Starting phenix.real_space_refine on Sat Feb 17 12:12:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrc_9195/02_2024/6mrc_9195_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrc_9195/02_2024/6mrc_9195.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrc_9195/02_2024/6mrc_9195.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrc_9195/02_2024/6mrc_9195.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrc_9195/02_2024/6mrc_9195_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrc_9195/02_2024/6mrc_9195_updated.pdb" } resolution = 3.08 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= 0.004 sd= 0.137 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: 7 Type Number sf(0) Gaussians P 28 5.49 5 Mg 14 5.21 5 S 210 5.16 5 C 41482 2.51 5 N 11256 2.21 5 O 13188 1.98 5 H 2954 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 422": "NH1" <-> "NH2" Residue "V ARG 15": "NH1" <-> "NH2" Residue "V ARG 92": "NH1" <-> "NH2" Residue "2 ARG 15": "NH1" <-> "NH2" Residue "2 ARG 92": "NH1" <-> "NH2" Residue "1 ARG 15": "NH1" <-> "NH2" Residue "1 ARG 92": "NH1" <-> "NH2" Residue "Z ARG 15": "NH1" <-> "NH2" Residue "Z ARG 92": "NH1" <-> "NH2" Residue "Y ARG 15": "NH1" <-> "NH2" Residue "Y ARG 92": "NH1" <-> "NH2" Residue "X ARG 15": "NH1" <-> "NH2" Residue "X ARG 92": "NH1" <-> "NH2" Residue "W ARG 15": "NH1" <-> "NH2" Residue "W ARG 92": "NH1" <-> "NH2" Residue "R ARG 15": "NH1" <-> "NH2" Residue "R ARG 92": "NH1" <-> "NH2" Residue "Q ARG 15": "NH1" <-> "NH2" Residue "Q ARG 92": "NH1" <-> "NH2" Residue "P ARG 15": "NH1" <-> "NH2" Residue "P ARG 92": "NH1" <-> "NH2" Residue "O ARG 15": "NH1" <-> "NH2" Residue "O ARG 92": "NH1" <-> "NH2" Residue "U ARG 15": "NH1" <-> "NH2" Residue "U ARG 92": "NH1" <-> "NH2" Residue "T ARG 15": "NH1" <-> "NH2" Residue "T ARG 92": "NH1" <-> "NH2" Residue "S ARG 15": "NH1" <-> "NH2" Residue "S ARG 92": "NH1" <-> "NH2" Residue "N TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 422": "NH1" <-> "NH2" Residue "M TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 422": "NH1" <-> "NH2" Residue "L TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 422": "NH1" <-> "NH2" Residue "K TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 422": "NH1" <-> "NH2" Residue "J TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 422": "NH1" <-> "NH2" Residue "I TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 422": "NH1" <-> "NH2" Residue "D TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 422": "NH1" <-> "NH2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 422": "NH1" <-> "NH2" Residue "B TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 422": "NH1" <-> "NH2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 422": "NH1" <-> "NH2" Residue "G TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 422": "NH1" <-> "NH2" Residue "F TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 422": "NH1" <-> "NH2" Residue "E TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 422": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 69132 Number of models: 1 Model: "" Number of chains: 56 Chain: "H" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4147 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 15, 'TRANS': 512} Chain: "V" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 756 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "2" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 756 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "1" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 756 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "Z" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 756 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "Y" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 756 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "X" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 756 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "W" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 756 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "R" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 756 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "Q" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 756 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "P" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 756 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "O" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 756 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "U" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 756 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "T" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 756 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "S" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 756 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "N" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4147 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 15, 'TRANS': 512} Chain: "M" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4147 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 15, 'TRANS': 512} Chain: "L" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4147 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 15, 'TRANS': 512} Chain: "K" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4147 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 15, 'TRANS': 512} Chain: "J" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4147 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 15, 'TRANS': 512} Chain: "I" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4147 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 15, 'TRANS': 512} Chain: "D" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4147 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 15, 'TRANS': 512} Chain: "C" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4147 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 15, 'TRANS': 512} Chain: "B" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4147 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 15, 'TRANS': 512} Chain: "A" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4147 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 15, 'TRANS': 512} Chain: "G" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4147 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 15, 'TRANS': 512} Chain: "F" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4147 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 15, 'TRANS': 512} Chain: "E" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4147 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 15, 'TRANS': 512} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "N" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "M" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "L" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "K" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "J" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "I" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "G" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "F" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 25.56, per 1000 atoms: 0.37 Number of scatterers: 69132 At special positions: 0 Unit cell: (159.43, 157.29, 260.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 210 16.00 P 28 15.00 Mg 14 11.99 O 13188 8.00 N 11256 7.00 C 41482 6.00 H 2954 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 21.93 Conformation dependent library (CDL) restraints added in 9.7 seconds 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15876 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 259 helices and 112 sheets defined 42.5% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.12 Creating SS restraints... Processing helix chain 'H' and resid 9 through 30 removed outlier: 3.809A pdb=" N VAL H 27 " --> pdb=" O LEU H 23 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL H 29 " --> pdb=" O ASP H 25 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N THR H 30 " --> pdb=" O ALA H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 59 Processing helix chain 'H' and resid 65 through 85 removed outlier: 3.752A pdb=" N VAL H 77 " --> pdb=" O LEU H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 103 Processing helix chain 'H' and resid 113 through 134 removed outlier: 3.556A pdb=" N GLU H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS H 132 " --> pdb=" O ILE H 128 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS H 133 " --> pdb=" O ALA H 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 151 removed outlier: 3.558A pdb=" N ALA H 145 " --> pdb=" O PRO H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 167 Processing helix chain 'H' and resid 230 through 243 Proline residue: H 235 - end of helix Processing helix chain 'H' and resid 256 through 267 Processing helix chain 'H' and resid 284 through 296 removed outlier: 3.833A pdb=" N LYS H 290 " --> pdb=" O LYS H 286 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 356 removed outlier: 3.863A pdb=" N LYS H 345 " --> pdb=" O ALA H 341 " (cutoff:3.500A) Processing helix chain 'H' and resid 362 through 371 Processing helix chain 'H' and resid 387 through 407 Processing helix chain 'H' and resid 418 through 429 removed outlier: 4.186A pdb=" N CYS H 423 " --> pdb=" O ALA H 419 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE H 424 " --> pdb=" O LEU H 420 " (cutoff:3.500A) Proline residue: H 425 - end of helix removed outlier: 3.940A pdb=" N SER H 429 " --> pdb=" O PRO H 425 " (cutoff:3.500A) Processing helix chain 'H' and resid 435 through 458 removed outlier: 4.615A pdb=" N LYS H 449 " --> pdb=" O LYS H 445 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE H 450 " --> pdb=" O ARG H 446 " (cutoff:3.500A) Proline residue: H 451 - end of helix Processing helix chain 'H' and resid 463 through 472 Processing helix chain 'H' and resid 498 through 517 removed outlier: 3.570A pdb=" N LEU H 514 " --> pdb=" O GLY H 510 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR H 517 " --> pdb=" O SER H 513 " (cutoff:3.500A) Processing helix chain 'V' and resid 93 through 95 No H-bonds generated for 'chain 'V' and resid 93 through 95' Processing helix chain '2' and resid 93 through 95 No H-bonds generated for 'chain '2' and resid 93 through 95' Processing helix chain '1' and resid 93 through 95 No H-bonds generated for 'chain '1' and resid 93 through 95' Processing helix chain 'Z' and resid 93 through 95 No H-bonds generated for 'chain 'Z' and resid 93 through 95' Processing helix chain 'Y' and resid 93 through 95 No H-bonds generated for 'chain 'Y' and resid 93 through 95' Processing helix chain 'X' and resid 93 through 95 No H-bonds generated for 'chain 'X' and resid 93 through 95' Processing helix chain 'W' and resid 93 through 95 No H-bonds generated for 'chain 'W' and resid 93 through 95' Processing helix chain 'R' and resid 93 through 95 No H-bonds generated for 'chain 'R' and resid 93 through 95' Processing helix chain 'Q' and resid 93 through 95 No H-bonds generated for 'chain 'Q' and resid 93 through 95' Processing helix chain 'P' and resid 93 through 95 No H-bonds generated for 'chain 'P' and resid 93 through 95' Processing helix chain 'U' and resid 93 through 95 No H-bonds generated for 'chain 'U' and resid 93 through 95' Processing helix chain 'T' and resid 93 through 95 No H-bonds generated for 'chain 'T' and resid 93 through 95' Processing helix chain 'S' and resid 93 through 95 No H-bonds generated for 'chain 'S' and resid 93 through 95' Processing helix chain 'N' and resid 9 through 30 removed outlier: 3.821A pdb=" N VAL N 27 " --> pdb=" O LEU N 23 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL N 29 " --> pdb=" O ASP N 25 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N THR N 30 " --> pdb=" O ALA N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 59 Processing helix chain 'N' and resid 65 through 85 removed outlier: 3.721A pdb=" N VAL N 77 " --> pdb=" O LEU N 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 89 through 103 Processing helix chain 'N' and resid 113 through 134 removed outlier: 3.553A pdb=" N GLU N 130 " --> pdb=" O ALA N 126 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS N 133 " --> pdb=" O ALA N 129 " (cutoff:3.500A) Processing helix chain 'N' and resid 141 through 151 removed outlier: 3.613A pdb=" N ALA N 145 " --> pdb=" O PRO N 141 " (cutoff:3.500A) Processing helix chain 'N' and resid 156 through 167 Processing helix chain 'N' and resid 230 through 243 Proline residue: N 235 - end of helix Processing helix chain 'N' and resid 256 through 269 removed outlier: 3.530A pdb=" N VAL N 269 " --> pdb=" O ASN N 265 " (cutoff:3.500A) Processing helix chain 'N' and resid 283 through 296 removed outlier: 3.802A pdb=" N ASN N 287 " --> pdb=" O ASP N 283 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS N 290 " --> pdb=" O LYS N 286 " (cutoff:3.500A) Processing helix chain 'N' and resid 340 through 356 removed outlier: 3.746A pdb=" N LYS N 345 " --> pdb=" O ALA N 341 " (cutoff:3.500A) Processing helix chain 'N' and resid 362 through 374 Processing helix chain 'N' and resid 387 through 407 Processing helix chain 'N' and resid 418 through 429 removed outlier: 4.158A pdb=" N CYS N 423 " --> pdb=" O ALA N 419 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE N 424 " --> pdb=" O LEU N 420 " (cutoff:3.500A) Proline residue: N 425 - end of helix removed outlier: 3.855A pdb=" N SER N 429 " --> pdb=" O PRO N 425 " (cutoff:3.500A) Processing helix chain 'N' and resid 435 through 458 removed outlier: 4.601A pdb=" N LYS N 449 " --> pdb=" O LYS N 445 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ILE N 450 " --> pdb=" O ARG N 446 " (cutoff:3.500A) Proline residue: N 451 - end of helix Processing helix chain 'N' and resid 463 through 472 Processing helix chain 'N' and resid 489 through 492 No H-bonds generated for 'chain 'N' and resid 489 through 492' Processing helix chain 'N' and resid 498 through 517 removed outlier: 3.509A pdb=" N LEU N 514 " --> pdb=" O GLY N 510 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR N 517 " --> pdb=" O SER N 513 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 30 removed outlier: 3.797A pdb=" N VAL M 27 " --> pdb=" O LEU M 23 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL M 29 " --> pdb=" O ASP M 25 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N THR M 30 " --> pdb=" O ALA M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 59 Processing helix chain 'M' and resid 65 through 85 removed outlier: 3.676A pdb=" N VAL M 77 " --> pdb=" O LEU M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 103 Processing helix chain 'M' and resid 113 through 134 removed outlier: 3.538A pdb=" N GLU M 130 " --> pdb=" O ALA M 126 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS M 132 " --> pdb=" O ILE M 128 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS M 133 " --> pdb=" O ALA M 129 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 151 removed outlier: 3.609A pdb=" N ALA M 145 " --> pdb=" O PRO M 141 " (cutoff:3.500A) Processing helix chain 'M' and resid 156 through 167 Processing helix chain 'M' and resid 230 through 243 Proline residue: M 235 - end of helix Processing helix chain 'M' and resid 256 through 269 Processing helix chain 'M' and resid 283 through 296 removed outlier: 4.025A pdb=" N LYS M 290 " --> pdb=" O LYS M 286 " (cutoff:3.500A) Processing helix chain 'M' and resid 340 through 356 removed outlier: 3.849A pdb=" N LYS M 345 " --> pdb=" O ALA M 341 " (cutoff:3.500A) Processing helix chain 'M' and resid 362 through 371 Processing helix chain 'M' and resid 387 through 407 Processing helix chain 'M' and resid 418 through 429 removed outlier: 4.139A pdb=" N CYS M 423 " --> pdb=" O ALA M 419 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE M 424 " --> pdb=" O LEU M 420 " (cutoff:3.500A) Proline residue: M 425 - end of helix removed outlier: 3.928A pdb=" N SER M 429 " --> pdb=" O PRO M 425 " (cutoff:3.500A) Processing helix chain 'M' and resid 435 through 458 removed outlier: 4.598A pdb=" N LYS M 449 " --> pdb=" O LYS M 445 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE M 450 " --> pdb=" O ARG M 446 " (cutoff:3.500A) Proline residue: M 451 - end of helix Processing helix chain 'M' and resid 463 through 472 Processing helix chain 'M' and resid 498 through 517 removed outlier: 3.563A pdb=" N LEU M 514 " --> pdb=" O GLY M 510 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR M 517 " --> pdb=" O SER M 513 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 30 removed outlier: 3.812A pdb=" N VAL L 27 " --> pdb=" O LEU L 23 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL L 29 " --> pdb=" O ASP L 25 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N THR L 30 " --> pdb=" O ALA L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 59 Processing helix chain 'L' and resid 65 through 85 removed outlier: 3.728A pdb=" N VAL L 77 " --> pdb=" O LEU L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 103 Processing helix chain 'L' and resid 113 through 134 removed outlier: 3.553A pdb=" N LYS L 132 " --> pdb=" O ILE L 128 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS L 133 " --> pdb=" O ALA L 129 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 151 removed outlier: 3.629A pdb=" N ALA L 145 " --> pdb=" O PRO L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 156 through 167 Processing helix chain 'L' and resid 230 through 243 Proline residue: L 235 - end of helix Processing helix chain 'L' and resid 256 through 267 Processing helix chain 'L' and resid 283 through 296 removed outlier: 4.039A pdb=" N LYS L 290 " --> pdb=" O LYS L 286 " (cutoff:3.500A) Processing helix chain 'L' and resid 340 through 356 removed outlier: 3.850A pdb=" N LYS L 345 " --> pdb=" O ALA L 341 " (cutoff:3.500A) Processing helix chain 'L' and resid 362 through 371 Processing helix chain 'L' and resid 387 through 407 Processing helix chain 'L' and resid 418 through 429 removed outlier: 4.168A pdb=" N CYS L 423 " --> pdb=" O ALA L 419 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE L 424 " --> pdb=" O LEU L 420 " (cutoff:3.500A) Proline residue: L 425 - end of helix removed outlier: 3.999A pdb=" N SER L 429 " --> pdb=" O PRO L 425 " (cutoff:3.500A) Processing helix chain 'L' and resid 435 through 458 removed outlier: 4.595A pdb=" N LYS L 449 " --> pdb=" O LYS L 445 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE L 450 " --> pdb=" O ARG L 446 " (cutoff:3.500A) Proline residue: L 451 - end of helix Processing helix chain 'L' and resid 463 through 472 Processing helix chain 'L' and resid 489 through 492 No H-bonds generated for 'chain 'L' and resid 489 through 492' Processing helix chain 'L' and resid 498 through 517 removed outlier: 3.521A pdb=" N LEU L 514 " --> pdb=" O GLY L 510 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR L 517 " --> pdb=" O SER L 513 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 30 removed outlier: 3.748A pdb=" N VAL K 27 " --> pdb=" O LEU K 23 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL K 29 " --> pdb=" O ASP K 25 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N THR K 30 " --> pdb=" O ALA K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 59 Processing helix chain 'K' and resid 65 through 85 removed outlier: 3.697A pdb=" N VAL K 77 " --> pdb=" O LEU K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 103 Processing helix chain 'K' and resid 113 through 134 removed outlier: 3.535A pdb=" N GLU K 130 " --> pdb=" O ALA K 126 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS K 132 " --> pdb=" O ILE K 128 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS K 133 " --> pdb=" O ALA K 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 141 through 151 removed outlier: 3.669A pdb=" N ALA K 145 " --> pdb=" O PRO K 141 " (cutoff:3.500A) Processing helix chain 'K' and resid 156 through 167 Processing helix chain 'K' and resid 230 through 243 Proline residue: K 235 - end of helix Processing helix chain 'K' and resid 256 through 267 Processing helix chain 'K' and resid 283 through 296 removed outlier: 3.682A pdb=" N ASN K 287 " --> pdb=" O ASP K 283 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS K 290 " --> pdb=" O LYS K 286 " (cutoff:3.500A) Processing helix chain 'K' and resid 340 through 356 removed outlier: 3.811A pdb=" N LYS K 345 " --> pdb=" O ALA K 341 " (cutoff:3.500A) Processing helix chain 'K' and resid 362 through 371 Processing helix chain 'K' and resid 387 through 407 Processing helix chain 'K' and resid 418 through 429 removed outlier: 4.133A pdb=" N CYS K 423 " --> pdb=" O ALA K 419 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE K 424 " --> pdb=" O LEU K 420 " (cutoff:3.500A) Proline residue: K 425 - end of helix removed outlier: 3.986A pdb=" N SER K 429 " --> pdb=" O PRO K 425 " (cutoff:3.500A) Processing helix chain 'K' and resid 435 through 458 removed outlier: 4.563A pdb=" N LYS K 449 " --> pdb=" O LYS K 445 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE