier: 3.732A pdb=" N LYS O 37 " --> pdb=" O ASP O 26 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP O 28 " --> pdb=" O THR O 35 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'E' and resid 9 through 14 removed outlier: 4.239A pdb=" N ILE E 11 " --> pdb=" O ILE E 28 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 25 through 28 current: chain 'E' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 68 through 75 current: chain 'E' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 119 through 122 current: chain 'E' and resid 143 through 159 removed outlier: 5.643A pdb=" N ILE E 152 " --> pdb=" O ASN E 172 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN E 172 " --> pdb=" O ILE E 152 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASN E 158 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ARG E 166 " --> pdb=" O ASN E 158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 166 through 173 current: chain 'E' and resid 221 through 222 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 221 through 222 current: chain 'E' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 260 through 268 current: chain 'E' and resid 309 through 319 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 309 through 319 current: chain 'E' and resid 331 through 338 Processing sheet with id=AI3, first strand: chain 'E' and resid 40 through 44 removed outlier: 3.917A pdb=" N SER E 64 " --> pdb=" O ASN E 41 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR E 43 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ASN E 62 " --> pdb=" O THR E 43 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'E' and resid 79 through 80 Processing sheet with id=AI5, first strand: chain 'E' and resid 238 through 239 Processing sheet with id=AI6, first strand: chain 'E' and resid 378 through 382 removed outlier: 3.558A pdb=" N ALA E 378 " --> pdb=" O THR E 403 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR E 380 " --> pdb=" O GLU E 401 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU E 401 " --> pdb=" O THR E 380 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'E' and resid 389 through 390 removed outlier: 3.915A pdb=" N LEU E 390 " --> pdb=" O THR E 459 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL E 440 " --> pdb=" O ILE E 458 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'E' and resid 396 through 397 Processing sheet with id=AI9, first strand: chain 'C' and resid 9 through 14 removed outlier: 3.581A pdb=" N VAL C 13 " --> pdb=" O GLN C 26 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN C 26 " --> pdb=" O VAL C 13 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 25 through 27 current: chain 'C' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 68 through 75 current: chain 'C' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 119 through 122 current: chain 'C' and resid 143 through 160 removed outlier: 5.715A pdb=" N ILE C 152 " --> pdb=" O ASN C 172 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASN C 172 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG C 166 " --> pdb=" O ASN C 158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 166 through 173 current: chain 'C' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 260 through 268 current: chain 'C' and resid 307 through 319 Processing sheet with id=AJ1, first strand: chain 'C' and resid 40 through 46 removed outlier: 6.773A pdb=" N ASN C 41 " --> pdb=" O ASP C 63 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'C' and resid 79 through 80 Processing sheet with id=AJ3, first strand: chain 'C' and resid 237 through 239 removed outlier: 4.149A pdb=" N THR C 238 " --> pdb=" O PHE C 255 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'C' and resid 378 through 382 removed outlier: 3.893A pdb=" N ALA C 378 " --> pdb=" O THR C 403 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR C 380 " --> pdb=" O GLU C 401 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU C 401 " --> pdb=" O THR C 380 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'C' and resid 389 through 390 removed outlier: 3.913A pdb=" N LEU C 390 " --> pdb=" O THR C 459 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS C 456 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL C 442 " --> pdb=" O LYS C 456 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL C 440 " --> pdb=" O ILE C 458 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'C' and resid 395 through 397 Processing sheet with id=AJ7, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.337A pdb=" N LEU J 10 " --> pdb=" O TYR J 133 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N SER J 135 " --> pdb=" O LEU J 10 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL J 12 " --> pdb=" O SER J 135 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL J 111 " --> pdb=" O ILE J 127 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU J 129 " --> pdb=" O TYR J 109 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TYR J 109 " --> pdb=" O GLU J 129 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LYS J 131 " --> pdb=" O GLY J 107 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLY J 107 " --> pdb=" O LYS J 131 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR J 133 " --> pdb=" O LEU J 105 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU J 105 " --> pdb=" O TYR J 133 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N SER J 135 " --> pdb=" O GLN J 103 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLN J 103 " --> pdb=" O SER J 135 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP J 110 " --> pdb=" O SER J 49 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE J 50 " --> pdb=" O VAL J 61 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'J' and resid 18 through 23 removed outlier: 3.784A pdb=" N LEU J 80 " --> pdb=" O TYR J 18 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL J 75 " --> pdb=" O ASP J 70 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER J 77 " --> pdb=" O ILE J 68 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ILE J 68 " --> pdb=" O SER J 77 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'J' and resid 25 through 27 Processing sheet with id=AK1, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.503A pdb=" N LEU L 10 " --> pdb=" O TYR L 133 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N SER L 135 " --> pdb=" O LEU L 10 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL L 12 " --> pdb=" O SER L 135 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N SER L 124 " --> pdb=" O ARG L 115 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ARG L 115 " --> pdb=" O SER L 124 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ARG L 126 " --> pdb=" O ILE L 113 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE L 113 " --> pdb=" O ARG L 126 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET L 128 " --> pdb=" O VAL L 111 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL L 111 " --> pdb=" O MET L 128 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE L 134 " --> pdb=" O LEU L 105 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU L 105 " --> pdb=" O ILE L 134 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER L 49 " --> pdb=" O ASP L 110 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N PHE L 44 " --> pdb=" O ILE L 68 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE L 68 " --> pdb=" O PHE L 44 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU L 46 " --> pdb=" O THR L 66 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N THR L 66 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLY L 48 " --> pdb=" O PHE L 64 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA L 62 " --> pdb=" O ILE L 50 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N THR L 66 " --> pdb=" O SER L 79 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N SER L 79 " --> pdb=" O THR L 66 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ILE L 68 " --> pdb=" O SER L 77 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N SER L 77 " --> pdb=" O ILE L 68 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'L' and resid 25 through 26 Processing sheet with id=AK3, first strand: chain 'W' and resid 79 through 81 removed outlier: 5.239A pdb=" N TRP W 48 " --> pdb=" O GLU W 202 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN W 25 " --> pdb=" O TYR W 47 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER W 19 " --> pdb=" O SER W 53 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL W 20 " --> pdb=" O LEU V 187 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N THR V 186 " --> pdb=" O SER V 194 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER V 194 " --> pdb=" O THR V 186 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'W' and resid 92 through 93 Processing sheet with id=AK5, first strand: chain 'W' and resid 108 through 112 removed outlier: 7.156A pdb=" N VAL W 147 " --> pdb=" O SER W 143 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N SER W 143 " --> pdb=" O VAL W 147 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN W 149 " --> pdb=" O PHE W 141 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE W 141 " --> pdb=" O ASN W 149 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N SER W 151 " --> pdb=" O THR W 139 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'U' and resid 10 through 13 removed outlier: 6.528A pdb=" N LEU U 10 " --> pdb=" O TYR U 133 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N SER U 135 " --> pdb=" O LEU U 10 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL U 12 " --> pdb=" O SER U 135 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ARG U 126 " --> pdb=" O ILE U 113 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE U 113 " --> pdb=" O ARG U 126 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET U 128 " --> pdb=" O VAL U 111 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY U 130 " --> pdb=" O TYR U 109 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ILE U 134 " --> pdb=" O LEU U 105 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LEU U 105 " --> pdb=" O ILE U 134 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA U 62 " --> pdb=" O ILE U 50 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'U' and resid 18 through 23 removed outlier: 7.474A pdb=" N VAL U 75 " --> pdb=" O VAL U 69 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL U 69 " --> pdb=" O VAL U 75 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'U' and resid 25 through 28 removed outlier: 3.812A pdb=" N THR U 35 " --> pdb=" O ASP U 28 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.415A pdb=" N LEU K 10 " --> pdb=" O TYR K 133 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N SER K 135 " --> pdb=" O LEU K 10 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL K 12 " --> pdb=" O SER K 135 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL K 111 " --> pdb=" O ILE K 127 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLU K 129 " --> pdb=" O TYR K 109 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR K 109 " --> pdb=" O GLU K 129 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LYS K 131 " --> pdb=" O GLY K 107 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLY K 107 " --> pdb=" O LYS K 131 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR K 133 " --> pdb=" O LEU K 105 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU K 105 " --> pdb=" O TYR K 133 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N SER K 135 " --> pdb=" O GLN K 103 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLN K 103 " --> pdb=" O SER K 135 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP K 110 " --> pdb=" O SER K 49 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER K 49 " --> pdb=" O ASP K 110 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'K' and resid 18 through 23 removed outlier: 3.750A pdb=" N TYR K 18 " --> pdb=" O LEU K 80 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'K' and resid 26 through 28 removed outlier: 3.732A pdb=" N LYS K 37 " --> pdb=" O ASP K 26 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP K 28 " --> pdb=" O THR K 35 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'D' and resid 9 through 14 removed outlier: 4.240A pdb=" N ILE D 11 " --> pdb=" O ILE D 28 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 25 through 28 current: chain 'D' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 68 through 75 current: chain 'D' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 119 through 122 current: chain 'D' and resid 143 through 159 removed outlier: 5.643A pdb=" N ILE D 152 " --> pdb=" O ASN D 172 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASN D 172 " --> pdb=" O ILE D 152 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASN D 158 " --> pdb=" O ARG D 166 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ARG D 166 " --> pdb=" O ASN D 158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 166 through 173 current: chain 'D' and resid 221 through 222 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 221 through 222 current: chain 'D' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 260 through 268 current: chain 'D' and resid 309 through 319 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 309 through 319 current: chain 'D' and resid 331 through 338 Processing sheet with id=AL4, first strand: chain 'D' and resid 40 through 44 removed outlier: 3.918A pdb=" N SER D 64 " --> pdb=" O ASN D 41 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR D 43 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ASN D 62 " --> pdb=" O THR D 43 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'D' and resid 79 through 80 Processing sheet with id=AL6, first strand: chain 'D' and resid 238 through 239 Processing sheet with id=AL7, first strand: chain 'D' and resid 378 through 382 removed outlier: 3.557A pdb=" N ALA D 378 " --> pdb=" O THR D 403 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR D 380 " --> pdb=" O GLU D 401 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU D 401 " --> pdb=" O THR D 380 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'D' and resid 389 through 390 removed outlier: 3.916A pdb=" N LEU D 390 " --> pdb=" O THR D 459 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL D 440 " --> pdb=" O ILE D 458 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'D' and resid 396 through 397 Processing sheet with id=AM1, first strand: chain 'A' and resid 9 through 14 removed outlier: 3.582A pdb=" N VAL A 13 " --> pdb=" O GLN A 26 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN A 26 " --> pdb=" O VAL A 13 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 25 through 27 current: chain 'A' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 68 through 75 current: chain 'A' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 119 through 122 current: chain 'A' and resid 143 through 160 removed outlier: 5.714A pdb=" N ILE A 152 " --> pdb=" O ASN A 172 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASN A 172 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG A 166 " --> pdb=" O ASN A 158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 166 through 173 current: chain 'A' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 260 through 268 current: chain 'A' and resid 307 through 319 Processing sheet with id=AM2, first strand: chain 'A' and resid 40 through 46 removed outlier: 6.773A pdb=" N ASN A 41 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'A' and resid 79 through 80 Processing sheet with id=AM4, first strand: chain 'A' and resid 237 through 239 removed outlier: 4.150A pdb=" N THR A 238 " --> pdb=" O PHE A 255 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'A' and resid 378 through 382 removed outlier: 3.892A pdb=" N ALA A 378 " --> pdb=" O THR A 403 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR A 380 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU A 401 " --> pdb=" O THR A 380 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'A' and resid 389 through 390 removed outlier: 3.912A pdb=" N LEU A 390 " --> pdb=" O THR A 459 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS A 456 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 442 " --> pdb=" O LYS A 456 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A 440 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'A' and resid 395 through 397 Processing sheet with id=AM8, first strand: chain 'B' and resid 9 through 14 removed outlier: 3.583A pdb=" N VAL B 13 " --> pdb=" O GLN B 26 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN B 26 " --> pdb=" O VAL B 13 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 25 through 27 current: chain 'B' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 68 through 75 current: chain 'B' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 119 through 122 current: chain 'B' and resid 143 through 160 removed outlier: 5.714A pdb=" N ILE B 152 " --> pdb=" O ASN B 172 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASN B 172 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ARG B 166 " --> pdb=" O ASN B 158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 166 through 173 current: chain 'B' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 260 through 268 current: chain 'B' and resid 307 through 319 Processing sheet with id=AM9, first strand: chain 'B' and resid 40 through 46 removed outlier: 6.773A pdb=" N ASN B 41 " --> pdb=" O ASP B 63 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'B' and resid 79 through 80 Processing sheet with id=AN2, first strand: chain 'B' and resid 237 through 239 removed outlier: 4.150A pdb=" N THR B 238 " --> pdb=" O PHE B 255 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'B' and resid 378 through 382 removed outlier: 3.892A pdb=" N ALA B 378 " --> pdb=" O THR B 403 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR B 380 " --> pdb=" O GLU B 401 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU B 401 " --> pdb=" O THR B 380 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'B' and resid 389 through 390 removed outlier: 3.913A pdb=" N LEU B 390 " --> pdb=" O THR B 459 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS B 456 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL B 442 " --> pdb=" O LYS B 456 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 440 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'B' and resid 395 through 397 Processing sheet with id=AN6, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.546A pdb=" N SER P 124 " --> pdb=" O ARG P 115 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ARG P 115 " --> pdb=" O SER P 124 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ARG