Starting phenix.real_space_refine on Wed Apr 17 12:13:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ey6_31321/04_2024/7ey6_31321.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ey6_31321/04_2024/7ey6_31321.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ey6_31321/04_2024/7ey6_31321.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ey6_31321/04_2024/7ey6_31321.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ey6_31321/04_2024/7ey6_31321.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ey6_31321/04_2024/7ey6_31321.pdb" } resolution = 4.3 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 ------------------------------------------------------------------------------- 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= 0.013 sd= 2.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 204 5.16 5 C 27756 2.51 5 N 7428 2.21 5 O 8640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A GLU 199": "OE1" <-> "OE2" Residue "A ARG 258": "NH1" <-> "NH2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A GLU 380": "OE1" <-> "OE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A ARG 435": "NH1" <-> "NH2" Residue "A ARG 444": "NH1" <-> "NH2" Residue "B TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B ARG 258": "NH1" <-> "NH2" Residue "B GLU 262": "OE1" <-> "OE2" Residue "B ARG 266": "NH1" <-> "NH2" Residue "B GLU 284": "OE1" <-> "OE2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "B ARG 364": "NH1" <-> "NH2" Residue "B GLU 367": "OE1" <-> "OE2" Residue "B GLU 380": "OE1" <-> "OE2" Residue "B GLU 431": "OE1" <-> "OE2" Residue "B ARG 435": "NH1" <-> "NH2" Residue "B ARG 444": "NH1" <-> "NH2" Residue "C TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C ARG 258": "NH1" <-> "NH2" Residue "C GLU 262": "OE1" <-> "OE2" Residue "C ARG 266": "NH1" <-> "NH2" Residue "C GLU 284": "OE1" <-> "OE2" Residue "C GLU 325": "OE1" <-> "OE2" Residue "C ARG 364": "NH1" <-> "NH2" Residue "C GLU 367": "OE1" <-> "OE2" Residue "C GLU 380": "OE1" <-> "OE2" Residue "C GLU 431": "OE1" <-> "OE2" Residue "C ARG 435": "NH1" <-> "NH2" Residue "C ARG 444": "NH1" <-> "NH2" Residue "D TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 182": "NH1" <-> "NH2" Residue "D GLU 199": "OE1" <-> "OE2" Residue "D ARG 258": "NH1" <-> "NH2" Residue "D GLU 262": "OE1" <-> "OE2" Residue "D ARG 266": "NH1" <-> "NH2" Residue "D GLU 284": "OE1" <-> "OE2" Residue "D GLU 325": "OE1" <-> "OE2" Residue "D ARG 364": "NH1" <-> "NH2" Residue "D GLU 367": "OE1" <-> "OE2" Residue "D GLU 380": "OE1" <-> "OE2" Residue "D GLU 431": "OE1" <-> "OE2" Residue "D ARG 435": "NH1" <-> "NH2" Residue "D ARG 444": "NH1" <-> "NH2" Residue "E TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 182": "NH1" <-> "NH2" Residue "E GLU 199": "OE1" <-> "OE2" Residue "E ARG 258": "NH1" <-> "NH2" Residue "E GLU 262": "OE1" <-> "OE2" Residue "E ARG 266": "NH1" <-> "NH2" Residue "E GLU 284": "OE1" <-> "OE2" Residue "E GLU 325": "OE1" <-> "OE2" Residue "E ARG 364": "NH1" <-> "NH2" Residue "E GLU 367": "OE1" <-> "OE2" Residue "E GLU 380": "OE1" <-> "OE2" Residue "E GLU 431": "OE1" <-> "OE2" Residue "E ARG 435": "NH1" <-> "NH2" Residue "E ARG 444": "NH1" <-> "NH2" Residue "F TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 182": "NH1" <-> "NH2" Residue "F GLU 199": "OE1" <-> "OE2" Residue "F ARG 258": "NH1" <-> "NH2" Residue "F GLU 262": "OE1" <-> "OE2" Residue "F ARG 266": "NH1" <-> "NH2" Residue "F GLU 284": "OE1" <-> "OE2" Residue "F GLU 325": "OE1" <-> "OE2" Residue "F ARG 364": "NH1" <-> "NH2" Residue "F GLU 367": "OE1" <-> "OE2" Residue "F GLU 380": "OE1" <-> "OE2" Residue "F GLU 431": "OE1" <-> "OE2" Residue "F ARG 435": "NH1" <-> "NH2" Residue "F ARG 444": "NH1" <-> "NH2" Residue "G TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 182": "NH1" <-> "NH2" Residue "G GLU 199": "OE1" <-> "OE2" Residue "G ARG 258": "NH1" <-> "NH2" Residue "G GLU 262": "OE1" <-> "OE2" Residue "G ARG 266": "NH1" <-> "NH2" Residue "G GLU 284": "OE1" <-> "OE2" Residue "G GLU 325": "OE1" <-> "OE2" Residue "G ARG 364": "NH1" <-> "NH2" Residue "G GLU 367": "OE1" <-> "OE2" Residue "G GLU 380": "OE1" <-> "OE2" Residue "G GLU 431": "OE1" <-> "OE2" Residue "G ARG 435": "NH1" <-> "NH2" Residue "G ARG 444": "NH1" <-> "NH2" Residue "H TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 182": "NH1" <-> "NH2" Residue "H GLU 199": "OE1" <-> "OE2" Residue "H ARG 258": "NH1" <-> "NH2" Residue "H GLU 262": "OE1" <-> "OE2" Residue "H ARG 266": "NH1" <-> "NH2" Residue "H GLU 284": "OE1" <-> "OE2" Residue "H GLU 325": "OE1" <-> "OE2" Residue "H ARG 364": "NH1" <-> "NH2" Residue "H GLU 367": "OE1" <-> "OE2" Residue "H GLU 380": "OE1" <-> "OE2" Residue "H GLU 431": "OE1" <-> "OE2" Residue "H ARG 435": "NH1" <-> "NH2" Residue "H ARG 444": "NH1" <-> "NH2" Residue "I TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 182": "NH1" <-> "NH2" Residue "I GLU 199": "OE1" <-> "OE2" Residue "I ARG 258": "NH1" <-> "NH2" Residue "I GLU 262": "OE1" <-> "OE2" Residue "I ARG 266": "NH1" <-> "NH2" Residue "I GLU 284": "OE1" <-> "OE2" Residue "I GLU 325": "OE1" <-> "OE2" Residue "I ARG 364": "NH1" <-> "NH2" Residue "I GLU 367": "OE1" <-> "OE2" Residue "I GLU 380": "OE1" <-> "OE2" Residue "I GLU 431": "OE1" <-> "OE2" Residue "I ARG 435": "NH1" <-> "NH2" Residue "I ARG 444": "NH1" <-> "NH2" Residue "J TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 182": "NH1" <-> "NH2" Residue "J GLU 199": "OE1" <-> "OE2" Residue "J ARG 258": "NH1" <-> "NH2" Residue "J GLU 262": "OE1" <-> "OE2" Residue "J ARG 266": "NH1" <-> "NH2" Residue "J GLU 284": "OE1" <-> "OE2" Residue "J GLU 325": "OE1" <-> "OE2" Residue "J ARG 364": "NH1" <-> "NH2" Residue "J GLU 367": "OE1" <-> "OE2" Residue "J GLU 380": "OE1" <-> "OE2" Residue "J GLU 431": "OE1" <-> "OE2" Residue "J ARG 435": "NH1" <-> "NH2" Residue "J ARG 444": "NH1" <-> "NH2" Residue "K TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 182": "NH1" <-> "NH2" Residue "K GLU 199": "OE1" <-> "OE2" Residue "K ARG 258": "NH1" <-> "NH2" Residue "K GLU 262": "OE1" <-> "OE2" Residue "K ARG 266": "NH1" <-> "NH2" Residue "K GLU 284": "OE1" <-> "OE2" Residue "K GLU 325": "OE1" <-> "OE2" Residue "K ARG 364": "NH1" <-> "NH2" Residue "K GLU 367": "OE1" <-> "OE2" Residue "K GLU 380": "OE1" <-> "OE2" Residue "K GLU 431": "OE1" <-> "OE2" Residue "K ARG 435": "NH1" <-> "NH2" Residue "K ARG 444": "NH1" <-> "NH2" Residue "L TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 182": "NH1" <-> "NH2" Residue "L GLU 199": "OE1" <-> "OE2" Residue "L ARG 258": "NH1" <-> "NH2" Residue "L GLU 262": "OE1" <-> "OE2" Residue "L ARG 266": "NH1" <-> "NH2" Residue "L GLU 284": "OE1" <-> "OE2" Residue "L GLU 325": "OE1" <-> "OE2" Residue "L ARG 364": "NH1" <-> "NH2" Residue "L GLU 367": "OE1" <-> "OE2" Residue "L GLU 380": "OE1" <-> "OE2" Residue "L GLU 431": "OE1" <-> "OE2" Residue "L ARG 435": "NH1" <-> "NH2" Residue "L ARG 444": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 44028 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3669 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 22, 'TRANS': 446} Chain breaks: 1 Chain: "B" Number of atoms: 3669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3669 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 22, 'TRANS': 446} Chain breaks: 1 Chain: "C" Number of atoms: 3669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3669 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 22, 'TRANS': 446} Chain breaks: 1 Chain: "D" Number of atoms: 3669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3669 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 22, 'TRANS': 446} Chain breaks: 1 Chain: "E" Number of atoms: 3669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3669 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 22, 'TRANS': 446} Chain breaks: 1 Chain: "F" Number of atoms: 3669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3669 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 22, 'TRANS': 446} Chain breaks: 1 Chain: "G" Number of atoms: 3669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3669 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 22, 'TRANS': 446} Chain breaks: 1 Chain: "H" Number of atoms: 3669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3669 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 22, 'TRANS': 446} Chain breaks: 1 Chain: "I" Number of atoms: 3669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3669 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 22, 'TRANS': 446} Chain breaks: 1 Chain: "J" Number of atoms: 3669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3669 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 22, 'TRANS': 446} Chain breaks: 1 Chain: "K" Number of atoms: 3669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3669 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 22, 'TRANS': 446} Chain breaks: 1 Chain: "L" Number of atoms: 3669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3669 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 22, 'TRANS': 446} Chain breaks: 1 Time building chain proxies: 21.97, per 1000 atoms: 0.50 Number of scatterers: 44028 At special positions: 0 Unit cell: (189.23, 189.23, 118.11, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 204 16.00 O 8640 8.00 N 7428 7.00 C 27756 6.00 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: 18.70 Conformation dependent library (CDL) restraints added in 8.3 seconds 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10512 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 60 sheets defined 51.8% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.41 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 removed outlier: 3.851A pdb=" N ALA A 9 " --> pdb=" O THR A 6 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU A 10 " --> pdb=" O GLY A 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 6 through 10' Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.647A pdb=" N ASP A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Proline residue: A 26 - end of helix Processing helix chain 'A' and resid 40 through 43 removed outlier: 3.696A pdb=" N PHE A 43 " --> pdb=" O PRO A 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 40 through 43' Processing helix chain 