K 450 " --> pdb=" O ARG K 446 " (cutoff:3.500A) Proline residue: K 451 - end of helix Processing helix chain 'K' and resid 463 through 471 Processing helix chain 'K' and resid 498 through 517 removed outlier: 4.067A pdb=" N THR K 517 " --> pdb=" O SER K 513 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 30 removed outlier: 3.822A pdb=" N VAL J 27 " --> pdb=" O LEU J 23 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL J 29 " --> pdb=" O ASP J 25 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N THR J 30 " --> pdb=" O ALA J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 59 Processing helix chain 'J' and resid 65 through 85 removed outlier: 3.721A pdb=" N VAL J 77 " --> pdb=" O LEU J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 103 Processing helix chain 'J' and resid 113 through 134 removed outlier: 3.565A pdb=" N GLU J 130 " --> pdb=" O ALA J 126 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS J 132 " --> pdb=" O ILE J 128 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS J 133 " --> pdb=" O ALA J 129 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 151 removed outlier: 3.608A pdb=" N ALA J 145 " --> pdb=" O PRO J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 167 Processing helix chain 'J' and resid 230 through 243 Proline residue: J 235 - end of helix Processing helix chain 'J' and resid 256 through 267 Processing helix chain 'J' and resid 283 through 296 removed outlier: 3.863A pdb=" N LYS J 290 " --> pdb=" O LYS J 286 " (cutoff:3.500A) Processing helix chain 'J' and resid 315 through 317 No H-bonds generated for 'chain 'J' and resid 315 through 317' Processing helix chain 'J' and resid 340 through 356 removed outlier: 3.854A pdb=" N LYS J 345 " --> pdb=" O ALA J 341 " (cutoff:3.500A) Processing helix chain 'J' and resid 362 through 371 Processing helix chain 'J' and resid 387 through 407 Processing helix chain 'J' and resid 418 through 429 removed outlier: 4.218A pdb=" N CYS J 423 " --> pdb=" O ALA J 419 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE J 424 " --> pdb=" O LEU J 420 " (cutoff:3.500A) Proline residue: J 425 - end of helix removed outlier: 3.945A pdb=" N SER J 429 " --> pdb=" O PRO J 425 " (cutoff:3.500A) Processing helix chain 'J' and resid 435 through 458 removed outlier: 4.533A pdb=" N LYS J 449 " --> pdb=" O LYS J 445 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE J 450 " --> pdb=" O ARG J 446 " (cutoff:3.500A) Proline residue: J 451 - end of helix Processing helix chain 'J' and resid 463 through 471 Processing helix chain 'J' and resid 498 through 517 removed outlier: 3.558A pdb=" N LEU J 514 " --> pdb=" O GLY J 510 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR J 517 " --> pdb=" O SER J 513 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 30 removed outlier: 3.767A pdb=" N VAL I 27 " --> pdb=" O LEU I 23 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL I 29 " --> pdb=" O ASP I 25 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N THR I 30 " --> pdb=" O ALA I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 59 Processing helix chain 'I' and resid 65 through 85 removed outlier: 3.700A pdb=" N VAL I 77 " --> pdb=" O LEU I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 103 Processing helix chain 'I' and resid 113 through 134 removed outlier: 3.527A pdb=" N GLU I 130 " --> pdb=" O ALA I 126 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS I 132 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS I 133 " --> pdb=" O ALA I 129 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 151 removed outlier: 3.613A pdb=" N ALA I 145 " --> pdb=" O PRO I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 167 Processing helix chain 'I' and resid 230 through 243 Proline residue: I 235 - end of helix Processing helix chain 'I' and resid 256 through 267 Processing helix chain 'I' and resid 283 through 296 removed outlier: 3.914A pdb=" N ASN I 287 " --> pdb=" O ASP I 283 " (cutoff:3.500A) Processing helix chain 'I' and resid 340 through 356 removed outlier: 3.828A pdb=" N LYS I 345 " --> pdb=" O ALA I 341 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 371 Processing helix chain 'I' and resid 387 through 407 Processing helix chain 'I' and resid 418 through 429 removed outlier: 4.170A pdb=" N CYS I 423 " --> pdb=" O ALA I 419 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE I 424 " --> pdb=" O LEU I 420 " (cutoff:3.500A) Proline residue: I 425 - end of helix removed outlier: 3.949A pdb=" N SER I 429 " --> pdb=" O PRO I 425 " (cutoff:3.500A) Processing helix chain 'I' and resid 435 through 458 removed outlier: 4.552A pdb=" N LYS I 449 " --> pdb=" O LYS I 445 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE I 450 " --> pdb=" O ARG I 446 " (cutoff:3.500A) Proline residue: I 451 - end of helix Processing helix chain 'I' and resid 463 through 471 Processing helix chain 'I' and resid 489 through 492 No H-bonds generated for 'chain 'I' and resid 489 through 492' Processing helix chain 'I' and resid 498 through 517 removed outlier: 3.543A pdb=" N LEU I 514 " --> pdb=" O GLY I 510 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR I 517 " --> pdb=" O SER I 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 30 removed outlier: 3.834A pdb=" N VAL D 27 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL D 29 " --> pdb=" O ASP D 25 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N THR D 30 " --> pdb=" O ALA D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'D' and resid 65 through 85 removed outlier: 3.745A pdb=" N VAL D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 103 Processing helix chain 'D' and resid 113 through 134 removed outlier: 3.528A pdb=" N GLU D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS D 133 " --> pdb=" O ALA D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 151 removed outlier: 3.603A pdb=" N ALA D 145 " --> pdb=" O PRO D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 167 Processing helix chain 'D' and resid 230 through 243 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 256 through 267 Processing helix chain 'D' and resid 283 through 296 removed outlier: 4.069A pdb=" N LYS D 290 " --> pdb=" O LYS D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 356 removed outlier: 3.812A pdb=" N LYS D 345 " --> pdb=" O ALA D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 373 Processing helix chain 'D' and resid 387 through 407 Processing helix chain 'D' and resid 418 through 429 removed outlier: 4.173A pdb=" N CYS D 423 " --> pdb=" O ALA D 419 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE D 424 " --> pdb=" O LEU D 420 " (cutoff:3.500A) Proline residue: D 425 - end of helix removed outlier: 3.874A pdb=" N SER D 429 " --> pdb=" O PRO D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 458 removed outlier: 4.577A pdb=" N LYS D 449 " --> pdb=" O LYS D 445 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE D 450 " --> pdb=" O ARG D 446 " (cutoff:3.500A) Proline residue: D 451 - end of helix Processing helix chain 'D' and resid 463 through 471 Processing helix chain 'D' and resid 489 through 492 No H-bonds generated for 'chain 'D' and resid 489 through 492' Processing helix chain 'D' and resid 498 through 517 removed outlier: 3.547A pdb=" N LEU D 514 " --> pdb=" O GLY D 510 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR D 517 " --> pdb=" O SER D 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 28 removed outlier: 3.781A pdb=" N VAL C 27 " --> pdb=" O LEU C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'C' and resid 65 through 85 removed outlier: 3.672A pdb=" N VAL C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 103 Processing helix chain 'C' and resid 113 through 134 removed outlier: 3.532A pdb=" N GLU C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS C 132 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 151 removed outlier: 3.615A pdb=" N ALA C 145 " --> pdb=" O PRO C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 167 Processing helix chain 'C' and resid 230 through 243 Proline residue: C 235 - end of helix Processing helix chain 'C' and resid 256 through 267 Processing helix chain 'C' and resid 283 through 296 removed outlier: 3.990A pdb=" N LYS C 290 " --> pdb=" O LYS C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 356 removed outlier: 3.849A pdb=" N LYS C 345 " --> pdb=" O ALA C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 371 Processing helix chain 'C' and resid 387 through 407 Processing helix chain 'C' and resid 418 through 429 removed outlier: 4.154A pdb=" N CYS C 423 " --> pdb=" O ALA C 419 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE C 424 " --> pdb=" O LEU C 420 " (cutoff:3.500A) Proline residue: C 425 - end of helix removed outlier: 3.956A pdb=" N SER C 429 " --> pdb=" O PRO C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 458 removed outlier: 4.592A pdb=" N LYS C 449 " --> pdb=" O LYS C 445 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE C 450 " --> pdb=" O ARG C 446 " (cutoff:3.500A) Proline residue: C 451 - end of helix Processing helix chain 'C' and resid 463 through 472 Processing helix chain 'C' and resid 498 through 517 removed outlier: 3.551A pdb=" N LEU C 514 " --> pdb=" O GLY C 510 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR C 517 " --> pdb=" O SER C 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 28 removed outlier: 3.818A pdb=" N VAL B 27 " --> pdb=" O LEU B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 65 through 85 removed outlier: 3.697A pdb=" N VAL B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 103 Processing helix chain 'B' and resid 113 through 134 removed outlier: 3.503A pdb=" N GLU B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS B 132 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 151 removed outlier: 3.750A pdb=" N ALA B 145 " --> pdb=" O PRO B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 167 Processing helix chain 'B' and resid 230 through 243 Proline residue: B 235 - end of helix Processing helix chain 'B' and resid 256 through 267 Processing helix chain 'B' and resid 283 through 296 Processing helix chain 'B' and resid 340 through 356 removed outlier: 3.704A pdb=" N LYS B 345 " --> pdb=" O ALA B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 373 Processing helix chain 'B' and resid 387 through 407 Processing helix chain 'B' and resid 418 through 429 removed outlier: 4.214A pdb=" N CYS B 423 " --> pdb=" O ALA B 419 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE B 424 " --> pdb=" O LEU B 420 " (cutoff:3.500A) Proline residue: B 425 - end of helix removed outlier: 3.961A pdb=" N SER B 429 " --> pdb=" O PRO B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 458 removed outlier: 4.632A pdb=" N LYS B 449 " --> pdb=" O LYS B 445 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE B 450 " --> pdb=" O ARG B 446 " (cutoff:3.500A) Proline residue: B 451 - end of helix Processing helix chain 'B' and resid 463 through 472 Processing helix chain 'B' and resid 489 through 492 No H-bonds generated for 'chain 'B' and resid 489 through 492' Processing helix chain 'B' and resid 498 through 517 removed outlier: 3.520A pdb=" N LEU B 514 " --> pdb=" O GLY B 510 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR B 517 " --> pdb=" O SER B 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 28 removed outlier: 3.721A pdb=" N VAL A 27 " --> pdb=" O LEU A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 65 through 85 removed outlier: 3.701A pdb=" N VAL A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 103 Processing helix chain 'A' and resid 113 through 134 removed outlier: 3.543A pdb=" N GLU A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS A 132 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 151 removed outlier: 3.660A pdb=" N ALA A 145 " --> pdb=" O PRO A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 167 Processing helix chain 'A' and resid 230 through 243 Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 256 through 267 Processing helix chain 'A' and resid 283 through 296 removed outlier: 4.769A pdb=" N LEU A 289 " --> pdb=" O LYS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 356 removed outlier: 3.835A pdb=" N LYS A 345 " --> pdb=" O ALA A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 371 Processing helix chain 'A' and resid 387 through 407 Processing helix chain 'A' and resid 418 through 429 removed outlier: 4.125A pdb=" N CYS A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE A 424 " --> pdb=" O LEU A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix removed outlier: 4.017A pdb=" N SER A 429 " --> pdb=" O PRO A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 458 removed outlier: 4.564A pdb=" N LYS A 449 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 463 through 471 Processing helix chain 'A' and resid 498 through 517 removed outlier: 3.558A pdb=" N LEU A 514 " --> pdb=" O GLY A 510 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR A 517 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 30 removed outlier: 3.805A pdb=" N VAL G 27 " --> pdb=" O LEU G 23 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL G 29 " --> pdb=" O ASP G 25 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N THR G 30 " --> pdb=" O ALA G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'G' and resid 65 through 85 removed outlier: 3.809A pdb=" N VAL G 77 " --> pdb=" O LEU G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 105 removed outlier: 3.838A pdb=" N GLU G 105 " --> pdb=" O LYS G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 131 removed outlier: 3.602A pdb=" N GLU G 130 " --> pdb=" O ALA G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 151 removed outlier: 3.539A pdb=" N ALA G 145 " --> pdb=" O PRO G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 167 Processing helix chain 'G' and resid 230 through 243 Proline residue: G 235 - end of helix Processing helix chain 'G' and resid 256 through 267 Processing helix chain 'G' and resid 283 through 296 removed outlier: 3.774A pdb=" N ASN G 287 " --> pdb=" O ASP G 283 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS G 290 " --> pdb=" O LYS G 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 340 through 356 removed outlier: 3.879A pdb=" N LYS G 345 " --> pdb=" O ALA G 341 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 371 Processing helix chain 'G' and resid 387 through 407 Processing helix chain 'G' and resid 418 through 429 removed outlier: 4.234A pdb=" N CYS G 423 " --> pdb=" O ALA G 419 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE G 424 " --> pdb=" O LEU G 420 " (cutoff:3.500A) Proline residue: G 425 - end of helix removed outlier: 3.904A pdb=" N SER G 429 " --> pdb=" O PRO G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 435 through 458 removed outlier: 4.574A pdb=" N LYS G 449 " --> pdb=" O LYS G 445 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE G 450 " --> pdb=" O ARG G 446 " (cutoff:3.500A) Proline residue: G 451 - end of helix Processing helix chain 'G' and resid 463 through 472 Processing helix chain 'G' and resid 498 through 517 removed outlier: 3.555A pdb=" N LEU G 514 " --> pdb=" O GLY G 510 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR G 517 " --> pdb=" O SER G 513 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 30 removed outlier: 3.744A pdb=" N VAL F 27 " --> pdb=" O LEU F 23 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL F 29 " --> pdb=" O ASP F 25 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N THR F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 59 Processing helix chain 'F' and resid 65 through 85 removed outlier: 3.751A pdb=" N VAL F 77 " --> pdb=" O LEU F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 103 Processing helix chain 'F' and resid 113 through 131 removed outlier: 3.549A pdb=" N GLU F 130 " --> pdb=" O ALA F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 151 removed outlier: 3.539A pdb=" N ALA F 145 " --> pdb=" O PRO F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 167 Processing helix chain 'F' and resid 230 through 243 Proline residue: F 235 - end of helix Processing helix chain 'F' and resid 256 through 267 Processing helix chain 'F' and resid 283 through 296 removed outlier: 4.012A pdb=" N ASN F 287 " --> pdb=" O ASP F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 317 No H-bonds generated for 'chain 'F' and resid 315 through 317' Processing helix chain 'F' and resid 340 through 356 removed outlier: 3.862A pdb=" N LYS F 345 " --> pdb=" O ALA F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 371 Processing helix chain 'F' and resid 387 through 407 Processing helix chain 'F' and resid 418 through 429 removed outlier: 4.199A pdb=" N CYS F 423 " --> pdb=" O ALA F 419 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE F 424 " --> pdb=" O LEU F 420 " (cutoff:3.500A) Proline residue: F 425 - end of helix removed outlier: 3.919A pdb=" N SER F 429 " --> pdb=" O PRO F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 458 removed outlier: 4.515A pdb=" N LYS F 449 " --> pdb=" O LYS F 445 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE F 450 " --> pdb=" O ARG F 446 " (cutoff:3.500A) Proline residue: F 451 - end of helix Processing helix chain 'F' and resid 463 through 472 Processing helix chain 'F' and resid 489 through 492 No H-bonds generated for 'chain 'F' and resid 489 through 492' Processing helix chain 'F' and resid 498 through 517 removed outlier: 4.000A pdb=" N THR F 517 " --> pdb=" O SER F 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 30 removed outlier: 3.793A pdb=" N VAL E 27 " --> pdb=" O LEU E 23 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL E 29 " --> pdb=" O ASP E 25 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N THR E 30 " --> pdb=" O ALA E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 59 Processing helix chain 'E' and resid 65 through 85 removed outlier: 3.744A pdb=" N VAL E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 103 Processing helix chain 'E' and resid 113 through 134 removed outlier: 3.502A pdb=" N GLU E 130 " --> pdb=" O ALA E 126 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS E 133 " --> pdb=" O ALA E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 151 removed outlier: 3.629A pdb=" N ALA E 145 " --> pdb=" O PRO E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 167 Processing helix chain 'E' and resid 230 through 243 Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 256 through 267 Processing helix chain 'E' and resid 283 through 296 removed outlier: 3.941A pdb=" N LYS E 290 " --> pdb=" O LYS E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 356 removed outlier: 3.771A pdb=" N LYS E 345 " --> pdb=" O ALA E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 373 Processing helix chain 'E' and resid 387 through 407 Processing helix chain 'E' and resid 418 through 429 removed outlier: 4.177A pdb=" N CYS E 423 " --> pdb=" O ALA E 419 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE E 424 " --> pdb=" O LEU E 420 " (cutoff:3.500A) Proline residue: E 425 - end of helix removed outlier: 3.956A pdb=" N SER E 429 " --> pdb=" O PRO E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 458 removed outlier: 4.621A pdb=" N LYS E 449 " --> pdb=" O LYS E 445 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE E 450 " --> pdb=" O ARG E 446 " (cutoff:3.500A) Proline residue: E 451 - end of helix Processing helix chain 'E' and resid 463 through 471 Processing helix chain 'E' and resid 498 through 517 removed outlier: 3.505A pdb=" N LEU E 514 " --> pdb=" O GLY E 510 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR E 517 " --> pdb=" O SER E 513 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'H' and resid 4 through 8 Processing sheet with id= B, first strand: chain 'H' and resid 38 through 40 Processing sheet with id= C, first strand: chain 'H' and resid 175 through 179 removed outlier: 6.595A pdb=" N ALA H 378 " --> pdb=" O THR H 176 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N LYS H 178 " --> pdb=" O ALA H 378 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU H 380 " --> pdb=" O LYS H 178 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 193 through 195 Processing sheet with id= E, first strand: chain 'H' and resid 319 through 321 Processing sheet with id= F, first strand: chain 'H' and resid 412 through 414 Processing sheet with id= G, first strand: chain 'H' and resid 477 through 480 Processing sheet with id= H, first strand: chain 'V' and resid 79 through 83 removed outlier: 8.918A pdb=" N ASP V 87 " --> pdb=" O ARG V 20 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ARG V 20 " --> pdb=" O ASP V 87 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLU V 19 " --> pdb=" O VAL V 46 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N VAL V 46 " --> pdb=" O GLU V 19 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '2' and resid 79 through 83 removed outlier: 8.908A pdb=" N ASP 2 87 " --> pdb=" O