P 126 " --> pdb=" O ILE P 113 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE P 113 " --> pdb=" O ARG P 126 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET P 128 " --> pdb=" O VAL P 111 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL P 111 " --> pdb=" O MET P 128 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE P 134 " --> pdb=" O LEU P 105 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU P 105 " --> pdb=" O ILE P 134 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER P 49 " --> pdb=" O ASP P 110 " (cutoff:3.500A) removed outlier: 10.080A pdb=" N PHE P 44 " --> pdb=" O ILE P 68 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE P 68 " --> pdb=" O PHE P 44 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU P 46 " --> pdb=" O THR P 66 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N THR P 66 " --> pdb=" O LEU P 46 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLY P 48 " --> pdb=" O PHE P 64 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA P 62 " --> pdb=" O ILE P 50 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N THR P 66 " --> pdb=" O SER P 79 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N SER P 79 " --> pdb=" O THR P 66 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ILE P 68 " --> pdb=" O SER P 77 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N SER P 77 " --> pdb=" O ILE P 68 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'P' and resid 25 through 26 Processing sheet with id=AN8, first strand: chain 'T' and resid 10 through 13 removed outlier: 6.505A pdb=" N LEU T 10 " --> pdb=" O TYR T 133 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N SER T 135 " --> pdb=" O LEU T 10 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL T 12 " --> pdb=" O SER T 135 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N SER T 124 " --> pdb=" O ARG T 115 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ARG T 115 " --> pdb=" O SER T 124 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ARG T 126 " --> pdb=" O ILE T 113 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE T 113 " --> pdb=" O ARG T 126 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET T 128 " --> pdb=" O VAL T 111 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL T 111 " --> pdb=" O MET T 128 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE T 134 " --> pdb=" O LEU T 105 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU T 105 " --> pdb=" O ILE T 134 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER T 49 " --> pdb=" O ASP T 110 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N PHE T 44 " --> pdb=" O ILE T 68 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE T 68 " --> pdb=" O PHE T 44 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU T 46 " --> pdb=" O THR T 66 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N THR T 66 " --> pdb=" O LEU T 46 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLY T 48 " --> pdb=" O PHE T 64 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA T 62 " --> pdb=" O ILE T 50 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N THR T 66 " --> pdb=" O SER T 79 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N SER T 79 " --> pdb=" O THR T 66 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE T 68 " --> pdb=" O SER T 77 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N SER T 77 " --> pdb=" O ILE T 68 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain 'T' and resid 25 through 26 Processing sheet with id=AO1, first strand: chain 'V' and resid 108 through 112 removed outlier: 6.966A pdb=" N VAL V 147 " --> pdb=" O SER V 143 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N SER V 143 " --> pdb=" O VAL V 147 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASN V 149 " --> pdb=" O PHE V 141 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE V 141 " --> pdb=" O ASN V 149 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N SER V 151 " --> pdb=" O THR V 139 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS V 128 " --> pdb=" O VAL V 167 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'Z' and resid 108 through 112 removed outlier: 6.966A pdb=" N VAL Z 147 " --> pdb=" O SER Z 143 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N SER Z 143 " --> pdb=" O VAL Z 147 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASN Z 149 " --> pdb=" O PHE Z 141 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N PHE Z 141 " --> pdb=" O ASN Z 149 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER Z 151 " --> pdb=" O THR Z 139 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS Z 128 " --> pdb=" O VAL Z 167 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'b' and resid 48 through 50 Processing sheet with id=AO4, first strand: chain 'b' and resid 181 through 183 Processing sheet with id=AO5, first strand: chain 'b' and resid 227 through 228 Processing sheet with id=AO6, first strand: chain 'b' and resid 304 through 308 removed outlier: 8.119A pdb=" N PHE b 304 " --> pdb=" O GLN b 438 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLN b 438 " --> pdb=" O PHE b 304 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP b 306 " --> pdb=" O GLU b 436 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY b 439 " --> pdb=" O GLY b 269 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N GLY b 269 " --> pdb=" O GLY b 439 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'b' and resid 276 through 282 removed outlier: 6.060A pdb=" N ALA b 295 " --> pdb=" O PRO b 277 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE b 279 " --> pdb=" O VAL b 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 289 through 295 current: chain 'b' and resid 365 through 367 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 365 through 367 current: chain 'b' and resid 416 through 422 Processing sheet with id=AO8, first strand: chain 'b' and resid 444 through 445 Processing sheet with id=AO9, first strand: chain 'b' and resid 551 through 553 removed outlier: 3.620A pdb=" N THR b 562 " --> pdb=" O ALA b 551 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'b' and resid 609 through 615 removed outlier: 3.519A pdb=" N VAL b 596 " --> pdb=" O PHE b 614 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N SER b 595 " --> pdb=" O LEU b 630 " (cutoff:3.500A) Processing sheet with id=AP2, first strand: chain 'b' and resid 740 through 745 removed outlier: 4.431A pdb=" N PHE b 742 " --> pdb=" O SER b 762 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N SER b 762 " --> pdb=" O PHE b 742 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N TYR b 744 " --> pdb=" O GLU b 760 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLU b 760 " --> pdb=" O TYR b 744 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLY b 759 " --> pdb=" O ILE b 802 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'b' and resid 785 through 788 removed outlier: 7.082A pdb=" N VAL b 817 " --> pdb=" O VAL b 772 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'b' and resid 808 through 814 removed outlier: 3.630A pdb=" N ALA b 810 " --> pdb=" O VAL b 831 " (cutoff:3.500A) Processing sheet with id=AP5, first strand: chain 'b' and resid 843 through 848 removed outlier: 6.006A pdb=" N ASN b 844 " --> pdb=" O ASP b 868 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP b 868 " --> pdb=" O ASN b 844 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS b 864 " --> pdb=" O VAL b 848 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL b 863 " --> pdb=" O TYR b 906 " (cutoff:3.500A) Processing sheet with id=AP6, first strand: chain 'b' and resid 892 through 898 Processing sheet with id=AP7, first strand: chain 'd' and resid 48 through 50 Processing sheet with id=AP8, first strand: chain 'd' and resid 181 through 183 Processing sheet with id=AP9, first strand: chain 'd' and resid 227 through 228 Processing sheet with id=AQ1, first strand: chain 'd' and resid 304 through 308 removed outlier: 8.119A pdb=" N PHE d 304 " --> pdb=" O GLN d 438 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLN d 438 " --> pdb=" O PHE d 304 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP d 306 " --> pdb=" O GLU d 436 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY d 439 " --> pdb=" O GLY d 269 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLY d 269 " --> pdb=" O GLY d 439 " (cutoff:3.500A) Processing sheet with id=AQ2, first strand: chain 'd' and resid 276 through 282 removed outlier: 6.058A pdb=" N ALA d 295 " --> pdb=" O PRO d 277 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE d 279 " --> pdb=" O VAL d 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 289 through 295 current: chain 'd' and resid 365 through 367 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 365 through 367 current: chain 'd' and resid 416 through 422 Processing sheet with id=AQ3, first strand: chain 'd' and resid 444 through 445 Processing sheet with id=AQ4, first strand: chain 'd' and resid 551 through 553 removed outlier: 3.618A pdb=" N THR d 562 " --> pdb=" O ALA d 551 " (cutoff:3.500A) Processing sheet with id=AQ5, first strand: chain 'd' and resid 609 through 615 removed outlier: 3.519A pdb=" N VAL d 596 " --> pdb=" O PHE d 614 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N SER d 595 " --> pdb=" O LEU d 630 " (cutoff:3.500A) Processing sheet with id=AQ6, first strand: chain 'd' and resid 740 through 745 removed outlier: 4.431A pdb=" N PHE d 742 " --> pdb=" O SER d 762 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N SER d 762 " --> pdb=" O PHE d 742 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N TYR d 744 " --> pdb=" O GLU d 760 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLU d 760 " --> pdb=" O TYR d 744 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLY d 759 " --> pdb=" O ILE d 802 " (cutoff:3.500A) Processing sheet with id=AQ7, first strand: chain 'd' and resid 785 through 788 removed outlier: 7.082A pdb=" N VAL d 817 " --> pdb=" O VAL d 772 " (cutoff:3.500A) Processing sheet with id=AQ8, first strand: chain 'd' and resid 808 through 814 removed outlier: 3.629A pdb=" N ALA d 810 " --> pdb=" O VAL d 831 " (cutoff:3.500A) Processing sheet with id=AQ9, first strand: chain 'd' and resid 843 through 848 removed outlier: 6.005A pdb=" N ASN d 844 " --> pdb=" O ASP d 868 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASP d 868 " --> pdb=" O ASN d 844 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS d 864 " --> pdb=" O VAL d 848 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL d 863 " --> pdb=" O TYR d 906 " (cutoff:3.500A) Processing sheet with id=AR1, first strand: chain 'd' and resid 892 through 898 Processing sheet with id=AR2, first strand: chain 'c' and resid 48 through 50 Processing sheet with id=AR3, first strand: chain 'c' and resid 181 through 183 Processing sheet with id=AR4, first strand: chain 'c' and resid 227 through 228 Processing sheet with id=AR5, first strand: chain 'c' and resid 304 through 308 removed outlier: 8.117A pdb=" N PHE c 304 " --> pdb=" O GLN c 438 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLN c 438 " --> pdb=" O PHE c 304 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP c 306 " --> pdb=" O GLU c 436 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY c 439 " --> pdb=" O GLY c 269 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N GLY c 269 " --> pdb=" O GLY c 439 " (cutoff:3.500A) Processing sheet with id=AR6, first strand: chain 'c' and resid 276 through 282 removed outlier: 6.059A pdb=" N ALA c 295 " --> pdb=" O PRO c 277 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE c 279 " --> pdb=" O VAL c 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 289 through 295 current: chain 'c' and resid 365 through 367 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 365 through 367 current: chain 'c' and resid 416 through 422 Processing sheet with id=AR7, first strand: chain 'c' and resid 444 through 445 Processing sheet with id=AR8, first strand: chain 'c' and resid 551 through 553 removed outlier: 3.621A pdb=" N THR c 562 " --> pdb=" O ALA c 551 " (cutoff:3.500A) Processing sheet with id=AR9, first strand: chain 'c' and resid 609 through 615 removed outlier: 3.518A pdb=" N VAL c 596 " --> pdb=" O PHE c 614 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER c 595 " --> pdb=" O LEU c 630 " (cutoff:3.500A) Processing sheet with id=AS1, first strand: chain 'c' and resid 740 through 745 removed outlier: 4.432A pdb=" N PHE c 742 " --> pdb=" O SER c 762 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N SER c 762 " --> pdb=" O PHE c 742 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N TYR c 744 " --> pdb=" O GLU c 760 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLU c 760 " --> pdb=" O TYR c 744 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLY c 759 " --> pdb=" O ILE c 802 " (cutoff:3.500A) Processing sheet with id=AS2, first strand: chain 'c' and resid 785 through 788 removed outlier: 7.082A pdb=" N VAL c 817 " --> pdb=" O VAL c 772 " (cutoff:3.500A) Processing sheet with id=AS3, first strand: chain 'c' and resid 808 through 814 removed outlier: 3.630A pdb=" N ALA c 810 " --> pdb=" O VAL c 831 " (cutoff:3.500A) Processing sheet with id=AS4, first strand: chain 'c' and resid 843 through 848 removed outlier: 6.006A pdb=" N ASN c 844 " --> pdb=" O ASP c 868 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP c 868 " --> pdb=" O ASN c 844 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS c 864 " --> pdb=" O VAL c 848 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL c 863 " --> pdb=" O TYR c 906 " (cutoff:3.500A) Processing sheet with id=AS5, first strand: chain 'c' and resid 892 through 898 1677 hydrogen bonds defined for protein. 4407 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: 41.41 Time building geometry restraints manager: 28.06 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: 27578 1.34 - 1.45: 13766 1.45 - 1.57: 46520 1.57 - 1.69: 0 1.69 - 1.81: 405 Bond restraints: 88269 Sorted by residual: bond pdb=" N VAL Z 41 " pdb=" CA VAL Z 41 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.20e-02 6.94e+03 8.49e+00 bond pdb=" N VAL X 41 " pdb=" CA VAL X 41 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.20e-02 6.94e+03 8.41e+00 bond pdb=" N VAL c 863 " pdb=" CA VAL c 863 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.24e-02 6.50e+03 8.15e+00 bond pdb=" N ILE d 898 " pdb=" CA ILE d 898 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.20e-02 6.94e+03 8.04e+00 bond pdb=" N VAL d 859 " pdb=" CA VAL d 859 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.84e+00 ... (remaining 88264 not shown) Histogram of bond angle deviations from ideal: 99.45 - 106.38: 2088 106.38 - 113.31: 48443 113.31 - 120.24: 29489 120.24 - 127.16: 39187 127.16 - 134.09: 736 Bond angle restraints: 119943 Sorted by residual: angle pdb=" CA PRO P 33 " pdb=" N PRO P 33 " pdb=" CD PRO P 33 " ideal model delta sigma weight residual 112.00 105.06 6.94 1.40e+00 5.10e-01 2.45e+01 angle pdb=" CA PRO T 33 " pdb=" N PRO T 33 " pdb=" CD PRO T 33 " ideal model delta sigma weight residual 112.00 105.07 6.93 1.40e+00 5.10e-01 2.45e+01 angle pdb=" CA PRO L 33 " pdb=" N PRO L 33 " pdb=" CD PRO L 33 " ideal model delta sigma weight residual 112.00 105.14 6.86 1.40e+00 5.10e-01 2.40e+01 angle pdb=" CA GLY d 924 " pdb=" C GLY d 924 " pdb=" O GLY d 924 " ideal model delta sigma weight residual 121.62 118.07 3.55 9.80e-01 1.04e+00 1.31e+01 angle pdb=" CA GLY b 924 " pdb=" C GLY b 924 " pdb=" O GLY b 924 " ideal model delta sigma weight residual 121.62 118.17 3.45 9.80e-01 1.04e+00 1.24e+01 ... (remaining 119938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 48444 17.80 - 35.60: 3656 35.60 - 53.40: 600 53.40 - 71.20: 85 71.20 - 89.00: 66 Dihedral angle restraints: 52851 sinusoidal: 20610 harmonic: 32241 Sorted by residual: dihedral pdb=" CB CYS b 316 " pdb=" SG CYS b 316 " pdb=" SG CYS b 327 " pdb=" CB CYS b 327 " ideal model delta sinusoidal sigma weight residual 93.00 43.93 49.07 1 1.00e+01 1.00e-02 3.31e+01 dihedral pdb=" CB CYS d 316 " pdb=" SG CYS d 316 " pdb=" SG CYS d 327 " pdb=" CB CYS d 327 " ideal model delta sinusoidal sigma weight residual 93.00 43.95 49.05 1 1.00e+01 1.00e-02 3.31e+01 dihedral pdb=" CB CYS c 316 " pdb=" SG CYS c 316 " pdb=" SG CYS c 327 " pdb=" CB CYS c 327 " ideal model delta sinusoidal sigma weight residual 93.00 43.98 49.02 1 1.00e+01 1.00e-02 3.30e+01 ... (remaining 52848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 9411 0.039 - 0.077: 2701 0.077 - 0.116: 1292 0.116 - 0.154: 258 0.154 - 0.193: 36 Chirality restraints: 13698 Sorted by residual: chirality pdb=" CA ILE L 78 " pdb=" N ILE L 78 " pdb=" C ILE L 78 " pdb=" CB ILE L 78 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.27e-01 chirality pdb=" CA ILE P 78 " pdb=" N ILE P 78 " pdb=" C ILE P 78 " pdb=" CB ILE P 78 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.17e-01 chirality pdb=" CA ILE T 78 " pdb=" N ILE T 78 " pdb=" C ILE T 78 " pdb=" CB ILE T 78 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.97e-01 ... (remaining 13695 not shown) Planarity restraints: 15528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR L 32 " 0.076 5.00e-02 4.00e+02 1.11e-01 1.98e+01 pdb=" N PRO L 33 " -0.192 5.00e-02 4.00e+02 pdb=" CA PRO L 33 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO L 33 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR P 32 " -0.076 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO P 33 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO P 33 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO P 33 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR T 32 " -0.076 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO T 33 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO T 33 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO T 33 " -0.060 5.00e-02 4.00e+02 ... (remaining 15525 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 317 2.43 - 3.05: 56240 3.05 - 3.66: 126267 3.66 - 4.28: 195402 4.28 - 4.90: 329370 Nonbonded interactions: 707596 Sorted by model distance: nonbonded pdb=" O LEU h 651 " pdb=" NE ARG j 662 " model vdw 1.812 2.520 nonbonded pdb=" NE ARG i 662 " pdb=" O LEU j 651 " model vdw 1.877 2.520 nonbonded pdb=" O LEU i 651 " pdb=" NE ARG h 662 " model vdw 1.905 2.520 nonbonded pdb=" O VAL i 645 " pdb=" O ALA h 641 " model vdw 1.937 3.040 nonbonded pdb=" O VAL h 645 " pdb=" O ALA j 641 " model vdw 1.979 3.040 ... (remaining 707591 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = (chain 'L' and resid 2 through 140) selection = (chain 'M' and resid 2 through 140) selection = chain 'N' selection = chain 'O' selection = (chain 'P' and resid 2 through 140) selection = (chain 'Q' and resid 2 through 140) selection = chain 'R' selection = chain 'S' selection = (chain 'T' and resid 2 through 140) selection = (chain 'U' and resid 2 through 140) } ncs_group { reference = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } ncs_group { reference = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'e' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'h' selection = chain 'i' selection = chain 'j' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 21.340 Check model and map are aligned: 0.940 Set scattering table: 0.620 Process input model: 184.220 Find NCS groups from input model: 4.570 Set up NCS constraints: 0.680 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 219.