'A' and resid 60 through 78 Processing helix chain 'A' and resid 91 through 96 Processing helix chain 'A' and resid 99 through 124 removed outlier: 3.717A pdb=" N LEU A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 140 Processing helix chain 'A' and resid 191 through 202 removed outlier: 3.521A pdb=" N GLN A 201 " --> pdb=" O ALA A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 272 removed outlier: 4.016A pdb=" N GLU A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR A 272 " --> pdb=" O TYR A 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 267 through 272' Processing helix chain 'A' and resid 272 through 295 removed outlier: 3.599A pdb=" N LYS A 295 " --> pdb=" O MET A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 314 removed outlier: 4.268A pdb=" N LEU A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 357 Processing helix chain 'A' and resid 372 through 385 removed outlier: 4.086A pdb=" N TYR A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A 379 " --> pdb=" O ARG A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 396 removed outlier: 3.609A pdb=" N ILE A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 412 removed outlier: 3.523A pdb=" N GLN A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 451 Processing helix chain 'A' and resid 462 through 474 removed outlier: 4.163A pdb=" N ILE A 474 " --> pdb=" O ILE A 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 10 removed outlier: 3.852A pdb=" N ALA B 9 " --> pdb=" O THR B 6 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU B 10 " --> pdb=" O GLY B 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 6 through 10' Processing helix chain 'B' and resid 12 through 39 removed outlier: 3.646A pdb=" N ASP B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Proline residue: B 26 - end of helix Processing helix chain 'B' and resid 40 through 43 removed outlier: 3.696A pdb=" N PHE B 43 " --> pdb=" O PRO B 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 43' Processing helix chain 'B' and resid 60 through 78 Processing helix chain 'B' and resid 91 through 96 Processing helix chain 'B' and resid 99 through 124 removed outlier: 3.716A pdb=" N LEU B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 140 Processing helix chain 'B' and resid 191 through 202 removed outlier: 3.520A pdb=" N GLN B 201 " --> pdb=" O ALA B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 272 removed outlier: 4.018A pdb=" N GLU B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR B 272 " --> pdb=" O TYR B 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 267 through 272' Processing helix chain 'B' and resid 272 through 295 removed outlier: 3.599A pdb=" N LYS B 295 " --> pdb=" O MET B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 314 removed outlier: 4.269A pdb=" N LEU B 311 " --> pdb=" O GLN B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 357 Processing helix chain 'B' and resid 372 through 385 removed outlier: 4.086A pdb=" N TYR B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER B 379 " --> pdb=" O ARG B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 396 removed outlier: 3.609A pdb=" N ILE B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 412 removed outlier: 3.523A pdb=" N GLN B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA B 410 " --> pdb=" O LYS B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 451 Processing helix chain 'B' and resid 462 through 474 removed outlier: 4.161A pdb=" N ILE B 474 " --> pdb=" O ILE B 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 10 removed outlier: 3.851A pdb=" N ALA C 9 " --> pdb=" O THR C 6 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU C 10 " --> pdb=" O GLY C 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 6 through 10' Processing helix chain 'C' and resid 12 through 39 removed outlier: 3.646A pdb=" N ASP C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Proline residue: C 26 - end of helix Processing helix chain 'C' and resid 40 through 43 removed outlier: 3.696A pdb=" N PHE C 43 " --> pdb=" O PRO C 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 40 through 43' Processing helix chain 'C' and resid 60 through 78 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'C' and resid 99 through 124 removed outlier: 3.717A pdb=" N LEU C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 140 Processing helix chain 'C' and resid 191 through 202 removed outlier: 3.521A pdb=" N GLN C 201 " --> pdb=" O ALA C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 272 removed outlier: 4.015A pdb=" N GLU C 271 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR C 272 " --> pdb=" O TYR C 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 267 through 272' Processing helix chain 'C' and resid 272 through 295 removed outlier: 3.600A pdb=" N LYS C 295 " --> pdb=" O MET C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 314 removed outlier: 4.268A pdb=" N LEU C 311 " --> pdb=" O GLN C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 357 Processing helix chain 'C' and resid 372 through 385 removed outlier: 4.086A pdb=" N TYR C 376 