ARG 2 20 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ARG 2 20 " --> pdb=" O ASP 2 87 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLU 2 19 " --> pdb=" O VAL 2 46 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N VAL 2 46 " --> pdb=" O GLU 2 19 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '1' and resid 79 through 83 removed outlier: 8.912A pdb=" N ASP 1 87 " --> pdb=" O ARG 1 20 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ARG 1 20 " --> pdb=" O ASP 1 87 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLU 1 19 " --> pdb=" O VAL 1 46 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N VAL 1 46 " --> pdb=" O GLU 1 19 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'Z' and resid 79 through 83 removed outlier: 8.888A pdb=" N ASP Z 87 " --> pdb=" O ARG Z 20 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ARG Z 20 " --> pdb=" O ASP Z 87 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLU Z 19 " --> pdb=" O VAL Z 46 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL Z 46 " --> pdb=" O GLU Z 19 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'Y' and resid 79 through 83 removed outlier: 8.889A pdb=" N ASP Y 87 " --> pdb=" O ARG Y 20 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ARG Y 20 " --> pdb=" O ASP Y 87 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLU Y 19 " --> pdb=" O VAL Y 46 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N VAL Y 46 " --> pdb=" O GLU Y 19 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'X' and resid 79 through 83 removed outlier: 8.909A pdb=" N ASP X 87 " --> pdb=" O ARG X 20 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ARG X 20 " --> pdb=" O ASP X 87 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLU X 19 " --> pdb=" O VAL X 46 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N VAL X 46 " --> pdb=" O GLU X 19 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'W' and resid 79 through 83 removed outlier: 8.926A pdb=" N ASP W 87 " --> pdb=" O ARG W 20 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ARG W 20 " --> pdb=" O ASP W 87 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLU W 19 " --> pdb=" O VAL W 46 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N VAL W 46 " --> pdb=" O GLU W 19 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'R' and resid 79 through 83 removed outlier: 8.888A pdb=" N ASP R 87 " --> pdb=" O ARG R 20 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ARG R 20 " --> pdb=" O ASP R 87 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLU R 19 " --> pdb=" O VAL R 46 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N VAL R 46 " --> pdb=" O GLU R 19 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'Q' and resid 79 through 83 removed outlier: 8.919A pdb=" N ASP Q 87 " --> pdb=" O ARG Q 20 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ARG Q 20 " --> pdb=" O ASP Q 87 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLU Q 19 " --> pdb=" O VAL Q 46 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N VAL Q 46 " --> pdb=" O GLU Q 19 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'P' and resid 79 through 83 removed outlier: 8.911A pdb=" N ASP P 87 " --> pdb=" O ARG P 20 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ARG P 20 " --> pdb=" O ASP P 87 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU P 19 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N VAL P 46 " --> pdb=" O GLU P 19 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'O' and resid 79 through 83 removed outlier: 8.899A pdb=" N ASP O 87 " --> pdb=" O ARG O 20 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ARG O 20 " --> pdb=" O ASP O 87 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLU O 19 " --> pdb=" O VAL O 46 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N VAL O 46 " --> pdb=" O GLU O 19 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'U' and resid 79 through 83 removed outlier: 8.930A pdb=" N ASP U 87 " --> pdb=" O ARG U 20 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ARG U 20 " --> pdb=" O ASP U 87 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLU U 19 " --> pdb=" O VAL U 46 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N VAL U 46 " --> pdb=" O GLU U 19 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'T' and resid 79 through 83 removed outlier: 8.957A pdb=" N ASP T 87 " --> pdb=" O ARG T 20 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ARG T 20 " --> pdb=" O ASP T 87 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLU T 19 " --> pdb=" O VAL T 46 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL T 46 " --> pdb=" O GLU T 19 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'S' and resid 79 through 83 removed outlier: 8.938A pdb=" N ASP S 87 " --> pdb=" O ARG S 20 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ARG S 20 " --> pdb=" O ASP S 87 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU S 19 " --> pdb=" O VAL S 46 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL S 46 " --> pdb=" O GLU S 19 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'N' and resid 4 through 8 Processing sheet with id= W, first strand: chain 'N' and resid 38 through 40 Processing sheet with id= X, first strand: chain 'N' and resid 175 through 179 removed outlier: 6.696A pdb=" N ALA N 378 " --> pdb=" O THR N 176 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N LYS N 178 " --> pdb=" O ALA N 378 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU N 380 " --> pdb=" O LYS N 178 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'N' and resid 193 through 195 Processing sheet with id= Z, first strand: chain 'N' and resid 319 through 321 Processing sheet with id= AA, first strand: chain 'N' and resid 412 through 414 Processing sheet with id= AB, first strand: chain 'N' and resid 477 through 480 Processing sheet with id= AC, first strand: chain 'M' and resid 4 through 8 Processing sheet with id= AD, first strand: chain 'M' and resid 38 through 40 Processing sheet with id= AE, first strand: chain 'M' and resid 175 through 179 removed outlier: 6.576A pdb=" N ALA M 378 " --> pdb=" O THR M 176 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N LYS M 178 " --> pdb=" O ALA M 378 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU M 380 " --> pdb=" O LYS M 178 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'M' and resid 193 through 195 Processing sheet with id= AG, first strand: chain 'M' and resid 319 through 321 Processing sheet with id= AH, first strand: chain 'M' and resid 412 through 414 Processing sheet with id= AI, first strand: chain 'M' and resid 477 through 480 Processing sheet with id= AJ, first strand: chain 'L' and resid 4 through 8 Processing sheet with id= AK, first strand: chain 'L' and resid 38 through 40 Processing sheet with id= AL, first strand: chain 'L' and resid 175 through 178 removed outlier: 6.557A pdb=" N ALA L 378 " --> pdb=" O THR L 176 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N LYS L 178 " --> pdb=" O ALA L 378 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU L 380 " --> pdb=" O LYS L 178 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'L' and resid 193 through 195 Processing sheet with id= AN, first strand: chain 'L' and resid 319 through 321 Processing sheet with id= AO, first strand: chain 'L' and resid 412 through 414 Processing sheet with id= AP, first strand: chain 'L' and resid 477 through 480 Processing sheet with id= AQ, first strand: chain 'K' and resid 4 through 8 Processing sheet with id= AR, first strand: chain 'K' and resid 38 through 40 Processing sheet with id= AS, first strand: chain 'K' and resid 175 through 179 removed outlier: 6.647A pdb=" N ALA K 378 " --> pdb=" O THR K 176 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N LYS K 178 " --> pdb=" O ALA K 378 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU K 380 " --> pdb=" O LYS K 178 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'K' and resid 193 through 195 Processing sheet with id= AU, first strand: chain 'K' and resid 319 through 321 Processing sheet with id= AV, first strand: chain 'K' and resid 412 through 414 Processing sheet with id= AW, first strand: chain 'K' and resid 477 through 480 Processing sheet with id= AX, first strand: chain 'J' and resid 4 through 8 Processing sheet with id= AY, first strand: chain 'J' and resid 38 through 40 Processing sheet with id= AZ, first strand: chain 'J' and resid 175 through 179 removed outlier: 6.544A pdb=" N ALA J 378 " --> pdb=" O THR J 176 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N LYS J 178 " --> pdb=" O ALA J 378 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU J 380 " --> pdb=" O LYS J 178 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'J' and resid 193 through 195 Processing sheet with id= BB, first strand: chain 'J' and resid 319 through 321 Processing sheet with id= BC, first strand: chain 'J' and resid 412 through 414 Processing sheet with id= BD, first strand: chain 'J' and resid 477 through 480 Processing sheet with id= BE, first strand: chain 'I' and resid 4 through 8 Processing sheet with id= BF, first strand: chain 'I' and resid 38 through 40 Processing sheet with id= BG, first strand: chain 'I' and resid 175 through 179 removed outlier: 6.505A pdb=" N ALA I 378 " --> pdb=" O THR I 176 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LYS I 178 " --> pdb=" O ALA I 378 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU I 380 " --> pdb=" O LYS I 178 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'I' and resid 193 through 195 Processing sheet with id= BI, first strand: chain 'I' and resid 319 through 321 Processing sheet with id= BJ, first strand: chain 'I' and resid 412 through 414 Processing sheet with id= BK, first strand: chain 'I' and resid 477 through 480 Processing sheet with id= BL, first strand: chain 'D' and resid 4 through 8 Processing sheet with id= BM, first strand: chain 'D' and resid 38 through 40 Processing sheet with id= BN, first strand: chain 'D' and resid 175 through 179 removed outlier: 6.603A pdb=" N ALA D 378 " --> pdb=" O THR D 176 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LYS D 178 " --> pdb=" O ALA D 378 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU D 380 " --> pdb=" O LYS D 178 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'D' and resid 193 through 195 Processing sheet with id= BP, first strand: chain 'D' and resid 319 through 321 Processing sheet with id= BQ, first strand: chain 'D' and resid 412 through 414 Processing sheet with id= BR, first strand: chain 'D' and resid 477 through 480 Processing sheet with id= BS, first strand: chain 'C' and resid 4 through 8 Processing sheet with id= BT, first strand: chain 'C' and resid 38 through 40 Processing sheet with id= BU, first strand: chain 'C' and resid 175 through 179 removed outlier: 6.578A pdb=" N ALA C 378 " --> pdb=" O THR C 176 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N LYS C 178 " --> pdb=" O ALA C 378 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU C 380 " --> pdb=" O LYS C 178 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'C' and resid 193 through 195 Processing sheet with id= BW, first strand: chain 'C' and resid 319 through 321 Processing sheet with id= BX, first strand: chain 'C' and resid 412 through 414 Processing sheet with id= BY, first strand: chain 'C' and resid 477 through 480 Processing sheet with id= BZ, first strand: chain 'B' and resid 4 through 8 Processing sheet with id= CA, first strand: chain 'B' and resid 38 through 40 Processing sheet with id= CB, first strand: chain 'B' and resid 175 through 179 removed outlier: 6.614A pdb=" N ALA B 378 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LYS B 178 " --> pdb=" O ALA B 378 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LEU B 380 " --> pdb=" O LYS B 178 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'B' and resid 193 through 195 Processing sheet with id= CD, first strand: chain 'B' and resid 319 through 321 Processing sheet with id= CE, first strand: chain 'B' and resid 412 through 414 Processing sheet with id= CF, first strand: chain 'B' and resid 477 through 480 Processing sheet with id= CG, first strand: chain 'A' and resid 4 through 8 Processing sheet with id= CH, first strand: chain 'A' and resid 38 through 40 Processing sheet with id= CI, first strand: chain 'A' and resid 175 through 179 removed outlier: 6.562A pdb=" N ALA A 378 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LYS A 178 " --> pdb=" O ALA A 378 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU A 380 " --> pdb=" O LYS A 178 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 'A' and resid 193 through 195 Processing sheet with id= CK, first strand: chain 'A' and resid 319 through 321 Processing sheet with id= CL, first strand: chain 'A' and resid 412 through 414 Processing sheet with id= CM, first strand: chain 'A' and resid 477 through 480 Processing sheet with id= CN, first strand: chain 'G' and resid 4 through 8 Processing sheet with id= CO, first strand: chain 'G' and resid 38 through 40 Processing sheet with id= CP, first strand: chain 'G' and resid 175 through 179 removed outlier: 6.628A pdb=" N ALA G 378 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LYS G 178 " --> pdb=" O ALA G 378 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU G 380 " --> pdb=" O LYS G 178 " (cutoff:3.500A) Processing sheet with id= CQ, first strand: chain 'G' and resid 193 through 195 Processing sheet with id= CR, first strand: chain 'G' and resid 319 through 321 Processing sheet with id= CS, first strand: chain 'G' and resid 412 through 414 Processing sheet with id= CT, first strand: chain 'G' and resid 477 through 480 Processing sheet with id= CU, first strand: chain 'F' and resid 4 through 8 Processing sheet with id= CV, first strand: chain 'F' and resid 38 through 40 Processing sheet with id= CW, first strand: chain 'F' and resid 175 through 179 removed outlier: 6.551A pdb=" N ALA F 378 " --> pdb=" O THR F 176 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LYS F 178 " --> pdb=" O ALA F 378 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU F 380 " --> pdb=" O LYS F 178 " (cutoff:3.500A) Processing sheet with id= CX, first strand: chain 'F' and resid 193 through 195 Processing sheet with id= CY, first strand: chain 'F' and resid 319 through 321 Processing sheet with id= CZ, first strand: chain 'F' and resid 412 through 414 Processing sheet with id= DA, first strand: chain 'F' and resid 477 through 480 Processing sheet with id= DB, first strand: chain 'E' and resid 4 through 8 Processing sheet with id= DC, first strand: chain 'E' and resid 38 through 40 Processing sheet with id= DD, first strand: chain 'E' and resid 175 through 179 removed outlier: 6.646A pdb=" N ALA E 378 " --> pdb=" O THR E 176 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LYS E 178 " --> pdb=" O ALA E 378 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU E 380 " --> pdb=" O LYS E 178 " (cutoff:3.500A) Processing sheet with id= DE, first strand: chain 'E' and resid 193 through 195 Processing sheet with id= DF, first strand: chain 'E' and resid 319 through 321 Processing sheet with id= DG, first strand: chain 'E' and resid 412 through 414 Processing sheet with id= DH, first strand: chain 'E' and resid 477 through 480 3129 hydrogen bonds defined for protein. 8853 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: 28.63 Time building geometry restraints manager: 24.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 2954 1.03 - 1.22: 0 1.22 - 1.42: 24903 1.42 - 1.61: 41373 1.61 - 1.81: 420 Bond restraints: 69650 Sorted by residual: bond pdb=" C1' ADP C 601 " pdb=" C2' ADP C 601 " ideal model delta sigma weight residual 1.524 1.298 0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C1' ADP H 601 " pdb=" C2' ADP H 601 " ideal model delta sigma weight residual 1.524 1.298 0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C1' ADP F 601 " pdb=" C2' ADP F 601 " ideal model delta sigma weight residual 1.524 1.298 0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C1' ADP G 601 " pdb=" C2' ADP G 601 " ideal model delta sigma weight residual 1.524 1.298 0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C1' ADP I 601 " pdb=" C2' ADP I 601 " ideal model delta sigma weight residual 1.524 1.298 0.226 2.00e-02 2.50e+03 1.27e+02 ... (remaining 69645 not shown) Histogram of bond angle deviations from ideal: 80.32 - 91.11: 42 91.11 - 101.90: 173 101.90 - 112.69: 44288 112.69 - 123.49: 50747 123.49 - 134.28: 1546 Bond angle restraints: 96796 Sorted by residual: angle pdb=" CG2 ILE A 494 " pdb=" CB ILE A 494 " pdb=" HB ILE A 494 " ideal model delta sigma weight residual 109.00 80.32 28.68 3.00e+00 1.11e-01 9.14e+01 angle pdb=" CG2 ILE K 494 " pdb=" CB ILE K 494 " pdb=" HB ILE K 494 " ideal model delta sigma weight residual 109.00 80.32 28.68 3.00e+00 1.11e-01 9.14e+01 angle pdb=" CG2 ILE H 494 " pdb=" CB ILE H 494 " pdb=" HB ILE H 494 " ideal model delta sigma weight residual 109.00 80.34 28.66 3.00e+00 1.11e-01 9.12e+01 angle pdb=" CG2 ILE N 494 " pdb=" CB ILE N 494 " pdb=" HB ILE N 494 " ideal model delta sigma weight residual 109.00 80.35 28.65 3.00e+00 1.11e-01 9.12e+01 angle pdb=" CG2 ILE D 494 " pdb=" CB ILE D 494 " pdb=" HB ILE D 494 " ideal model delta sigma weight residual 109.00 80.41 28.59 3.00e+00 1.11e-01 9.08e+01 ... (remaining 96791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.28: 41872 33.28 - 66.56: 226 66.56 - 99.84: 49 99.84 - 133.12: 17 133.12 - 166.39: 18 Dihedral angle restraints: 42182 sinusoidal: 17360 harmonic: 24822 Sorted by residual: dihedral pdb=" CA LYS G 268 " pdb=" C LYS G 268 " pdb=" N VAL G 269 " pdb=" CA VAL G 269 " ideal model delta harmonic sigma weight residual 180.00 -132.25 -47.75 0 5.00e+00 4.00e-02 9.12e+01 dihedral pdb=" CA LYS I 268 " pdb=" C LYS I 268 " pdb=" N VAL I 269 " pdb=" CA VAL I 269 " ideal model delta harmonic sigma weight residual -180.00 -132.35 -47.65 0 5.00e+00 4.00e-02 9.08e+01 dihedral pdb=" CA LYS J 268 " pdb=" C LYS J 268 " pdb=" N VAL J 269 " pdb=" CA VAL J 269 " ideal model delta harmonic sigma weight residual -180.00 -134.34 -45.66 0 5.00e+00 4.00e-02 8.34e+01 ... (remaining 42179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.300: 10836 0.300 - 0.600: 0 0.600 - 0.900: 0 0.900 - 1.200: 0 1.200 - 1.501: 14 Chirality restraints: 10850 Sorted by residual: chirality pdb=" CB ILE I 494 " pdb=" CA ILE I 494 " pdb=" CG1 ILE I 494 " pdb=" CG2 ILE I 494 " both_signs ideal model delta sigma weight residual False 2.64 1.14 1.50 2.00e-01 2.50e+01 5.63e+01 chirality pdb=" CB ILE F 494 " pdb=" CA ILE F 494 " pdb=" CG1 ILE F 494 " pdb=" CG2 ILE F 494 " both_signs ideal model delta sigma weight residual False 2.64 1.15 1.50 2.00e-01 2.50e+01 5.60e+01 chirality pdb=" CB ILE M 494 " pdb=" CA ILE M 494 " pdb=" CG1 ILE M 494 " pdb=" CG2 ILE M 494 " both_signs ideal model delta sigma weight residual False 2.64 1.17 1.48 2.00e-01 2.50e+01 5.47e+01 ... (remaining 10847 not shown) Planarity restraints: 11774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA H 278 " -0.038 5.00e-02 4.00e+02 5.79e-02 5.36e+00 pdb=" N PRO H 279 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO H 279 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO H 279 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE K 450 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO K 451 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO K 451 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO K 451 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 278 " -0.034 5.00e-02 4.00e+02 5.12e-02 4.19e+00 pdb=" N PRO G 279 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO G 279 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 279 " -0.028 5.00e-02 4.00e+02 ... (remaining 11771 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 910 2.25 - 2.84: 31947 2.84 - 3.43: 89266 3.43 - 4.01: 136610 4.01 - 4.60: 206259 Nonbonded interactions: 464992 Sorted by model distance: nonbonded pdb=" H GLY A 32 " pdb=" O1A ADP A 601 " model vdw 1.663 1.850 nonbonded pdb=" H GLY M 32 " pdb=" O2A ADP M 601 " model vdw 1.693 1.850 nonbonded pdb=" H GLY B 32 " pdb=" O1A ADP B 601 " model vdw 1.693 1.850 nonbonded pdb=" H GLY J 32 " pdb=" O2A ADP J 601 " model vdw 1.694 1.850 nonbonded pdb=" H GLY K 32 " pdb=" O2A ADP K 601 " model vdw 1.694 1.850 ... (remaining 464987 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 '1' selection = chain '2' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.280 Extract box with map and model: 11.540 Check model and map are aligned: 0.750 Set scattering table: 0.480 Process input model: 142.440 Find NCS groups from input model: 3.660 Set up NCS constraints: 0.580 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 166.