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 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 : 0.003 0.078 88269 Z= 0.211 Angle : 0.556 8.669 119943 Z= 0.324 Chirality : 0.046 0.193 13698 Planarity : 0.004 0.111 15528 Dihedral : 13.099 88.998 32190 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.57 % Favored : 95.40 % Rotamer: Outliers : 0.03 % Allowed : 0.35 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % 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: -1.99 (0.08), residues: 11031 helix: -0.40 (0.16), residues: 1089 sheet: -1.05 (0.08), residues: 3843 loop : -1.67 (0.07), residues: 6099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 369 HIS 0.008 0.001 HIS b 339 PHE 0.014 0.001 PHE H 92 TYR 0.022 0.001 TYR B 239 ARG 0.009 0.001 ARG F 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22062 Ramachandran restraints generated. 11031 Oldfield, 0 Emsley, 11031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22062 Ramachandran restraints generated. 11031 Oldfield, 0 Emsley, 11031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2182 residues out of total 9600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 2179 time to evaluate : 7.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: i 405 ASN cc_start: 0.6966 (t0) cc_final: 0.6220 (m110) REVERT: i 627 MET cc_start: 0.1648 (ptm) cc_final: 0.1268 (mtm) REVERT: i 633 MET cc_start: -0.3553 (mmt) cc_final: -0.4060 (mtt) REVERT: i 677 LYS cc_start: 0.5652 (ttmt) cc_final: 0.5290 (ttmt) REVERT: h 143 LEU cc_start: 0.5474 (mt) cc_final: 0.5259 (mm) REVERT: h 405 ASN cc_start: 0.6455 (t0) cc_final: 0.6138 (m-40) REVERT: h 676 MET cc_start: -0.1285 (pmm) cc_final: -0.1633 (pmm) REVERT: j 166 MET cc_start: 0.4445 (ptt) cc_final: 0.4227 (ptt) REVERT: j 627 MET cc_start: 0.1240 (ptm) cc_final: 0.0994 (ptp) REVERT: R 65 THR cc_start: 0.7811 (m) cc_final: 0.7585 (t) REVERT: I 275 GLN cc_start: 0.8678 (mt0) cc_final: 0.8343 (mt0) REVERT: Q 1 MET cc_start: 0.5236 (mtp) cc_final: 0.4939 (mtp) REVERT: Q 54 LEU cc_start: 0.8911 (mt) cc_final: 0.8207 (mt) REVERT: S 37 LYS cc_start: 0.8725 (tmmt) cc_final: 0.8267 (ttpp) REVERT: S 73 GLN cc_start: 0.7061 (tp40) cc_final: 0.6120 (tm-30) REVERT: F 91 ASP cc_start: 0.6909 (p0) cc_final: 0.6621 (p0) REVERT: F 196 TYR cc_start: 0.8163 (t80) cc_final: 0.7708 (t80) REVERT: F 239 TYR cc_start: 0.8603 (m-80) cc_final: 0.8402 (m-80) REVERT: F 262 THR cc_start: 0.8660 (p) cc_final: 0.7873 (t) REVERT: H 144 SER cc_start: 0.8439 (t) cc_final: 0.8070 (p) REVERT: X 105 LYS cc_start: 0.7875 (ptpp) cc_final: 0.7661 (mttp) REVERT: X 160 THR cc_start: 0.7826 (p) cc_final: 0.7566 (t) REVERT: X 178 MET cc_start: 0.8743 (mmm) cc_final: 0.8345 (mmt) REVERT: Y 1 MET cc_start: 0.6748 (ttt) cc_final: 0.5955 (ttm) REVERT: Y 66 ASP cc_start: 0.7658 (t70) cc_final: 0.7383 (t0) REVERT: M 54 LEU cc_start: 0.8708 (mt) cc_final: 0.8402 (mp) REVERT: M 128 MET cc_start: 0.7270 (mtp) cc_final: 0.6886 (mtm) REVERT: O 37 LYS cc_start: 0.8387 (tmmt) cc_final: 0.7926 (ttpp) REVERT: E 77 LEU cc_start: 0.8640 (mt) cc_final: 0.8439 (mp) REVERT: E 262 THR cc_start: 0.8728 (p) cc_final: 0.8345 (t) REVERT: C 339 ILE cc_start: 0.8672 (pt) cc_final: 0.8428 (mm) REVERT: J 46 LEU cc_start: 0.8306 (pt) cc_final: 0.7918 (pt) REVERT: J 100 ASN cc_start: 0.7046 (t0) cc_final: 0.6835 (t0) REVERT: L 1 MET cc_start: 0.4596 (tpt) cc_final: 0.4379 (ttm) REVERT: L 9 ASP cc_start: 0.8022 (m-30) cc_final: 0.7611 (m-30) REVERT: L 24 PHE cc_start: 0.8063 (m-80) cc_final: 0.7834 (m-80) REVERT: L 61 VAL cc_start: 0.8496 (t) cc_final: 0.8260 (t) REVERT: L 126 ARG cc_start: 0.7991 (ttp-170) cc_final: 0.7504 (ttm170) REVERT: G 82 MET cc_start: 0.8443 (ttp) cc_final: 0.8040 (ttm) REVERT: G 144 SER cc_start: 0.8883 (t) cc_final: 0.8093 (p) REVERT: G 182 LEU cc_start: 0.8276 (tp) cc_final: 0.7988 (tt) REVERT: G 275 GLN cc_start: 0.8574 (mt0) cc_final: 0.8337 (mt0) REVERT: W 1 MET cc_start: 0.6421 (ttt) cc_final: 0.5073 (ttm) REVERT: W 66 ASP cc_start: 0.7720 (t70) cc_final: 0.7485 (t0) REVERT: W 189 ASN cc_start: 0.8470 (p0) cc_final: 0.8232 (p0) REVERT: K 18 TYR cc_start: 0.7614 (t80) cc_final: 0.7167 (t80) REVERT: K 37 LYS cc_start: 0.8592 (tmmt) cc_final: 0.8191 (ttpp) REVERT: K 73 GLN cc_start: 0.6831 (tp40) cc_final: 0.6501 (tp40) REVERT: D 91 ASP cc_start: 0.7217 (p0) cc_final: 0.6986 (p0) REVERT: D 262 THR cc_start: 0.8663 (p) cc_final: 0.8137 (t) REVERT: A 98 LEU cc_start: 0.8811 (tp) cc_final: 0.8605 (tp) REVERT: P 61 VAL cc_start: 0.8470 (t) cc_final: 0.8150 (t) REVERT: P 126 ARG cc_start: 0.8300 (ttp-170) cc_final: 0.7872 (ttm170) REVERT: T 61 VAL cc_start: 0.8667 (t) cc_final: 0.8418 (t) REVERT: T 109 TYR cc_start: 0.8052 (p90) cc_final: 0.7741 (p90) REVERT: T 126 ARG cc_start: 0.8082 (ttp-170) cc_final: 0.7506 (ttm170) REVERT: f 1204 LEU cc_start: 0.8393 (tp) cc_final: 0.8123 (tp) REVERT: V 105 LYS cc_start: 0.7936 (ptpp) cc_final: 0.7618 (mttp) REVERT: V 160 THR cc_start: 0.7569 (p) cc_final: 0.7294 (t) REVERT: Z 160 THR cc_start: 0.6839 (p) cc_final: 0.6410 (t) REVERT: b 257 PHE cc_start: 0.8122 (m-80) cc_final: 0.7854 (m-80) REVERT: b 360 ASN cc_start: 0.7610 (t0) cc_final: 0.6937 (t0) REVERT: b 419 VAL cc_start: 0.9419 (p) cc_final: 0.9109 (m) REVERT: b 650 GLU cc_start: 0.7427 (mm-30) cc_final: 0.7167 (tp30) REVERT: b 898 ILE cc_start: 0.7781 (mp) cc_final: 0.7145 (mt) REVERT: d 257 PHE cc_start: 0.8124 (m-80) cc_final: 0.7799 (m-80) REVERT: d 898 ILE cc_start: 0.7505 (mp) cc_final: 0.7106 (mt) REVERT: d 908 LEU cc_start: 0.8113 (mt) cc_final: 0.7882 (mt) REVERT: c 360 ASN cc_start: 0.7492 (t0) cc_final: 0.7209 (t0) REVERT: c 419 VAL cc_start: 0.9331 (p) cc_final: 0.9128 (m) REVERT: c 657 SER cc_start: 0.7830 (m) cc_final: 0.7546 (t) REVERT: c 809 LEU cc_start: 0.8110 (tp) cc_final: 0.7780 (tt) REVERT: c 898 ILE cc_start: 0.7621 (mp) cc_final: 0.7271 (mp) outliers start: 3 outliers final: 3 residues processed: 2182 average time/residue: 0.7902 time to fit residues: 2958.8825 Evaluate side-chains 1067 residues out of total 9600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1064 time to evaluate : 7.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 863 VAL Chi-restraints excluded: chain d residue 863 VAL Chi-restraints excluded: chain c residue 863 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1092 random chunks: chunk 922 optimal weight: 1.9990 chunk 827 optimal weight: 2.9990 chunk 459 optimal weight: 5.9990 chunk 282 optimal weight: 8.9990 chunk 558 optimal weight: 5.9990 chunk 442 optimal weight: 10.0000 chunk 855 optimal weight: 6.9990 chunk 331 optimal weight: 1.9990 chunk 520 optimal weight: 0.9990 chunk 637 optimal weight: 6.9990 chunk 991 optimal weight: 0.0470 overall best weight: 1.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 217 ASN ** j 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 103 GLN F 31 GLN O 103 GLN E 26 GLN E 31 GLN E 153 ASN E 386 ASN C 31 GLN J 103 GLN L 103 GLN K 103 GLN D 31 GLN D 386 ASN B 409 ASN P 100 ASN T 100 ASN T 103 GLN b 178 HIS ** b 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 735 ASN b 849 ASN d 178 HIS ** d 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 554 ASN d 735 ASN d 849 ASN c 178 HIS c 189 GLN c 849 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 88269 Z= 0.311 Angle : 0.627 9.583 119943 Z= 0.330 Chirality : 0.047 0.274 13698 Planarity : 0.004 0.075 15528 Dihedral : 4.888 62.790 12075 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.60 % Favored : 95.37 % Rotamer: Outliers : 2.15 % Allowed : 10.97 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % 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: -1.76 (0.08), residues: 11031 helix: -0.02 (0.16), residues: 1116 sheet: -0.88 (0.08), residues: 3864 loop : -1.58 (0.07), residues: 6051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP b 369 HIS 0.006 0.002 HIS d 207 PHE 0.031 0.002 PHE h 354 TYR 0.026 0.002 TYR i 129 ARG 0.011 0.001 ARG A 292 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22062 Ramachandran restraints generated. 11031 Oldfield, 0 Emsley, 11031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22062 Ramachandran restraints generated. 11031 Oldfield, 0 Emsley, 11031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1286 residues out of total 9600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 1080 time to evaluate : 7.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: i 405 ASN cc_start: 0.7031 (t0) cc_final: 0.6441 (m110) REVERT: j 241 ASN cc_start: 0.3660 (p0) cc_final: 0.3341 (p0) REVERT: j 392 ILE cc_start: 0.4788 (pt) cc_final: 0.4225 (mp) REVERT: R 20 LEU cc_start: 0.9019 (tp) cc_final: 0.8799 (tt) REVERT: I 275 GLN cc_start: 0.8800 (mt0) cc_final: 0.8490 (mt0) REVERT: a 66 ASP cc_start: 0.7464 (t0) cc_final: 0.7218 (t0) REVERT: S 37 LYS cc_start: 0.8740 (tmmt) cc_final: 0.8349 (ttpp) REVERT: S 73 GLN cc_start: 0.7136 (tp40) cc_final: 0.6268 (tm-30) REVERT: S 108 TYR cc_start: 0.7339 (m-80) cc_final: 0.7133 (m-10) REVERT: F 91 ASP cc_start: 0.7453 (p0) cc_final: 0.7175 (p0) REVERT: F 280 TYR cc_start: 0.8429 (t80) cc_final: 0.8153 (t80) REVERT: X 178 MET cc_start: 0.8551 (mmm) cc_final: 0.8167 (mmt) REVERT: Y 66 ASP cc_start: 0.7563 (t70) cc_final: 0.7154 (t0) REVERT: Y 71 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7433 (tm-30) REVERT: O 37 LYS cc_start: 0.8514 (tmmt) cc_final: 0.8029 (ttpp) REVERT: E 77 LEU cc_start: 0.8934 (mt) cc_final: 0.8600 (mt) REVERT: C 134 LEU cc_start: 0.9205 (mm) cc_final: 0.8981 (tp) REVERT: C 197 MET cc_start: 0.7841 (mmp) cc_final: 0.7625 (mmp) REVERT: C 293 PHE cc_start: 0.6714 (m-80) cc_final: 0.6305 (m-80) REVERT: G 144 SER cc_start: 0.8578 (t) cc_final: 0.8117 (p) REVERT: W 66 ASP cc_start: 0.7809 (t70) cc_final: 0.7561 (t0) REVERT: U 28 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.7220 (t0) REVERT: K 18 TYR cc_start: 0.7796 (t80) cc_final: 0.7551 (t80) REVERT: K 37 LYS cc_start: 0.8723 (tmmt) cc_final: 0.8233 (ttpp) REVERT: K 73 GLN cc_start: 0.6881 (tp40) cc_final: 0.6603 (tp40) REVERT: A 95 TRP cc_start: 0.7478 (m-90) cc_final: 0.7119 (m-90) REVERT: B 187 ASP cc_start: 0.8598 (m-30) cc_final: 0.8357 (p0) REVERT: B 397 GLN cc_start: 0.7185 (tm-30) cc_final: 0.6842 (tm-30) REVERT: B 398 MET cc_start: 0.0461 (tpp) cc_final: 0.0153 (tpp) REVERT: d 257 PHE cc_start: 0.8392 (m-80) cc_final: 0.7938 (m-80) REVERT: c 68 GLN cc_start: 0.7371 (mm-40) cc_final: 0.7018 (mm-40) REVERT: c 419 VAL cc_start: 0.9371 (p) cc_final: 0.9158 (m) REVERT: c 657 SER cc_start: 0.7898 (m) cc_final: 0.7605 (t) REVERT: c 798 MET cc_start: 0.6848 (mtp) cc_final: 0.6541 (mtp) REVERT: c 892 MET cc_start: 0.6568 (tpt) cc_final: 0.6333 (tpt) REVERT: c 908 LEU cc_start: 0.7981 (mt) cc_final: 0.7726 (mt) outliers start: 206 outliers final: 125 residues processed: 1218 average time/residue: 0.7984 time to fit residues: 1720.7544 Evaluate side-chains 1009 residues out of total 9600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 883 time to evaluate : 7.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 45 SER Chi-restraints excluded: chain i residue 97 ASP Chi-restraints excluded: chain i residue 113 ARG Chi-restraints excluded: chain i residue 115 GLU Chi-restraints excluded: chain i residue 216 ILE Chi-restraints excluded: chain h residue 16 LEU Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain h residue 103 MET Chi-restraints excluded: chain h residue 652 SER Chi-restraints excluded: chain j residue 32 TYR Chi-restraints excluded: chain j residue 121 VAL Chi-restraints excluded: chain j residue 216 ILE Chi-restraints excluded: chain j residue 328 VAL Chi-restraints excluded: chain j residue 447 THR Chi-restraints excluded: chain j residue 633 MET Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain I residue 233 VAL Chi-restraints excluded: chain a residue 199 SER Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 113 ILE Chi-restraints excluded: chain S residue 24 PHE Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain N residue 134 ILE Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 193 CYS Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 251 LYS Chi-restraints excluded: chain X residue 181 ASP Chi-restraints excluded: chain X residue 196 ILE Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 200 LEU Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain E residue 150 CYS Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain L residue 8 ILE Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 128 MET Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain W residue 200 LEU Chi-restraints excluded: chain U residue 28 ASP Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 138 VAL Chi-restraints excluded: chain K residue 24 PHE Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain T residue 10 LEU Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 68 ILE Chi-restraints excluded: chain f residue 1206 LEU Chi-restraints excluded: chain f residue 1209 ASN Chi-restraints excluded: chain g residue 1209 ASN Chi-restraints excluded: chain V residue 23 VAL Chi-restraints excluded: chain V residue 39 LYS Chi-restraints excluded: chain V residue 181 ASP Chi-restraints excluded: chain V residue 196 ILE Chi-restraints excluded: chain Z residue 181 ASP Chi-restraints excluded: chain Z residue 196 ILE Chi-restraints excluded: chain Z residue 200 LEU Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 118 LEU Chi-restraints excluded: chain b residue 187 THR Chi-restraints excluded: chain b residue 236 LEU Chi-restraints excluded: chain b residue 242 LEU Chi-restraints excluded: chain b residue 338 MET Chi-restraints excluded: chain b residue 612 ILE Chi-restraints excluded: chain b residue 776 ILE Chi-restraints excluded: chain b residue 848 VAL Chi-restraints excluded: chain b residue 849 ASN Chi-restraints excluded: chain b residue 863 VAL Chi-restraints excluded: chain d residue 20 THR Chi-restraints excluded: chain d residue 242 LEU Chi-restraints excluded: chain d residue 255 LEU Chi-restraints excluded: chain d residue 285 ASN Chi-restraints excluded: chain d residue 530 ILE Chi-restraints excluded: chain d residue 706 LEU Chi-restraints excluded: chain d residue 849 ASN Chi-restraints excluded: chain d residue 863 VAL Chi-restraints excluded: chain c residue 72 LEU Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 255 LEU Chi-restraints excluded: chain c residue 338 MET Chi-restraints excluded: chain c residue 530 ILE Chi-restraints excluded: chain c residue 612 ILE Chi-restraints excluded: chain c residue 706 LEU Chi-restraints excluded: chain c residue 803 ILE Chi-restraints excluded: chain c residue 835 SER Chi-restraints excluded: chain c residue 863 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1092 random chunks: chunk 551 optimal weight: 0.8980 chunk 307 optimal weight: 4.9990 chunk 825 optimal weight: 3.9990 chunk 675 optimal weight: 3.9990 chunk 273 optimal weight: 3.9990 chunk 993 optimal weight: 0.0980 chunk 1073 optimal weight: 6.9990 chunk 884 optimal weight: 1.9990 chunk 985 optimal weight: 5.9990 chunk 338 optimal weight: 0.8980 chunk 796 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 336 ASN h 182 GLN h 336 ASN ** j 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 217 ASN j 336 ASN j 455 ASN Y 104 GLN G 112 HIS ** G 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 104 GLN A 62 ASN B 62 ASN B 409 ASN ** b 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 591 ASN ** d 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 554 ASN ** d 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 698 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 88269 Z= 0.259 Angle : 0.566 9.102 119943 Z= 0.296 Chirality : 0.045 0.234 13698 Planarity : 0.004 0.077 15528 Dihedral : 4.764 66.634 12075 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.31 % Favored : 95.66 % Rotamer: Outliers : 2.38 % Allowed : 13.52 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % 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: -1.66 (0.08), residues: 11031 helix: 0.10 (0.16), residues: 1128 sheet: -0.82 (0.08), residues: 3804 loop : -1.51 (0.07), residues: 6099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP B 95 HIS 0.005 0.001 HIS B 135 PHE 0.021 0.001 PHE S 64 TYR 0.020 0.001 TYR G 28 ARG 0.018 0.001 ARG D 431 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22062 Ramachandran restraints generated. 11031 Oldfield, 0 Emsley, 11031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22062 Ramachandran restraints generated. 11031 Oldfield, 0 Emsley, 11031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1169 residues out of total 9600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 941 time to evaluate : 7.