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 379 " --> pdb=" O ARG C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 396 removed outlier: 3.609A pdb=" N ILE C 391 " --> pdb=" O GLY C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 412 removed outlier: 3.523A pdb=" N GLN C 409 " --> pdb=" O LEU C 405 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA C 410 " --> pdb=" O LYS C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 451 Processing helix chain 'C' and resid 462 through 474 removed outlier: 4.162A pdb=" N ILE C 474 " --> pdb=" O ILE C 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 10 removed outlier: 3.852A pdb=" N ALA D 9 " --> pdb=" O THR D 6 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU D 10 " --> pdb=" O GLY D 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 6 through 10' Processing helix chain 'D' and resid 12 through 39 removed outlier: 3.646A pdb=" N ASP D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) Proline residue: D 26 - end of helix Processing helix chain 'D' and resid 40 through 43 removed outlier: 3.697A pdb=" N PHE D 43 " --> pdb=" O PRO D 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 40 through 43' Processing helix chain 'D' and resid 60 through 78 Processing helix chain 'D' and resid 91 through 96 Processing helix chain 'D' and resid 99 through 124 removed outlier: 3.717A pdb=" N LEU D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 140 Processing helix chain 'D' and resid 191 through 202 removed outlier: 3.522A pdb=" N GLN D 201 " --> pdb=" O ALA D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 272 removed outlier: 4.016A pdb=" N GLU D 271 " --> pdb=" O SER D 267 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR D 272 " --> pdb=" O TYR D 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 267 through 272' Processing helix chain 'D' and resid 272 through 295 removed outlier: 3.600A pdb=" N LYS D 295 " --> pdb=" O MET D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 314 removed outlier: 4.269A pdb=" N LEU D 311 " --> pdb=" O GLN D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 357 Processing helix chain 'D' and resid 372 through 385 removed outlier: 4.086A pdb=" N TYR D 376 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER D 379 " --> pdb=" O ARG D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 396 removed outlier: 3.610A pdb=" N ILE D 391 " --> pdb=" O GLY D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 412 removed outlier: 3.522A pdb=" N GLN D 409 " --> pdb=" O LEU D 405 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA D 410 " --> pdb=" O LYS D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 451 Processing helix chain 'D' and resid 462 through 474 removed outlier: 4.163A pdb=" N ILE D 474 " --> pdb=" O ILE D 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 10 removed outlier: 3.851A pdb=" N ALA E 9 " --> pdb=" O THR E 6 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU E 10 " --> pdb=" O GLY E 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 6 through 10' Processing helix chain 'E' and resid 12 through 39 removed outlier: 3.646A pdb=" N ASP E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) Proline residue: E 26 - end of helix Processing helix chain 'E' and resid 40 through 43 removed outlier: 3.695A pdb=" N PHE E 43 " --> pdb=" O PRO E 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 40 through 43' Processing helix chain 'E' and resid 60 through 78 Processing helix chain 'E' and resid 91 through 96 Processing helix chain 'E' and resid 99 through 124 removed outlier: 3.717A pdb=" N LEU E 103 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 140 Processing helix chain 'E' and resid 191 through 202 removed outlier: 3.520A pdb=" N GLN E 201 " --> pdb=" O ALA E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 272 removed outlier: 4.015A pdb=" N GLU E 271 " --> pdb=" O SER E 267 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR E 272 " --> pdb=" O TYR E 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 267 through 272' Processing helix chain 'E' and resid 272 through 295 removed outlier: 3.600A pdb=" N LYS E 295 " --> pdb=" O MET E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 314 removed outlier: 4.269A pdb=" N LEU E 311 " --> pdb=" O GLN E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 357 Processing helix chain 'E' and resid 372 through 385 removed outlier: 4.085A pdb=" N TYR E 376 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER E 379 " --> pdb=" O ARG E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 396 removed outlier: 3.609A pdb=" N ILE E 391 " --> pdb=" O GLY E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 412 removed outlier: 3.524A pdb=" N GLN E 409 " --> pdb=" O LEU E 405 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA E 410 " --> pdb=" O LYS E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 451 Processing helix chain 'E' and resid 462 through 474 removed outlier: 4.162A pdb=" N ILE E 474 " --> pdb=" O ILE E 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 10 removed outlier: 3.852A pdb=" N ALA