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 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 : 0.007 0.226 66696 Z= 0.462 Angle : 0.808 15.333 89978 Z= 0.408 Chirality : 0.069 1.501 10850 Planarity : 0.004 0.058 11522 Dihedral : 10.507 166.395 25368 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 27.58 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.51 % Favored : 92.27 % Rotamer: Outliers : 0.18 % Allowed : 1.36 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.08), residues: 8736 helix: -1.13 (0.07), residues: 3892 sheet: -2.38 (0.14), residues: 980 loop : -2.64 (0.08), residues: 3864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 44 HIS 0.002 0.001 HIS B 316 PHE 0.023 0.002 PHE B 104 TYR 0.015 0.002 TYR Y 88 ARG 0.005 0.001 ARG O 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1709 residues out of total 7112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1696 time to evaluate : 6.469 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: H 79 ASN cc_start: 0.8144 (t0) cc_final: 0.7920 (t0) REVERT: H 83 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7509 (mt-10) REVERT: H 121 MET cc_start: 0.8533 (mmm) cc_final: 0.8306 (mmm) REVERT: H 183 LEU cc_start: 0.8525 (mm) cc_final: 0.8308 (tp) REVERT: H 190 ILE cc_start: 0.8645 (mm) cc_final: 0.8384 (mt) REVERT: H 344 GLU cc_start: 0.8121 (tp30) cc_final: 0.7812 (tp30) REVERT: V 24 GLU cc_start: 0.7649 (tp30) cc_final: 0.7447 (tp30) REVERT: 2 24 GLU cc_start: 0.7579 (tp30) cc_final: 0.7232 (tp30) REVERT: 2 33 LEU cc_start: 0.8985 (mp) cc_final: 0.8690 (mp) REVERT: 1 24 GLU cc_start: 0.7607 (tp30) cc_final: 0.7328 (tp30) REVERT: 1 25 THR cc_start: 0.8181 (p) cc_final: 0.7885 (p) REVERT: 1 26 VAL cc_start: 0.7490 (m) cc_final: 0.7236 (p) REVERT: Z 24 GLU cc_start: 0.7648 (tp30) cc_final: 0.7409 (tp30) REVERT: Y 24 GLU cc_start: 0.7672 (tp30) cc_final: 0.7276 (tp30) REVERT: X 24 GLU cc_start: 0.7454 (tp30) cc_final: 0.7248 (tp30) REVERT: X 69 ASP cc_start: 0.7522 (m-30) cc_final: 0.7215 (m-30) REVERT: W 53 SER cc_start: 0.8237 (t) cc_final: 0.8002 (p) REVERT: R 24 GLU cc_start: 0.7554 (tp30) cc_final: 0.7305 (tp30) REVERT: R 85 ASP cc_start: 0.7954 (m-30) cc_final: 0.7676 (m-30) REVERT: Q 24 GLU cc_start: 0.7752 (tp30) cc_final: 0.7508 (tp30) REVERT: Q 25 THR cc_start: 0.8195 (p) cc_final: 0.7904 (p) REVERT: Q 42 LEU cc_start: 0.8509 (mt) cc_final: 0.8181 (mt) REVERT: Q 43 GLN cc_start: 0.8346 (mp10) cc_final: 0.8094 (mp10) REVERT: Q 80 LYS cc_start: 0.9168 (tttt) cc_final: 0.8888 (tttm) REVERT: Q 87 ASP cc_start: 0.8353 (m-30) cc_final: 0.8051 (m-30) REVERT: P 10 LEU cc_start: 0.8437 (tp) cc_final: 0.8184 (mt) REVERT: U 66 LYS cc_start: 0.8476 (pttp) cc_final: 0.8239 (pttp) REVERT: U 69 ASP cc_start: 0.7369 (m-30) cc_final: 0.7090 (m-30) REVERT: T 24 GLU cc_start: 0.7530 (tp30) cc_final: 0.7287 (tp30) REVERT: S 24 GLU cc_start: 0.7691 (tp30) cc_final: 0.7430 (tp30) REVERT: S 25 THR cc_start: 0.8165 (p) cc_final: 0.7951 (p) REVERT: S 85 ASP cc_start: 0.8106 (m-30) cc_final: 0.7893 (m-30) REVERT: N 79 ASN cc_start: 0.8288 (t0) cc_final: 0.7979 (t0) REVERT: N 121 MET cc_start: 0.8593 (mmm) cc_final: 0.8263 (mmm) REVERT: N 183 LEU cc_start: 0.8484 (mm) cc_final: 0.8241 (tp) REVERT: N 190 ILE cc_start: 0.8599 (mm) cc_final: 0.8384 (mt) REVERT: N 342 GLN cc_start: 0.8116 (tt0) cc_final: 0.7791 (tm-30) REVERT: N 361 TYR cc_start: 0.7710 (t80) cc_final: 0.7460 (t80) REVERT: M 79 ASN cc_start: 0.8130 (t0) cc_final: 0.7865 (t0) REVERT: M 183 LEU cc_start: 0.8492 (mm) cc_final: 0.8276 (tp) REVERT: M 190 ILE cc_start: 0.8753 (mm) cc_final: 0.8534 (mt) REVERT: M 292 MET cc_start: 0.8725 (mtp) cc_final: 0.8291 (ttm) REVERT: M 344 GLU cc_start: 0.8158 (tp30) cc_final: 0.7693 (tp30) REVERT: L 183 LEU cc_start: 0.8409 (mm) cc_final: 0.8174 (tp) REVERT: L 190 ILE cc_start: 0.8681 (mm) cc_final: 0.8363 (mt) REVERT: L 292 MET cc_start: 0.8825 (mtp) cc_final: 0.8529 (ttm) REVERT: L 344 GLU cc_start: 0.8342 (tp30) cc_final: 0.8072 (tp30) REVERT: K 183 LEU cc_start: 0.8359 (mm) cc_final: 0.7959 (tp) REVERT: K 344 GLU cc_start: 0.8052 (tp30) cc_final: 0.7820 (tp30) REVERT: J 79 ASN cc_start: 0.8157 (t0) cc_final: 0.7865 (t0) REVERT: J 292 MET cc_start: 0.8760 (mtp) cc_final: 0.8517 (mtm) REVERT: J 344 GLU cc_start: 0.8241 (tp30) cc_final: 0.7922 (tp30) REVERT: I 168 LYS cc_start: 0.8537 (mttp) cc_final: 0.8305 (mtpp) REVERT: I 183 LEU cc_start: 0.8387 (mm) cc_final: 0.8104 (tp) REVERT: I 344 GLU cc_start: 0.8248 (tp30) cc_final: 0.7971 (tp30) REVERT: D 79 ASN cc_start: 0.8296 (t0) cc_final: 0.8001 (t0) REVERT: D 121 MET cc_start: 0.8584 (mmm) cc_final: 0.8310 (mmm) REVERT: D 183 LEU cc_start: 0.8454 (mm) cc_final: 0.8100 (tp) REVERT: D 190 ILE cc_start: 0.8594 (mm) cc_final: 0.8389 (mt) REVERT: D 342 GLN cc_start: 0.8338 (tt0) cc_final: 0.7949 (tm-30) REVERT: D 386 SER cc_start: 0.9133 (p) cc_final: 0.8910 (t) REVERT: C 79 ASN cc_start: 0.8120 (t0) cc_final: 0.7872 (t0) REVERT: C 183 LEU cc_start: 0.8473 (mm) cc_final: 0.8217 (tp) REVERT: C 190 ILE cc_start: 0.8741 (mm) cc_final: 0.8537 (mt) REVERT: C 264 LEU cc_start: 0.9105 (tp) cc_final: 0.8862 (tt) REVERT: C 292 MET cc_start: 0.8725 (mtp) cc_final: 0.8521 (mtm) REVERT: C 332 MET cc_start: 0.7629 (ttm) cc_final: 0.7320 (tpp) REVERT: C 342 GLN cc_start: 0.8290 (tt0) cc_final: 0.8026 (tm-30) REVERT: C 344 GLU cc_start: 0.8138 (tp30) cc_final: 0.7690 (tp30) REVERT: B 183 LEU cc_start: 0.8410 (mm) cc_final: 0.8118 (tp) REVERT: B 190 ILE cc_start: 0.8640 (mm) cc_final: 0.8316 (mt) REVERT: B 264 LEU cc_start: 0.8987 (tp) cc_final: 0.8753 (tt) REVERT: B 332 MET cc_start: 0.7654 (ttm) cc_final: 0.7221 (ttm) REVERT: B 342 GLN cc_start: 0.8194 (tt0) cc_final: 0.7926 (tm-30) REVERT: A 183 LEU cc_start: 0.8390 (mm) cc_final: 0.8005 (tp) REVERT: A 342 GLN cc_start: 0.8226 (tt0) cc_final: 0.7961 (tm-30) REVERT: A 344 GLU cc_start: 0.8108 (tp30) cc_final: 0.7510 (tp30) REVERT: G 79 ASN cc_start: 0.8142 (t0) cc_final: 0.7937 (t0) REVERT: G 121 MET cc_start: 0.8418 (mmm) cc_final: 0.8205 (mmt) REVERT: G 183 LEU cc_start: 0.8582 (mm) cc_final: 0.8144 (tp) REVERT: G 344 GLU cc_start: 0.8219 (tp30) cc_final: 0.7977 (tp30) REVERT: F 307 THR cc_start: 0.8642 (m) cc_final: 0.8294 (p) REVERT: F 344 GLU cc_start: 0.8114 (tp30) cc_final: 0.7672 (tp30) REVERT: E 121 MET cc_start: 0.8605 (mmm) cc_final: 0.8392 (mmm) REVERT: E 183 LEU cc_start: 0.8546 (mm) cc_final: 0.8229 (tp) REVERT: E 342 GLN cc_start: 0.8193 (tt0) cc_final: 0.7875 (tm-30) REVERT: E 386 SER cc_start: 0.9097 (p) cc_final: 0.8744 (t) outliers start: 13 outliers final: 0 residues processed: 1709 average time/residue: 0.7078 time to fit residues: 1974.7541 Evaluate side-chains 885 residues out of total 7112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 885 time to evaluate : 6.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 732 optimal weight: 9.9990 chunk 657 optimal weight: 0.9990 chunk 365 optimal weight: 8.9990 chunk 224 optimal weight: 8.9990 chunk 443 optimal weight: 0.7980 chunk 351 optimal weight: 0.9980 chunk 680 optimal weight: 0.9990 chunk 263 optimal weight: 4.9990 chunk 413 optimal weight: 5.9990 chunk 506 optimal weight: 2.9990 chunk 788 optimal weight: 0.0050 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 134 GLN ** H 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 367 ASN ** 2 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 4 GLN ** X 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 231 GLN N 284 ASN N 367 ASN M 134 GLN M 284 ASN M 288 GLN M 367 ASN L 80 ASN ** L 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 288 GLN L 367 ASN K 79 ASN K 134 GLN K 243 HIS ** K 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 367 ASN J 75 GLN J 80 ASN J 134 GLN ** J 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 367 ASN I 243 HIS I 284 ASN I 367 ASN D 80 ASN ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 367 ASN C 134 GLN C 284 ASN C 288 GLN C 367 ASN B 80 ASN B 284 ASN B 288 GLN B 367 ASN A 75 GLN A 79 ASN A 134 GLN A 243 HIS A 367 ASN G 80 ASN G 134 GLN G 243 HIS ** G 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 314 GLN ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 367 ASN E 80 ASN E 231 GLN E 284 ASN E 367 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 66696 Z= 0.133 Angle : 0.560 15.406 89978 Z= 0.273 Chirality : 0.071 1.638 10850 Planarity : 0.003 0.053 11522 Dihedral : 8.976 176.643 9338 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 36.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.14 % Favored : 94.69 % Rotamer: Outliers : 1.32 % Allowed : 7.97 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.31 (0.09), residues: 8736 helix: 0.44 (0.08), residues: 3892 sheet: -1.98 (0.15), residues: 980 loop : -1.93 (0.09), residues: 3864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP I 44 HIS 0.002 0.001 HIS N 316 PHE 0.024 0.001 PHE F 281 TYR 0.010 0.001 TYR H 66 ARG 0.007 0.000 ARG L 405 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1059 residues out of total 7112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 965 time to evaluate : 5.792 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: H 79 ASN cc_start: 0.8087 (t0) cc_final: 0.7852 (t0) REVERT: H 83 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7428 (mt-10) REVERT: H 121 MET cc_start: 0.8529 (mmm) cc_final: 0.8193 (mmm) REVERT: H 183 LEU cc_start: 0.8526 (mm) cc_final: 0.8294 (tp) REVERT: H 190 ILE cc_start: 0.8591 (mm) cc_final: 0.8374 (mt) REVERT: H 344 GLU cc_start: 0.8105 (tp30) cc_final: 0.7854 (tp30) REVERT: V 24 GLU cc_start: 0.7550 (tp30) cc_final: 0.7286 (tp30) REVERT: V 26 VAL cc_start: 0.7729 (OUTLIER) cc_final: 0.7284 (t) REVERT: V 69 ASP cc_start: 0.7476 (m-30) cc_final: 0.7205 (m-30) REVERT: 2 24 GLU cc_start: 0.7454 (tp30) cc_final: 0.7098 (tp30) REVERT: 2 26 VAL cc_start: 0.7808 (p) cc_final: 0.7606 (t) REVERT: 2 33 LEU cc_start: 0.9033 (mp) cc_final: 0.8824 (mp) REVERT: 2 69 ASP cc_start: 0.7826 (m-30) cc_final: 0.7552 (m-30) REVERT: 2 86 LYS cc_start: 0.7952 (mtpt) cc_final: 0.7573 (tttt) REVERT: 1 80 LYS cc_start: 0.9097 (tttm) cc_final: 0.8206 (tttm) REVERT: Z 24 GLU cc_start: 0.7589 (tp30) cc_final: 0.7381 (tp30) REVERT: Z 26 VAL cc_start: 0.7771 (OUTLIER) cc_final: 0.7371 (t) REVERT: Z 33 LEU cc_start: 0.8987 (mp) cc_final: 0.8756 (mp) REVERT: Z 80 LYS cc_start: 0.8973 (tttm) cc_final: 0.8256 (tptp) REVERT: Z 86 LYS cc_start: 0.7963 (mtpt) cc_final: 0.7641 (tttt) REVERT: Y 24 GLU cc_start: 0.7614 (tp30) cc_final: 0.7228 (tp30) REVERT: Y 32 MET cc_start: 0.7992 (ptm) cc_final: 0.7768 (ptp) REVERT: Y 80 LYS cc_start: 0.9108 (tttp) cc_final: 0.8476 (tttp) REVERT: X 24 GLU cc_start: 0.7246 (tp30) cc_final: 0.6983 (tp30) REVERT: X 80 LYS cc_start: 0.8914 (tttp) cc_final: 0.8303 (tttm) REVERT: X 86 LYS cc_start: 0.8008 (mtpt) cc_final: 0.7485 (tttt) REVERT: W 43 GLN cc_start: 0.8289 (mp10) cc_final: 0.8085 (mp10) REVERT: R 24 GLU cc_start: 0.7413 (tp30) cc_final: 0.7042 (tp30) REVERT: R 33 LEU cc_start: 0.9104 (mp) cc_final: 0.8821 (mp) REVERT: Q 26 VAL cc_start: 0.7531 (OUTLIER) cc_final: 0.7219 (t) REVERT: Q 42 LEU cc_start: 0.8441 (mt) cc_final: 0.8193 (mt) REVERT: Q 43 GLN cc_start: 0.8320 (mp10) cc_final: 0.8041 (mp10) REVERT: P 10 LEU cc_start: 0.8466 (tp) cc_final: 0.8225 (mt) REVERT: P 43 GLN cc_start: 0.8237 (mp10) cc_final: 0.7966 (mp10) REVERT: U 69 ASP cc_start: 0.7411 (m-30) cc_final: 0.7156 (m-30) REVERT: T 24 GLU cc_start: 0.7597 (tp30) cc_final: 0.7346 (tp30) REVERT: T 26 VAL cc_start: 0.8016 (p) cc_final: 0.7706 (t) REVERT: T 69 ASP cc_start: 0.7345 (m-30) cc_final: 0.7103 (m-30) REVERT: T 86 LYS cc_start: 0.7976 (mtpt) cc_final: 0.7737 (tttt) REVERT: S 4 GLN cc_start: 0.8359 (tt0) cc_final: 0.8149 (tt0) REVERT: S 26 VAL cc_start: 0.7640 (OUTLIER) cc_final: 0.7348 (t) REVERT: N 79 ASN cc_start: 0.8184 (t0) cc_final: 0.7898 (t0) REVERT: N 121 MET cc_start: 0.8556 (mmm) cc_final: 0.8353 (mmm) REVERT: N 183 LEU cc_start: 0.8471 (mm) cc_final: 0.8219 (tp) REVERT: N 342 GLN cc_start: 0.8145 (tt0) cc_final: 0.7814 (tm-30) REVERT: N 361 TYR cc_start: 0.7810 (t80) cc_final: 0.7532 (t80) REVERT: M 183 LEU cc_start: 0.8444 (mm) cc_final: 0.8234 (tp) REVERT: M 190 ILE cc_start: 0.8720 (mm) cc_final: 0.8460 (mt) REVERT: M 214 GLU cc_start: 0.8630 (tt0) cc_final: 0.8404 (mt-10) REVERT: M 292 MET cc_start: 0.8692 (mtp) cc_final: 0.8322 (ttm) REVERT: M 332 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7386 (tpp) REVERT: M 344 GLU cc_start: 0.8100 (tp30) cc_final: 0.7672 (tp30) REVERT: L 183 LEU cc_start: 0.8326 (mm) cc_final: 0.8062 (tp) REVERT: L 190 ILE cc_start: 0.8663 (mm) cc_final: 0.8359 (mt) REVERT: L 292 MET cc_start: 0.8719 (mtp) cc_final: 0.8449 (ttm) REVERT: L 344 GLU cc_start: 0.8322 (tp30) cc_final: 0.8037 (tp30) REVERT: L 482 MET cc_start: 0.8408 (mmt) cc_final: 0.8145 (tpt) REVERT: K 183 LEU cc_start: 0.8347 (mm) cc_final: 0.7963 (tp) REVERT: K 332 MET cc_start: 0.8066 (mtp) cc_final: 0.7792 (tpp) REVERT: K 342 GLN cc_start: 0.8245 (tt0) cc_final: 0.7944 (tm-30) REVERT: J 344 GLU cc_start: 0.8232 (tp30) cc_final: 0.7704 (tp30) REVERT: I 121 MET cc_start: 0.8547 (mmm) cc_final: 0.8279 (mmm) REVERT: I 168 LYS cc_start: 0.8526 (mttp) cc_final: 0.8312 (mtpp) REVERT: I 183 LEU cc_start: 0.8409 (mm) cc_final: 0.8093 (tp) REVERT: I 332 MET cc_start: 0.8083 (mtp) cc_final: 0.7594 (tpp) REVERT: I 344 GLU cc_start: 0.8222 (tp30) cc_final: 0.7977 (tp30) REVERT: I 352 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7115 (pt0) REVERT: I 394 LYS cc_start: 0.8571 (ttpt) cc_final: 0.8214 (ttpp) REVERT: D 79 ASN cc_start: 0.8193 (t0) cc_final: 0.7898 (t0) REVERT: D 183 LEU cc_start: 0.8503 (mm) cc_final: 0.8142 (tp) REVERT: D 332 MET cc_start: 0.7902 (mtp) cc_final: 0.7333 (tpp) REVERT: D 342 GLN cc_start: 0.8330 (tt0) cc_final: 0.8016 (tm-30) REVERT: C 183 LEU cc_start: 0.8468 (mm) cc_final: 0.8205 (tp) REVERT: C 190 ILE cc_start: 0.8707 (mm) cc_final: 0.8488 (mt) REVERT: C 344 GLU cc_start: 0.8127 (tp30) cc_final: 0.7713 (tp30) REVERT: C 394 LYS cc_start: 0.8614 (ttpt) cc_final: 0.8332 (ttpp) REVERT: B 183 LEU cc_start: 0.8457 (mm) cc_final: 0.8175 (tp) REVERT: B 190 ILE cc_start: 0.8620 (mm) cc_final: 0.8319 (mt) REVERT: B 405 ARG cc_start: 0.7747 (mtm180) cc_final: 0.7489 (mtm-85) REVERT: A 183 LEU cc_start: 0.8349 (mm) cc_final: 0.7957 (tp) REVERT: A 342 GLN cc_start: 0.8223 (tt0) cc_final: 0.7922 (tm-30) REVERT: A 344 GLU cc_start: 0.8055 (tp30) cc_final: 0.7537 (tp30) REVERT: A 352 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7247 (pt0) REVERT: A 394 LYS cc_start: 0.8620 (ttpt) cc_final: 0.8291 (ttpp) REVERT: G 183 LEU cc_start: 0.8601 (mm) cc_final: 0.8129 (tp) REVERT: G 344 GLU cc_start: 0.8180 (tp30) cc_final: 0.7952 (tp30) REVERT: G 394 LYS cc_start: 0.8681 (ttpt) cc_final: 0.8461 (ttpp) REVERT: F 121 MET cc_start: 0.8592 (mmm) cc_final: 0.8306 (mmm) REVERT: F 190 ILE cc_start: 0.8620 (mm) cc_final: 0.8244 (mt) REVERT: F 307 THR cc_start: 0.8658 (m) cc_final: 0.8358 (p) REVERT: F 332 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.7168 (tpp) REVERT: F 344 GLU cc_start: 0.8048 (tp30) cc_final: 0.7664 (tp30) REVERT: E 121 MET cc_start: 0.8533 (mmm) cc_final: 0.8247 (mmm) REVERT: E 183 LEU cc_start: 0.8560 (mm) cc_final: 0.8246 (tp) outliers start: 94 outliers final: 71 residues processed: 1039 average time/residue: 0.6803 time to fit residues: 1175.6939 Evaluate side-chains 887 residues out of total 7112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 810 time to evaluate : 5.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 230 ILE Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain V residue 26 VAL Chi-restraints excluded: chain V residue 64 SER Chi-restraints excluded: chain Z residue 13 PHE Chi-restraints excluded: chain Z residue 26 VAL Chi-restraints excluded: chain X residue 13 PHE Chi-restraints excluded: chain X residue 72 LEU Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain Q residue 26 VAL Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain T residue 10 LEU Chi-restraints excluded: chain S residue 26 VAL Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 230 ILE Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 370 LEU Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 195 PHE Chi-restraints excluded: chain M residue 250 ILE Chi-restraints excluded: chain M residue 332 MET Chi-restraints excluded: chain M residue 366 LEU Chi-restraints excluded: chain L residue 185 ASP Chi-restraints excluded: chain L residue 195 PHE Chi-restraints excluded: chain L residue 230 ILE Chi-restraints excluded: chain L residue 250 ILE Chi-restraints excluded: chain L residue 374 SER Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 121 MET Chi-restraints excluded: chain K residue 230 ILE Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 366 LEU Chi-restraints excluded: chain K residue 370 LEU Chi-restraints excluded: chain K residue 374 SER Chi-restraints excluded: chain J residue 195 PHE Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain J residue 230 ILE Chi-restraints excluded: chain J residue 289 LEU Chi-restraints excluded: chain J residue 370 LEU Chi-restraints excluded: chain J residue 374 SER Chi-restraints excluded: chain I residue 181 LYS Chi-restraints excluded: chain I residue 195 PHE Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 370 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 525 ILE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 268 LYS Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 374 SER Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 195 PHE Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 370 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 438 optimal weight: 0.6980 chunk 244 optimal weight: 3.9990 chunk 656 optimal weight: 5.9990 chunk 536 optimal weight: 10.0000 chunk 217 optimal weight: 6.9990 chunk 789 optimal weight: 3.9990 chunk 853 optimal weight: 5.9990 chunk 703 optimal weight: 0.9980 chunk 783 optimal weight: 10.0000 chunk 269 optimal weight: 4.9990 chunk 633 optimal weight: 0.8980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 134 GLN ** H 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 4 GLN X 4 GLN ** W 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 231 GLN M 134 GLN ** L 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 ASN K 134 GLN ** K 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 75 GLN J 134 GLN ** J 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 288 GLN J 367 ASN ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN A 75 GLN A 134 GLN G 134 GLN G 231 GLN ** G 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 66696 Z= 0.246 Angle : 0.590 15.511 89978 Z= 0.290 Chirality : 0.071 1.622 10850 Planarity : 0.003 0.046 11522 Dihedral : 8.257 179.991 9338 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 33.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.58 % Favored : 93.28 % Rotamer: Outliers : 2.24 % Allowed : 9.15 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.09), residues: 8736 helix: 0.84 (0.09), residues: 3878 sheet: -1.82 (0.14), residues: 1232 loop : -1.88 (0.10), residues: 3626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 44 HIS 0.002 0.001 HIS K 316 PHE 0.024 0.002 PHE G 104 TYR 0.013 0.001 TYR G 66 ARG 0.003 0.000 ARG H 405 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 993 residues out of total 7112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 834 time to evaluate : 5.