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: i 405 ASN cc_start: 0.6914 (t0) cc_final: 0.6334 (m110) REVERT: h 340 ILE cc_start: 0.6706 (OUTLIER) cc_final: 0.6299 (mt) REVERT: j 241 ASN cc_start: 0.4164 (p0) cc_final: 0.3838 (p0) REVERT: j 392 ILE cc_start: 0.4719 (OUTLIER) cc_final: 0.4141 (mp) REVERT: j 685 ILE cc_start: 0.2876 (mt) cc_final: 0.2671 (tp) REVERT: I 155 ASP cc_start: 0.7554 (OUTLIER) cc_final: 0.7270 (p0) REVERT: I 275 GLN cc_start: 0.8794 (mt0) cc_final: 0.8584 (mt0) REVERT: Q 18 TYR cc_start: 0.8090 (t80) cc_final: 0.7724 (t80) REVERT: Q 55 GLU cc_start: 0.7674 (mp0) cc_final: 0.7474 (mp0) REVERT: S 64 PHE cc_start: 0.7365 (m-80) cc_final: 0.7030 (m-80) REVERT: S 108 TYR cc_start: 0.7388 (m-80) cc_final: 0.7151 (m-10) REVERT: F 280 TYR cc_start: 0.8370 (t80) cc_final: 0.7949 (t80) REVERT: N 54 LEU cc_start: 0.8937 (tp) cc_final: 0.8715 (tt) REVERT: N 59 GLU cc_start: 0.7858 (pt0) cc_final: 0.7649 (pt0) REVERT: H 155 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7011 (p0) REVERT: X 178 MET cc_start: 0.8497 (mmm) cc_final: 0.8153 (mmt) REVERT: Y 1 MET cc_start: 0.6346 (ttt) cc_final: 0.5923 (ttt) REVERT: Y 18 GLU cc_start: 0.7495 (tp30) cc_final: 0.7207 (tp30) REVERT: Y 66 ASP cc_start: 0.7478 (t70) cc_final: 0.7050 (t0) REVERT: Y 71 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7543 (tm-30) REVERT: M 54 LEU cc_start: 0.8911 (mt) cc_final: 0.8694 (mp) REVERT: O 37 LYS cc_start: 0.8594 (tmmt) cc_final: 0.8121 (ttpp) REVERT: E 77 LEU cc_start: 0.8842 (mt) cc_final: 0.8549 (mt) REVERT: E 260 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.7054 (tm-30) REVERT: C 293 PHE cc_start: 0.6518 (m-80) cc_final: 0.6088 (m-80) REVERT: J 22 MET cc_start: 0.7618 (mtp) cc_final: 0.7394 (mtp) REVERT: J 54 LEU cc_start: 0.9157 (tp) cc_final: 0.8937 (tt) REVERT: L 91 LYS cc_start: 0.8676 (mtmm) cc_final: 0.8441 (mtmm) REVERT: L 109 TYR cc_start: 0.8607 (p90) cc_final: 0.8296 (p90) REVERT: G 108 TYR cc_start: 0.8430 (m-80) cc_final: 0.8175 (m-80) REVERT: G 144 SER cc_start: 0.8635 (t) cc_final: 0.8136 (p) REVERT: W 66 ASP cc_start: 0.7590 (t70) cc_final: 0.7299 (t0) REVERT: U 1 MET cc_start: 0.5217 (mmt) cc_final: 0.4678 (mmp) REVERT: U 28 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7176 (t0) REVERT: U 55 GLU cc_start: 0.7821 (mp0) cc_final: 0.7575 (mp0) REVERT: K 37 LYS cc_start: 0.8727 (tmmt) cc_final: 0.8279 (ttpp) REVERT: K 73 GLN cc_start: 0.6869 (tp40) cc_final: 0.6662 (tp40) REVERT: D 260 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7366 (tm-30) REVERT: A 95 TRP cc_start: 0.7485 (m-90) cc_final: 0.7099 (m-90) REVERT: B 277 MET cc_start: 0.6911 (mtt) cc_final: 0.6382 (mtt) REVERT: B 397 GLN cc_start: 0.7047 (tm-30) cc_final: 0.6737 (tm-30) REVERT: B 398 MET cc_start: 0.1031 (tpp) cc_final: 0.0201 (tpp) REVERT: P 25 MET cc_start: 0.7458 (mmm) cc_final: 0.7075 (pmm) REVERT: T 59 GLU cc_start: 0.7077 (tm-30) cc_final: 0.6834 (tm-30) REVERT: b 12 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8965 (mm) REVERT: b 695 GLU cc_start: 0.7624 (tp30) cc_final: 0.7281 (tp30) REVERT: b 892 MET cc_start: 0.6923 (tpt) cc_final: 0.6460 (tpt) REVERT: d 257 PHE cc_start: 0.8347 (m-80) cc_final: 0.7906 (m-80) REVERT: d 583 ASP cc_start: 0.7624 (m-30) cc_final: 0.7424 (m-30) REVERT: c 657 SER cc_start: 0.7897 (m) cc_final: 0.7579 (t) REVERT: c 798 MET cc_start: 0.7101 (mtp) cc_final: 0.6884 (mtp) REVERT: c 892 MET cc_start: 0.6580 (tpt) cc_final: 0.6377 (tpt) outliers start: 228 outliers final: 150 residues processed: 1107 average time/residue: 0.7415 time to fit residues: 1457.0531 Evaluate side-chains 982 residues out of total 9600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 824 time to evaluate : 7.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 93 ILE Chi-restraints excluded: chain i residue 97 ASP Chi-restraints excluded: chain i residue 115 GLU Chi-restraints excluded: chain i residue 216 ILE Chi-restraints excluded: chain h residue 16 LEU Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain h residue 93 ILE Chi-restraints excluded: chain h residue 340 ILE Chi-restraints excluded: chain h residue 349 THR Chi-restraints excluded: chain h residue 645 VAL Chi-restraints excluded: chain h residue 652 SER Chi-restraints excluded: chain j residue 32 TYR Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain j residue 103 MET Chi-restraints excluded: chain j residue 121 VAL Chi-restraints excluded: chain j residue 216 ILE Chi-restraints excluded: chain j residue 217 ASN Chi-restraints excluded: chain j residue 328 VAL Chi-restraints excluded: chain j residue 392 ILE Chi-restraints excluded: chain j residue 421 TRP Chi-restraints excluded: chain j residue 447 THR Chi-restraints excluded: chain j residue 633 MET Chi-restraints excluded: chain j residue 644 ILE Chi-restraints excluded: chain R residue 131 LYS Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain a residue 69 LEU Chi-restraints excluded: chain a residue 199 SER Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 54 LEU Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 113 ILE Chi-restraints excluded: chain S residue 24 PHE Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain N residue 134 ILE Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 133 LYS Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 193 CYS Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain X residue 181 ASP Chi-restraints excluded: chain X residue 196 ILE Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 113 ILE Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain L residue 8 ILE Chi-restraints excluded: chain L residue 128 MET Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain U residue 28 ASP Chi-restraints excluded: chain U residue 56 ASP Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 138 VAL Chi-restraints excluded: chain K residue 24 PHE Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain P residue 10 LEU Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 68 ILE Chi-restraints excluded: chain f residue 1206 LEU Chi-restraints excluded: chain f residue 1209 ASN Chi-restraints excluded: chain g residue 1209 ASN Chi-restraints excluded: chain V residue 5 ASP Chi-restraints excluded: chain V residue 23 VAL Chi-restraints excluded: chain V residue 181 ASP Chi-restraints excluded: chain V residue 196 ILE Chi-restraints excluded: chain Z residue 5 ASP Chi-restraints excluded: chain Z residue 181 ASP Chi-restraints excluded: chain Z residue 196 ILE Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 236 LEU Chi-restraints excluded: chain b residue 242 LEU Chi-restraints excluded: chain b residue 259 LEU Chi-restraints excluded: chain b residue 338 MET Chi-restraints excluded: chain b residue 419 VAL Chi-restraints excluded: chain b residue 528 ASN Chi-restraints excluded: chain b residue 612 ILE Chi-restraints excluded: chain b residue 736 VAL Chi-restraints excluded: chain b residue 776 ILE Chi-restraints excluded: chain b residue 787 VAL Chi-restraints excluded: chain b residue 832 ASP Chi-restraints excluded: chain b residue 848 VAL Chi-restraints excluded: chain b residue 863 VAL Chi-restraints excluded: chain d residue 20 THR Chi-restraints excluded: chain d residue 242 LEU Chi-restraints excluded: chain d residue 254 ASP Chi-restraints excluded: chain d residue 255 LEU Chi-restraints excluded: chain d residue 285 ASN Chi-restraints excluded: chain d residue 292 VAL Chi-restraints excluded: chain d residue 338 MET Chi-restraints excluded: chain d residue 612 ILE Chi-restraints excluded: chain d residue 657 SER Chi-restraints excluded: chain d residue 706 LEU Chi-restraints excluded: chain d residue 832 ASP Chi-restraints excluded: chain d residue 863 VAL Chi-restraints excluded: chain c residue 72 LEU Chi-restraints excluded: chain c residue 140 ILE Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 255 LEU Chi-restraints excluded: chain c residue 273 ILE Chi-restraints excluded: chain c residue 337 THR Chi-restraints excluded: chain c residue 338 MET Chi-restraints excluded: chain c residue 530 ILE Chi-restraints excluded: chain c residue 612 ILE Chi-restraints excluded: chain c residue 706 LEU Chi-restraints excluded: chain c residue 803 ILE Chi-restraints excluded: chain c residue 835 SER Chi-restraints excluded: chain c residue 863 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1092 random chunks: chunk 981 optimal weight: 3.9990 chunk 746 optimal weight: 1.9990 chunk 515 optimal weight: 4.9990 chunk 109 optimal weight: 20.0000 chunk 474 optimal weight: 6.9990 chunk 667 optimal weight: 9.9990 chunk 997 optimal weight: 2.9990 chunk 1055 optimal weight: 0.4980 chunk 520 optimal weight: 2.9990 chunk 944 optimal weight: 3.9990 chunk 284 optimal weight: 10.0000 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 417 GLN ** j 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 217 ASN j 237 GLN j 417 GLN j 686 HIS ** R 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 4 GLN ** N 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 GLN A 236 ASN A 318 HIS ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 591 ASN b 800 GLN ** d 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 778 HIS d 800 GLN ** d 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 800 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 88269 Z= 0.423 Angle : 0.659 9.951 119943 Z= 0.343 Chirality : 0.047 0.264 13698 Planarity : 0.005 0.083 15528 Dihedral : 5.066 71.946 12075 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.84 % Favored : 94.11 % Rotamer: Outliers : 3.51 % Allowed : 15.28 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % 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: -1.68 (0.08), residues: 11031 helix: -0.00 (0.15), residues: 1122 sheet: -0.87 (0.08), residues: 3849 loop : -1.48 (0.07), residues: 6060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 95 HIS 0.009 0.002 HIS j 686 PHE 0.028 0.002 PHE S 64 TYR 0.026 0.002 TYR h 232 ARG 0.018 0.001 ARG J 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22062 Ramachandran restraints generated. 11031 Oldfield, 0 Emsley, 11031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22062 Ramachandran restraints generated. 11031 Oldfield, 0 Emsley, 11031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1179 residues out of total 9600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 337 poor density : 842 time to evaluate : 9.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: i 162 MET cc_start: 0.4096 (mmm) cc_final: 0.3860 (mmp) REVERT: i 405 ASN cc_start: 0.6919 (t0) cc_final: 0.6369 (m110) REVERT: i 645 VAL cc_start: 0.3585 (OUTLIER) cc_final: 0.3222 (m) REVERT: i 658 ILE cc_start: 0.2658 (OUTLIER) cc_final: 0.2028 (mp) REVERT: h 340 ILE cc_start: 0.6537 (OUTLIER) cc_final: 0.6147 (mt) REVERT: h 430 MET cc_start: 0.1747 (tmm) cc_final: 0.1195 (ppp) REVERT: h 654 ILE cc_start: 0.1547 (OUTLIER) cc_final: 0.1101 (tp) REVERT: j 241 ASN cc_start: 0.4903 (p0) cc_final: 0.4639 (p0) REVERT: j 392 ILE cc_start: 0.4863 (OUTLIER) cc_final: 0.4263 (mp) REVERT: j 403 MET cc_start: 0.2026 (mmt) cc_final: 0.1685 (mmt) REVERT: j 654 ILE cc_start: 0.3061 (OUTLIER) cc_final: 0.2419 (tp) REVERT: j 685 ILE cc_start: 0.2195 (mt) cc_final: 0.1552 (tp) REVERT: Q 18 TYR cc_start: 0.8247 (t80) cc_final: 0.7895 (t80) REVERT: F 348 GLU cc_start: 0.6430 (mt-10) cc_final: 0.6223 (mt-10) REVERT: X 178 MET cc_start: 0.8341 (mmm) cc_final: 0.7953 (mmt) REVERT: Y 66 ASP cc_start: 0.7460 (t70) cc_final: 0.7061 (t0) REVERT: M 55 GLU cc_start: 0.8167 (mp0) cc_final: 0.7701 (mp0) REVERT: O 37 LYS cc_start: 0.8783 (tmmt) cc_final: 0.8330 (ttpp) REVERT: E 1 MET cc_start: 0.6596 (tpp) cc_final: 0.6104 (tpp) REVERT: C 95 TRP cc_start: 0.7264 (m-90) cc_final: 0.6927 (m-90) REVERT: C 405 SER cc_start: 0.7394 (m) cc_final: 0.7159 (t) REVERT: J 7 VAL cc_start: 0.8686 (m) cc_final: 0.8405 (p) REVERT: J 25 MET cc_start: 0.7415 (ttt) cc_final: 0.7093 (ttt) REVERT: J 54 LEU cc_start: 0.9086 (tp) cc_final: 0.8872 (tt) REVERT: L 4 GLU cc_start: 0.3747 (mm-30) cc_final: 0.3490 (mm-30) REVERT: L 99 TYR cc_start: 0.8001 (m-10) cc_final: 0.7763 (m-10) REVERT: W 66 ASP cc_start: 0.7555 (t70) cc_final: 0.7249 (t0) REVERT: U 1 MET cc_start: 0.5606 (mmt) cc_final: 0.4534 (mmp) REVERT: U 28 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7157 (t0) REVERT: U 54 LEU cc_start: 0.8978 (mt) cc_final: 0.8684 (mp) REVERT: U 55 GLU cc_start: 0.8040 (mp0) cc_final: 0.7644 (mp0) REVERT: K 18 TYR cc_start: 0.7903 (t80) cc_final: 0.7543 (t80) REVERT: K 20 LEU cc_start: 0.8861 (tp) cc_final: 0.8438 (tp) REVERT: K 37 LYS cc_start: 0.8875 (tmmt) cc_final: 0.8428 (ttpp) REVERT: K 73 GLN cc_start: 0.7183 (tp40) cc_final: 0.6835 (tp40) REVERT: D 260 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7300 (tm-30) REVERT: A 95 TRP cc_start: 0.7820 (m-90) cc_final: 0.7383 (m-90) REVERT: B 17 LYS cc_start: 0.7479 (OUTLIER) cc_final: 0.6857 (tppt) REVERT: P 127 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8913 (tp) REVERT: e 1188 ARG cc_start: 0.8023 (mmm160) cc_final: 0.7654 (mmm-85) REVERT: Z 37 LYS cc_start: 0.8700 (mtmt) cc_final: 0.8499 (mtmm) REVERT: b 12 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8984 (mm) REVERT: b 695 GLU cc_start: 0.7602 (tp30) cc_final: 0.7345 (tp30) REVERT: b 892 MET cc_start: 0.7406 (tpt) cc_final: 0.6991 (tpt) REVERT: c 657 SER cc_start: 0.8055 (m) cc_final: 0.7774 (t) outliers start: 337 outliers final: 235 residues processed: 1113 average time/residue: 0.7568 time to fit residues: 1501.7833 Evaluate side-chains 990 residues out of total 9600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 744 time to evaluate : 7.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 45 SER Chi-restraints excluded: chain i residue 93 ILE Chi-restraints excluded: chain i residue 97 ASP Chi-restraints excluded: chain i residue 113 ARG Chi-restraints excluded: chain i residue 115 GLU Chi-restraints excluded: chain i residue 216 ILE Chi-restraints excluded: chain i residue 349 THR Chi-restraints excluded: chain i residue 395 THR Chi-restraints excluded: chain i residue 645 VAL Chi-restraints excluded: chain i residue 658 ILE Chi-restraints excluded: chain h residue 16 LEU Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain h residue 93 ILE Chi-restraints excluded: chain h residue 121 VAL Chi-restraints excluded: chain h residue 340 ILE Chi-restraints excluded: chain h residue 349 THR Chi-restraints excluded: chain h residue 393 THR Chi-restraints excluded: chain h residue 447 THR Chi-restraints excluded: chain h residue 645 VAL Chi-restraints excluded: chain h residue 652 SER Chi-restraints excluded: chain h residue 654 ILE Chi-restraints excluded: chain h residue 656 VAL Chi-restraints excluded: chain j residue 5 ASN Chi-restraints excluded: chain j residue 32 TYR Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain j residue 121 VAL Chi-restraints excluded: chain j residue 216 ILE Chi-restraints excluded: chain j residue 227 ASP Chi-restraints excluded: chain j residue 328 VAL Chi-restraints excluded: chain j residue 392 ILE Chi-restraints excluded: chain j residue 393 THR Chi-restraints excluded: chain j residue 421 TRP Chi-restraints excluded: chain j residue 447 THR Chi-restraints excluded: chain j residue 633 MET Chi-restraints excluded: chain j residue 644 ILE Chi-restraints excluded: chain j residue 645 VAL Chi-restraints excluded: chain j residue 654 ILE Chi-restraints excluded: chain R residue 68 ILE Chi-restraints excluded: chain R residue 131 LYS Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain I residue 233 VAL Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain a residue 69 LEU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain a residue 196 ILE Chi-restraints excluded: chain a residue 199 SER Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 54 LEU Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 113 ILE Chi-restraints excluded: chain Q residue 126 ARG Chi-restraints excluded: chain S residue 24 PHE Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain N residue 134 ILE Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 133 LYS Chi-restraints excluded: chain H residue 193 CYS Chi-restraints excluded: chain H residue 229 VAL Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 249 ILE Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain X residue 181 ASP Chi-restraints excluded: chain X residue 196 ILE Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 56 ASP Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 113 ILE Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 134 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 150 CYS Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 20 HIS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain L residue 8 ILE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain L residue 127 ILE Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain U residue 28 ASP Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 138 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 24 PHE Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 295 ILE Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 243 ASN Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 17 LYS Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain P residue 127 ILE Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 68 ILE Chi-restraints excluded: chain T residue 113 ILE Chi-restraints excluded: chain f residue 1196 THR Chi-restraints excluded: chain f residue 1206 LEU Chi-restraints excluded: chain f residue 1209 ASN Chi-restraints excluded: chain g residue 1209 ASN Chi-restraints excluded: chain e residue 1196 THR Chi-restraints excluded: chain V residue 5 ASP Chi-restraints excluded: chain V residue 23 VAL Chi-restraints excluded: chain V residue 181 ASP Chi-restraints excluded: chain Z residue 5 ASP Chi-restraints excluded: chain Z residue 57 LEU Chi-restraints excluded: chain Z residue 181 ASP Chi-restraints excluded: chain Z residue 192 THR Chi-restraints excluded: chain Z residue 200 LEU Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 140 ILE Chi-restraints excluded: chain b residue 155 THR Chi-restraints excluded: chain b residue 187 THR Chi-restraints excluded: chain b residue 242 LEU Chi-restraints excluded: chain b residue 255 LEU Chi-restraints excluded: chain b residue 259 LEU Chi-restraints excluded: chain b residue 292 VAL Chi-restraints excluded: chain b residue 338 MET Chi-restraints excluded: chain b residue 419 VAL Chi-restraints excluded: chain b residue 528 ASN Chi-restraints excluded: chain b residue 594 ASN Chi-restraints excluded: chain b residue 612 ILE Chi-restraints excluded: chain b residue 696 VAL Chi-restraints excluded: chain b residue 736 VAL Chi-restraints excluded: chain b residue 787 VAL Chi-restraints excluded: chain b residue 832 ASP Chi-restraints excluded: chain b residue 848 VAL Chi-restraints excluded: chain b residue 863 VAL Chi-restraints excluded: chain b residue 897 ARG Chi-restraints excluded: chain b residue 908 LEU Chi-restraints excluded: chain d residue 20 THR Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 155 THR Chi-restraints excluded: chain d residue 187 THR Chi-restraints excluded: chain d residue 242 LEU Chi-restraints excluded: chain d residue 254 ASP Chi-restraints excluded: chain d residue 255 LEU Chi-restraints excluded: chain d residue 259 LEU Chi-restraints excluded: chain d residue 266 VAL Chi-restraints excluded: chain d residue 285 ASN Chi-restraints excluded: chain d residue 290 VAL Chi-restraints excluded: chain d residue 292 VAL Chi-restraints excluded: chain d residue 338 MET Chi-restraints excluded: chain d residue 594 ASN Chi-restraints excluded: chain d residue 612 ILE Chi-restraints excluded: chain d residue 657 SER Chi-restraints excluded: chain d residue 695 GLU Chi-restraints excluded: chain d residue 706 LEU Chi-restraints excluded: chain d residue 848 VAL Chi-restraints excluded: chain d residue 863 VAL Chi-restraints excluded: chain c residue 72 LEU Chi-restraints excluded: chain c residue 140 ILE Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 155 THR Chi-restraints excluded: chain c residue 273 ILE Chi-restraints excluded: chain c residue 290 VAL Chi-restraints excluded: chain c residue 337 THR Chi-restraints excluded: chain c residue 338 MET Chi-restraints excluded: chain c residue 419 VAL Chi-restraints excluded: chain c residue 530 ILE Chi-restraints excluded: chain c residue 612 ILE Chi-restraints excluded: chain c residue 705 ASN Chi-restraints excluded: chain c residue 706 LEU Chi-restraints excluded: chain c residue 803 ILE Chi-restraints excluded: chain c residue 835 SER Chi-restraints excluded: chain c residue 863 VAL Chi-restraints excluded: chain c residue 870 ILE Chi-restraints excluded: chain c residue 901 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1092 random chunks: chunk 879 optimal weight: 0.9990 chunk 599 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 785 optimal weight: 0.9990 chunk 435 optimal weight: 0.7980 chunk 900 optimal weight: 7.9990 chunk 729 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 538 optimal weight: 0.9990 chunk 947 optimal weight: 1.9990 chunk 266 optimal weight: 3.