F 9 " --> pdb=" O THR F 6 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU F 10 " --> pdb=" O GLY F 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 6 through 10' Processing helix chain 'F' and resid 12 through 39 removed outlier: 3.647A pdb=" N ASP F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) Proline residue: F 26 - end of helix Processing helix chain 'F' and resid 40 through 43 removed outlier: 3.696A pdb=" N PHE F 43 " --> pdb=" O PRO F 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 40 through 43' Processing helix chain 'F' and resid 60 through 78 Processing helix chain 'F' and resid 91 through 96 Processing helix chain 'F' and resid 99 through 124 removed outlier: 3.716A pdb=" N LEU F 103 " --> pdb=" O ASP F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 140 Processing helix chain 'F' and resid 191 through 202 removed outlier: 3.521A pdb=" N GLN F 201 " --> pdb=" O ALA F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 272 removed outlier: 4.017A pdb=" N GLU F 271 " --> pdb=" O SER F 267 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR F 272 " --> pdb=" O TYR F 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 267 through 272' Processing helix chain 'F' and resid 272 through 295 removed outlier: 3.600A pdb=" N LYS F 295 " --> pdb=" O MET F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 314 removed outlier: 4.269A pdb=" N LEU F 311 " --> pdb=" O GLN F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 357 Processing helix chain 'F' and resid 372 through 385 removed outlier: 4.086A pdb=" N TYR F 376 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER F 379 " --> pdb=" O ARG F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 396 removed outlier: 3.608A pdb=" N ILE F 391 " --> pdb=" O GLY F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 412 removed outlier: 3.523A pdb=" N GLN F 409 " --> pdb=" O LEU F 405 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA F 410 " --> pdb=" O LYS F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 451 Processing helix chain 'F' and resid 462 through 474 removed outlier: 4.163A pdb=" N ILE F 474 " --> pdb=" O ILE F 470 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 10 removed outlier: 3.851A pdb=" N ALA G 9 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU G 10 " --> pdb=" O GLY G 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 6 through 10' Processing helix chain 'G' and resid 12 through 39 removed outlier: 3.647A pdb=" N ASP G 23 " --> pdb=" O ARG G 19 " (cutoff:3.500A) Proline residue: G 26 - end of helix Processing helix chain 'G' and resid 40 through 43 removed outlier: 3.695A pdb=" N PHE G 43 " --> pdb=" O PRO G 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 40 through 43' Processing helix chain 'G' and resid 60 through 78 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'G' and resid 99 through 124 removed outlier: 3.717A pdb=" N LEU G 103 " --> pdb=" O ASP G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 140 Processing helix chain 'G' and resid 191 through 202 removed outlier: 3.521A pdb=" N GLN G 201 " --> pdb=" O ALA G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 267 through 272 removed outlier: 4.016A pdb=" N GLU G 271 " --> pdb=" O SER G 267 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR G 272 " --> pdb=" O TYR G 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 267 through 272' Processing helix chain 'G' and resid 272 through 295 removed outlier: 3.600A pdb=" N LYS G 295 " --> pdb=" O MET G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 314 removed outlier: 4.269A pdb=" N LEU G 311 " --> pdb=" O GLN G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 357 Processing helix chain 'G' and resid 372 through 385 removed outlier: 4.086A pdb=" N TYR G 376 " --> pdb=" O GLU G 372 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER G 379 " --> pdb=" O ARG G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 396 removed outlier: 3.609A pdb=" N ILE G 391 " --> pdb=" O GLY G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 396 through 412 removed outlier: 3.522A pdb=" N GLN G 409 " --> pdb=" O LEU G 405 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA G 410 " --> pdb=" O LYS G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 440 through 451 Processing helix chain 'G' and resid 462 through 474 removed outlier: 4.163A pdb=" N ILE G 474 " --> pdb=" O ILE G 470 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 10 removed outlier: 3.851A pdb=" N ALA H 9 " --> pdb=" O THR H 6 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU H 10 " --> pdb=" O GLY H 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 6 through 10' Processing helix chain 'H' and resid 12 through 39 removed outlier: 3.648A pdb=" N ASP H 23 " --> pdb=" O ARG H 19 " (cutoff:3.500A) Proline residue: H 26 - end of helix Processing helix chain 'H' and resid 40 through 43 removed outlier: 3.696A pdb=" N PHE H 43 " --> pdb=" O PRO H 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 40 through 43' Processing helix chain 'H' and resid 60 through 78 Processing helix chain 