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 79 ASN cc_start: 0.8130 (t0) cc_final: 0.7910 (t0) REVERT: H 83 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7490 (mt-10) REVERT: H 183 LEU cc_start: 0.8604 (mm) cc_final: 0.8335 (tp) REVERT: H 190 ILE cc_start: 0.8598 (mm) cc_final: 0.8293 (mt) REVERT: H 344 GLU cc_start: 0.8188 (tp30) cc_final: 0.7972 (tp30) REVERT: V 24 GLU cc_start: 0.7550 (tp30) cc_final: 0.7275 (tp30) REVERT: V 26 VAL cc_start: 0.7727 (OUTLIER) cc_final: 0.7326 (t) REVERT: V 69 ASP cc_start: 0.7472 (m-30) cc_final: 0.7261 (m-30) REVERT: 2 24 GLU cc_start: 0.7476 (tp30) cc_final: 0.7219 (tp30) REVERT: 2 33 LEU cc_start: 0.9053 (mp) cc_final: 0.8801 (mp) REVERT: 2 86 LYS cc_start: 0.8022 (mtpt) cc_final: 0.7519 (tttt) REVERT: 1 43 GLN cc_start: 0.8296 (mp10) cc_final: 0.7893 (mp10) REVERT: 1 69 ASP cc_start: 0.7844 (m-30) cc_final: 0.7567 (m-30) REVERT: 1 80 LYS cc_start: 0.9140 (tttm) cc_final: 0.8842 (tttp) REVERT: Z 24 GLU cc_start: 0.7603 (tp30) cc_final: 0.7308 (tp30) REVERT: Z 26 VAL cc_start: 0.7808 (OUTLIER) cc_final: 0.7419 (t) REVERT: Z 33 LEU cc_start: 0.9014 (mp) cc_final: 0.8804 (mp) REVERT: Z 86 LYS cc_start: 0.7996 (mtpt) cc_final: 0.7666 (tttt) REVERT: Y 24 GLU cc_start: 0.7504 (tp30) cc_final: 0.7223 (tp30) REVERT: Y 85 ASP cc_start: 0.8004 (m-30) cc_final: 0.7779 (m-30) REVERT: X 24 GLU cc_start: 0.7290 (tp30) cc_final: 0.7022 (tp30) REVERT: X 69 ASP cc_start: 0.7890 (m-30) cc_final: 0.7585 (m-30) REVERT: X 86 LYS cc_start: 0.8080 (mtpt) cc_final: 0.7749 (tttt) REVERT: W 43 GLN cc_start: 0.8300 (mp10) cc_final: 0.8059 (mp10) REVERT: R 24 GLU cc_start: 0.7469 (tp30) cc_final: 0.7016 (tp30) REVERT: R 33 LEU cc_start: 0.9144 (mp) cc_final: 0.8865 (mp) REVERT: R 86 LYS cc_start: 0.7866 (tttt) cc_final: 0.7623 (tttt) REVERT: Q 42 LEU cc_start: 0.8507 (mt) cc_final: 0.8242 (mt) REVERT: Q 43 GLN cc_start: 0.8421 (mp10) cc_final: 0.8110 (mp10) REVERT: Q 69 ASP cc_start: 0.7688 (m-30) cc_final: 0.7349 (m-30) REVERT: Q 80 LYS cc_start: 0.9056 (tttp) cc_final: 0.8546 (tttm) REVERT: P 10 LEU cc_start: 0.8479 (tp) cc_final: 0.8244 (mt) REVERT: P 80 LYS cc_start: 0.9072 (tttm) cc_final: 0.8753 (tptm) REVERT: P 86 LYS cc_start: 0.7932 (mtpt) cc_final: 0.7481 (tttt) REVERT: U 69 ASP cc_start: 0.7477 (m-30) cc_final: 0.7157 (m-30) REVERT: T 24 GLU cc_start: 0.7430 (tp30) cc_final: 0.7222 (tp30) REVERT: T 26 VAL cc_start: 0.7981 (p) cc_final: 0.7678 (t) REVERT: T 86 LYS cc_start: 0.8025 (mtpt) cc_final: 0.7814 (tttt) REVERT: S 80 LYS cc_start: 0.9235 (tttm) cc_final: 0.8844 (tttm) REVERT: N 79 ASN cc_start: 0.8255 (t0) cc_final: 0.7961 (t0) REVERT: N 183 LEU cc_start: 0.8544 (mm) cc_final: 0.8289 (tp) REVERT: N 332 MET cc_start: 0.8103 (mtp) cc_final: 0.7872 (mtp) REVERT: N 342 GLN cc_start: 0.8180 (tt0) cc_final: 0.7872 (tm-30) REVERT: N 361 TYR cc_start: 0.7783 (t80) cc_final: 0.7522 (t80) REVERT: M 183 LEU cc_start: 0.8516 (mm) cc_final: 0.8253 (tp) REVERT: M 190 ILE cc_start: 0.8684 (mm) cc_final: 0.8450 (mt) REVERT: M 342 GLN cc_start: 0.8278 (tt0) cc_final: 0.8009 (tm-30) REVERT: M 344 GLU cc_start: 0.8185 (tp30) cc_final: 0.7671 (tp30) REVERT: L 183 LEU cc_start: 0.8444 (mm) cc_final: 0.8120 (tp) REVERT: L 292 MET cc_start: 0.8705 (mtp) cc_final: 0.8431 (ttm) REVERT: L 332 MET cc_start: 0.8096 (mtp) cc_final: 0.7870 (tpp) REVERT: L 342 GLN cc_start: 0.8362 (tt0) cc_final: 0.7916 (tm-30) REVERT: L 344 GLU cc_start: 0.8379 (tp30) cc_final: 0.7881 (tp30) REVERT: L 482 MET cc_start: 0.8682 (mmt) cc_final: 0.8247 (tpt) REVERT: K 183 LEU cc_start: 0.8525 (mm) cc_final: 0.8144 (tp) REVERT: K 264 LEU cc_start: 0.8856 (tp) cc_final: 0.8620 (tp) REVERT: K 352 GLU cc_start: 0.7574 (mt-10) cc_final: 0.6905 (pt0) REVERT: J 344 GLU cc_start: 0.8199 (tp30) cc_final: 0.7764 (tp30) REVERT: I 183 LEU cc_start: 0.8568 (mm) cc_final: 0.8219 (tp) REVERT: I 344 GLU cc_start: 0.8297 (tp30) cc_final: 0.8069 (tp30) REVERT: I 352 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7105 (pt0) REVERT: I 394 LYS cc_start: 0.8590 (ttpt) cc_final: 0.8332 (ttpp) REVERT: D 79 ASN cc_start: 0.8249 (t0) cc_final: 0.7990 (t0) REVERT: D 183 LEU cc_start: 0.8567 (mm) cc_final: 0.8204 (tp) REVERT: D 344 GLU cc_start: 0.8079 (tp30) cc_final: 0.7534 (tp30) REVERT: C 31 MET cc_start: 0.8413 (ttt) cc_final: 0.7856 (ttt) REVERT: C 183 LEU cc_start: 0.8561 (mm) cc_final: 0.8247 (tp) REVERT: C 190 ILE cc_start: 0.8697 (mm) cc_final: 0.8486 (mt) REVERT: C 230 ILE cc_start: 0.8625 (pt) cc_final: 0.8203 (mt) REVERT: C 286 LYS cc_start: 0.8292 (mptt) cc_final: 0.8009 (mmtm) REVERT: C 342 GLN cc_start: 0.8287 (tt0) cc_final: 0.8019 (tm-30) REVERT: C 344 GLU cc_start: 0.8213 (tp30) cc_final: 0.7711 (tp30) REVERT: B 183 LEU cc_start: 0.8431 (mm) cc_final: 0.8109 (tp) REVERT: B 190 ILE cc_start: 0.8657 (mm) cc_final: 0.8332 (mt) REVERT: B 230 ILE cc_start: 0.8511 (pt) cc_final: 0.8255 (pt) REVERT: B 489 MET cc_start: 0.8489 (mmt) cc_final: 0.8075 (mmt) REVERT: A 183 LEU cc_start: 0.8355 (mm) cc_final: 0.8011 (tp) REVERT: A 344 GLU cc_start: 0.8100 (tp30) cc_final: 0.7595 (tp30) REVERT: A 352 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7356 (pt0) REVERT: G 183 LEU cc_start: 0.8651 (mm) cc_final: 0.8187 (tp) REVERT: G 344 GLU cc_start: 0.8245 (tp30) cc_final: 0.8015 (tp30) REVERT: F 190 ILE cc_start: 0.8595 (mm) cc_final: 0.8221 (mt) REVERT: F 230 ILE cc_start: 0.8402 (pt) cc_final: 0.7958 (mt) REVERT: F 332 MET cc_start: 0.7875 (mtp) cc_final: 0.7435 (tpp) REVERT: F 344 GLU cc_start: 0.8136 (tp30) cc_final: 0.7761 (tp30) REVERT: F 352 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7573 (mp0) REVERT: E 31 MET cc_start: 0.8738 (ttt) cc_final: 0.8441 (ttt) REVERT: E 183 LEU cc_start: 0.8622 (mm) cc_final: 0.8310 (tp) outliers start: 159 outliers final: 136 residues processed: 940 average time/residue: 0.6795 time to fit residues: 1074.1047 Evaluate side-chains 914 residues out of total 7112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 775 time to evaluate : 5.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 199 TYR Chi-restraints excluded: chain H residue 230 ILE Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain H residue 343 ILE Chi-restraints excluded: chain H residue 354 LEU Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 13 PHE Chi-restraints excluded: chain V residue 14 ASP Chi-restraints excluded: chain V residue 25 THR Chi-restraints excluded: chain V residue 26 VAL Chi-restraints excluded: chain V residue 27 THR Chi-restraints excluded: chain V residue 64 SER Chi-restraints excluded: chain 2 residue 12 LEU Chi-restraints excluded: chain 2 residue 13 PHE Chi-restraints excluded: chain 2 residue 25 THR Chi-restraints excluded: chain 1 residue 25 THR Chi-restraints excluded: chain Z residue 13 PHE Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 26 VAL Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Y residue 26 VAL Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Y residue 66 LYS Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 13 PHE Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 27 THR Chi-restraints excluded: chain X residue 60 ILE Chi-restraints excluded: chain X residue 72 LEU Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain W residue 85 ASP Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain R residue 13 PHE Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain Q residue 14 ASP Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 66 LYS Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain O residue 13 PHE Chi-restraints excluded: chain O residue 14 ASP Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain U residue 14 ASP Chi-restraints excluded: chain U residue 60 ILE Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain T residue 10 LEU Chi-restraints excluded: chain T residue 25 THR Chi-restraints excluded: chain S residue 14 ASP Chi-restraints excluded: chain S residue 25 THR Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain S residue 66 LYS Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 230 ILE Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 370 LEU Chi-restraints excluded: chain N residue 388 VAL Chi-restraints excluded: chain M residue 185 ASP Chi-restraints excluded: chain M residue 228 SER Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 409 GLU Chi-restraints excluded: chain L residue 185 ASP Chi-restraints excluded: chain L residue 195 PHE Chi-restraints excluded: chain L residue 230 ILE Chi-restraints excluded: chain L residue 250 ILE Chi-restraints excluded: chain L residue 343 ILE Chi-restraints excluded: chain L residue 374 SER Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 195 PHE Chi-restraints excluded: chain K residue 230 ILE Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 366 LEU Chi-restraints excluded: chain K residue 370 LEU Chi-restraints excluded: chain K residue 374 SER Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain J residue 230 ILE Chi-restraints excluded: chain J residue 289 LEU Chi-restraints excluded: chain J residue 343 ILE Chi-restraints excluded: chain J residue 370 LEU Chi-restraints excluded: chain J residue 374 SER Chi-restraints excluded: chain I residue 195 PHE Chi-restraints excluded: chain I residue 199 TYR Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 327 THR Chi-restraints excluded: chain I residue 343 ILE Chi-restraints excluded: chain I residue 370 LEU Chi-restraints excluded: chain I residue 388 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 525 ILE Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 268 LYS Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 195 PHE Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 388 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 374 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 780 optimal weight: 0.9990 chunk 593 optimal weight: 7.9990 chunk 409 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 376 optimal weight: 8.9990 chunk 530 optimal weight: 2.9990 chunk 792 optimal weight: 9.9990 chunk 839 optimal weight: 0.4980 chunk 414 optimal weight: 2.9990 chunk 751 optimal weight: 0.7980 chunk 226 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 4 GLN ** X 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 ASN ** K 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 HIS G 79 ASN ** G 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 66696 Z= 0.123 Angle : 0.529 15.532 89978 Z= 0.253 Chirality : 0.070 1.618 10850 Planarity : 0.002 0.042 11522 Dihedral : 7.519 179.123 9338 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 35.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.22 % Favored : 94.68 % Rotamer: Outliers : 1.65 % Allowed : 10.85 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.09), residues: 8736 helix: 1.49 (0.09), residues: 3962 sheet: -1.37 (0.15), residues: 1078 loop : -1.84 (0.10), residues: 3696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP N 44 HIS 0.003 0.000 HIS B 316 PHE 0.015 0.001 PHE P 13 TYR 0.010 0.001 TYR G 66 ARG 0.002 0.000 ARG N 285 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 970 residues out of total 7112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 853 time to evaluate : 5.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 183 LEU cc_start: 0.8619 (mm) cc_final: 0.8338 (tp) REVERT: H 332 MET cc_start: 0.8058 (mtp) cc_final: 0.7561 (tpp) REVERT: H 344 GLU cc_start: 0.8200 (tp30) cc_final: 0.7995 (tp30) REVERT: V 24 GLU cc_start: 0.7445 (tp30) cc_final: 0.7229 (tp30) REVERT: V 26 VAL cc_start: 0.7757 (OUTLIER) cc_final: 0.7437 (t) REVERT: 2 24 GLU cc_start: 0.7365 (tp30) cc_final: 0.6976 (tp30) REVERT: 2 33 LEU cc_start: 0.9064 (mp) cc_final: 0.8847 (mp) REVERT: 2 69 ASP cc_start: 0.7776 (m-30) cc_final: 0.7486 (m-30) REVERT: 2 86 LYS cc_start: 0.8023 (mtpt) cc_final: 0.7569 (tttt) REVERT: 1 43 GLN cc_start: 0.8262 (mp10) cc_final: 0.7818 (mp10) REVERT: 1 69 ASP cc_start: 0.7753 (m-30) cc_final: 0.7516 (m-30) REVERT: Z 24 GLU cc_start: 0.7569 (tp30) cc_final: 0.7317 (tp30) REVERT: Z 26 VAL cc_start: 0.7738 (OUTLIER) cc_final: 0.7393 (t) REVERT: Z 33 LEU cc_start: 0.9037 (mp) cc_final: 0.8837 (mp) REVERT: Z 66 LYS cc_start: 0.8859 (ptpp) cc_final: 0.8645 (pttp) REVERT: Z 80 LYS cc_start: 0.9022 (tptp) cc_final: 0.8521 (tptp) REVERT: Z 86 LYS cc_start: 0.7783 (mtpt) cc_final: 0.7399 (tttt) REVERT: Z 87 ASP cc_start: 0.8559 (m-30) cc_final: 0.8078 (t0) REVERT: Y 24 GLU cc_start: 0.7494 (tp30) cc_final: 0.7190 (tp30) REVERT: Y 32 MET cc_start: 0.7921 (ptm) cc_final: 0.7684 (ptp) REVERT: Y 85 ASP cc_start: 0.7920 (m-30) cc_final: 0.7718 (m-30) REVERT: X 24 GLU cc_start: 0.7367 (tp30) cc_final: 0.7044 (tp30) REVERT: X 33 LEU cc_start: 0.9073 (mp) cc_final: 0.8855 (mp) REVERT: X 69 ASP cc_start: 0.7984 (m-30) cc_final: 0.7745 (m-30) REVERT: X 86 LYS cc_start: 0.8055 (mtpt) cc_final: 0.7750 (tttt) REVERT: W 43 GLN cc_start: 0.8310 (mp10) cc_final: 0.8088 (mp10) REVERT: R 24 GLU cc_start: 0.7386 (tp30) cc_final: 0.6960 (tp30) REVERT: R 86 LYS cc_start: 0.7850 (tttt) cc_final: 0.7645 (tttt) REVERT: Q 42 LEU cc_start: 0.8418 (mt) cc_final: 0.8157 (mt) REVERT: Q 43 GLN cc_start: 0.8354 (mp10) cc_final: 0.7979 (mp10) REVERT: Q 69 ASP cc_start: 0.7598 (m-30) cc_final: 0.7269 (m-30) REVERT: P 10 LEU cc_start: 0.8509 (tp) cc_final: 0.8271 (mt) REVERT: P 43 GLN cc_start: 0.8302 (mp10) cc_final: 0.8005 (mp10) REVERT: U 69 ASP cc_start: 0.7522 (m-30) cc_final: 0.7236 (m-30) REVERT: T 24 GLU cc_start: 0.7395 (tp30) cc_final: 0.7094 (tp30) REVERT: T 26 VAL cc_start: 0.7869 (OUTLIER) cc_final: 0.7591 (t) REVERT: T 80 LYS cc_start: 0.9072 (tttp) cc_final: 0.8220 (tptp) REVERT: T 86 LYS cc_start: 0.8024 (mtpt) cc_final: 0.7823 (tttt) REVERT: S 80 LYS cc_start: 0.9237 (tttm) cc_final: 0.8741 (tttm) REVERT: S 87 ASP cc_start: 0.8650 (OUTLIER) cc_final: 0.7555 (t0) REVERT: N 79 ASN cc_start: 0.8114 (t0) cc_final: 0.7828 (t0) REVERT: N 183 LEU cc_start: 0.8528 (mm) cc_final: 0.8256 (tp) REVERT: N 342 GLN cc_start: 0.8144 (tt0) cc_final: 0.7875 (tm-30) REVERT: N 361 TYR cc_start: 0.7764 (t80) cc_final: 0.7530 (t80) REVERT: M 183 LEU cc_start: 0.8506 (mm) cc_final: 0.8236 (tp) REVERT: M 190 ILE cc_start: 0.8667 (mm) cc_final: 0.8434 (mt) REVERT: M 230 ILE cc_start: 0.8604 (pt) cc_final: 0.8199 (mt) REVERT: M 332 MET cc_start: 0.8049 (mtp) cc_final: 0.7681 (tpp) REVERT: M 344 GLU cc_start: 0.8159 (tp30) cc_final: 0.7670 (tp30) REVERT: L 183 LEU cc_start: 0.8375 (mm) cc_final: 0.8071 (tp) REVERT: L 190 ILE cc_start: 0.8632 (mm) cc_final: 0.8374 (mt) REVERT: L 292 MET cc_start: 0.8678 (mtp) cc_final: 0.8292 (ttm) REVERT: L 342 GLN cc_start: 0.8343 (tt0) cc_final: 0.7919 (tm-30) REVERT: L 344 GLU cc_start: 0.8368 (tp30) cc_final: 0.7894 (tp30) REVERT: L 489 MET cc_start: 0.8657 (mmt) cc_final: 0.8074 (mmt) REVERT: K 183 LEU cc_start: 0.8537 (mm) cc_final: 0.8135 (tp) REVERT: K 264 LEU cc_start: 0.8782 (tp) cc_final: 0.8550 (tp) REVERT: K 332 MET cc_start: 0.7925 (mtp) cc_final: 0.7463 (tpp) REVERT: K 342 GLN cc_start: 0.8191 (tt0) cc_final: 0.7878 (tm-30) REVERT: J 344 GLU cc_start: 0.8155 (tp30) cc_final: 0.7779 (tp30) REVERT: J 489 MET cc_start: 0.8554 (mmt) cc_final: 0.8004 (mmt) REVERT: I 121 MET cc_start: 0.8532 (mmm) cc_final: 0.8310 (mmm) REVERT: I 183 LEU cc_start: 0.8524 (mm) cc_final: 0.8198 (tp) REVERT: I 332 MET cc_start: 0.8092 (mtp) cc_final: 0.7763 (tpp) REVERT: I 344 GLU cc_start: 0.8224 (tp30) cc_final: 0.8023 (tp30) REVERT: D 183 LEU cc_start: 0.8558 (mm) cc_final: 0.8175 (tp) REVERT: D 332 MET cc_start: 0.8053 (mtp) cc_final: 0.7604 (tpp) REVERT: C 183 LEU cc_start: 0.8585 (mm) cc_final: 0.8255 (tp) REVERT: C 230 ILE cc_start: 0.8582 (pt) cc_final: 0.8135 (mt) REVERT: C 332 MET cc_start: 0.7633 (ttm) cc_final: 0.7348 (ttp) REVERT: C 344 GLU cc_start: 0.8145 (tp30) cc_final: 0.7677 (tp30) REVERT: C 394 LYS cc_start: 0.8590 (ttpt) cc_final: 0.8324 (ttpp) REVERT: B 183 LEU cc_start: 0.8379 (mm) cc_final: 0.8070 (tp) REVERT: B 190 ILE cc_start: 0.8634 (mm) cc_final: 0.8352 (mt) REVERT: B 230 ILE cc_start: 0.8426 (pt) cc_final: 0.8183 (pt) REVERT: B 239 ILE cc_start: 0.8221 (mt) cc_final: 0.7982 (mt) REVERT: B 339 ASP cc_start: 0.7723 (t0) cc_final: 0.7154 (p0) REVERT: B 489 MET cc_start: 0.8606 (mmt) cc_final: 0.8120 (mmt) REVERT: A 183 LEU cc_start: 0.8370 (mm) cc_final: 0.7997 (tp) REVERT: A 286 LYS cc_start: 0.8388 (mptt) cc_final: 0.8180 (mmtm) REVERT: A 332 MET cc_start: 0.8102 (mtp) cc_final: 0.7643 (tpp) REVERT: A 344 GLU cc_start: 0.8089 (tp30) cc_final: 0.7585 (tp30) REVERT: A 352 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7349 (pt0) REVERT: G 183 LEU cc_start: 0.8649 (mm) cc_final: 0.8179 (tp) REVERT: G 225 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7590 (ptpp) REVERT: G 268 LYS cc_start: 0.7272 (OUTLIER) cc_final: 0.6659 (mptt) REVERT: G 344 GLU cc_start: 0.8223 (tp30) cc_final: 0.7981 (tp30) REVERT: F 121 MET cc_start: 0.8530 (mmm) cc_final: 0.8324 (mmm) REVERT: F 190 ILE cc_start: 0.8647 (mm) cc_final: 0.8299 (mt) REVERT: F 230 ILE cc_start: 0.8418 (pt) cc_final: 0.8076 (mt) REVERT: F 332 MET cc_start: 0.7905 (mtp) cc_final: 0.7532 (tpp) REVERT: F 344 GLU cc_start: 0.8142 (tp30) cc_final: 0.7789 (tp30) REVERT: E 31 MET cc_start: 0.8661 (ttt) cc_final: 0.8332 (ttt) REVERT: E 183 LEU cc_start: 0.8604 (mm) cc_final: 0.8295 (tp) outliers start: 117 outliers final: 90 residues processed: 937 average time/residue: 0.6932 time to fit residues: 1109.8456 Evaluate side-chains 872 residues out of total 7112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 776 time to evaluate : 6.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 13 PHE Chi-restraints excluded: chain V residue 26 VAL Chi-restraints excluded: chain V residue 64 SER Chi-restraints excluded: chain 2 residue 12 LEU Chi-restraints excluded: chain 2 residue 13 PHE Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 87 ASP Chi-restraints excluded: chain 1 residue 13 PHE Chi-restraints excluded: chain 1 residue 27 THR Chi-restraints excluded: chain Z residue 13 PHE Chi-restraints excluded: chain Z residue 26 VAL Chi-restraints excluded: chain Z residue 27 THR Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Y residue 27 THR Chi-restraints excluded: chain Y residue 66 LYS Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 13 PHE Chi-restraints excluded: chain X residue 32 MET Chi-restraints excluded: chain X residue 72 LEU Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain R residue 13 PHE Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 32 MET Chi-restraints excluded: chain Q residue 14 ASP Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain Q residue 66 LYS Chi-restraints excluded: chain P residue 13 PHE Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain O residue 13 PHE Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 66 LYS Chi-restraints excluded: chain U residue 13 PHE Chi-restraints excluded: chain U residue 14 ASP Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain T residue 13 PHE Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain S residue 13 PHE Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain N residue 230 ILE Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 370 LEU Chi-restraints excluded: chain N residue 374 SER Chi-restraints excluded: chain L residue 185 ASP Chi-restraints excluded: chain L residue 195 PHE Chi-restraints excluded: chain L residue 250 ILE Chi-restraints excluded: chain L residue 374 SER Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 121 MET Chi-restraints excluded: chain K residue 195 PHE Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 370 LEU Chi-restraints excluded: chain K residue 374 SER Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 195 PHE Chi-restraints excluded: chain J residue 230 ILE Chi-restraints excluded: chain J residue 328 LYS Chi-restraints excluded: chain J residue 370 LEU Chi-restraints excluded: chain J residue 374 SER Chi-restraints excluded: chain I residue 195 PHE Chi-restraints excluded: chain I residue 370 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 525 ILE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain G residue 225 LYS Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 268 LYS Chi-restraints excluded: chain G residue 327 THR Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 374 SER Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 195 PHE Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 374 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 698 optimal weight: 7.9990 chunk 476 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 624 optimal weight: 5.9990 chunk 346 optimal weight: 1.9990 chunk 715 optimal weight: 4.9990 chunk 579 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 428 optimal weight: 0.7980 chunk 753 optimal weight: 0.6980 chunk 211 optimal weight: 10.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 79 ASN X 4 GLN ** W 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 ASN ** K 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 231 GLN ** G 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 GLN ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 66696 Z= 0.184 Angle : 0.547 15.479 89978 Z= 0.263 Chirality : 0.070 1.614 10850 Planarity : 0.003 0.042 11522 Dihedral : 7.015 177.850 9338 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 33.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.38 % Favored : 93.52 % Rotamer: Outliers : 2.43 % Allowed : 10.90 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.09), residues: 8736 helix: 1.70 (0.09), residues: 3878 sheet: -1.39 (0.14), residues: 1232 loop : -1.68 (0.10), residues: 3626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N 44 HIS 0.004 0.001 HIS F 316 PHE 0.017 0.002 PHE G 104 TYR 0.011 0.001 TYR F 66 ARG 0.002 0.000 ARG K 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 983 residues out of total 7112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 810 time to evaluate : 5.