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 217 ASN ** h 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 686 HIS ** R 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 GLN D 4 GLN ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 591 ASN ** b 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 554 ASN ** d 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 88269 Z= 0.217 Angle : 0.549 8.779 119943 Z= 0.284 Chirality : 0.045 0.199 13698 Planarity : 0.004 0.083 15528 Dihedral : 4.786 70.855 12075 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.25 % Favored : 95.70 % Rotamer: Outliers : 2.98 % Allowed : 17.18 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % 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: -1.52 (0.08), residues: 11031 helix: 0.34 (0.16), residues: 1104 sheet: -0.86 (0.08), residues: 3861 loop : -1.35 (0.07), residues: 6066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP B 95 HIS 0.005 0.001 HIS B 113 PHE 0.034 0.001 PHE S 64 TYR 0.021 0.001 TYR S 108 ARG 0.008 0.000 ARG V 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22062 Ramachandran restraints generated. 11031 Oldfield, 0 Emsley, 11031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22062 Ramachandran restraints generated. 11031 Oldfield, 0 Emsley, 11031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1146 residues out of total 9600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 860 time to evaluate : 8.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: i 405 ASN cc_start: 0.6961 (t0) cc_final: 0.6318 (m110) REVERT: i 645 VAL cc_start: 0.3529 (OUTLIER) cc_final: 0.3164 (m) REVERT: i 658 ILE cc_start: 0.2400 (OUTLIER) cc_final: 0.2038 (tt) REVERT: h 340 ILE cc_start: 0.6562 (OUTLIER) cc_final: 0.6162 (mt) REVERT: h 430 MET cc_start: 0.2642 (tmm) cc_final: 0.1837 (ppp) REVERT: j 241 ASN cc_start: 0.4657 (p0) cc_final: 0.4410 (p0) REVERT: j 392 ILE cc_start: 0.4993 (OUTLIER) cc_final: 0.4344 (mp) REVERT: j 654 ILE cc_start: 0.3155 (OUTLIER) cc_final: 0.2523 (tp) REVERT: R 41 LEU cc_start: 0.7686 (mp) cc_final: 0.7433 (mp) REVERT: Q 18 TYR cc_start: 0.8251 (t80) cc_final: 0.7752 (t80) REVERT: H 155 ASP cc_start: 0.7505 (OUTLIER) cc_final: 0.7121 (p0) REVERT: Y 1 MET cc_start: 0.6806 (ttm) cc_final: 0.6527 (ttt) REVERT: Y 66 ASP cc_start: 0.7360 (t70) cc_final: 0.6915 (t0) REVERT: Y 71 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7416 (tm-30) REVERT: M 55 GLU cc_start: 0.8140 (mp0) cc_final: 0.7823 (mp0) REVERT: O 37 LYS cc_start: 0.8939 (tmmt) cc_final: 0.8599 (ttpp) REVERT: O 78 ILE cc_start: 0.8457 (tp) cc_final: 0.8250 (tp) REVERT: E 1 MET cc_start: 0.6767 (tpp) cc_final: 0.6135 (tpp) REVERT: C 95 TRP cc_start: 0.7264 (m-90) cc_final: 0.6944 (m-90) REVERT: C 120 MET cc_start: 0.3758 (ptt) cc_final: 0.3330 (ptt) REVERT: C 398 MET cc_start: 0.0090 (tpp) cc_final: -0.0178 (tpp) REVERT: C 405 SER cc_start: 0.7390 (m) cc_final: 0.7164 (t) REVERT: J 54 LEU cc_start: 0.9049 (tp) cc_final: 0.8844 (tt) REVERT: W 66 ASP cc_start: 0.7531 (t70) cc_final: 0.7233 (t0) REVERT: U 1 MET cc_start: 0.5322 (mmt) cc_final: 0.4310 (mmp) REVERT: U 18 TYR cc_start: 0.8052 (t80) cc_final: 0.7532 (t80) REVERT: U 55 GLU cc_start: 0.8025 (mp0) cc_final: 0.7542 (mp0) REVERT: K 37 LYS cc_start: 0.8831 (tmmt) cc_final: 0.8391 (ttpp) REVERT: K 73 GLN cc_start: 0.7239 (tp40) cc_final: 0.6888 (tp40) REVERT: D 260 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7158 (tm-30) REVERT: A 17 LYS cc_start: 0.7215 (OUTLIER) cc_final: 0.6151 (tptp) REVERT: A 95 TRP cc_start: 0.7681 (m-90) cc_final: 0.7431 (m-90) REVERT: A 120 MET cc_start: 0.4107 (ptt) cc_final: 0.3828 (ptm) REVERT: A 216 MET cc_start: 0.8101 (mpp) cc_final: 0.7231 (mmm) REVERT: B 95 TRP cc_start: 0.8058 (m-90) cc_final: 0.7828 (m-90) REVERT: e 1188 ARG cc_start: 0.7851 (mmm160) cc_final: 0.7622 (mmm-85) REVERT: Z 40 GLU cc_start: 0.6713 (tm-30) cc_final: 0.6510 (tm-30) REVERT: b 12 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8932 (mm) REVERT: b 82 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8912 (t) REVERT: d 695 GLU cc_start: 0.7548 (tp30) cc_final: 0.7316 (tp30) REVERT: c 82 THR cc_start: 0.9123 (OUTLIER) cc_final: 0.8768 (t) REVERT: c 657 SER cc_start: 0.7934 (m) cc_final: 0.7607 (t) outliers start: 286 outliers final: 193 residues processed: 1085 average time/residue: 0.7382 time to fit residues: 1420.7020 Evaluate side-chains 964 residues out of total 9600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 760 time to evaluate : 7.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 45 SER Chi-restraints excluded: chain i residue 93 ILE Chi-restraints excluded: chain i residue 97 ASP Chi-restraints excluded: chain i residue 113 ARG Chi-restraints excluded: chain i residue 115 GLU Chi-restraints excluded: chain i residue 121 VAL Chi-restraints excluded: chain i residue 177 VAL Chi-restraints excluded: chain i residue 216 ILE Chi-restraints excluded: chain i residue 217 ASN Chi-restraints excluded: chain i residue 645 VAL Chi-restraints excluded: chain i residue 658 ILE Chi-restraints excluded: chain h residue 16 LEU Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain h residue 130 ILE Chi-restraints excluded: chain h residue 340 ILE Chi-restraints excluded: chain h residue 349 THR Chi-restraints excluded: chain h residue 393 THR Chi-restraints excluded: chain h residue 447 THR Chi-restraints excluded: chain h residue 645 VAL Chi-restraints excluded: chain h residue 652 SER Chi-restraints excluded: chain h residue 656 VAL Chi-restraints excluded: chain j residue 32 TYR Chi-restraints excluded: chain j residue 58 PHE Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain j residue 121 VAL Chi-restraints excluded: chain j residue 177 VAL Chi-restraints excluded: chain j residue 216 ILE Chi-restraints excluded: chain j residue 328 VAL Chi-restraints excluded: chain j residue 392 ILE Chi-restraints excluded: chain j residue 393 THR Chi-restraints excluded: chain j residue 421 TRP Chi-restraints excluded: chain j residue 447 THR Chi-restraints excluded: chain j residue 633 MET Chi-restraints excluded: chain j residue 654 ILE Chi-restraints excluded: chain R residue 131 LYS Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain a residue 69 LEU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 43 ASP Chi-restraints excluded: chain Q residue 54 LEU Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 113 ILE Chi-restraints excluded: chain Q residue 126 ARG Chi-restraints excluded: chain S residue 24 PHE Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain N residue 134 ILE Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 133 LYS Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 193 CYS Chi-restraints excluded: chain H residue 229 VAL Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain X residue 181 ASP Chi-restraints excluded: chain M residue 56 ASP Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 134 ILE Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 150 CYS Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 20 HIS Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain L residue 8 ILE Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain L residue 128 MET Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain W residue 177 LEU Chi-restraints excluded: chain U residue 56 ASP Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 138 VAL Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 24 PHE Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 113 ILE Chi-restraints excluded: chain f residue 1206 LEU Chi-restraints excluded: chain f residue 1209 ASN Chi-restraints excluded: chain g residue 1196 THR Chi-restraints excluded: chain g residue 1209 ASN Chi-restraints excluded: chain V residue 5 ASP Chi-restraints excluded: chain V residue 23 VAL Chi-restraints excluded: chain V residue 181 ASP Chi-restraints excluded: chain Z residue 5 ASP Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain Z residue 57 LEU Chi-restraints excluded: chain Z residue 181 ASP Chi-restraints excluded: chain Z residue 192 THR Chi-restraints excluded: chain Z residue 200 LEU Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 82 THR Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 140 ILE Chi-restraints excluded: chain b residue 242 LEU Chi-restraints excluded: chain b residue 254 ASP Chi-restraints excluded: chain b residue 255 LEU Chi-restraints excluded: chain b residue 259 LEU Chi-restraints excluded: chain b residue 292 VAL Chi-restraints excluded: chain b residue 337 THR Chi-restraints excluded: chain b residue 338 MET Chi-restraints excluded: chain b residue 419 VAL Chi-restraints excluded: chain b residue 528 ASN Chi-restraints excluded: chain b residue 612 ILE Chi-restraints excluded: chain b residue 832 ASP Chi-restraints excluded: chain b residue 848 VAL Chi-restraints excluded: chain b residue 863 VAL Chi-restraints excluded: chain b residue 897 ARG Chi-restraints excluded: chain d residue 20 THR Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 155 THR Chi-restraints excluded: chain d residue 242 LEU Chi-restraints excluded: chain d residue 254 ASP Chi-restraints excluded: chain d residue 255 LEU Chi-restraints excluded: chain d residue 259 LEU Chi-restraints excluded: chain d residue 266 VAL Chi-restraints excluded: chain d residue 285 ASN Chi-restraints excluded: chain d residue 290 VAL Chi-restraints excluded: chain d residue 292 VAL Chi-restraints excluded: chain d residue 337 THR Chi-restraints excluded: chain d residue 338 MET Chi-restraints excluded: chain d residue 528 ASN Chi-restraints excluded: chain d residue 612 ILE Chi-restraints excluded: chain d residue 657 SER Chi-restraints excluded: chain d residue 863 VAL Chi-restraints excluded: chain c residue 20 THR Chi-restraints excluded: chain c residue 72 LEU Chi-restraints excluded: chain c residue 82 THR Chi-restraints excluded: chain c residue 140 ILE Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 155 THR Chi-restraints excluded: chain c residue 273 ILE Chi-restraints excluded: chain c residue 337 THR Chi-restraints excluded: chain c residue 338 MET Chi-restraints excluded: chain c residue 419 VAL Chi-restraints excluded: chain c residue 530 ILE Chi-restraints excluded: chain c residue 594 ASN Chi-restraints excluded: chain c residue 612 ILE Chi-restraints excluded: chain c residue 803 ILE Chi-restraints excluded: chain c residue 863 VAL Chi-restraints excluded: chain c residue 901 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1092 random chunks: chunk 355 optimal weight: 3.9990 chunk 950 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 619 optimal weight: 0.0370 chunk 260 optimal weight: 1.9990 chunk 1056 optimal weight: 0.9990 chunk 877 optimal weight: 2.9990 chunk 489 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 349 optimal weight: 3.9990 chunk 554 optimal weight: 2.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 GLN ** I 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 88269 Z= 0.256 Angle : 0.554 9.178 119943 Z= 0.287 Chirality : 0.045 0.260 13698 Planarity : 0.004 0.082 15528 Dihedral : 4.697 70.806 12075 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.04 % Favored : 94.93 % Rotamer: Outliers : 3.03 % Allowed : 18.21 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % 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: -1.45 (0.08), residues: 11031 helix: 0.25 (0.16), residues: 1155 sheet: -0.79 (0.08), residues: 3888 loop : -1.29 (0.08), residues: 5988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 95 HIS 0.005 0.001 HIS A 135 PHE 0.023 0.001 PHE B 255 TYR 0.032 0.001 TYR h 232 ARG 0.009 0.000 ARG V 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22062 Ramachandran restraints generated. 11031 Oldfield, 0 Emsley, 11031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22062 Ramachandran restraints generated. 11031 Oldfield, 0 Emsley, 11031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1087 residues out of total 9600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 796 time to evaluate : 7.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: i 405 ASN cc_start: 0.6960 (t0) cc_final: 0.6328 (m110) REVERT: i 645 VAL cc_start: 0.3025 (OUTLIER) cc_final: 0.2644 (m) REVERT: h 340 ILE cc_start: 0.6431 (OUTLIER) cc_final: 0.5995 (mt) REVERT: h 392 ILE cc_start: 0.6880 (OUTLIER) cc_final: 0.6376 (tp) REVERT: h 430 MET cc_start: 0.2627 (tmm) cc_final: 0.1984 (ppp) REVERT: j 12 LEU cc_start: 0.4847 (OUTLIER) cc_final: 0.4460 (mp) REVERT: j 241 ASN cc_start: 0.4871 (p0) cc_final: 0.4657 (p0) REVERT: j 392 ILE cc_start: 0.5342 (OUTLIER) cc_final: 0.4664 (mp) REVERT: j 403 MET cc_start: 0.2068 (mmt) cc_final: 0.1671 (mmt) REVERT: j 654 ILE cc_start: 0.3048 (OUTLIER) cc_final: 0.2486 (tp) REVERT: R 22 MET cc_start: 0.6701 (mtp) cc_final: 0.6296 (mtp) REVERT: Q 37 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8372 (mmtm) REVERT: F 120 MET cc_start: 0.6333 (ptt) cc_final: 0.5701 (ptt) REVERT: N 37 LYS cc_start: 0.8098 (ptmt) cc_final: 0.7798 (tttm) REVERT: Y 66 ASP cc_start: 0.7330 (t70) cc_final: 0.6834 (t0) REVERT: M 1 MET cc_start: 0.6696 (mmt) cc_final: 0.6220 (mmm) REVERT: M 55 GLU cc_start: 0.8193 (mp0) cc_final: 0.7871 (mp0) REVERT: O 37 LYS cc_start: 0.8941 (tmmt) cc_final: 0.8616 (ttpp) REVERT: E 1 MET cc_start: 0.6781 (tpp) cc_final: 0.5873 (tpp) REVERT: E 77 LEU cc_start: 0.9015 (mt) cc_final: 0.8710 (mp) REVERT: E 260 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7104 (tm-30) REVERT: E 284 ILE cc_start: 0.9478 (pt) cc_final: 0.9052 (mm) REVERT: C 95 TRP cc_start: 0.7399 (m-90) cc_final: 0.6999 (m-90) REVERT: C 120 MET cc_start: 0.3855 (ptt) cc_final: 0.3483 (ptt) REVERT: C 245 MET cc_start: 0.7888 (mtp) cc_final: 0.7622 (mtp) REVERT: C 405 SER cc_start: 0.7408 (m) cc_final: 0.7189 (t) REVERT: J 54 LEU cc_start: 0.9048 (tp) cc_final: 0.8841 (tt) REVERT: W 66 ASP cc_start: 0.7532 (t70) cc_final: 0.7241 (t0) REVERT: U 1 MET cc_start: 0.5367 (mmt) cc_final: 0.4337 (mmp) REVERT: U 18 TYR cc_start: 0.8117 (t80) cc_final: 0.7645 (t80) REVERT: U 28 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.6951 (p0) REVERT: U 54 LEU cc_start: 0.8831 (mt) cc_final: 0.8595 (mp) REVERT: U 55 GLU cc_start: 0.8085 (mp0) cc_final: 0.7659 (mp0) REVERT: K 37 LYS cc_start: 0.8867 (tmmt) cc_final: 0.8389 (ttpp) REVERT: D 260 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7286 (tm-30) REVERT: A 17 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.6302 (tptp) REVERT: A 95 TRP cc_start: 0.7784 (m-90) cc_final: 0.7537 (m-90) REVERT: A 120 MET cc_start: 0.4181 (ptt) cc_final: 0.3967 (ptm) REVERT: A 133 MET cc_start: 0.8769 (tpp) cc_final: 0.8456 (tpp) REVERT: A 216 MET cc_start: 0.8097 (mpp) cc_final: 0.7124 (mmm) REVERT: B 216 MET cc_start: 0.8307 (mpp) cc_final: 0.7367 (mmm) REVERT: B 397 GLN cc_start: 0.7385 (tm-30) cc_final: 0.6947 (tm-30) REVERT: B 398 MET cc_start: 0.1023 (tpp) cc_final: 0.0284 (tpp) REVERT: P 1 MET cc_start: 0.5104 (tpp) cc_final: 0.4740 (mtp) REVERT: e 1188 ARG cc_start: 0.7865 (mmm160) cc_final: 0.7565 (mmm-85) REVERT: b 82 THR cc_start: 0.9114 (OUTLIER) cc_final: 0.8862 (t) REVERT: b 602 ASP cc_start: 0.7216 (p0) cc_final: 0.6829 (p0) REVERT: b 695 GLU cc_start: 0.7445 (tp30) cc_final: 0.7133 (tp30) REVERT: d 695 GLU cc_start: 0.7637 (tp30) cc_final: 0.7166 (tp30) REVERT: c 82 THR cc_start: 0.9089 (OUTLIER) cc_final: 0.8729 (t) REVERT: c 657 SER cc_start: 0.8059 (m) cc_final: 0.7698 (t) outliers start: 291 outliers final: 221 residues processed: 1033 average time/residue: 0.7511 time to fit residues: 1380.5299 Evaluate side-chains 983 residues out of total 9600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 749 time to evaluate : 7.