'H' and resid 91 through 96 Processing helix chain 'H' and resid 99 through 124 removed outlier: 3.716A pdb=" N LEU H 103 " --> pdb=" O ASP H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 140 Processing helix chain 'H' and resid 191 through 202 removed outlier: 3.521A pdb=" N GLN H 201 " --> pdb=" O ALA H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 272 removed outlier: 4.016A pdb=" N GLU H 271 " --> pdb=" O SER H 267 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR H 272 " --> pdb=" O TYR H 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 267 through 272' Processing helix chain 'H' and resid 272 through 295 removed outlier: 3.600A pdb=" N LYS H 295 " --> pdb=" O MET H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 307 through 314 removed outlier: 4.269A pdb=" N LEU H 311 " --> pdb=" O GLN H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 335 through 357 Processing helix chain 'H' and resid 372 through 385 removed outlier: 4.086A pdb=" N TYR H 376 " --> pdb=" O GLU H 372 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER H 379 " --> pdb=" O ARG H 375 " (cutoff:3.500A) Processing helix chain 'H' and resid 387 through 396 removed outlier: 3.610A pdb=" N ILE H 391 " --> pdb=" O GLY H 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 396 through 412 removed outlier: 3.523A pdb=" N GLN H 409 " --> pdb=" O LEU H 405 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA H 410 " --> pdb=" O LYS H 406 " (cutoff:3.500A) Processing helix chain 'H' and resid 440 through 451 Processing helix chain 'H' and resid 462 through 474 removed outlier: 4.162A pdb=" N ILE H 474 " --> pdb=" O ILE H 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 10 removed outlier: 3.852A pdb=" N ALA I 9 " --> pdb=" O THR I 6 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU I 10 " --> pdb=" O GLY I 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 6 through 10' Processing helix chain 'I' and resid 12 through 39 removed outlier: 3.646A pdb=" N ASP I 23 " --> pdb=" O ARG I 19 " (cutoff:3.500A) Proline residue: I 26 - end of helix Processing helix chain 'I' and resid 40 through 43 removed outlier: 3.696A pdb=" N PHE I 43 " --> pdb=" O PRO I 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 40 through 43' Processing helix chain 'I' and resid 60 through 78 Processing helix chain 'I' and resid 91 through 96 Processing helix chain 'I' and resid 99 through 124 removed outlier: 3.716A pdb=" N LEU I 103 " --> pdb=" O ASP I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 140 Processing helix chain 'I' and resid 191 through 202 removed outlier: 3.521A pdb=" N GLN I 201 " --> pdb=" O ALA I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 267 through 272 removed outlier: 4.016A pdb=" N GLU I 271 " --> pdb=" O SER I 267 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR I 272 " --> pdb=" O TYR I 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 267 through 272' Processing helix chain 'I' and resid 272 through 295 removed outlier: 3.600A pdb=" N LYS I 295 " --> pdb=" O MET I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 307 through 314 removed outlier: 4.269A pdb=" N LEU I 311 " --> pdb=" O GLN I 307 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 357 Processing helix chain 'I' and resid 372 through 385 removed outlier: 4.085A pdb=" N TYR I 376 " --> pdb=" O GLU I 372 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER I 379 " --> pdb=" O ARG I 375 " (cutoff:3.500A) Processing helix chain 'I' and resid 387 through 396 removed outlier: 3.609A pdb=" N ILE I 391 " --> pdb=" O GLY I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 396 through 412 removed outlier: 3.523A pdb=" N GLN I 409 " --> pdb=" O LEU I 405 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA I 410 " --> pdb=" O LYS I 406 " (cutoff:3.500A) Processing helix chain 'I' and resid 440 through 451 Processing helix chain 'I' and resid 462 through 474 removed outlier: 4.163A pdb=" N ILE I 474 " --> pdb=" O ILE I 470 " (cutoff:3.500A) Processing helix chain 'J' and resid 6 through 10 removed outlier: 3.851A pdb=" N ALA J 9 " --> pdb=" O THR J 6 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU J 10 " --> pdb=" O GLY J 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 6 through 10' Processing helix chain 'J' and resid 12 through 39 removed outlier: 3.646A pdb=" N ASP J 23 " --> pdb=" O ARG J 19 " (cutoff:3.500A) Proline residue: J 26 - end of helix Processing helix chain 'J' and resid 40 through 43 removed outlier: 3.696A pdb=" N PHE J 43 " --> pdb=" O PRO J 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 40 through 43' Processing helix chain 'J' and resid 60 through 78 Processing helix chain 'J' and resid 91 through 96 Processing helix chain 'J' and resid 99 through 124 removed outlier: 3.717A pdb=" N LEU J 103 " --> pdb=" O ASP J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 140 Processing helix chain 'J' and resid 191 through 202 removed outlier: 3.521A pdb=" N GLN J 201 " --> pdb=" O ALA J 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 267 through 272 removed outlier: 4.016A pdb=" N GLU J 271 " --> pdb=" O SER J 267 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR J 272 " --> pdb=" O TYR J 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 267 through 272' Processing helix chain 'J' and resid 272 through 295 removed outlier: 3.601A pdb=" N LYS J 295 " --> pdb=" O MET J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 307 through 314 removed outlier: 4.268A pdb=" N LEU J 311 " --> pdb=" O GLN J 307 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 357 Processing helix chain 'J' and resid 372 through 385 removed outlier: 4.086A pdb=" N TYR J 376 " --> pdb=" O GLU J 372 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER J 379 " --> pdb=" O ARG J 375 " (cutoff:3.500A) Processing helix chain 'J' and resid 387 through 396 removed outlier: 3.609A pdb=" N ILE J 391 " --> pdb=" O GLY J 387 " (cutoff:3.500A) Processing helix chain 'J' and resid 396 through 412 removed outlier: 3.523A pdb=" N GLN J 409 " --> pdb=" O LEU J 405 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA J 410 " --> pdb=" O LYS J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 440 through 451 Processing helix chain 'J' and resid 462 through 474 removed outlier: 4.163A pdb=" N ILE J 474 " --> pdb=" O ILE J 470 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 10 removed outlier: 3.851A pdb=" N ALA K 9 " --> pdb=" O THR K 6 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU K 10 " --> pdb=" O GLY K 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 6 through 10' Processing helix chain 'K' and resid 12 through 39 removed outlier: 3.647A pdb=" N ASP K 23 " --> pdb=" O ARG K 19 " (cutoff:3.500A) Proline residue: K 26 - end of helix Processing helix chain 'K' and resid 40 through 43 removed outlier: 3.696A pdb=" N PHE K 43 " --> pdb=" O PRO K 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 40 through 43' Processing helix chain 'K' and resid 60 through 78 Processing helix chain 'K' and resid 91 through 96 Processing helix chain 'K' and resid 99 through 124 removed outlier: 3.717A pdb=" N LEU K 103 " --> pdb=" O ASP K 99 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 140 Processing helix chain 'K' and resid 191 through 202 removed outlier: 3.521A pdb=" N GLN K 201 " --> pdb=" O ALA K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 267 through 272 removed outlier: 4.016A pdb=" N GLU K 271 " --> pdb=" O SER K 267 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR K 272 " --> pdb=" O TYR K 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 267 through 272' Processing helix chain 'K' and resid 272 through 295 removed outlier: 3.600A pdb=" N LYS K 295 " --> pdb=" O MET K 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 307 through 314 removed outlier: 4.269A pdb=" N LEU K 311 " --> pdb=" O GLN K 307 " (cutoff:3.500A) Processing helix chain 'K' and resid 335 through 357 Processing helix chain 'K' and resid 372 through 385 removed outlier: 4.086A pdb=" N TYR K 376 " --> pdb=" O GLU K 372 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER K 379 " --> pdb=" O ARG K 375 " (cutoff:3.500A) Processing helix chain 'K' and resid 387 through 396 removed outlier: 3.609A pdb=" N ILE K 391 " --> pdb=" O GLY K 387 " (cutoff:3.500A) Processing helix chain 'K' and resid 396 through 412 removed outlier: 3.522A pdb=" N GLN K 409 " --> pdb=" O LEU K 405 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA K 410 " --> pdb=" O LYS K 406 " (cutoff:3.500A) Processing helix chain 'K' and resid 440 through 451 Processing helix chain 'K' and resid 462 through 474 removed outlier: 4.162A pdb=" N ILE K 474 " --> pdb=" O ILE K 470 " (cutoff:3.500A) Processing helix chain 'L' and resid 6 through 10 removed outlier: 3.851A pdb=" N ALA L 9 " --> pdb=" O THR L 6 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU L 10 " --> pdb=" O GLY L 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 6 through 10' Processing helix chain 'L' and resid 12 through 39 removed outlier: 3.647A pdb=" N ASP L 23 " --> pdb=" O ARG L 19 " (cutoff:3.500A) Proline residue: L 26 - end of helix Processing helix chain 'L' and resid 40 through 43 removed outlier: 3.697A pdb=" N PHE L 43 " --> pdb=" O PRO L 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 40 through 43' Processing helix chain 'L' and resid 60 through 78 Processing helix chain 'L' and resid 91 through 96 Processing helix chain 'L' and resid 99 through 124 removed outlier: 3.716A pdb=" N LEU L 103 " --> pdb=" O ASP L 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 140 Processing helix chain 'L' and resid 191 through 202 removed outlier: 3.519A pdb=" N GLN L 201 " --> pdb=" O ALA L 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 267 through 272 removed outlier: 4.017A pdb=" N GLU L 271 " --> pdb=" O SER L 267 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR L 272 " --> pdb=" O TYR L 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 267 through 272' Processing helix chain 'L' and resid 272 through 295 removed outlier: 3.600A pdb=" N LYS L 295 " --> pdb=" O MET L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 307 through 314 removed outlier: 4.268A pdb=" N