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 79 ASN cc_start: 0.8032 (OUTLIER) cc_final: 0.7812 (t0) REVERT: H 183 LEU cc_start: 0.8681 (mm) cc_final: 0.8379 (tp) REVERT: H 344 GLU cc_start: 0.8199 (tp30) cc_final: 0.7995 (tp30) REVERT: H 361 TYR cc_start: 0.7771 (t80) cc_final: 0.7525 (t80) REVERT: V 14 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.8023 (t0) REVERT: V 24 GLU cc_start: 0.7454 (tp30) cc_final: 0.7150 (tp30) REVERT: V 26 VAL cc_start: 0.7846 (OUTLIER) cc_final: 0.7492 (t) REVERT: 2 24 GLU cc_start: 0.7347 (tp30) cc_final: 0.7087 (tp30) REVERT: 2 86 LYS cc_start: 0.8038 (mtpt) cc_final: 0.7605 (tttt) REVERT: 1 43 GLN cc_start: 0.8360 (mp10) cc_final: 0.7899 (mp10) REVERT: 1 69 ASP cc_start: 0.7779 (m-30) cc_final: 0.7513 (m-30) REVERT: Z 24 GLU cc_start: 0.7580 (tp30) cc_final: 0.7276 (tp30) REVERT: Z 26 VAL cc_start: 0.7826 (OUTLIER) cc_final: 0.7442 (t) REVERT: Z 33 LEU cc_start: 0.9055 (mp) cc_final: 0.8833 (mp) REVERT: Z 80 LYS cc_start: 0.9028 (tptp) cc_final: 0.8538 (tptp) REVERT: Z 86 LYS cc_start: 0.7830 (mtpt) cc_final: 0.7420 (tttt) REVERT: Z 87 ASP cc_start: 0.8500 (m-30) cc_final: 0.7906 (t0) REVERT: Y 24 GLU cc_start: 0.7445 (tp30) cc_final: 0.7119 (tp30) REVERT: Y 32 MET cc_start: 0.7868 (ptm) cc_final: 0.7629 (ptp) REVERT: X 24 GLU cc_start: 0.7252 (tp30) cc_final: 0.6929 (tp30) REVERT: X 33 LEU cc_start: 0.9032 (mp) cc_final: 0.8748 (mp) REVERT: W 43 GLN cc_start: 0.8373 (mp10) cc_final: 0.8123 (mp10) REVERT: R 24 GLU cc_start: 0.7324 (tp30) cc_final: 0.6996 (tp30) REVERT: R 86 LYS cc_start: 0.7775 (tttt) cc_final: 0.7567 (tttt) REVERT: Q 32 MET cc_start: 0.7922 (ptm) cc_final: 0.7707 (ptp) REVERT: Q 42 LEU cc_start: 0.8437 (mt) cc_final: 0.8147 (mt) REVERT: Q 43 GLN cc_start: 0.8419 (mp10) cc_final: 0.7932 (mp10) REVERT: Q 69 ASP cc_start: 0.7662 (m-30) cc_final: 0.7333 (m-30) REVERT: P 10 LEU cc_start: 0.8509 (tp) cc_final: 0.8272 (mt) REVERT: P 43 GLN cc_start: 0.8242 (mp10) cc_final: 0.7921 (mp10) REVERT: U 69 ASP cc_start: 0.7547 (m-30) cc_final: 0.7253 (m-30) REVERT: T 26 VAL cc_start: 0.7782 (OUTLIER) cc_final: 0.7541 (t) REVERT: S 43 GLN cc_start: 0.8265 (mp10) cc_final: 0.7683 (mp10) REVERT: N 79 ASN cc_start: 0.8210 (t0) cc_final: 0.7915 (t0) REVERT: N 183 LEU cc_start: 0.8573 (mm) cc_final: 0.8291 (tp) REVERT: N 219 TYR cc_start: 0.8664 (m-80) cc_final: 0.8278 (m-80) REVERT: N 332 MET cc_start: 0.7944 (mtp) cc_final: 0.7504 (tpp) REVERT: N 342 GLN cc_start: 0.8130 (tt0) cc_final: 0.7834 (tm-30) REVERT: N 361 TYR cc_start: 0.7782 (t80) cc_final: 0.7536 (t80) REVERT: M 183 LEU cc_start: 0.8584 (mm) cc_final: 0.8293 (tp) REVERT: M 190 ILE cc_start: 0.8642 (mm) cc_final: 0.8416 (mt) REVERT: M 230 ILE cc_start: 0.8612 (pt) cc_final: 0.8225 (mt) REVERT: M 332 MET cc_start: 0.8054 (mtp) cc_final: 0.7598 (tpp) REVERT: M 342 GLN cc_start: 0.8220 (tt0) cc_final: 0.8013 (tm-30) REVERT: M 344 GLU cc_start: 0.8206 (tp30) cc_final: 0.7712 (tp30) REVERT: L 183 LEU cc_start: 0.8462 (mm) cc_final: 0.8124 (tp) REVERT: L 190 ILE cc_start: 0.8636 (mm) cc_final: 0.8375 (mt) REVERT: L 292 MET cc_start: 0.8668 (mtp) cc_final: 0.8379 (ttm) REVERT: L 342 GLN cc_start: 0.8353 (tt0) cc_final: 0.7918 (tm-30) REVERT: L 344 GLU cc_start: 0.8432 (tp30) cc_final: 0.7958 (tp30) REVERT: K 183 LEU cc_start: 0.8635 (mm) cc_final: 0.8230 (tp) REVERT: J 230 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7874 (pt) REVERT: J 344 GLU cc_start: 0.8173 (tp30) cc_final: 0.7787 (tp30) REVERT: I 121 MET cc_start: 0.8555 (mmm) cc_final: 0.8333 (mmm) REVERT: I 183 LEU cc_start: 0.8520 (mm) cc_final: 0.8219 (tp) REVERT: I 332 MET cc_start: 0.8152 (mtp) cc_final: 0.7755 (tpp) REVERT: I 352 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7128 (pt0) REVERT: D 183 LEU cc_start: 0.8506 (mm) cc_final: 0.8223 (tp) REVERT: D 332 MET cc_start: 0.8010 (mtp) cc_final: 0.7510 (tpp) REVERT: C 31 MET cc_start: 0.8333 (ttt) cc_final: 0.7592 (ttt) REVERT: C 183 LEU cc_start: 0.8596 (mm) cc_final: 0.8264 (tp) REVERT: C 230 ILE cc_start: 0.8575 (pt) cc_final: 0.8135 (mt) REVERT: C 332 MET cc_start: 0.7624 (ttm) cc_final: 0.7012 (ttm) REVERT: C 344 GLU cc_start: 0.8232 (tp30) cc_final: 0.7787 (tp30) REVERT: B 183 LEU cc_start: 0.8486 (mm) cc_final: 0.8170 (tp) REVERT: B 190 ILE cc_start: 0.8653 (mm) cc_final: 0.8364 (mt) REVERT: B 230 ILE cc_start: 0.8471 (pt) cc_final: 0.8249 (pt) REVERT: B 489 MET cc_start: 0.8782 (mmt) cc_final: 0.8273 (mmt) REVERT: A 183 LEU cc_start: 0.8470 (mm) cc_final: 0.8086 (tp) REVERT: A 286 LYS cc_start: 0.8428 (mptt) cc_final: 0.8223 (mmtm) REVERT: A 308 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.6967 (mt) REVERT: A 332 MET cc_start: 0.8122 (mtp) cc_final: 0.7585 (tpp) REVERT: A 344 GLU cc_start: 0.8129 (tp30) cc_final: 0.7594 (tp30) REVERT: A 352 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7361 (pt0) REVERT: G 183 LEU cc_start: 0.8600 (mm) cc_final: 0.8194 (tp) REVERT: G 268 LYS cc_start: 0.7346 (OUTLIER) cc_final: 0.6609 (mptt) REVERT: G 344 GLU cc_start: 0.8256 (tp30) cc_final: 0.8019 (tp30) REVERT: G 489 MET cc_start: 0.8302 (mmt) cc_final: 0.7872 (mmt) REVERT: F 190 ILE cc_start: 0.8635 (mm) cc_final: 0.8289 (mt) REVERT: F 230 ILE cc_start: 0.8445 (pt) cc_final: 0.7988 (mt) REVERT: F 332 MET cc_start: 0.8018 (mtp) cc_final: 0.7574 (tpp) REVERT: F 344 GLU cc_start: 0.8182 (tp30) cc_final: 0.7820 (tp30) REVERT: F 352 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7589 (mp0) REVERT: E 31 MET cc_start: 0.8742 (ttt) cc_final: 0.8523 (ttt) REVERT: E 183 LEU cc_start: 0.8594 (mm) cc_final: 0.8290 (tp) outliers start: 173 outliers final: 136 residues processed: 921 average time/residue: 0.6536 time to fit residues: 1020.5245 Evaluate side-chains 924 residues out of total 7112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 779 time to evaluate : 5.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 79 ASN Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 230 ILE Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 343 ILE Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 13 PHE Chi-restraints excluded: chain V residue 14 ASP Chi-restraints excluded: chain V residue 25 THR Chi-restraints excluded: chain V residue 26 VAL Chi-restraints excluded: chain V residue 27 THR Chi-restraints excluded: chain V residue 64 SER Chi-restraints excluded: chain V residue 87 ASP Chi-restraints excluded: chain 2 residue 12 LEU Chi-restraints excluded: chain 2 residue 13 PHE Chi-restraints excluded: chain 2 residue 25 THR Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 1 residue 27 THR Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 1 residue 87 ASP Chi-restraints excluded: chain Z residue 12 LEU Chi-restraints excluded: chain Z residue 13 PHE Chi-restraints excluded: chain Z residue 26 VAL Chi-restraints excluded: chain Z residue 27 THR Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Y residue 13 PHE Chi-restraints excluded: chain Y residue 14 ASP Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 27 THR Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Y residue 66 LYS Chi-restraints excluded: chain Y residue 86 LYS Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 13 PHE Chi-restraints excluded: chain X residue 27 THR Chi-restraints excluded: chain X residue 72 LEU Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain R residue 13 PHE Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 32 MET Chi-restraints excluded: chain R residue 87 ASP Chi-restraints excluded: chain Q residue 13 PHE Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain Q residue 66 LYS Chi-restraints excluded: chain P residue 13 PHE Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain O residue 13 PHE Chi-restraints excluded: chain O residue 14 ASP Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 66 LYS Chi-restraints excluded: chain U residue 13 PHE Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain T residue 13 PHE Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain S residue 14 ASP Chi-restraints excluded: chain S residue 25 THR Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 230 ILE Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 370 LEU Chi-restraints excluded: chain N residue 374 SER Chi-restraints excluded: chain M residue 195 PHE Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 409 GLU Chi-restraints excluded: chain L residue 185 ASP Chi-restraints excluded: chain L residue 195 PHE Chi-restraints excluded: chain L residue 230 ILE Chi-restraints excluded: chain L residue 250 ILE Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 195 PHE Chi-restraints excluded: chain K residue 230 ILE Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 370 LEU Chi-restraints excluded: chain K residue 374 SER Chi-restraints excluded: chain K residue 386 SER Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 195 PHE Chi-restraints excluded: chain J residue 230 ILE Chi-restraints excluded: chain J residue 328 LYS Chi-restraints excluded: chain J residue 343 ILE Chi-restraints excluded: chain J residue 370 LEU Chi-restraints excluded: chain J residue 374 SER Chi-restraints excluded: chain I residue 195 PHE Chi-restraints excluded: chain I residue 199 TYR Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 327 THR Chi-restraints excluded: chain I residue 370 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 525 ILE Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 409 GLU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 268 LYS Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 327 THR Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 374 SER Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 195 PHE Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 424 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 282 optimal weight: 4.9990 chunk 755 optimal weight: 3.9990 chunk 165 optimal weight: 0.0970 chunk 492 optimal weight: 0.5980 chunk 207 optimal weight: 4.9990 chunk 839 optimal weight: 2.9990 chunk 697 optimal weight: 8.9990 chunk 388 optimal weight: 0.9980 chunk 69 optimal weight: 8.9990 chunk 277 optimal weight: 9.9990 chunk 440 optimal weight: 3.9990 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN ** X 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 4 GLN ** L 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 ASN ** J 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 367 ASN ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 GLN ** G 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 GLN ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 66696 Z= 0.200 Angle : 0.550 15.523 89978 Z= 0.265 Chirality : 0.071 1.617 10850 Planarity : 0.003 0.040 11522 Dihedral : 6.489 173.302 9338 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 33.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.90 % Favored : 94.00 % Rotamer: Outliers : 2.36 % Allowed : 11.83 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.09), residues: 8736 helix: 1.74 (0.09), residues: 3962 sheet: -1.12 (0.15), residues: 1092 loop : -1.64 (0.10), residues: 3682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 44 HIS 0.001 0.000 HIS N 316 PHE 0.016 0.002 PHE G 104 TYR 0.011 0.001 TYR F 66 ARG 0.002 0.000 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 978 residues out of total 7112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 810 time to evaluate : 5.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 183 LEU cc_start: 0.8680 (mm) cc_final: 0.8370 (tp) REVERT: V 14 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.8141 (t0) REVERT: V 24 GLU cc_start: 0.7464 (tp30) cc_final: 0.7228 (tp30) REVERT: V 26 VAL cc_start: 0.7955 (OUTLIER) cc_final: 0.7655 (t) REVERT: 2 86 LYS cc_start: 0.8068 (mtpt) cc_final: 0.7656 (tttt) REVERT: 2 93 ASP cc_start: 0.8304 (t70) cc_final: 0.8102 (t0) REVERT: 1 43 GLN cc_start: 0.8417 (mp10) cc_final: 0.8003 (mp10) REVERT: 1 69 ASP cc_start: 0.7854 (m-30) cc_final: 0.7555 (m-30) REVERT: Z 24 GLU cc_start: 0.7521 (tp30) cc_final: 0.7215 (tp30) REVERT: Z 26 VAL cc_start: 0.7828 (OUTLIER) cc_final: 0.7453 (t) REVERT: Z 33 LEU cc_start: 0.9061 (mp) cc_final: 0.8859 (mp) REVERT: Z 80 LYS cc_start: 0.9043 (tptp) cc_final: 0.8503 (tptp) REVERT: Z 85 ASP cc_start: 0.7789 (m-30) cc_final: 0.7515 (m-30) REVERT: Z 86 LYS cc_start: 0.7877 (mtpt) cc_final: 0.7458 (tttt) REVERT: Z 87 ASP cc_start: 0.8525 (m-30) cc_final: 0.7879 (t0) REVERT: X 24 GLU cc_start: 0.7261 (tp30) cc_final: 0.6925 (tp30) REVERT: X 33 LEU cc_start: 0.9015 (mp) cc_final: 0.8731 (mp) REVERT: X 93 ASP cc_start: 0.8256 (t70) cc_final: 0.7690 (t0) REVERT: W 43 GLN cc_start: 0.8385 (mp10) cc_final: 0.8144 (mp10) REVERT: R 24 GLU cc_start: 0.7341 (tp30) cc_final: 0.7058 (tp30) REVERT: Q 32 MET cc_start: 0.7977 (ptm) cc_final: 0.7725 (ptp) REVERT: Q 42 LEU cc_start: 0.8480 (mt) cc_final: 0.8225 (mt) REVERT: Q 43 GLN cc_start: 0.8425 (mp10) cc_final: 0.7983 (mp10) REVERT: Q 69 ASP cc_start: 0.7700 (m-30) cc_final: 0.7364 (m-30) REVERT: P 32 MET cc_start: 0.7656 (mtp) cc_final: 0.7124 (ptm) REVERT: P 43 GLN cc_start: 0.8260 (mp10) cc_final: 0.7904 (mp10) REVERT: U 69 ASP cc_start: 0.7550 (m-30) cc_final: 0.7246 (m-30) REVERT: U 93 ASP cc_start: 0.8311 (t0) cc_final: 0.8089 (t0) REVERT: T 54 LYS cc_start: 0.4959 (OUTLIER) cc_final: 0.4437 (pttm) REVERT: S 43 GLN cc_start: 0.8295 (mp10) cc_final: 0.7688 (mp10) REVERT: S 80 LYS cc_start: 0.9255 (tttm) cc_final: 0.8850 (tttm) REVERT: N 79 ASN cc_start: 0.8222 (t0) cc_final: 0.7927 (t0) REVERT: N 183 LEU cc_start: 0.8644 (mm) cc_final: 0.8347 (tp) REVERT: N 342 GLN cc_start: 0.8162 (tt0) cc_final: 0.7888 (tm-30) REVERT: N 361 TYR cc_start: 0.7709 (t80) cc_final: 0.7476 (t80) REVERT: M 183 LEU cc_start: 0.8586 (mm) cc_final: 0.8282 (tp) REVERT: M 190 ILE cc_start: 0.8605 (mm) cc_final: 0.8382 (mt) REVERT: M 230 ILE cc_start: 0.8622 (pt) cc_final: 0.8246 (mt) REVERT: M 332 MET cc_start: 0.8019 (mtp) cc_final: 0.7574 (tpp) REVERT: M 342 GLN cc_start: 0.8219 (tt0) cc_final: 0.7962 (tm-30) REVERT: M 344 GLU cc_start: 0.8213 (tp30) cc_final: 0.7764 (tp30) REVERT: L 44 TRP cc_start: 0.8117 (p90) cc_final: 0.7754 (p90) REVERT: L 183 LEU cc_start: 0.8507 (mm) cc_final: 0.8146 (tp) REVERT: L 190 ILE cc_start: 0.8619 (mm) cc_final: 0.8364 (mt) REVERT: L 292 MET cc_start: 0.8719 (mtp) cc_final: 0.8398 (ttm) REVERT: L 342 GLN cc_start: 0.8353 (tt0) cc_final: 0.7888 (tm-30) REVERT: L 344 GLU cc_start: 0.8424 (tp30) cc_final: 0.7966 (tp30) REVERT: K 183 LEU cc_start: 0.8653 (mm) cc_final: 0.8247 (tp) REVERT: K 342 GLN cc_start: 0.8209 (tt0) cc_final: 0.7874 (tm-30) REVERT: K 352 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7243 (pt0) REVERT: J 230 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7925 (pt) REVERT: J 344 GLU cc_start: 0.8211 (tp30) cc_final: 0.7810 (tp30) REVERT: I 121 MET cc_start: 0.8553 (mmm) cc_final: 0.8334 (mmm) REVERT: I 183 LEU cc_start: 0.8553 (mm) cc_final: 0.8244 (tp) REVERT: I 190 ILE cc_start: 0.8470 (mm) cc_final: 0.8152 (mt) REVERT: I 304 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7550 (mm-30) REVERT: I 352 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7101 (pt0) REVERT: D 183 LEU cc_start: 0.8544 (mm) cc_final: 0.8230 (tp) REVERT: D 332 MET cc_start: 0.7998 (mtp) cc_final: 0.7467 (tpp) REVERT: C 31 MET cc_start: 0.8426 (ttt) cc_final: 0.7652 (ttt) REVERT: C 183 LEU cc_start: 0.8582 (mm) cc_final: 0.8255 (tp) REVERT: C 230 ILE cc_start: 0.8566 (pt) cc_final: 0.8126 (mt) REVERT: C 332 MET cc_start: 0.7676 (ttm) cc_final: 0.7173 (ttm) REVERT: C 344 GLU cc_start: 0.8184 (tp30) cc_final: 0.7735 (tp30) REVERT: B 183 LEU cc_start: 0.8503 (mm) cc_final: 0.8183 (tp) REVERT: B 190 ILE cc_start: 0.8650 (mm) cc_final: 0.8351 (mt) REVERT: B 339 ASP cc_start: 0.7753 (t0) cc_final: 0.7154 (p0) REVERT: B 489 MET cc_start: 0.8891 (mmt) cc_final: 0.8411 (mmt) REVERT: A 183 LEU cc_start: 0.8492 (mm) cc_final: 0.8110 (tp) REVERT: A 286 LYS cc_start: 0.8469 (mptt) cc_final: 0.8257 (mmtm) REVERT: A 342 GLN cc_start: 0.8202 (tt0) cc_final: 0.7863 (tm-30) REVERT: A 344 GLU cc_start: 0.8110 (tp30) cc_final: 0.7578 (tp30) REVERT: A 352 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7308 (pt0) REVERT: G 183 LEU cc_start: 0.8642 (mm) cc_final: 0.8216 (tp) REVERT: G 268 LYS cc_start: 0.7294 (OUTLIER) cc_final: 0.6590 (mptt) REVERT: G 344 GLU cc_start: 0.8287 (tp30) cc_final: 0.8025 (tp30) REVERT: F 190 ILE cc_start: 0.8626 (mm) cc_final: 0.8276 (mt) REVERT: F 230 ILE cc_start: 0.8452 (pt) cc_final: 0.8039 (mt) REVERT: F 332 MET cc_start: 0.8004 (mtp) cc_final: 0.7528 (tpp) REVERT: F 344 GLU cc_start: 0.8208 (tp30) cc_final: 0.7847 (tp30) REVERT: F 352 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: E 183 LEU cc_start: 0.8596 (mm) cc_final: 0.8292 (tp) REVERT: E 217 ASP cc_start: 0.7815 (m-30) cc_final: 0.7593 (t0) REVERT: E 389 GLU cc_start: 0.7625 (mp0) cc_final: 0.7093 (mp0) outliers start: 168 outliers final: 142 residues processed: 929 average time/residue: 0.6566 time to fit residues: 1035.2327 Evaluate side-chains 924 residues out of total 7112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 775 time to evaluate : 5.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 195 PHE Chi-restraints excluded: chain H residue 199 TYR Chi-restraints excluded: chain H residue 230 ILE Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 343 ILE Chi-restraints excluded: chain H residue 354 LEU Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 13 PHE Chi-restraints excluded: chain V residue 14 ASP Chi-restraints excluded: chain V residue 26 VAL Chi-restraints excluded: chain V residue 27 THR Chi-restraints excluded: chain 2 residue 12 LEU Chi-restraints excluded: chain 2 residue 13 PHE Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 1 residue 25 THR Chi-restraints excluded: chain 1 residue 27 THR Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 1 residue 87 ASP Chi-restraints excluded: chain Z residue 13 PHE Chi-restraints excluded: chain Z residue 26 VAL Chi-restraints excluded: chain Z residue 27 THR Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Y residue 14 ASP Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 27 THR Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Y residue 66 LYS Chi-restraints excluded: chain Y residue 86 LYS Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 13 PHE Chi-restraints excluded: chain X residue 27 THR Chi-restraints excluded: chain X residue 60 ILE Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 87 ASP Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain R residue 13 PHE Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 32 MET Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain Q residue 66 LYS Chi-restraints excluded: chain Q residue 87 ASP Chi-restraints excluded: chain P residue 13 PHE Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain O residue 13 PHE Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain U residue 13 PHE Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 87 ASP Chi-restraints excluded: chain T residue 13 PHE Chi-restraints excluded: chain T residue 25 THR Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain T residue 54 LYS Chi-restraints excluded: chain T residue 87 ASP Chi-restraints excluded: chain S residue 13 PHE Chi-restraints excluded: chain S residue 25 THR Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain S residue 66 LYS Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 230 ILE Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 370 LEU Chi-restraints excluded: chain N residue 374 SER Chi-restraints excluded: chain M residue 185 ASP Chi-restraints excluded: chain M residue 195 PHE Chi-restraints excluded: chain M residue 401 LEU Chi-restraints excluded: chain M residue 409 GLU Chi-restraints excluded: chain L residue 185 ASP Chi-restraints excluded: chain L residue 195 PHE Chi-restraints excluded: chain L residue 230 ILE Chi-restraints excluded: chain L residue 250 ILE Chi-restraints excluded: chain L residue 289 LEU Chi-restraints excluded: chain L residue 343 ILE Chi-restraints excluded: chain L residue 374 SER Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 79 ASN Chi-restraints excluded: chain K residue 195 PHE Chi-restraints excluded: chain K residue 230 ILE Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 370 LEU Chi-restraints excluded: chain K residue 374 SER Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 195 PHE Chi-restraints excluded: chain J residue 230 ILE Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 328 LYS Chi-restraints excluded: chain J residue 370 LEU Chi-restraints excluded: chain J residue 374 SER Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 195 PHE Chi-restraints excluded: chain I residue 199 TYR Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 327 THR Chi-restraints excluded: chain I residue 343 ILE Chi-restraints excluded: chain I residue 370 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 525 ILE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 409 GLU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 268 LYS Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 327 THR Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 374 SER Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 195 PHE Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 424 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 809 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 478 optimal weight: 7.9990 chunk 613 optimal weight: 1.9990 chunk 475 optimal weight: 8.9990 chunk 706 optimal weight: 0.6980 chunk 468 optimal weight: 0.8980 chunk 836 optimal weight: 10.0000 chunk 523 optimal weight: 6.9990 chunk 510 optimal weight: 0.9980 chunk 386 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 79 ASN H 80 ASN ** X 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 231 GLN ** L 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 288 GLN K 79 ASN ** J 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 284 ASN E 243 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 66696 Z= 0.164 Angle : 0.529 15.491 89978 Z= 0.254 Chirality : 0.070 1.621 10850 Planarity : 0.002 0.040 11522 Dihedral : 6.147 164.776 9338 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 34.