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 45 SER Chi-restraints excluded: chain i residue 93 ILE Chi-restraints excluded: chain i residue 97 ASP Chi-restraints excluded: chain i residue 113 ARG Chi-restraints excluded: chain i residue 115 GLU Chi-restraints excluded: chain i residue 121 VAL Chi-restraints excluded: chain i residue 177 VAL Chi-restraints excluded: chain i residue 395 THR Chi-restraints excluded: chain i residue 645 VAL Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 16 LEU Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain h residue 93 ILE Chi-restraints excluded: chain h residue 121 VAL Chi-restraints excluded: chain h residue 340 ILE Chi-restraints excluded: chain h residue 349 THR Chi-restraints excluded: chain h residue 392 ILE Chi-restraints excluded: chain h residue 393 THR Chi-restraints excluded: chain h residue 447 THR Chi-restraints excluded: chain h residue 645 VAL Chi-restraints excluded: chain h residue 652 SER Chi-restraints excluded: chain h residue 656 VAL Chi-restraints excluded: chain j residue 5 ASN Chi-restraints excluded: chain j residue 12 LEU Chi-restraints excluded: chain j residue 32 TYR Chi-restraints excluded: chain j residue 58 PHE Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain j residue 95 LEU Chi-restraints excluded: chain j residue 121 VAL Chi-restraints excluded: chain j residue 130 ILE Chi-restraints excluded: chain j residue 177 VAL Chi-restraints excluded: chain j residue 328 VAL Chi-restraints excluded: chain j residue 392 ILE Chi-restraints excluded: chain j residue 393 THR Chi-restraints excluded: chain j residue 421 TRP Chi-restraints excluded: chain j residue 633 MET Chi-restraints excluded: chain j residue 654 ILE Chi-restraints excluded: chain R residue 68 ILE Chi-restraints excluded: chain R residue 131 LYS Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain a residue 69 LEU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 37 LYS Chi-restraints excluded: chain Q residue 43 ASP Chi-restraints excluded: chain Q residue 54 LEU Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 113 ILE Chi-restraints excluded: chain Q residue 126 ARG Chi-restraints excluded: chain S residue 24 PHE Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain N residue 134 ILE Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 133 LYS Chi-restraints excluded: chain H residue 193 CYS Chi-restraints excluded: chain H residue 229 VAL Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain X residue 181 ASP Chi-restraints excluded: chain Y residue 28 MET Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 56 ASP Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 134 ILE Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 150 CYS Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain C residue 20 HIS Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain L residue 8 ILE Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain W residue 177 LEU Chi-restraints excluded: chain U residue 28 ASP Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 138 VAL Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 24 PHE Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 320 ASN Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain P residue 8 ILE Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 113 ILE Chi-restraints excluded: chain f residue 1196 THR Chi-restraints excluded: chain f residue 1206 LEU Chi-restraints excluded: chain f residue 1209 ASN Chi-restraints excluded: chain g residue 1209 ASN Chi-restraints excluded: chain e residue 1189 ASP Chi-restraints excluded: chain e residue 1196 THR Chi-restraints excluded: chain V residue 5 ASP Chi-restraints excluded: chain V residue 23 VAL Chi-restraints excluded: chain V residue 181 ASP Chi-restraints excluded: chain Z residue 5 ASP Chi-restraints excluded: chain Z residue 57 LEU Chi-restraints excluded: chain Z residue 181 ASP Chi-restraints excluded: chain Z residue 192 THR Chi-restraints excluded: chain Z residue 200 LEU Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 42 THR Chi-restraints excluded: chain b residue 82 THR Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 140 ILE Chi-restraints excluded: chain b residue 155 THR Chi-restraints excluded: chain b residue 187 THR Chi-restraints excluded: chain b residue 242 LEU Chi-restraints excluded: chain b residue 254 ASP Chi-restraints excluded: chain b residue 255 LEU Chi-restraints excluded: chain b residue 259 LEU Chi-restraints excluded: chain b residue 292 VAL Chi-restraints excluded: chain b residue 337 THR Chi-restraints excluded: chain b residue 419 VAL Chi-restraints excluded: chain b residue 594 ASN Chi-restraints excluded: chain b residue 612 ILE Chi-restraints excluded: chain b residue 787 VAL Chi-restraints excluded: chain b residue 832 ASP Chi-restraints excluded: chain b residue 848 VAL Chi-restraints excluded: chain b residue 863 VAL Chi-restraints excluded: chain b residue 897 ARG Chi-restraints excluded: chain d residue 20 THR Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 187 THR Chi-restraints excluded: chain d residue 242 LEU Chi-restraints excluded: chain d residue 254 ASP Chi-restraints excluded: chain d residue 259 LEU Chi-restraints excluded: chain d residue 266 VAL Chi-restraints excluded: chain d residue 285 ASN Chi-restraints excluded: chain d residue 292 VAL Chi-restraints excluded: chain d residue 337 THR Chi-restraints excluded: chain d residue 419 VAL Chi-restraints excluded: chain d residue 594 ASN Chi-restraints excluded: chain d residue 612 ILE Chi-restraints excluded: chain d residue 657 SER Chi-restraints excluded: chain d residue 706 LEU Chi-restraints excluded: chain d residue 848 VAL Chi-restraints excluded: chain d residue 863 VAL Chi-restraints excluded: chain c residue 20 THR Chi-restraints excluded: chain c residue 72 LEU Chi-restraints excluded: chain c residue 82 THR Chi-restraints excluded: chain c residue 140 ILE Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 155 THR Chi-restraints excluded: chain c residue 289 ILE Chi-restraints excluded: chain c residue 290 VAL Chi-restraints excluded: chain c residue 337 THR Chi-restraints excluded: chain c residue 338 MET Chi-restraints excluded: chain c residue 419 VAL Chi-restraints excluded: chain c residue 530 ILE Chi-restraints excluded: chain c residue 612 ILE Chi-restraints excluded: chain c residue 803 ILE Chi-restraints excluded: chain c residue 855 VAL Chi-restraints excluded: chain c residue 863 VAL Chi-restraints excluded: chain c residue 901 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1092 random chunks: chunk 1018 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 601 optimal weight: 4.9990 chunk 771 optimal weight: 0.5980 chunk 597 optimal weight: 4.9990 chunk 889 optimal weight: 0.4980 chunk 589 optimal weight: 3.9990 chunk 1052 optimal weight: 0.6980 chunk 658 optimal weight: 7.9990 chunk 641 optimal weight: 0.9980 chunk 485 optimal weight: 7.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 4 ASN ** i 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 217 ASN ** h 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 686 HIS ** R 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN ** I 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 ASN ** G 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 849 ASN ** d 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 88269 Z= 0.244 Angle : 0.553 10.621 119943 Z= 0.284 Chirality : 0.045 0.302 13698 Planarity : 0.004 0.084 15528 Dihedral : 4.634 70.344 12075 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.67 % Favored : 95.30 % Rotamer: Outliers : 3.23 % Allowed : 18.43 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % 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: -1.39 (0.08), residues: 11031 helix: 0.29 (0.16), residues: 1155 sheet: -0.74 (0.08), residues: 3879 loop : -1.26 (0.08), residues: 5997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 95 HIS 0.005 0.001 HIS A 318 PHE 0.021 0.001 PHE S 64 TYR 0.032 0.001 TYR j 684 ARG 0.010 0.000 ARG i 451 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22062 Ramachandran restraints generated. 11031 Oldfield, 0 Emsley, 11031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22062 Ramachandran restraints generated. 11031 Oldfield, 0 Emsley, 11031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1110 residues out of total 9600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 310 poor density : 800 time to evaluate : 7.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: i 405 ASN cc_start: 0.6886 (t0) cc_final: 0.6285 (m110) REVERT: i 645 VAL cc_start: 0.3071 (OUTLIER) cc_final: 0.2677 (m) REVERT: h 340 ILE cc_start: 0.6465 (OUTLIER) cc_final: 0.6011 (mt) REVERT: h 392 ILE cc_start: 0.6386 (OUTLIER) cc_final: 0.6107 (tp) REVERT: h 430 MET cc_start: 0.2693 (tmm) cc_final: 0.1889 (ppp) REVERT: j 12 LEU cc_start: 0.4663 (OUTLIER) cc_final: 0.4309 (mp) REVERT: j 392 ILE cc_start: 0.5428 (OUTLIER) cc_final: 0.4762 (mp) REVERT: j 654 ILE cc_start: 0.3058 (OUTLIER) cc_final: 0.2494 (tp) REVERT: R 22 MET cc_start: 0.6722 (mtp) cc_final: 0.6176 (mtp) REVERT: R 128 MET cc_start: 0.8032 (mmm) cc_final: 0.7677 (mtt) REVERT: Q 37 LYS cc_start: 0.8627 (mmtm) cc_final: 0.8372 (mmtm) REVERT: F 120 MET cc_start: 0.6888 (OUTLIER) cc_final: 0.6287 (ptt) REVERT: F 325 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7470 (tm-30) REVERT: N 37 LYS cc_start: 0.8163 (ptmt) cc_final: 0.7853 (tttm) REVERT: H 155 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7177 (p0) REVERT: Y 66 ASP cc_start: 0.7304 (t70) cc_final: 0.6814 (t0) REVERT: M 1 MET cc_start: 0.6412 (mmt) cc_final: 0.5948 (mmm) REVERT: O 37 LYS cc_start: 0.8943 (tmmt) cc_final: 0.8615 (ttpp) REVERT: E 1 MET cc_start: 0.6761 (tpp) cc_final: 0.5701 (tpp) REVERT: E 164 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7930 (mt) REVERT: E 260 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7148 (tm-30) REVERT: E 284 ILE cc_start: 0.9471 (pt) cc_final: 0.9085 (mm) REVERT: C 17 LYS cc_start: 0.6651 (OUTLIER) cc_final: 0.5731 (tptp) REVERT: C 95 TRP cc_start: 0.7411 (m-90) cc_final: 0.7024 (m-90) REVERT: C 120 MET cc_start: 0.4307 (ptt) cc_final: 0.4031 (ptt) REVERT: C 245 MET cc_start: 0.7830 (mtp) cc_final: 0.7576 (mtp) REVERT: C 405 SER cc_start: 0.7435 (m) cc_final: 0.7227 (t) REVERT: J 22 MET cc_start: 0.7455 (mtp) cc_final: 0.6698 (mtp) REVERT: J 50 ILE cc_start: 0.9413 (mt) cc_final: 0.9202 (tp) REVERT: W 66 ASP cc_start: 0.7521 (t70) cc_final: 0.7208 (t0) REVERT: U 1 MET cc_start: 0.5402 (mmt) cc_final: 0.4330 (mmp) REVERT: U 18 TYR cc_start: 0.8109 (t80) cc_final: 0.7637 (t80) REVERT: U 28 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.6970 (p0) REVERT: U 54 LEU cc_start: 0.8899 (mt) cc_final: 0.8634 (mp) REVERT: U 55 GLU cc_start: 0.8159 (mp0) cc_final: 0.7618 (mp0) REVERT: K 24 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.7700 (m-10) REVERT: K 37 LYS cc_start: 0.8893 (tmmt) cc_final: 0.8487 (ttpp) REVERT: D 133 MET cc_start: 0.8106 (tpp) cc_final: 0.7647 (tpt) REVERT: D 260 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7349 (tm-30) REVERT: D 284 ILE cc_start: 0.9398 (pt) cc_final: 0.8979 (mm) REVERT: A 95 TRP cc_start: 0.7812 (m-90) cc_final: 0.7523 (m-90) REVERT: A 216 MET cc_start: 0.8061 (mpp) cc_final: 0.7040 (mmm) REVERT: B 216 MET cc_start: 0.8147 (mpp) cc_final: 0.7366 (mmm) REVERT: B 277 MET cc_start: 0.7134 (mtt) cc_final: 0.6851 (ptp) REVERT: B 397 GLN cc_start: 0.7315 (tm-30) cc_final: 0.6920 (tm-30) REVERT: B 398 MET cc_start: 0.0878 (tpp) cc_final: 0.0131 (tpp) REVERT: P 1 MET cc_start: 0.5118 (tpp) cc_final: 0.4766 (mtp) REVERT: b 82 THR cc_start: 0.9103 (OUTLIER) cc_final: 0.8877 (t) REVERT: b 695 GLU cc_start: 0.7421 (tp30) cc_final: 0.7092 (tp30) REVERT: d 695 GLU cc_start: 0.7586 (tp30) cc_final: 0.7235 (tp30) REVERT: c 76 SER cc_start: 0.8373 (m) cc_final: 0.8112 (p) REVERT: c 82 THR cc_start: 0.9101 (OUTLIER) cc_final: 0.8742 (t) REVERT: c 657 SER cc_start: 0.8080 (m) cc_final: 0.7654 (t) outliers start: 310 outliers final: 233 residues processed: 1050 average time/residue: 0.7609 time to fit residues: 1416.3174 Evaluate side-chains 1000 residues out of total 9600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 751 time to evaluate : 7.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 45 SER Chi-restraints excluded: chain i residue 93 ILE Chi-restraints excluded: chain i residue 97 ASP Chi-restraints excluded: chain i residue 113 ARG Chi-restraints excluded: chain i residue 115 GLU Chi-restraints excluded: chain i residue 177 VAL Chi-restraints excluded: chain i residue 216 ILE Chi-restraints excluded: chain i residue 394 LYS Chi-restraints excluded: chain i residue 395 THR Chi-restraints excluded: chain i residue 645 VAL Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 16 LEU Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain h residue 93 ILE Chi-restraints excluded: chain h residue 121 VAL Chi-restraints excluded: chain h residue 130 ILE Chi-restraints excluded: chain h residue 340 ILE Chi-restraints excluded: chain h residue 349 THR Chi-restraints excluded: chain h residue 392 ILE Chi-restraints excluded: chain h residue 393 THR Chi-restraints excluded: chain h residue 447 THR Chi-restraints excluded: chain h residue 645 VAL Chi-restraints excluded: chain h residue 652 SER Chi-restraints excluded: chain h residue 656 VAL Chi-restraints excluded: chain j residue 12 LEU Chi-restraints excluded: chain j residue 32 TYR Chi-restraints excluded: chain j residue 58 PHE Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain j residue 95 LEU Chi-restraints excluded: chain j residue 121 VAL Chi-restraints excluded: chain j residue 130 ILE Chi-restraints excluded: chain j residue 177 VAL Chi-restraints excluded: chain j residue 216 ILE Chi-restraints excluded: chain j residue 328 VAL Chi-restraints excluded: chain j residue 392 ILE Chi-restraints excluded: chain j residue 393 THR Chi-restraints excluded: chain j residue 421 TRP Chi-restraints excluded: chain j residue 633 MET Chi-restraints excluded: chain j residue 654 ILE Chi-restraints excluded: chain R residue 68 ILE Chi-restraints excluded: chain R residue 131 LYS Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain a residue 69 LEU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 113 ILE Chi-restraints excluded: chain Q residue 126 ARG Chi-restraints excluded: chain S residue 24 PHE Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 129 HIS Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain N residue 134 ILE Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 133 LYS Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 193 CYS Chi-restraints excluded: chain H residue 229 VAL Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 249 ILE Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain X residue 81 VAL Chi-restraints excluded: chain X residue 181 ASP Chi-restraints excluded: chain Y residue 28 MET Chi-restraints excluded: chain Y residue 189 ASN Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 56 ASP Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain O residue 22 MET Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 134 ILE Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 150 CYS Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 20 HIS Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain L residue 8 ILE Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain W residue 177 LEU Chi-restraints excluded: chain U residue 28 ASP Chi-restraints excluded: chain U residue 56 ASP Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 138 VAL Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 24 PHE Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 134 ILE Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 320 ASN Chi-restraints excluded: chain P residue 8 ILE Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 129 GLU Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 113 ILE Chi-restraints excluded: chain f residue 1196 THR Chi-restraints excluded: chain f residue 1206 LEU Chi-restraints excluded: chain f residue 1209 ASN Chi-restraints excluded: chain g residue 1196 THR Chi-restraints excluded: chain g residue 1209 ASN Chi-restraints excluded: chain e residue 1189 ASP Chi-restraints excluded: chain e residue 1196 THR Chi-restraints excluded: chain V residue 5 ASP Chi-restraints excluded: chain V residue 23 VAL Chi-restraints excluded: chain V residue 147 VAL Chi-restraints excluded: chain V residue 181 ASP Chi-restraints excluded: chain Z residue 5 ASP Chi-restraints excluded: chain Z residue 57 LEU Chi-restraints excluded: chain Z residue 181 ASP Chi-restraints excluded: chain Z residue 192 THR Chi-restraints excluded: chain Z residue 200 LEU Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 42 THR Chi-restraints excluded: chain b residue 82 THR Chi-restraints excluded: chain b residue 140 ILE Chi-restraints excluded: chain b residue 155 THR Chi-restraints excluded: chain b residue 242 LEU Chi-restraints excluded: chain b residue 254 ASP Chi-restraints excluded: chain b residue 255 LEU Chi-restraints excluded: chain b residue 259 LEU Chi-restraints excluded: chain b residue 292 VAL Chi-restraints excluded: chain b residue 337 THR Chi-restraints excluded: chain b residue 338 MET Chi-restraints excluded: chain b residue 419 VAL Chi-restraints excluded: chain b residue 594 ASN Chi-restraints excluded: chain b residue 612 ILE Chi-restraints excluded: chain b residue 787 VAL Chi-restraints excluded: chain b residue 832 ASP Chi-restraints excluded: chain b residue 848 VAL Chi-restraints excluded: chain b residue 863 VAL Chi-restraints excluded: chain b residue 897 ARG Chi-restraints excluded: chain d residue 20 THR Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 242 LEU Chi-restraints excluded: chain d residue 254 ASP Chi-restraints excluded: chain d residue 259 LEU Chi-restraints excluded: chain d residue 266 VAL Chi-restraints excluded: chain d residue 285 ASN Chi-restraints excluded: chain d residue 292 VAL Chi-restraints excluded: chain d residue 337 THR Chi-restraints excluded: chain d residue 419 VAL Chi-restraints excluded: chain d residue 612 ILE Chi-restraints excluded: chain d residue 657 SER Chi-restraints excluded: chain d residue 706 LEU Chi-restraints excluded: chain d residue 768 THR Chi-restraints excluded: chain d residue 848 VAL Chi-restraints excluded: chain d residue 863 VAL Chi-restraints excluded: chain c residue 20 THR Chi-restraints excluded: chain c residue 72 LEU Chi-restraints excluded: chain c residue 82 THR Chi-restraints excluded: chain c residue 140 ILE Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 155 THR Chi-restraints excluded: chain c residue 273 ILE Chi-restraints excluded: chain c residue 290 VAL Chi-restraints excluded: chain c residue 337 THR Chi-restraints excluded: chain c residue 419 VAL Chi-restraints excluded: chain c residue 530 ILE Chi-restraints excluded: chain c residue 612 ILE Chi-restraints excluded: chain c residue 803 ILE Chi-restraints excluded: chain c residue 863 VAL Chi-restraints excluded: chain c residue 901 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1092 random chunks: chunk 651 optimal weight: 6.9990 chunk 420 optimal weight: 0.8980 chunk 628 optimal weight: 2.9990 chunk 317 optimal weight: 1.9990 chunk 206 optimal weight: 0.8980 chunk 203 optimal weight: 0.7980 chunk 669 optimal weight: 6.9990 chunk 717 optimal weight: 10.0000 chunk 520 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 827 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 686 HIS ** R 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN ** I 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 GLN ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 ASN ** G 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 GLN A 41 ASN A 66 ASN ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 849 ASN ** d 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.5066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 88269 Z= 0.268 Angle : 0.565 10.486 119943 Z= 0.290 Chirality : 0.045 0.186 13698 Planarity : 0.004 0.084 15528 Dihedral : 4.629 70.239 12075 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.01 % Favored : 94.95 % Rotamer: Outliers : 3.07 % Allowed : 18.88 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % 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: -1.40 (0.08), residues: 11031 helix: 0.19 (0.15), residues: 1182 sheet: -0.70 (0.08), residues: 3888 loop : -1.29 (0.08), residues: 5961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 95 HIS 0.011 0.001 HIS E 113 PHE 0.025 0.001 PHE S 64 TYR 0.030 0.001 TYR P 109 ARG 0.012 0.000 ARG h 458 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22062 Ramachandran restraints generated. 