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.24 % Favored : 93.67 % Rotamer: Outliers : 2.47 % Allowed : 12.18 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.09), residues: 8736 helix: 1.91 (0.08), residues: 3990 sheet: -0.97 (0.15), residues: 1092 loop : -1.60 (0.10), residues: 3654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP H 44 HIS 0.001 0.000 HIS N 316 PHE 0.014 0.001 PHE S 13 TYR 0.010 0.001 TYR F 66 ARG 0.001 0.000 ARG O 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 977 residues out of total 7112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 801 time to evaluate : 5.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 178 LYS cc_start: 0.8540 (mtpt) cc_final: 0.7870 (mmtm) REVERT: H 183 LEU cc_start: 0.8675 (mm) cc_final: 0.8350 (tp) REVERT: H 332 MET cc_start: 0.8010 (mtp) cc_final: 0.7795 (tpp) REVERT: V 14 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.8092 (t0) REVERT: V 24 GLU cc_start: 0.7436 (tp30) cc_final: 0.7188 (tp30) REVERT: V 26 VAL cc_start: 0.7919 (OUTLIER) cc_final: 0.7621 (t) REVERT: V 93 ASP cc_start: 0.8351 (t0) cc_final: 0.7985 (t0) REVERT: 2 86 LYS cc_start: 0.8078 (mtpt) cc_final: 0.7679 (tttt) REVERT: 2 93 ASP cc_start: 0.8348 (t70) cc_final: 0.8075 (t0) REVERT: 1 43 GLN cc_start: 0.8445 (mp10) cc_final: 0.8096 (mp10) REVERT: 1 69 ASP cc_start: 0.7856 (m-30) cc_final: 0.7556 (m-30) REVERT: 1 93 ASP cc_start: 0.8288 (t70) cc_final: 0.8039 (t0) REVERT: Z 24 GLU cc_start: 0.7526 (tp30) cc_final: 0.7236 (tp30) REVERT: Z 26 VAL cc_start: 0.7807 (OUTLIER) cc_final: 0.7443 (t) REVERT: Z 32 MET cc_start: 0.7469 (mtp) cc_final: 0.7146 (ptm) REVERT: Z 80 LYS cc_start: 0.9013 (tptp) cc_final: 0.8502 (tptp) REVERT: Z 85 ASP cc_start: 0.7762 (m-30) cc_final: 0.7471 (m-30) REVERT: Z 86 LYS cc_start: 0.7797 (mtpt) cc_final: 0.7439 (tttt) REVERT: Z 87 ASP cc_start: 0.8536 (m-30) cc_final: 0.7874 (t0) REVERT: Y 32 MET cc_start: 0.7666 (ptp) cc_final: 0.7412 (ptm) REVERT: X 24 GLU cc_start: 0.7232 (tp30) cc_final: 0.6945 (tp30) REVERT: X 93 ASP cc_start: 0.8282 (t70) cc_final: 0.7758 (t0) REVERT: W 43 GLN cc_start: 0.8367 (mp10) cc_final: 0.8124 (mp10) REVERT: R 24 GLU cc_start: 0.7256 (tp30) cc_final: 0.6960 (tp30) REVERT: R 93 ASP cc_start: 0.8240 (t70) cc_final: 0.7954 (t0) REVERT: Q 32 MET cc_start: 0.7838 (ptm) cc_final: 0.7630 (ptp) REVERT: Q 42 LEU cc_start: 0.8444 (mt) cc_final: 0.8183 (mt) REVERT: Q 43 GLN cc_start: 0.8418 (mp10) cc_final: 0.7932 (mp10) REVERT: Q 69 ASP cc_start: 0.7735 (m-30) cc_final: 0.7399 (m-30) REVERT: P 32 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.7080 (ptm) REVERT: P 43 GLN cc_start: 0.8255 (mp10) cc_final: 0.7902 (mp10) REVERT: U 69 ASP cc_start: 0.7612 (m-30) cc_final: 0.7312 (m-30) REVERT: U 93 ASP cc_start: 0.8355 (t0) cc_final: 0.8131 (t0) REVERT: S 80 LYS cc_start: 0.9257 (tttm) cc_final: 0.8853 (tttm) REVERT: S 93 ASP cc_start: 0.8433 (t0) cc_final: 0.8035 (t0) REVERT: N 79 ASN cc_start: 0.8140 (t0) cc_final: 0.7836 (t0) REVERT: N 183 LEU cc_start: 0.8616 (mm) cc_final: 0.8295 (tp) REVERT: N 332 MET cc_start: 0.7821 (mtp) cc_final: 0.7467 (tpp) REVERT: N 342 GLN cc_start: 0.8152 (tt0) cc_final: 0.7914 (tm-30) REVERT: N 361 TYR cc_start: 0.7700 (t80) cc_final: 0.7480 (t80) REVERT: M 183 LEU cc_start: 0.8577 (mm) cc_final: 0.8270 (tp) REVERT: M 230 ILE cc_start: 0.8602 (pt) cc_final: 0.8274 (mt) REVERT: M 344 GLU cc_start: 0.8228 (tp30) cc_final: 0.7788 (tp30) REVERT: L 44 TRP cc_start: 0.8118 (p90) cc_final: 0.7764 (p90) REVERT: L 183 LEU cc_start: 0.8504 (mm) cc_final: 0.8135 (tp) REVERT: L 190 ILE cc_start: 0.8588 (mm) cc_final: 0.8343 (mt) REVERT: L 292 MET cc_start: 0.8715 (mtp) cc_final: 0.8392 (ttm) REVERT: L 342 GLN cc_start: 0.8361 (tt0) cc_final: 0.7917 (tm-30) REVERT: L 344 GLU cc_start: 0.8414 (tp30) cc_final: 0.7961 (tp30) REVERT: L 489 MET cc_start: 0.8846 (mmt) cc_final: 0.8550 (mmt) REVERT: J 344 GLU cc_start: 0.8228 (tp30) cc_final: 0.7832 (tp30) REVERT: I 190 ILE cc_start: 0.8435 (mm) cc_final: 0.8140 (mt) REVERT: I 332 MET cc_start: 0.8153 (mtp) cc_final: 0.7881 (tpp) REVERT: I 352 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7135 (pt0) REVERT: D 183 LEU cc_start: 0.8526 (mm) cc_final: 0.8216 (tp) REVERT: D 286 LYS cc_start: 0.8467 (mptt) cc_final: 0.8225 (mptt) REVERT: D 352 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7151 (pt0) REVERT: C 31 MET cc_start: 0.8450 (ttt) cc_final: 0.7756 (ttt) REVERT: C 183 LEU cc_start: 0.8657 (mm) cc_final: 0.8269 (tp) REVERT: C 230 ILE cc_start: 0.8558 (pt) cc_final: 0.8121 (mt) REVERT: C 332 MET cc_start: 0.7666 (ttm) cc_final: 0.7169 (ttm) REVERT: C 344 GLU cc_start: 0.8216 (tp30) cc_final: 0.7775 (tp30) REVERT: B 183 LEU cc_start: 0.8504 (mm) cc_final: 0.8184 (tp) REVERT: B 190 ILE cc_start: 0.8625 (mm) cc_final: 0.8351 (mt) REVERT: B 489 MET cc_start: 0.8929 (mmt) cc_final: 0.8707 (mmt) REVERT: A 183 LEU cc_start: 0.8490 (mm) cc_final: 0.8106 (tp) REVERT: A 286 LYS cc_start: 0.8483 (mptt) cc_final: 0.8265 (mmtm) REVERT: A 344 GLU cc_start: 0.8100 (tp30) cc_final: 0.7533 (tp30) REVERT: A 352 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7366 (pt0) REVERT: G 183 LEU cc_start: 0.8571 (mm) cc_final: 0.8195 (tp) REVERT: G 344 GLU cc_start: 0.8275 (tp30) cc_final: 0.8016 (tp30) REVERT: F 190 ILE cc_start: 0.8635 (mm) cc_final: 0.8309 (mt) REVERT: F 230 ILE cc_start: 0.8466 (pt) cc_final: 0.8055 (mt) REVERT: F 332 MET cc_start: 0.7993 (mtp) cc_final: 0.7526 (tpp) REVERT: F 344 GLU cc_start: 0.8269 (tp30) cc_final: 0.7909 (tp30) REVERT: F 352 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7597 (mp0) REVERT: E 183 LEU cc_start: 0.8590 (mm) cc_final: 0.8276 (tp) REVERT: E 389 GLU cc_start: 0.7617 (mp0) cc_final: 0.7092 (mp0) outliers start: 176 outliers final: 152 residues processed: 918 average time/residue: 0.6413 time to fit residues: 1004.1001 Evaluate side-chains 928 residues out of total 7112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 771 time to evaluate : 5.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 195 PHE Chi-restraints excluded: chain H residue 230 ILE Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 343 ILE Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 13 PHE Chi-restraints excluded: chain V residue 14 ASP Chi-restraints excluded: chain V residue 26 VAL Chi-restraints excluded: chain V residue 27 THR Chi-restraints excluded: chain 2 residue 12 LEU Chi-restraints excluded: chain 2 residue 13 PHE Chi-restraints excluded: chain 2 residue 25 THR Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 1 residue 13 PHE Chi-restraints excluded: chain 1 residue 27 THR Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 1 residue 87 ASP Chi-restraints excluded: chain Z residue 12 LEU Chi-restraints excluded: chain Z residue 13 PHE Chi-restraints excluded: chain Z residue 26 VAL Chi-restraints excluded: chain Z residue 27 THR Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Y residue 13 PHE Chi-restraints excluded: chain Y residue 14 ASP Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 27 THR Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Y residue 53 SER Chi-restraints excluded: chain Y residue 66 LYS Chi-restraints excluded: chain Y residue 87 ASP Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 13 PHE Chi-restraints excluded: chain X residue 27 THR Chi-restraints excluded: chain X residue 60 ILE Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain W residue 13 PHE Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 87 ASP Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain R residue 13 PHE Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 32 MET Chi-restraints excluded: chain R residue 87 ASP Chi-restraints excluded: chain Q residue 13 PHE Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain Q residue 66 LYS Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain P residue 13 PHE Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 32 MET Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain O residue 13 PHE Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain U residue 13 PHE Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 60 ILE Chi-restraints excluded: chain U residue 87 ASP Chi-restraints excluded: chain T residue 10 LEU Chi-restraints excluded: chain T residue 13 PHE Chi-restraints excluded: chain T residue 25 THR Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain T residue 87 ASP Chi-restraints excluded: chain S residue 13 PHE Chi-restraints excluded: chain S residue 25 THR Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 66 LYS Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 230 ILE Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 370 LEU Chi-restraints excluded: chain N residue 374 SER Chi-restraints excluded: chain M residue 185 ASP Chi-restraints excluded: chain M residue 195 PHE Chi-restraints excluded: chain M residue 401 LEU Chi-restraints excluded: chain M residue 409 GLU Chi-restraints excluded: chain L residue 185 ASP Chi-restraints excluded: chain L residue 195 PHE Chi-restraints excluded: chain L residue 230 ILE Chi-restraints excluded: chain L residue 250 ILE Chi-restraints excluded: chain L residue 289 LEU Chi-restraints excluded: chain L residue 343 ILE Chi-restraints excluded: chain L residue 374 SER Chi-restraints excluded: chain K residue 195 PHE Chi-restraints excluded: chain K residue 230 ILE Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 327 THR Chi-restraints excluded: chain K residue 370 LEU Chi-restraints excluded: chain K residue 374 SER Chi-restraints excluded: chain K residue 386 SER Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 195 PHE Chi-restraints excluded: chain J residue 199 TYR Chi-restraints excluded: chain J residue 230 ILE Chi-restraints excluded: chain J residue 328 LYS Chi-restraints excluded: chain J residue 370 LEU Chi-restraints excluded: chain J residue 374 SER Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 195 PHE Chi-restraints excluded: chain I residue 199 TYR Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 327 THR Chi-restraints excluded: chain I residue 343 ILE Chi-restraints excluded: chain I residue 370 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 525 ILE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 268 LYS Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 327 THR Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 374 SER Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 195 PHE Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 424 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 517 optimal weight: 6.9990 chunk 334 optimal weight: 5.9990 chunk 499 optimal weight: 4.9990 chunk 252 optimal weight: 5.9990 chunk 164 optimal weight: 8.9990 chunk 162 optimal weight: 10.0000 chunk 531 optimal weight: 8.9990 chunk 569 optimal weight: 0.4980 chunk 413 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 657 optimal weight: 0.7980 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 367 ASN X 4 GLN ** U 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 GLN L 80 ASN ** L 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 ASN K 243 HIS J 42 GLN J 231 GLN ** J 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 GLN ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 ASN B 367 ASN A 42 GLN G 42 GLN ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 367 ASN E 80 ASN E 367 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 66696 Z= 0.391 Angle : 0.647 15.618 89978 Z= 0.318 Chirality : 0.073 1.625 10850 Planarity : 0.003 0.043 11522 Dihedral : 6.315 141.696 9338 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 32.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.43 % Favored : 92.45 % Rotamer: Outliers : 2.47 % Allowed : 12.72 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.09), residues: 8736 helix: 1.25 (0.08), residues: 3948 sheet: -1.11 (0.15), residues: 1106 loop : -1.63 (0.10), residues: 3682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 44 HIS 0.002 0.001 HIS N 316 PHE 0.027 0.002 PHE M 104 TYR 0.015 0.002 TYR I 219 ARG 0.004 0.001 ARG K 422 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 7112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 781 time to evaluate : 5.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 183 LEU cc_start: 0.8691 (mm) cc_final: 0.8349 (tp) REVERT: V 14 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.8051 (t0) REVERT: V 24 GLU cc_start: 0.7410 (tp30) cc_final: 0.7193 (tp30) REVERT: V 26 VAL cc_start: 0.7853 (OUTLIER) cc_final: 0.7568 (t) REVERT: V 93 ASP cc_start: 0.8514 (t0) cc_final: 0.8065 (t0) REVERT: 2 86 LYS cc_start: 0.8086 (mtpt) cc_final: 0.7653 (tttt) REVERT: 2 93 ASP cc_start: 0.8429 (t70) cc_final: 0.8191 (t0) REVERT: 1 28 LYS cc_start: 0.8962 (ptmt) cc_final: 0.8505 (mmtt) REVERT: 1 43 GLN cc_start: 0.8452 (mp10) cc_final: 0.8190 (mp10) REVERT: 1 69 ASP cc_start: 0.7949 (m-30) cc_final: 0.7596 (m-30) REVERT: 1 93 ASP cc_start: 0.8386 (t70) cc_final: 0.8076 (t0) REVERT: Z 24 GLU cc_start: 0.7308 (tp30) cc_final: 0.6891 (tp30) REVERT: Z 26 VAL cc_start: 0.7799 (OUTLIER) cc_final: 0.7312 (t) REVERT: Z 28 LYS cc_start: 0.9036 (ptmt) cc_final: 0.8414 (mmtt) REVERT: Z 32 MET cc_start: 0.7512 (mtp) cc_final: 0.7117 (ptm) REVERT: Z 80 LYS cc_start: 0.8998 (tptp) cc_final: 0.8574 (tptp) REVERT: Z 85 ASP cc_start: 0.7961 (m-30) cc_final: 0.7716 (m-30) REVERT: Z 86 LYS cc_start: 0.7898 (mtpt) cc_final: 0.7507 (tttt) REVERT: Y 32 MET cc_start: 0.7619 (ptp) cc_final: 0.7369 (ptm) REVERT: Y 93 ASP cc_start: 0.8669 (t0) cc_final: 0.8451 (t0) REVERT: X 93 ASP cc_start: 0.8372 (t70) cc_final: 0.7811 (t0) REVERT: W 43 GLN cc_start: 0.8414 (mp10) cc_final: 0.8150 (mp10) REVERT: R 32 MET cc_start: 0.7650 (mtp) cc_final: 0.7053 (ptm) REVERT: R 93 ASP cc_start: 0.8357 (t70) cc_final: 0.8111 (t0) REVERT: Q 28 LYS cc_start: 0.8917 (ptmt) cc_final: 0.8494 (mmtt) REVERT: Q 42 LEU cc_start: 0.8550 (mt) cc_final: 0.8279 (mt) REVERT: Q 43 GLN cc_start: 0.8462 (mp10) cc_final: 0.8101 (mp10) REVERT: Q 69 ASP cc_start: 0.7712 (m-30) cc_final: 0.7364 (m-30) REVERT: Q 93 ASP cc_start: 0.8401 (t70) cc_final: 0.8103 (t0) REVERT: U 69 ASP cc_start: 0.7548 (m-30) cc_final: 0.7217 (m-30) REVERT: U 93 ASP cc_start: 0.8471 (t0) cc_final: 0.8194 (t0) REVERT: T 32 MET cc_start: 0.7689 (mtm) cc_final: 0.6990 (ptm) REVERT: T 93 ASP cc_start: 0.8555 (t70) cc_final: 0.8281 (t0) REVERT: S 28 LYS cc_start: 0.8898 (ptmm) cc_final: 0.8359 (mmtt) REVERT: S 43 GLN cc_start: 0.8322 (mp10) cc_final: 0.7863 (mp10) REVERT: S 80 LYS cc_start: 0.9265 (tttm) cc_final: 0.8841 (tttm) REVERT: S 93 ASP cc_start: 0.8537 (t0) cc_final: 0.8099 (t0) REVERT: N 79 ASN cc_start: 0.8384 (t0) cc_final: 0.8113 (t0) REVERT: N 183 LEU cc_start: 0.8559 (mm) cc_final: 0.8303 (tp) REVERT: N 286 LYS cc_start: 0.8410 (mptt) cc_final: 0.8192 (mmtm) REVERT: N 332 MET cc_start: 0.7770 (mtp) cc_final: 0.7316 (tpp) REVERT: N 342 GLN cc_start: 0.8144 (tt0) cc_final: 0.7886 (tm-30) REVERT: N 361 TYR cc_start: 0.7713 (t80) cc_final: 0.7477 (t80) REVERT: M 183 LEU cc_start: 0.8607 (mm) cc_final: 0.8300 (tp) REVERT: M 230 ILE cc_start: 0.8599 (pt) cc_final: 0.8210 (mt) REVERT: M 332 MET cc_start: 0.8099 (mtp) cc_final: 0.7866 (tpp) REVERT: M 344 GLU cc_start: 0.8268 (tp30) cc_final: 0.7809 (tp30) REVERT: L 44 TRP cc_start: 0.8213 (p90) cc_final: 0.7732 (p90) REVERT: L 183 LEU cc_start: 0.8498 (mm) cc_final: 0.8177 (tp) REVERT: L 292 MET cc_start: 0.8707 (mtp) cc_final: 0.8496 (ttm) REVERT: L 342 GLN cc_start: 0.8410 (tt0) cc_final: 0.7929 (tm-30) REVERT: L 344 GLU cc_start: 0.8432 (tp30) cc_final: 0.8213 (tp30) REVERT: K 342 GLN cc_start: 0.8218 (tt0) cc_final: 0.7878 (tm-30) REVERT: K 352 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7292 (pt0) REVERT: J 344 GLU cc_start: 0.8274 (tp30) cc_final: 0.8053 (tp30) REVERT: J 489 MET cc_start: 0.8918 (mmt) cc_final: 0.8549 (mmt) REVERT: I 332 MET cc_start: 0.8160 (mtp) cc_final: 0.7851 (tpp) REVERT: I 507 ASP cc_start: 0.7750 (m-30) cc_final: 0.7484 (m-30) REVERT: D 183 LEU cc_start: 0.8617 (mm) cc_final: 0.8256 (tp) REVERT: D 286 LYS cc_start: 0.8502 (mptt) cc_final: 0.8211 (mptt) REVERT: D 344 GLU cc_start: 0.8175 (tp30) cc_final: 0.7674 (tp30) REVERT: C 31 MET cc_start: 0.8707 (ttt) cc_final: 0.8104 (ttt) REVERT: C 183 LEU cc_start: 0.8633 (mm) cc_final: 0.8291 (tp) REVERT: C 230 ILE cc_start: 0.8558 (pt) cc_final: 0.8111 (mt) REVERT: C 308 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6915 (mt) REVERT: C 344 GLU cc_start: 0.8278 (tp30) cc_final: 0.7842 (tp30) REVERT: B 183 LEU cc_start: 0.8541 (mm) cc_final: 0.8217 (tp) REVERT: B 352 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7000 (pt0) REVERT: A 183 LEU cc_start: 0.8579 (mm) cc_final: 0.8189 (tp) REVERT: A 286 LYS cc_start: 0.8524 (mptt) cc_final: 0.8314 (mmtm) REVERT: A 342 GLN cc_start: 0.8259 (tt0) cc_final: 0.7911 (tm-30) REVERT: A 344 GLU cc_start: 0.8192 (tp30) cc_final: 0.7664 (tp30) REVERT: G 183 LEU cc_start: 0.8626 (mm) cc_final: 0.8239 (tp) REVERT: G 344 GLU cc_start: 0.8260 (tp30) cc_final: 0.7987 (tp30) REVERT: G 489 MET cc_start: 0.8748 (mmt) cc_final: 0.8474 (mmt) REVERT: F 230 ILE cc_start: 0.8496 (pt) cc_final: 0.8143 (mt) REVERT: F 332 MET cc_start: 0.7901 (mtp) cc_final: 0.7625 (tpp) REVERT: F 344 GLU cc_start: 0.8307 (tp30) cc_final: 0.7980 (tp30) REVERT: F 352 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: F 489 MET cc_start: 0.8674 (mmt) cc_final: 0.8466 (mmt) REVERT: E 183 LEU cc_start: 0.8580 (mm) cc_final: 0.8310 (tp) REVERT: E 389 GLU cc_start: 0.7592 (mp0) cc_final: 0.7145 (mp0) outliers start: 176 outliers final: 156 residues processed: 901 average time/residue: 0.6603 time to fit residues: 1012.1532 Evaluate side-chains 890 residues out of total 7112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 729 time to evaluate : 5.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain H residue 199 TYR Chi-restraints excluded: chain H residue 230 ILE Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 343 ILE Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain V residue 13 PHE Chi-restraints excluded: chain V residue 14 ASP Chi-restraints excluded: chain V residue 25 THR Chi-restraints excluded: chain V residue 26 VAL Chi-restraints excluded: chain V residue 27 THR Chi-restraints excluded: chain 2 residue 12 LEU Chi-restraints excluded: chain 2 residue 13 PHE Chi-restraints excluded: chain 2 residue 25 THR Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 87 ASP Chi-restraints excluded: chain 1 residue 25 THR Chi-restraints excluded: chain 1 residue 27 THR Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 1 residue 87 ASP Chi-restraints excluded: chain Z residue 12 LEU Chi-restraints excluded: chain Z residue 13 PHE Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 26 VAL Chi-restraints excluded: chain Z residue 27 THR Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Y residue 14 ASP Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 27 THR Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Y residue 66 LYS Chi-restraints excluded: chain Y residue 85 ASP Chi-restraints excluded: chain Y residue 87 ASP Chi-restraints excluded: chain X residue 13 PHE Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 27 THR Chi-restraints excluded: chain X residue 60 ILE Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 87 ASP Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain R residue 13 PHE Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 87 ASP Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain Q residue 66 LYS Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 13 PHE Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 85 ASP Chi-restraints excluded: chain U residue 13 PHE Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 87 ASP Chi-restraints excluded: chain T residue 25 THR Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain T residue 87 ASP Chi-restraints excluded: chain S residue 25 THR Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 66 LYS Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 230 ILE Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 343 ILE Chi-restraints excluded: chain N residue 370 LEU Chi-restraints excluded: chain N residue 374 SER Chi-restraints excluded: chain N residue 392 GLU Chi-restraints excluded: chain M residue 185 ASP Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 370 LEU Chi-restraints excluded: chain M residue 401 LEU Chi-restraints excluded: chain M residue 409 GLU Chi-restraints excluded: chain L residue 185 ASP Chi-restraints excluded: chain L residue 230 ILE Chi-restraints excluded: chain L residue 250 ILE Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 289 LEU Chi-restraints excluded: chain L residue 343 ILE Chi-restraints excluded: chain L residue 374 SER Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 79 ASN Chi-restraints excluded: chain K residue 195 PHE Chi-restraints excluded: chain K residue 230 ILE Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 327 THR Chi-restraints excluded: chain K residue 370 LEU Chi-restraints excluded: chain K residue 374 SER Chi-restraints excluded: chain K residue 386 SER Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 199 TYR Chi-restraints excluded: chain J residue 230 ILE Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 328 LYS Chi-restraints excluded: chain J residue 343 ILE Chi-restraints excluded: chain J residue 370 LEU Chi-restraints excluded: chain J residue 374 SER Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 195 PHE Chi-restraints excluded: chain I residue 199 TYR Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 327 THR Chi-restraints excluded: chain I residue 343 ILE Chi-restraints excluded: chain I residue 370 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 525 ILE Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 409 GLU Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 268 LYS Chi-restraints excluded: chain G residue 310 LEU Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 327 THR Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 374 SER Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 195 PHE Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 374 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 761 optimal weight: 0.6980 chunk 801 optimal weight: 5.9990 chunk 731 optimal weight: 10.0000 chunk 779 optimal weight: 2.9990 chunk 469 optimal weight: 4.9990 chunk 339 optimal weight: 0.8980 chunk 612 optimal weight: 0.0770 chunk 239 optimal weight: 0.4980 chunk 704 optimal weight: 3.9990 chunk 737 optimal weight: 9.9990 chunk 776 optimal weight: 0.8980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 4 GLN ** U 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 ASN K 80 ASN ** J 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 66696 Z= 0.112 Angle : 0.517 15.457 89978 Z= 0.249 Chirality : 0.070 1.611 10850 Planarity : 0.002 0.041 11522 Dihedral : 5.687 106.630 9338 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 35.