11031 Oldfield, 0 Emsley, 11031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22062 Ramachandran restraints generated. 11031 Oldfield, 0 Emsley, 11031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1074 residues out of total 9600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 295 poor density : 779 time to evaluate : 8.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: i 405 ASN cc_start: 0.6872 (t0) cc_final: 0.6285 (m110) REVERT: i 645 VAL cc_start: 0.3024 (OUTLIER) cc_final: 0.2633 (m) REVERT: h 340 ILE cc_start: 0.6542 (OUTLIER) cc_final: 0.6070 (mt) REVERT: h 392 ILE cc_start: 0.6382 (OUTLIER) cc_final: 0.6140 (tp) REVERT: h 430 MET cc_start: 0.2727 (tmm) cc_final: 0.1967 (ppp) REVERT: j 392 ILE cc_start: 0.5257 (OUTLIER) cc_final: 0.4475 (mp) REVERT: R 22 MET cc_start: 0.6720 (mtp) cc_final: 0.6152 (mtp) REVERT: R 128 MET cc_start: 0.8087 (mmm) cc_final: 0.7787 (mtt) REVERT: Q 37 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8343 (mmtm) REVERT: Q 55 GLU cc_start: 0.8061 (mp0) cc_final: 0.7751 (mp0) REVERT: F 120 MET cc_start: 0.7010 (ptt) cc_final: 0.6413 (ptt) REVERT: F 315 LYS cc_start: 0.8764 (tptt) cc_final: 0.8512 (mmmt) REVERT: N 37 LYS cc_start: 0.8098 (ptmt) cc_final: 0.7780 (tttm) REVERT: H 155 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7188 (p0) REVERT: Y 66 ASP cc_start: 0.7316 (t70) cc_final: 0.6812 (t0) REVERT: M 1 MET cc_start: 0.6252 (mmt) cc_final: 0.5702 (mmm) REVERT: M 28 ASP cc_start: 0.6749 (t0) cc_final: 0.6515 (t0) REVERT: O 37 LYS cc_start: 0.9002 (tmmt) cc_final: 0.8702 (ttpp) REVERT: E 1 MET cc_start: 0.6764 (tpp) cc_final: 0.5508 (tpp) REVERT: E 245 MET cc_start: 0.8141 (mtt) cc_final: 0.7778 (mtp) REVERT: E 260 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7202 (tm-30) REVERT: E 284 ILE cc_start: 0.9475 (pt) cc_final: 0.9096 (mm) REVERT: C 17 LYS cc_start: 0.6831 (OUTLIER) cc_final: 0.5908 (tptp) REVERT: C 95 TRP cc_start: 0.7505 (m-90) cc_final: 0.7113 (m-90) REVERT: C 120 MET cc_start: 0.4674 (ptt) cc_final: 0.4420 (ptt) REVERT: C 245 MET cc_start: 0.7799 (mtp) cc_final: 0.7559 (mtp) REVERT: W 1 MET cc_start: 0.6672 (ttp) cc_final: 0.6421 (ttp) REVERT: W 66 ASP cc_start: 0.7502 (t70) cc_final: 0.7154 (t0) REVERT: U 1 MET cc_start: 0.5431 (mmt) cc_final: 0.4926 (mmp) REVERT: U 28 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7023 (p0) REVERT: U 54 LEU cc_start: 0.9065 (mt) cc_final: 0.8832 (mp) REVERT: U 55 GLU cc_start: 0.8187 (mp0) cc_final: 0.7616 (mp0) REVERT: K 37 LYS cc_start: 0.8968 (tmmt) cc_final: 0.8496 (ttpp) REVERT: D 133 MET cc_start: 0.8157 (tpp) cc_final: 0.7836 (tpt) REVERT: D 199 ILE cc_start: 0.9075 (tp) cc_final: 0.8798 (pt) REVERT: D 260 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7339 (tm-30) REVERT: D 284 ILE cc_start: 0.9425 (pt) cc_final: 0.9019 (mm) REVERT: A 95 TRP cc_start: 0.7930 (m-90) cc_final: 0.7599 (m-90) REVERT: A 216 MET cc_start: 0.8093 (mpp) cc_final: 0.7052 (mmm) REVERT: P 1 MET cc_start: 0.5154 (tpp) cc_final: 0.4787 (mtp) REVERT: T 8 ILE cc_start: 0.8719 (mp) cc_final: 0.8043 (mm) REVERT: e 1188 ARG cc_start: 0.8056 (mtp180) cc_final: 0.7817 (mmm-85) REVERT: e 1203 GLU cc_start: 0.7386 (mm-30) cc_final: 0.6843 (tm-30) REVERT: b 82 THR cc_start: 0.9111 (OUTLIER) cc_final: 0.8875 (t) REVERT: b 695 GLU cc_start: 0.7437 (tp30) cc_final: 0.7101 (tp30) REVERT: d 695 GLU cc_start: 0.7598 (tp30) cc_final: 0.7254 (tp30) REVERT: c 76 SER cc_start: 0.8284 (m) cc_final: 0.8031 (p) REVERT: c 82 THR cc_start: 0.9092 (OUTLIER) cc_final: 0.8728 (t) REVERT: c 657 SER cc_start: 0.8131 (m) cc_final: 0.7725 (t) outliers start: 295 outliers final: 244 residues processed: 1013 average time/residue: 0.7718 time to fit residues: 1398.6244 Evaluate side-chains 1004 residues out of total 9600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 748 time to evaluate : 7.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 45 SER Chi-restraints excluded: chain i residue 93 ILE Chi-restraints excluded: chain i residue 97 ASP Chi-restraints excluded: chain i residue 113 ARG Chi-restraints excluded: chain i residue 115 GLU Chi-restraints excluded: chain i residue 130 ILE Chi-restraints excluded: chain i residue 177 VAL Chi-restraints excluded: chain i residue 216 ILE Chi-restraints excluded: chain i residue 394 LYS Chi-restraints excluded: chain i residue 395 THR Chi-restraints excluded: chain i residue 645 VAL Chi-restraints excluded: chain h residue 16 LEU Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain h residue 93 ILE Chi-restraints excluded: chain h residue 121 VAL Chi-restraints excluded: chain h residue 130 ILE Chi-restraints excluded: chain h residue 340 ILE Chi-restraints excluded: chain h residue 349 THR Chi-restraints excluded: chain h residue 392 ILE Chi-restraints excluded: chain h residue 393 THR Chi-restraints excluded: chain h residue 447 THR Chi-restraints excluded: chain h residue 645 VAL Chi-restraints excluded: chain h residue 652 SER Chi-restraints excluded: chain h residue 656 VAL Chi-restraints excluded: chain j residue 12 LEU Chi-restraints excluded: chain j residue 32 TYR Chi-restraints excluded: chain j residue 58 PHE Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain j residue 95 LEU Chi-restraints excluded: chain j residue 121 VAL Chi-restraints excluded: chain j residue 130 ILE Chi-restraints excluded: chain j residue 177 VAL Chi-restraints excluded: chain j residue 216 ILE Chi-restraints excluded: chain j residue 328 VAL Chi-restraints excluded: chain j residue 392 ILE Chi-restraints excluded: chain j residue 393 THR Chi-restraints excluded: chain j residue 421 TRP Chi-restraints excluded: chain R residue 68 ILE Chi-restraints excluded: chain R residue 131 LYS Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain a residue 69 LEU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 37 LYS Chi-restraints excluded: chain Q residue 43 ASP Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 113 ILE Chi-restraints excluded: chain Q residue 126 ARG Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 108 TYR Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 129 HIS Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain N residue 134 ILE Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 193 CYS Chi-restraints excluded: chain H residue 229 VAL Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 249 ILE Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain X residue 81 VAL Chi-restraints excluded: chain X residue 181 ASP Chi-restraints excluded: chain Y residue 189 ASN Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 56 ASP Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 22 MET Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 134 ILE Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 150 CYS Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 20 HIS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain L residue 8 ILE Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain U residue 28 ASP Chi-restraints excluded: chain U residue 56 ASP Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 138 VAL Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 134 ILE Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 243 ASN Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 320 ASN Chi-restraints excluded: chain P residue 8 ILE Chi-restraints excluded: chain P residue 10 LEU Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 129 GLU Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 113 ILE Chi-restraints excluded: chain f residue 1196 THR Chi-restraints excluded: chain f residue 1206 LEU Chi-restraints excluded: chain f residue 1209 ASN Chi-restraints excluded: chain g residue 1196 THR Chi-restraints excluded: chain g residue 1209 ASN Chi-restraints excluded: chain e residue 1189 ASP Chi-restraints excluded: chain e residue 1196 THR Chi-restraints excluded: chain V residue 5 ASP Chi-restraints excluded: chain V residue 23 VAL Chi-restraints excluded: chain V residue 147 VAL Chi-restraints excluded: chain Z residue 5 ASP Chi-restraints excluded: chain Z residue 57 LEU Chi-restraints excluded: chain Z residue 69 LEU Chi-restraints excluded: chain Z residue 181 ASP Chi-restraints excluded: chain Z residue 192 THR Chi-restraints excluded: chain Z residue 200 LEU Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 42 THR Chi-restraints excluded: chain b residue 82 THR Chi-restraints excluded: chain b residue 140 ILE Chi-restraints excluded: chain b residue 155 THR Chi-restraints excluded: chain b residue 187 THR Chi-restraints excluded: chain b residue 242 LEU Chi-restraints excluded: chain b residue 254 ASP Chi-restraints excluded: chain b residue 255 LEU Chi-restraints excluded: chain b residue 259 LEU Chi-restraints excluded: chain b residue 292 VAL Chi-restraints excluded: chain b residue 337 THR Chi-restraints excluded: chain b residue 419 VAL Chi-restraints excluded: chain b residue 594 ASN Chi-restraints excluded: chain b residue 612 ILE Chi-restraints excluded: chain b residue 787 VAL Chi-restraints excluded: chain b residue 832 ASP Chi-restraints excluded: chain b residue 848 VAL Chi-restraints excluded: chain b residue 863 VAL Chi-restraints excluded: chain b residue 897 ARG Chi-restraints excluded: chain d residue 20 THR Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 187 THR Chi-restraints excluded: chain d residue 242 LEU Chi-restraints excluded: chain d residue 254 ASP Chi-restraints excluded: chain d residue 259 LEU Chi-restraints excluded: chain d residue 266 VAL Chi-restraints excluded: chain d residue 285 ASN Chi-restraints excluded: chain d residue 292 VAL Chi-restraints excluded: chain d residue 337 THR Chi-restraints excluded: chain d residue 338 MET Chi-restraints excluded: chain d residue 419 VAL Chi-restraints excluded: chain d residue 612 ILE Chi-restraints excluded: chain d residue 706 LEU Chi-restraints excluded: chain d residue 768 THR Chi-restraints excluded: chain d residue 848 VAL Chi-restraints excluded: chain d residue 863 VAL Chi-restraints excluded: chain c residue 20 THR Chi-restraints excluded: chain c residue 72 LEU Chi-restraints excluded: chain c residue 82 THR Chi-restraints excluded: chain c residue 140 ILE Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 155 THR Chi-restraints excluded: chain c residue 273 ILE Chi-restraints excluded: chain c residue 289 ILE Chi-restraints excluded: chain c residue 290 VAL Chi-restraints excluded: chain c residue 337 THR Chi-restraints excluded: chain c residue 338 MET Chi-restraints excluded: chain c residue 419 VAL Chi-restraints excluded: chain c residue 530 ILE Chi-restraints excluded: chain c residue 612 ILE Chi-restraints excluded: chain c residue 705 ASN Chi-restraints excluded: chain c residue 706 LEU Chi-restraints excluded: chain c residue 803 ILE Chi-restraints excluded: chain c residue 848 VAL Chi-restraints excluded: chain c residue 855 VAL Chi-restraints excluded: chain c residue 863 VAL Chi-restraints excluded: chain c residue 901 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1092 random chunks: chunk 957 optimal weight: 0.9990 chunk 1008 optimal weight: 3.9990 chunk 919 optimal weight: 0.9980 chunk 980 optimal weight: 2.9990 chunk 590 optimal weight: 1.9990 chunk 427 optimal weight: 1.9990 chunk 770 optimal weight: 0.9980 chunk 300 optimal weight: 5.9990 chunk 886 optimal weight: 0.5980 chunk 927 optimal weight: 3.9990 chunk 977 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 GLN ** S 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 ASN ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 88269 Z= 0.218 Angle : 0.558 13.884 119943 Z= 0.284 Chirality : 0.045 0.237 13698 Planarity : 0.004 0.085 15528 Dihedral : 4.564 69.962 12075 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.42 % Favored : 95.54 % Rotamer: Outliers : 2.80 % Allowed : 19.29 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % 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: -1.33 (0.08), residues: 11031 helix: 0.26 (0.16), residues: 1185 sheet: -0.63 (0.08), residues: 3861 loop : -1.27 (0.07), residues: 5985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 95 HIS 0.004 0.001 HIS A 113 PHE 0.030 0.001 PHE S 64 TYR 0.024 0.001 TYR S 108 ARG 0.015 0.000 ARG Y 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22062 Ramachandran restraints generated. 11031 Oldfield, 0 Emsley, 11031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22062 Ramachandran restraints generated. 11031 Oldfield, 0 Emsley, 11031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1070 residues out of total 9600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 801 time to evaluate : 8.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: i 405 ASN cc_start: 0.6800 (t0) cc_final: 0.6258 (m110) REVERT: h 340 ILE cc_start: 0.6550 (OUTLIER) cc_final: 0.6082 (mt) REVERT: h 392 ILE cc_start: 0.6369 (OUTLIER) cc_final: 0.6140 (tp) REVERT: h 430 MET cc_start: 0.2644 (tmm) cc_final: 0.1925 (ppp) REVERT: j 392 ILE cc_start: 0.5266 (OUTLIER) cc_final: 0.4501 (mp) REVERT: j 654 ILE cc_start: 0.3621 (OUTLIER) cc_final: 0.2981 (tp) REVERT: R 22 MET cc_start: 0.6607 (mtp) cc_final: 0.6011 (mtp) REVERT: R 128 MET cc_start: 0.8075 (mmm) cc_final: 0.7829 (mtt) REVERT: a 1 MET cc_start: 0.6648 (OUTLIER) cc_final: 0.6374 (ttt) REVERT: Q 55 GLU cc_start: 0.8096 (mp0) cc_final: 0.7776 (mp0) REVERT: F 120 MET cc_start: 0.6982 (ptt) cc_final: 0.6398 (ptt) REVERT: F 315 LYS cc_start: 0.8748 (tptt) cc_final: 0.8501 (mmmt) REVERT: N 37 LYS cc_start: 0.8115 (ptmt) cc_final: 0.7794 (tttm) REVERT: H 155 ASP cc_start: 0.7457 (OUTLIER) cc_final: 0.7097 (p0) REVERT: Y 66 ASP cc_start: 0.7275 (t70) cc_final: 0.6785 (t0) REVERT: M 1 MET cc_start: 0.6131 (mmt) cc_final: 0.5639 (mmt) REVERT: E 245 MET cc_start: 0.8109 (mtt) cc_final: 0.7704 (mtp) REVERT: E 260 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7165 (tm-30) REVERT: E 284 ILE cc_start: 0.9457 (pt) cc_final: 0.9122 (mm) REVERT: E 376 VAL cc_start: 0.8856 (OUTLIER) cc_final: 0.8546 (p) REVERT: C 17 LYS cc_start: 0.6823 (OUTLIER) cc_final: 0.5937 (tptp) REVERT: C 95 TRP cc_start: 0.7484 (m-90) cc_final: 0.7108 (m-90) REVERT: W 1 MET cc_start: 0.6661 (ttp) cc_final: 0.6440 (ttp) REVERT: W 66 ASP cc_start: 0.7450 (t70) cc_final: 0.7122 (t0) REVERT: U 1 MET cc_start: 0.5364 (mmt) cc_final: 0.4800 (mmp) REVERT: U 18 TYR cc_start: 0.8016 (t80) cc_final: 0.7778 (t80) REVERT: U 28 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.7085 (p0) REVERT: U 54 LEU cc_start: 0.9047 (mt) cc_final: 0.8824 (mp) REVERT: U 55 GLU cc_start: 0.8221 (mp0) cc_final: 0.7634 (mp0) REVERT: K 37 LYS cc_start: 0.9022 (tmmt) cc_final: 0.8632 (ttpp) REVERT: D 133 MET cc_start: 0.8117 (tpp) cc_final: 0.7826 (tpt) REVERT: D 199 ILE cc_start: 0.9088 (tp) cc_final: 0.8835 (pt) REVERT: D 260 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7314 (tm-30) REVERT: D 284 ILE cc_start: 0.9407 (pt) cc_final: 0.9028 (mm) REVERT: A 95 TRP cc_start: 0.7891 (m-90) cc_final: 0.7617 (m-90) REVERT: A 120 MET cc_start: 0.4209 (ptt) cc_final: 0.3981 (ptm) REVERT: A 211 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7877 (tp) REVERT: A 216 MET cc_start: 0.8122 (mpp) cc_final: 0.7049 (mmm) REVERT: B 397 GLN cc_start: 0.7389 (tm-30) cc_final: 0.6961 (tm-30) REVERT: P 1 MET cc_start: 0.5146 (tpp) cc_final: 0.4801 (mtp) REVERT: T 8 ILE cc_start: 0.8378 (mp) cc_final: 0.8178 (mm) REVERT: T 25 MET cc_start: 0.7481 (mmm) cc_final: 0.7273 (pmm) REVERT: g 1188 ARG cc_start: 0.7905 (mmm160) cc_final: 0.7563 (mmt180) REVERT: e 1203 GLU cc_start: 0.7371 (mm-30) cc_final: 0.6774 (tm-30) REVERT: Z 40 GLU cc_start: 0.6331 (tm-30) cc_final: 0.6016 (tm-30) REVERT: b 82 THR cc_start: 0.9076 (OUTLIER) cc_final: 0.8845 (t) REVERT: b 695 GLU cc_start: 0.7391 (tp30) cc_final: 0.6717 (tp30) REVERT: d 695 GLU cc_start: 0.7499 (tp30) cc_final: 0.7167 (tp30) REVERT: c 76 SER cc_start: 0.8189 (m) cc_final: 0.7923 (p) REVERT: c 82 THR cc_start: 0.9077 (OUTLIER) cc_final: 0.8715 (t) REVERT: c 657 SER cc_start: 0.8124 (m) cc_final: 0.7677 (t) outliers start: 269 outliers final: 220 residues processed: 1016 average time/residue: 0.7684 time to fit residues: 1391.7440 Evaluate side-chains 988 residues out of total 9600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 754 time to evaluate : 8.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 45 SER Chi-restraints excluded: chain i residue 93 ILE Chi-restraints excluded: chain i residue 97 ASP Chi-restraints excluded: chain i residue 115 GLU Chi-restraints excluded: chain i residue 130 ILE Chi-restraints excluded: chain i residue 177 VAL Chi-restraints excluded: chain i residue 216 ILE Chi-restraints excluded: chain i residue 384 ILE Chi-restraints excluded: chain i residue 395 THR Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 16 LEU Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain h residue 93 ILE Chi-restraints excluded: chain h residue 121 VAL Chi-restraints excluded: chain h residue 130 ILE Chi-restraints excluded: chain h residue 340 ILE Chi-restraints excluded: chain h residue 349 THR Chi-restraints excluded: chain h residue 392 ILE Chi-restraints excluded: chain h residue 393 THR Chi-restraints excluded: chain h residue 447 THR Chi-restraints excluded: chain h residue 645 VAL Chi-restraints excluded: chain h residue 652 SER Chi-restraints excluded: chain j residue 32 TYR Chi-restraints excluded: chain j residue 58 PHE Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain j residue 95 LEU Chi-restraints excluded: chain j residue 121 VAL Chi-restraints excluded: chain j residue 130 ILE Chi-restraints excluded: chain j residue 177 VAL Chi-restraints excluded: chain j residue 216 ILE Chi-restraints excluded: chain j residue 328 VAL Chi-restraints excluded: chain j residue 392 ILE Chi-restraints excluded: chain j residue 393 THR Chi-restraints excluded: chain j residue 421 TRP Chi-restraints excluded: chain j residue 654 ILE Chi-restraints excluded: chain R residue 68 ILE Chi-restraints excluded: chain R residue 131 LYS Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 69 LEU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 43 ASP Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 113 ILE Chi-restraints excluded: chain Q residue 126 ARG Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 129 HIS Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain N residue 134 ILE Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 193 CYS Chi-restraints excluded: chain H residue 229 VAL Chi-restraints excluded: chain H residue 246 THR Chi-restraints excluded: chain H residue 249 ILE Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain X residue 81 VAL Chi-restraints excluded: chain X residue 181 ASP Chi-restraints excluded: chain Y residue 189 ASN Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain O residue 22 MET Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 134 ILE Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 150 CYS Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 20 HIS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain L residue 8 ILE Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain U residue 28 ASP Chi-restraints excluded: chain U residue 56 ASP Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 138 VAL Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 134 ILE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 320 ASN Chi-restraints excluded: chain P residue 8 ILE Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 129 GLU Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 113 ILE Chi-restraints excluded: chain f residue 1206 LEU Chi-restraints excluded: chain f residue 1209 ASN Chi-restraints excluded: chain g residue 1196 THR Chi-restraints excluded: chain g residue 1209 ASN Chi-restraints excluded: chain e residue 1189 ASP Chi-restraints excluded: chain e residue 1196 THR Chi-restraints excluded: chain V residue 23 VAL Chi-restraints excluded: chain V residue 147 VAL Chi-restraints excluded: chain Z residue 5 ASP Chi-restraints excluded: chain Z residue 57 LEU Chi-restraints excluded: chain Z residue 69 LEU Chi-restraints excluded: chain Z residue 181 ASP Chi-restraints excluded: chain Z residue 192 THR Chi-restraints excluded: chain Z residue 200 LEU Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 42 THR Chi-restraints excluded: chain b residue 82 THR Chi-restraints excluded: chain b residue 140 ILE Chi-restraints excluded: chain b residue 242 LEU Chi-restraints excluded: chain b residue 254 ASP Chi-restraints excluded: chain b residue 255 LEU Chi-restraints excluded: chain b residue 259 LEU Chi-restraints excluded: chain b residue 290 VAL Chi-restraints excluded: chain b residue 292 VAL Chi-restraints excluded: chain b residue 337 THR Chi-restraints excluded: chain b residue 419 VAL Chi-restraints excluded: chain b residue 594 ASN Chi-restraints excluded: chain b residue 612 ILE Chi-restraints excluded: chain b residue 787 VAL Chi-restraints excluded: chain b residue 832 ASP Chi-restraints excluded: chain b residue 848 VAL Chi-restraints excluded: chain b residue 855 VAL Chi-restraints excluded: chain b residue 863 VAL Chi-restraints excluded: chain b residue 897 ARG Chi-restraints excluded: chain d residue 20 THR Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 242 LEU Chi-restraints excluded: chain d residue 254 ASP Chi-restraints excluded: chain d residue 259 LEU Chi-restraints excluded: chain d residue 266 VAL Chi-restraints excluded: chain d residue 285 ASN Chi-restraints excluded: chain d residue 292 VAL Chi-restraints excluded: chain d residue 337 THR Chi-restraints excluded: chain d residue 338 MET Chi-restraints excluded: chain d residue 419 VAL Chi-restraints excluded: chain d residue 612 ILE Chi-restraints excluded: chain d residue 706 LEU Chi-restraints excluded: chain d residue 768 THR Chi-restraints excluded: chain d residue 848 VAL Chi-restraints excluded: chain d residue 859 VAL Chi-restraints excluded: chain d residue 863 VAL Chi-restraints excluded: chain c residue 20 THR Chi-restraints excluded: chain c residue 42 THR Chi-restraints excluded: chain c residue 72 LEU Chi-restraints excluded: chain c residue 82 THR Chi-restraints excluded: chain c residue 140 ILE Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 155 THR Chi-restraints excluded: chain c residue 290 VAL Chi-restraints excluded: chain c residue 337 THR Chi-restraints excluded: chain c residue 338 MET Chi-restraints excluded: chain c residue 419 VAL Chi-restraints excluded: chain c residue 530 ILE Chi-restraints excluded: chain c residue 612 ILE Chi-restraints excluded: chain c residue 705 ASN Chi-restraints excluded: chain c residue 706 LEU Chi-restraints excluded: chain c residue 803 ILE Chi-restraints excluded: chain c residue 848 VAL Chi-restraints excluded: chain c residue 855 VAL Chi-restraints excluded: chain c residue 863 VAL Chi-restraints excluded: chain c residue 901 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1092 random chunks: chunk 644 optimal weight: 0.5980 chunk 1037 optimal weight: 0.5980 chunk 633 optimal weight: 8.9990 chunk 492 optimal weight: 5.9990 chunk 720 optimal weight: 9.9990 chunk 1087 optimal weight: 10.0000 chunk 1001 optimal weight: 3.9990 chunk 866 optimal weight: 0.5980 chunk 89 optimal weight: 20.0000 chunk 669 optimal weight: 3.9990 chunk 531 optimal weight: 3.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 217 ASN ** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 237 GLN ** R 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 GLN ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 849 ASN ** d 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 400 ASN c 735 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.5437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 88269 Z= 0.332 Angle : 0.615 13.518 119943 Z= 0.314 Chirality : 0.046 0.250 13698 Planarity : 0.004 0.086 15528 Dihedral : 4.775 71.241 12075 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.63 % Favored : 94.33 % Rotamer: Outliers : 2.71 % Allowed : 19.57 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % 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: -1.42 (0.08), residues: 11031 helix: 0.14 (0.15), residues: 1176 sheet: -0.71 (0.08), residues: 3894 loop : -1.30 (0.08), residues: 5961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP j 287 HIS 0.005 0.001 HIS F 113 PHE 0.038 0.002 PHE S 64 TYR 0.027 0.002 TYR P 109 ARG 0.012 0.001 ARG a 201 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22062 Ramachandran restraints generated. 11031 Oldfield, 0 Emsley, 11031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22062 Ramachandran restraints generated. 11031 Oldfield, 0 Emsley, 11031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1030 residues out of total 9600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 770 time to evaluate : 7.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: i 405 ASN cc_start: 0.6767 (t0) cc_final: 0.6222 (m110) REVERT: h 232 TYR cc_start: 0.4122 (OUTLIER) cc_final: 0.3478 (t80) REVERT: h 340 ILE cc_start: 0.6681 (OUTLIER) cc_final: 0.6177 (mt) REVERT: h 392 ILE cc_start: 0.6492 (OUTLIER) cc_final: 0.6126 (tp) REVERT: h 430 MET cc_start: 0.2623 (tmm) cc_final: 0.1901 (ppp) REVERT: j 392 ILE cc_start: 0.5458 (OUTLIER) cc_final: 0.4700 (mp) REVERT: j 654 ILE cc_start: 0.3613 (OUTLIER) cc_final: 0.2978 (tp) REVERT: R 22 MET cc_start: 0.6454 (mtp) cc_final: 0.5786 (mtp) REVERT: R 128 MET cc_start: 0.8073 (mmm) cc_final: 0.7867 (mtt) REVERT: a 1 MET cc_start: 0.6678 (OUTLIER) cc_final: 0.6432 (ttt) REVERT: F 315 LYS cc_start: 0.8801 (tptt) cc_final: 0.8543 (mmmt) REVERT: N 37 LYS cc_start: 0.8162 (ptmt) cc_final: 0.7088 (tttm) REVERT: H 155 ASP cc_start: 0.7452 (OUTLIER) cc_final: 0.7084 (p0) REVERT: Y 66 ASP cc_start: 0.7376 (t70) cc_final: 0.6891 (t0) REVERT: M 1 MET cc_start: 0.6302 (mmt) cc_final: 0.5705 (mmt) REVERT: E 260 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7269 (tm-30) REVERT: C 17 LYS cc_start: 0.6399 (OUTLIER) cc_final: 0.5370 (tptp) REVERT: C 95 TRP cc_start: 0.7684 (m-90) cc_final: 0.7271 (m-90) REVERT: C 216 MET cc_start: 0.7787 (mpp) cc_final: 0.7229 (mpp) REVERT: C 245 MET cc_start: 0.7939 (mtp) cc_final: 0.7684 (mtp) REVERT: J 22 MET cc_start: 0.6934 (mtp) cc_final: 0.6677 (mtp) REVERT: J 25 MET cc_start: 0.7061 (tpt) cc_final: 0.6435 (tpt) REVERT: L 4 GLU cc_start: 0.4069 (mm-30) cc_final: 0.3821 (mm-30) REVERT: W 66 ASP cc_start: 0.7416 (t70) cc_final: 0.7093 (t0) REVERT: U 1 MET cc_start: 0.5502 (mmt) cc_final: 0.4167 (mmp) REVERT: U 18 TYR cc_start: 0.8111 (t80) cc_final: 0.7690 (t80) REVERT: U 28 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.6803 (p0) REVERT: U 55 GLU cc_start: 0.8343 (mp0) cc_final: 0.7648 (mp0) REVERT: K 37 LYS cc_start: 0.9087 (tmmt) cc_final: 0.8700 (tmmt) REVERT: D 133 MET cc_start: 0.8120 (tpp) cc_final: 0.7906 (tpt) REVERT: D 199 ILE cc_start: 0.9088 (tp) cc_final: 0.8838 (pt) REVERT: A 120 MET cc_start: 0.4374 (ptt) cc_final: 0.4065 (ptm) REVERT: A 216 MET cc_start: 0.8145 (mpp) cc_final: 0.7305 (mmm) REVERT: B 398 MET cc_start: -0.0400 (tpp) cc_final: -0.0660 (tpp) REVERT: P 1 MET cc_start: 0.5496 (tpp) cc_final: 0.5070 (mtp) REVERT: P 129 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6411 (mt-10) REVERT: T 25 MET cc_start: 0.7577 (mmm) cc_final: 0.7253 (pmm) REVERT: e 1200 ASP cc_start: 0.6844 (t0) cc_final: 0.6642 (t0) REVERT: e 1203 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7008 (tm-30) REVERT: Z 40 GLU cc_start: 0.6311 (tm-30) cc_final: 0.6104 (tm-30) REVERT: b 82 THR cc_start: 0.9150 (OUTLIER) cc_final: 0.8923 (t) REVERT: b 897 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.7085 (ttm-80) REVERT: d 695 GLU cc_start: 0.7625 (tp30) cc_final: 0.7210 (tp30) REVERT: c 76 SER cc_start: 0.8307 (m) cc_final: 0.8069 (p) REVERT: c 82 THR cc_start: 0.9115 (OUTLIER) cc_final: 0.8733 (t) REVERT: c 657 SER cc_start: 0.8160 (m) cc_final: 0.7803 (t) outliers start: 260 outliers final: 222 residues processed: 983 average time/residue: 0.7741 time to fit residues: 1354.0731 Evaluate side-chains 970 residues out of total 9600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 734 time to evaluate : 7.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 45 SER Chi-restraints excluded: chain i residue 93 ILE Chi-restraints excluded: chain i residue 97 ASP Chi-restraints excluded: chain i residue 130 ILE Chi-restraints excluded: chain i residue 177 VAL Chi-restraints excluded: chain i residue 216 ILE Chi-restraints excluded: chain i residue 384 ILE Chi-restraints excluded: chain i residue 395 THR Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 16 LEU Chi-restraints excluded: chain h residue 93 ILE Chi-restraints excluded: chain h residue 121 VAL Chi-restraints excluded: chain h residue 130 ILE Chi-restraints excluded: chain h residue 232 TYR Chi-restraints excluded: chain h residue 340 ILE Chi-restraints excluded: chain h residue 349 THR Chi-restraints excluded: chain h residue 392 ILE Chi-restraints excluded: chain h residue 393 THR Chi-restraints excluded: chain h residue 447 THR Chi-restraints excluded: chain h residue 645 VAL Chi-restraints excluded: chain h residue 652 SER Chi-restraints excluded: chain j residue 58 PHE Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain j residue 95 LEU Chi-restraints excluded: chain j residue 121 VAL Chi-restraints excluded: chain j residue 130 ILE Chi-restraints excluded: chain j residue 177 VAL Chi-restraints excluded: chain j residue 216 ILE Chi-restraints excluded: chain j residue 328 VAL Chi-restraints excluded: chain j residue 392 ILE Chi-restraints excluded: chain j residue 421 TRP Chi-restraints excluded: chain j residue 654 ILE Chi-restraints excluded: chain R residue 68 ILE Chi-restraints excluded: chain R residue 131 LYS Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 69 LEU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 43 ASP Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 113 ILE Chi-restraints excluded: chain Q residue 126 ARG Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 108 TYR Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 129 HIS Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain N residue 134 ILE Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 193 CYS Chi-restraints excluded: chain H residue 229 VAL Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 246 THR Chi-restraints excluded: chain H residue 249 ILE Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain X residue 81 VAL Chi-restraints excluded: chain X residue 181 ASP Chi-restraints excluded: chain Y residue 69 LEU Chi-restraints excluded: chain Y residue 189 ASN Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 134 ILE Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 150 CYS Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 20 HIS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain L residue 8 ILE Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 122 CYS Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain U residue 28 ASP Chi-restraints excluded: chain U residue 56 ASP Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 138 VAL Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 134 ILE Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 243 ASN Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 320 ASN Chi-restraints excluded: chain P residue 8 ILE Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 129 GLU Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 113 ILE Chi-restraints excluded: chain f residue 1196 THR Chi-restraints excluded: chain f residue 1206 LEU Chi-restraints excluded: chain f residue 1209 ASN Chi-restraints excluded: chain g residue 1196 THR Chi-restraints excluded: chain e residue 1189 ASP Chi-restraints excluded: chain e residue 1196 THR Chi-restraints excluded: chain V residue 23 VAL Chi-restraints excluded: chain V residue 28 MET Chi-restraints excluded: chain V residue 147 VAL Chi-restraints excluded: chain Z residue 5 ASP Chi-restraints excluded: chain Z residue 57 LEU Chi-restraints excluded: chain Z residue 192 THR Chi-restraints excluded: chain Z residue 200 LEU Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 42 THR Chi-restraints excluded: chain b residue 82 THR Chi-restraints excluded: chain b residue 140 ILE Chi-restraints excluded: chain b residue 242 LEU Chi-restraints excluded: chain b residue 254 ASP Chi-restraints excluded: chain b residue 255 LEU Chi-restraints excluded: chain b residue 259 LEU Chi-restraints excluded: chain b residue 290 VAL Chi-restraints excluded: chain b residue 292 VAL Chi-restraints excluded: chain b residue 337 THR Chi-restraints excluded: chain b residue 419 VAL Chi-restraints excluded: chain b residue 594 ASN Chi-restraints excluded: chain b residue 612 ILE Chi-restraints excluded: chain b residue 787 VAL Chi-restraints excluded: chain b residue 832 ASP Chi-restraints excluded: chain b residue 848 VAL Chi-restraints excluded: chain b residue 855 VAL Chi-restraints excluded: chain b residue 863 VAL Chi-restraints excluded: chain b residue 897 ARG Chi-restraints excluded: chain d residue 20 THR Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 242 LEU Chi-restraints excluded: chain d residue 254 ASP Chi-restraints excluded: chain d residue 259 LEU Chi-restraints excluded: chain d residue 266 VAL Chi-restraints excluded: chain d residue 285 ASN Chi-restraints excluded: chain d residue 292 VAL Chi-restraints excluded: chain d residue 337 THR Chi-restraints excluded: chain d residue 338 MET Chi-restraints excluded: chain d residue 419 VAL Chi-restraints excluded: chain d residue 612 ILE Chi-restraints excluded: chain d residue 706 LEU Chi-restraints excluded: chain d residue 768 THR Chi-restraints excluded: chain d residue 848 VAL Chi-restraints excluded: chain d residue 855 VAL Chi-restraints excluded: chain d residue 859 VAL Chi-restraints excluded: chain d residue 863 VAL Chi-restraints excluded: chain c residue 20 THR Chi-restraints excluded: chain c residue 42 THR Chi-restraints excluded: chain c residue 72 LEU Chi-restraints excluded: chain c residue 82 THR Chi-restraints excluded: chain c residue 140 ILE Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 155 THR Chi-restraints excluded: chain c residue 273 ILE Chi-restraints excluded: chain c residue 290 VAL Chi-restraints excluded: chain c residue 337 THR Chi-restraints excluded: chain c residue 338 MET Chi-restraints excluded: chain c residue 419 VAL Chi-restraints excluded: chain c residue 530 ILE Chi-restraints excluded: chain c residue 612 ILE Chi-restraints excluded: chain c residue 705 ASN Chi-restraints excluded: chain c residue 706 LEU Chi-restraints excluded: chain c residue 848 VAL Chi-restraints excluded: chain c residue 855 VAL Chi-restraints excluded: chain c residue 863 VAL Chi-restraints excluded: chain c residue 901 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1092 random chunks: chunk 688 optimal weight: 5.9990 chunk 922 optimal weight: 2.9990 chunk 265 optimal weight: 2.9990 chunk 798 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 240 optimal weight: 3.9990 chunk 867 optimal weight: 0.6980 chunk 363 optimal weight: 7.9990 chunk 890 optimal weight: 0.0070 chunk 109 optimal weight: 4.9990 chunk 159 optimal weight: 9.9990 overall best weight: 1.9404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 325 ASN i 417 GLN ** h 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 5 ASN ** O 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 GLN C 320 ASN ** C 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 ASN ** G 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 ASN A 62 ASN ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 161 GLN ** b 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 849 ASN ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 734 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.081796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.055681 restraints weight = 308470.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.057155 restraints weight = 151321.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.058156 restraints weight = 91559.918| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 72 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 72 | |-----------------------------------------------------------------------------| r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.5584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 88269 Z= 0.326 Angle : 0.610 14.140 119943 Z= 0.312 Chirality : 0.046 0.226 13698 Planarity : 0.004 0.088 15528 Dihedral : 4.807 71.503 12075 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.15 % Favored : 94.81 % Rotamer: Outliers : 2.89 % Allowed : 19.82 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % 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: -1.44 (0.08), residues: 11031 helix: 0.12 (0.15), residues: 1179 sheet: -0.74 (0.08), residues: 3864 loop : -1.30 (0.07), residues: 5988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP j 287 HIS 0.006 0.001 HIS F 113 PHE 0.039 0.001 PHE S 64 TYR 0.030 0.001 TYR O 18 ARG 0.011 0.001 ARG a 201 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22949.98 seconds wall clock time: 405 minutes 12.77 seconds (24312.77 seconds total)