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.33 % Favored : 94.57 % Rotamer: Outliers : 1.29 % Allowed : 14.10 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.09), residues: 8736 helix: 2.16 (0.09), residues: 3878 sheet: -0.93 (0.15), residues: 1148 loop : -1.49 (0.10), residues: 3710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 44 HIS 0.001 0.000 HIS N 316 PHE 0.016 0.001 PHE P 13 TYR 0.008 0.001 TYR G 66 ARG 0.001 0.000 ARG C 97 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 863 residues out of total 7112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 771 time to evaluate : 5.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 178 LYS cc_start: 0.8499 (mtpt) cc_final: 0.7871 (mmtm) REVERT: H 183 LEU cc_start: 0.8676 (mm) cc_final: 0.8345 (tp) REVERT: V 14 ASP cc_start: 0.8369 (m-30) cc_final: 0.8071 (t0) REVERT: V 24 GLU cc_start: 0.7269 (tp30) cc_final: 0.6940 (tp30) REVERT: V 93 ASP cc_start: 0.8467 (t0) cc_final: 0.8042 (t0) REVERT: 2 93 ASP cc_start: 0.8351 (t70) cc_final: 0.8126 (t0) REVERT: 1 43 GLN cc_start: 0.8389 (mp10) cc_final: 0.8097 (mp10) REVERT: 1 69 ASP cc_start: 0.7995 (m-30) cc_final: 0.7616 (m-30) REVERT: 1 93 ASP cc_start: 0.8331 (t70) cc_final: 0.8059 (t0) REVERT: Z 24 GLU cc_start: 0.7344 (tp30) cc_final: 0.7061 (tp30) REVERT: Z 32 MET cc_start: 0.7452 (mtp) cc_final: 0.7121 (ptp) REVERT: Z 85 ASP cc_start: 0.7920 (m-30) cc_final: 0.7692 (m-30) REVERT: Y 93 ASP cc_start: 0.8623 (t0) cc_final: 0.8399 (t0) REVERT: X 32 MET cc_start: 0.7442 (mtp) cc_final: 0.7180 (ptp) REVERT: X 93 ASP cc_start: 0.8339 (t70) cc_final: 0.7793 (t0) REVERT: W 43 GLN cc_start: 0.8326 (mp10) cc_final: 0.8104 (mp10) REVERT: R 32 MET cc_start: 0.7563 (mtp) cc_final: 0.6872 (ptm) REVERT: R 93 ASP cc_start: 0.8317 (t70) cc_final: 0.8083 (t0) REVERT: Q 32 MET cc_start: 0.7820 (ptm) cc_final: 0.7611 (ptp) REVERT: Q 42 LEU cc_start: 0.8486 (mt) cc_final: 0.8237 (mt) REVERT: Q 43 GLN cc_start: 0.8376 (mp10) cc_final: 0.7963 (mp10) REVERT: Q 69 ASP cc_start: 0.7701 (m-30) cc_final: 0.7364 (m-30) REVERT: Q 93 ASP cc_start: 0.8329 (t70) cc_final: 0.8056 (t0) REVERT: P 43 GLN cc_start: 0.8275 (mp10) cc_final: 0.7957 (mp10) REVERT: U 69 ASP cc_start: 0.7627 (m-30) cc_final: 0.7324 (m-30) REVERT: U 93 ASP cc_start: 0.8466 (t0) cc_final: 0.8223 (t0) REVERT: T 32 MET cc_start: 0.7543 (mtm) cc_final: 0.6891 (ptm) REVERT: T 93 ASP cc_start: 0.8504 (t70) cc_final: 0.8245 (t0) REVERT: S 93 ASP cc_start: 0.8505 (t0) cc_final: 0.8082 (t0) REVERT: N 79 ASN cc_start: 0.8119 (t0) cc_final: 0.7796 (t0) REVERT: N 183 LEU cc_start: 0.8571 (mm) cc_final: 0.8205 (tp) REVERT: N 219 TYR cc_start: 0.8620 (m-80) cc_final: 0.8276 (m-80) REVERT: N 286 LYS cc_start: 0.8379 (mptt) cc_final: 0.8166 (mmtm) REVERT: N 332 MET cc_start: 0.7718 (mtp) cc_final: 0.7466 (tpp) REVERT: N 342 GLN cc_start: 0.8161 (tt0) cc_final: 0.7947 (tm-30) REVERT: N 352 GLU cc_start: 0.7692 (mt-10) cc_final: 0.6964 (pt0) REVERT: M 183 LEU cc_start: 0.8575 (mm) cc_final: 0.8199 (tp) REVERT: M 230 ILE cc_start: 0.8582 (pt) cc_final: 0.8233 (mt) REVERT: M 344 GLU cc_start: 0.8244 (tp30) cc_final: 0.7814 (tp30) REVERT: L 183 LEU cc_start: 0.8510 (mm) cc_final: 0.8136 (tp) REVERT: L 190 ILE cc_start: 0.8553 (mm) cc_final: 0.8330 (mt) REVERT: L 292 MET cc_start: 0.8704 (mtp) cc_final: 0.8435 (ttm) REVERT: L 342 GLN cc_start: 0.8385 (tt0) cc_final: 0.7949 (tm-30) REVERT: L 344 GLU cc_start: 0.8379 (tp30) cc_final: 0.7949 (tp30) REVERT: K 84 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6351 (mp0) REVERT: K 342 GLN cc_start: 0.8192 (tt0) cc_final: 0.7883 (tm-30) REVERT: K 352 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7345 (pt0) REVERT: J 344 GLU cc_start: 0.8224 (tp30) cc_final: 0.7846 (tp30) REVERT: I 190 ILE cc_start: 0.8427 (mm) cc_final: 0.8125 (mt) REVERT: I 332 MET cc_start: 0.8130 (mtp) cc_final: 0.7859 (tpp) REVERT: D 183 LEU cc_start: 0.8545 (mm) cc_final: 0.8188 (tp) REVERT: D 286 LYS cc_start: 0.8493 (mptt) cc_final: 0.8164 (mptt) REVERT: C 183 LEU cc_start: 0.8590 (mm) cc_final: 0.8251 (tp) REVERT: C 230 ILE cc_start: 0.8506 (pt) cc_final: 0.8077 (mt) REVERT: C 344 GLU cc_start: 0.8236 (tp30) cc_final: 0.7822 (tp30) REVERT: C 394 LYS cc_start: 0.8601 (ttpt) cc_final: 0.8393 (ttpp) REVERT: C 453 MET cc_start: 0.7986 (mtp) cc_final: 0.7694 (mtt) REVERT: B 84 GLU cc_start: 0.6805 (mt-10) cc_final: 0.6568 (mt-10) REVERT: B 183 LEU cc_start: 0.8508 (mm) cc_final: 0.8186 (tp) REVERT: B 190 ILE cc_start: 0.8595 (mm) cc_final: 0.8328 (mt) REVERT: B 332 MET cc_start: 0.8042 (mtp) cc_final: 0.7752 (mtp) REVERT: A 183 LEU cc_start: 0.8501 (mm) cc_final: 0.8120 (tp) REVERT: A 193 MET cc_start: 0.7453 (mtp) cc_final: 0.7120 (mtp) REVERT: A 286 LYS cc_start: 0.8474 (mptt) cc_final: 0.8257 (mmtm) REVERT: A 342 GLN cc_start: 0.8215 (tt0) cc_final: 0.7901 (tm-30) REVERT: A 344 GLU cc_start: 0.8103 (tp30) cc_final: 0.7551 (tp30) REVERT: G 183 LEU cc_start: 0.8552 (mm) cc_final: 0.8174 (tp) REVERT: G 268 LYS cc_start: 0.7135 (OUTLIER) cc_final: 0.6329 (mptt) REVERT: G 344 GLU cc_start: 0.8215 (tp30) cc_final: 0.7966 (tp30) REVERT: F 166 MET cc_start: 0.8376 (mtt) cc_final: 0.8053 (mtt) REVERT: F 190 ILE cc_start: 0.8604 (mm) cc_final: 0.8286 (mt) REVERT: F 230 ILE cc_start: 0.8531 (pt) cc_final: 0.8138 (mt) REVERT: F 332 MET cc_start: 0.7989 (mtp) cc_final: 0.7496 (tpp) REVERT: F 344 GLU cc_start: 0.8319 (tp30) cc_final: 0.7978 (tp30) REVERT: F 352 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7596 (mp0) REVERT: F 386 SER cc_start: 0.9024 (p) cc_final: 0.8809 (t) REVERT: E 183 LEU cc_start: 0.8562 (mm) cc_final: 0.8306 (tp) REVERT: E 389 GLU cc_start: 0.7607 (mp0) cc_final: 0.7164 (mp0) outliers start: 92 outliers final: 81 residues processed: 837 average time/residue: 0.6589 time to fit residues: 942.7021 Evaluate side-chains 819 residues out of total 7112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 736 time to evaluate : 5.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 195 PHE Chi-restraints excluded: chain H residue 230 ILE Chi-restraints excluded: chain V residue 13 PHE Chi-restraints excluded: chain V residue 27 THR Chi-restraints excluded: chain 2 residue 12 LEU Chi-restraints excluded: chain 2 residue 13 PHE Chi-restraints excluded: chain 2 residue 25 THR Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 37 SER Chi-restraints excluded: chain 2 residue 80 LYS Chi-restraints excluded: chain 1 residue 25 THR Chi-restraints excluded: chain 1 residue 27 THR Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain Z residue 13 PHE Chi-restraints excluded: chain Z residue 27 THR Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Y residue 13 PHE Chi-restraints excluded: chain Y residue 27 THR Chi-restraints excluded: chain Y residue 66 LYS Chi-restraints excluded: chain X residue 13 PHE Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain R residue 13 PHE Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain Q residue 13 PHE Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain Q residue 66 LYS Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain P residue 13 PHE Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain O residue 4 GLN Chi-restraints excluded: chain O residue 13 PHE Chi-restraints excluded: chain O residue 14 ASP Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain U residue 13 PHE Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain T residue 10 LEU Chi-restraints excluded: chain T residue 13 PHE Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain S residue 13 PHE Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain N residue 230 ILE Chi-restraints excluded: chain N residue 370 LEU Chi-restraints excluded: chain L residue 250 ILE Chi-restraints excluded: chain L residue 289 LEU Chi-restraints excluded: chain L residue 374 SER Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 195 PHE Chi-restraints excluded: chain K residue 327 THR Chi-restraints excluded: chain K residue 370 LEU Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 230 ILE Chi-restraints excluded: chain J residue 328 LYS Chi-restraints excluded: chain J residue 370 LEU Chi-restraints excluded: chain I residue 195 PHE Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 370 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 525 ILE Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain G residue 268 LYS Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 327 THR Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 374 SER Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 195 PHE Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 374 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 511 optimal weight: 4.9990 chunk 824 optimal weight: 6.9990 chunk 503 optimal weight: 1.9990 chunk 391 optimal weight: 1.9990 chunk 573 optimal weight: 9.9990 chunk 864 optimal weight: 0.9980 chunk 795 optimal weight: 0.8980 chunk 688 optimal weight: 0.0170 chunk 71 optimal weight: 9.9990 chunk 531 optimal weight: 5.9990 chunk 422 optimal weight: 10.0000 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 367 ASN ** L 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 66696 Z= 0.155 Angle : 0.526 15.523 89978 Z= 0.253 Chirality : 0.070 1.621 10850 Planarity : 0.002 0.044 11522 Dihedral : 5.473 91.719 9338 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 35.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.20 % Favored : 93.69 % Rotamer: Outliers : 1.14 % Allowed : 14.55 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.09), residues: 8736 helix: 2.25 (0.08), residues: 3892 sheet: -0.83 (0.15), residues: 1148 loop : -1.45 (0.10), residues: 3696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 44 HIS 0.002 0.000 HIS N 316 PHE 0.017 0.001 PHE P 13 TYR 0.010 0.001 TYR F 66 ARG 0.004 0.000 ARG O 7 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 7112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 753 time to evaluate : 5.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 178 LYS cc_start: 0.8526 (mtpt) cc_final: 0.7894 (mmtm) REVERT: H 183 LEU cc_start: 0.8670 (mm) cc_final: 0.8333 (tp) REVERT: V 14 ASP cc_start: 0.8385 (m-30) cc_final: 0.8075 (t0) REVERT: V 24 GLU cc_start: 0.7263 (tp30) cc_final: 0.7009 (tp30) REVERT: V 93 ASP cc_start: 0.8478 (t0) cc_final: 0.8032 (t0) REVERT: 1 43 GLN cc_start: 0.8395 (mp10) cc_final: 0.8102 (mp10) REVERT: 1 69 ASP cc_start: 0.8027 (m-30) cc_final: 0.7645 (m-30) REVERT: 1 93 ASP cc_start: 0.8335 (t70) cc_final: 0.8083 (t0) REVERT: Z 32 MET cc_start: 0.7393 (mtp) cc_final: 0.7075 (ptp) REVERT: Z 85 ASP cc_start: 0.7897 (m-30) cc_final: 0.7674 (m-30) REVERT: Y 93 ASP cc_start: 0.8644 (t0) cc_final: 0.8409 (t0) REVERT: X 32 MET cc_start: 0.7523 (mtp) cc_final: 0.7189 (ptp) REVERT: X 93 ASP cc_start: 0.8346 (t70) cc_final: 0.7816 (t0) REVERT: W 43 GLN cc_start: 0.8348 (mp10) cc_final: 0.8099 (mp10) REVERT: R 32 MET cc_start: 0.7626 (mtp) cc_final: 0.6960 (ptm) REVERT: R 93 ASP cc_start: 0.8319 (t70) cc_final: 0.8112 (t0) REVERT: Q 28 LYS cc_start: 0.8860 (ptmt) cc_final: 0.8305 (mmtt) REVERT: Q 32 MET cc_start: 0.7902 (ptm) cc_final: 0.7684 (ptp) REVERT: Q 42 LEU cc_start: 0.8506 (mt) cc_final: 0.8221 (mt) REVERT: Q 43 GLN cc_start: 0.8475 (mp10) cc_final: 0.8059 (mp10) REVERT: Q 69 ASP cc_start: 0.7687 (m-30) cc_final: 0.7347 (m-30) REVERT: Q 93 ASP cc_start: 0.8333 (t70) cc_final: 0.8084 (t0) REVERT: P 32 MET cc_start: 0.7739 (mtp) cc_final: 0.7007 (ptm) REVERT: O 28 LYS cc_start: 0.8935 (ptmt) cc_final: 0.8405 (mmtt) REVERT: U 69 ASP cc_start: 0.7634 (m-30) cc_final: 0.7326 (m-30) REVERT: U 93 ASP cc_start: 0.8486 (t0) cc_final: 0.8240 (t0) REVERT: T 32 MET cc_start: 0.7486 (mtm) cc_final: 0.6862 (ptm) REVERT: T 93 ASP cc_start: 0.8520 (t70) cc_final: 0.8251 (t0) REVERT: S 93 ASP cc_start: 0.8510 (t0) cc_final: 0.8090 (t0) REVERT: N 183 LEU cc_start: 0.8567 (mm) cc_final: 0.8202 (tp) REVERT: N 219 TYR cc_start: 0.8617 (m-80) cc_final: 0.8259 (m-80) REVERT: N 286 LYS cc_start: 0.8371 (mptt) cc_final: 0.8161 (mmtm) REVERT: N 332 MET cc_start: 0.7778 (mtp) cc_final: 0.7448 (tpp) REVERT: N 342 GLN cc_start: 0.8154 (tt0) cc_final: 0.7948 (tm-30) REVERT: M 183 LEU cc_start: 0.8599 (mm) cc_final: 0.8278 (tp) REVERT: M 230 ILE cc_start: 0.8633 (pt) cc_final: 0.8242 (mt) REVERT: M 344 GLU cc_start: 0.8201 (tp30) cc_final: 0.7745 (tp30) REVERT: L 183 LEU cc_start: 0.8541 (mm) cc_final: 0.8164 (tp) REVERT: L 190 ILE cc_start: 0.8550 (mm) cc_final: 0.8319 (mt) REVERT: L 292 MET cc_start: 0.8705 (mtp) cc_final: 0.8473 (ttm) REVERT: L 342 GLN cc_start: 0.8357 (tt0) cc_final: 0.7888 (tm-30) REVERT: L 344 GLU cc_start: 0.8369 (tp30) cc_final: 0.7916 (tp30) REVERT: K 342 GLN cc_start: 0.8188 (tt0) cc_final: 0.7883 (tm-30) REVERT: K 352 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7269 (pt0) REVERT: J 344 GLU cc_start: 0.8256 (tp30) cc_final: 0.7862 (tp30) REVERT: I 190 ILE cc_start: 0.8430 (mm) cc_final: 0.8131 (mt) REVERT: I 332 MET cc_start: 0.8120 (mtp) cc_final: 0.7818 (tpp) REVERT: D 183 LEU cc_start: 0.8557 (mm) cc_final: 0.8185 (tp) REVERT: D 286 LYS cc_start: 0.8493 (mptt) cc_final: 0.8168 (mptt) REVERT: C 183 LEU cc_start: 0.8617 (mm) cc_final: 0.8260 (tp) REVERT: C 230 ILE cc_start: 0.8546 (pt) cc_final: 0.8105 (mt) REVERT: C 344 GLU cc_start: 0.8256 (tp30) cc_final: 0.7829 (tp30) REVERT: B 183 LEU cc_start: 0.8524 (mm) cc_final: 0.8205 (tp) REVERT: B 190 ILE cc_start: 0.8596 (mm) cc_final: 0.8331 (mt) REVERT: A 183 LEU cc_start: 0.8538 (mm) cc_final: 0.8157 (tp) REVERT: A 193 MET cc_start: 0.7476 (mtp) cc_final: 0.7143 (mtp) REVERT: A 286 LYS cc_start: 0.8540 (mptt) cc_final: 0.8327 (mmtm) REVERT: A 342 GLN cc_start: 0.8202 (tt0) cc_final: 0.7853 (tm-30) REVERT: A 344 GLU cc_start: 0.8133 (tp30) cc_final: 0.7583 (tp30) REVERT: G 183 LEU cc_start: 0.8577 (mm) cc_final: 0.8210 (tp) REVERT: G 268 LYS cc_start: 0.7159 (OUTLIER) cc_final: 0.6428 (mptt) REVERT: G 332 MET cc_start: 0.8204 (mtp) cc_final: 0.7963 (tpp) REVERT: G 344 GLU cc_start: 0.8232 (tp30) cc_final: 0.7970 (tp30) REVERT: F 166 MET cc_start: 0.8374 (mtt) cc_final: 0.8074 (mtt) REVERT: F 190 ILE cc_start: 0.8610 (mm) cc_final: 0.8287 (mt) REVERT: F 230 ILE cc_start: 0.8496 (pt) cc_final: 0.8164 (mt) REVERT: F 332 MET cc_start: 0.7991 (mtp) cc_final: 0.7520 (tpp) REVERT: F 344 GLU cc_start: 0.8323 (tp30) cc_final: 0.7962 (tp30) REVERT: F 352 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: E 389 GLU cc_start: 0.7615 (mp0) cc_final: 0.7172 (mp0) outliers start: 81 outliers final: 75 residues processed: 817 average time/residue: 0.6389 time to fit residues: 893.1984 Evaluate side-chains 813 residues out of total 7112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 736 time to evaluate : 5.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 230 ILE Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain V residue 13 PHE Chi-restraints excluded: chain V residue 27 THR Chi-restraints excluded: chain 2 residue 12 LEU Chi-restraints excluded: chain 2 residue 13 PHE Chi-restraints excluded: chain 2 residue 25 THR Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 37 SER Chi-restraints excluded: chain 2 residue 80 LYS Chi-restraints excluded: chain 1 residue 25 THR Chi-restraints excluded: chain 1 residue 27 THR Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain Z residue 13 PHE Chi-restraints excluded: chain Z residue 27 THR Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Y residue 27 THR Chi-restraints excluded: chain X residue 13 PHE Chi-restraints excluded: chain W residue 13 PHE Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain R residue 13 PHE Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain Q residue 66 LYS Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain O residue 13 PHE Chi-restraints excluded: chain O residue 14 ASP Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain U residue 13 PHE Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain T residue 10 LEU Chi-restraints excluded: chain T residue 13 PHE Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain T residue 87 ASP Chi-restraints excluded: chain S residue 25 THR Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain N residue 230 ILE Chi-restraints excluded: chain N residue 370 LEU Chi-restraints excluded: chain N residue 388 VAL Chi-restraints excluded: chain L residue 230 ILE Chi-restraints excluded: chain L residue 250 ILE Chi-restraints excluded: chain L residue 289 LEU Chi-restraints excluded: chain L residue 374 SER Chi-restraints excluded: chain K residue 195 PHE Chi-restraints excluded: chain K residue 230 ILE Chi-restraints excluded: chain K residue 327 THR Chi-restraints excluded: chain K residue 370 LEU Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 230 ILE Chi-restraints excluded: chain J residue 328 LYS Chi-restraints excluded: chain J residue 370 LEU Chi-restraints excluded: chain I residue 195 PHE Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 370 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 525 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain G residue 268 LYS Chi-restraints excluded: chain G residue 327 THR Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 374 SER Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 195 PHE Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 374 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 546 optimal weight: 4.9990 chunk 733 optimal weight: 0.7980 chunk 210 optimal weight: 6.9990 chunk 634 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 191 optimal weight: 6.9990 chunk 689 optimal weight: 5.9990 chunk 288 optimal weight: 0.2980 chunk 708 optimal weight: 5.9990 chunk 87 optimal weight: 20.0000 chunk 127 optimal weight: 6.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 4 GLN ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 4 GLN ** U 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 243 HIS ** J 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.122202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.085368 restraints weight = 115813.467| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.27 r_work: 0.2945 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 66696 Z= 0.287 Angle : 0.586 15.733 89978 Z= 0.286 Chirality : 0.071 1.619 10850 Planarity : 0.003 0.044 11522 Dihedral : 5.681 89.689 9338 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 33.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.18 % Favored : 92.71 % Rotamer: Outliers : 1.39 % Allowed : 14.51 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.09), residues: 8736 helix: 1.82 (0.08), residues: 3920 sheet: -0.82 (0.15), residues: 1106 loop : -1.50 (0.10), residues: 3710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 44 HIS 0.002 0.000 HIS N 316 PHE 0.021 0.002 PHE G 104 TYR 0.013 0.002 TYR F 66 ARG 0.003 0.000 ARG K 422 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17751.12 seconds wall clock time: 312 minutes 1.08 seconds (18721.08 seconds total)