LEU L 311 " --> pdb=" O GLN L 307 " (cutoff:3.500A) Processing helix chain 'L' and resid 335 through 357 Processing helix chain 'L' and resid 372 through 385 removed outlier: 4.086A pdb=" N TYR L 376 " --> pdb=" O GLU L 372 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER L 379 " --> pdb=" O ARG L 375 " (cutoff:3.500A) Processing helix chain 'L' and resid 387 through 396 removed outlier: 3.609A pdb=" N ILE L 391 " --> pdb=" O GLY L 387 " (cutoff:3.500A) Processing helix chain 'L' and resid 396 through 412 removed outlier: 3.524A pdb=" N GLN L 409 " --> pdb=" O LEU L 405 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA L 410 " --> pdb=" O LYS L 406 " (cutoff:3.500A) Processing helix chain 'L' and resid 440 through 451 Processing helix chain 'L' and resid 462 through 474 removed outlier: 4.162A pdb=" N ILE L 474 " --> pdb=" O ILE L 470 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 162 removed outlier: 3.720A pdb=" N LYS A 159 " --> pdb=" O TYR A 146 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR A 146 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL A 143 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 145 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN A 178 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR A 215 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN A 178 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR A 215 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 298 through 300 Processing sheet with id=AA6, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA7, first strand: chain 'B' and resid 159 through 162 removed outlier: 3.721A pdb=" N LYS B 159 " --> pdb=" O TYR B 146 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR B 146 " --> pdb=" O LYS B 159 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL B 143 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B 145 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 166 through 169 removed outlier: 3.759A pdb=" N GLN B 178 " --> pdb=" O GLN B 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR B 215 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 166 through 169 removed outlier: 3.759A pdb=" N GLN B 178 " --> pdb=" O GLN B 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR B 215 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 298 through 300 Processing sheet with id=AB2, first strand: chain 'C' and resid 85 through 86 Processing sheet with id=AB3, first strand: chain 'C' and resid 159 through 162 removed outlier: 3.721A pdb=" N LYS C 159 " --> pdb=" O TYR C 146 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR C 146 " --> pdb=" O LYS C 159 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL C 143 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 145 " --> pdb=" O ILE C 252 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN C 178 " --> pdb=" O GLN C 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR C 215 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN C 178 " --> pdb=" O GLN C 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR C 215 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 298 through 300 Processing sheet with id=AB7, first strand: chain 'D' and resid 85 through 86 Processing sheet with id=AB8, first strand: chain 'D' and resid 159 through 162 removed outlier: 3.719A pdb=" N LYS D 159 " --> pdb=" O TYR D 146 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR D 146 " --> pdb=" O LYS D 159 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL D 143 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D 145 " --> pdb=" O ILE D 252 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 166 through 169 removed outlier: 3.761A pdb=" N GLN D 178 " --> pdb=" O GLN D 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR D 215 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 166 through 169 removed outlier: 3.761A pdb=" N GLN D 178 " --> pdb=" O GLN D 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR D 215 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 298 through 300 Processing sheet with id=AC3, first strand: chain 'E' and resid 85 through 86 Processing sheet with id=AC4, first strand: chain 'E' and resid 159 through 162 removed outlier: 3.720A pdb=" N LYS E 159 " --> pdb=" O TYR E 146 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR E 146 " --> pdb=" O LYS E 159 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL E 143 " --> pdb=" O ILE E 254 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU E 145 " --> pdb=" O ILE E 252 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 166 through 169 removed outlier: 3.762A pdb=" N GLN E 178 " --> pdb=" O GLN E 169 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR E 215 " --> pdb=" O THR E 181 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 166 through 169 removed outlier: 3.762A pdb=" N GLN E 178 " --> pdb=" O GLN E 169 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR E 215 " --> pdb=" O THR E 181 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 298 through 300 Processing sheet with id=AC8, first strand: chain 'F' and resid 85 through 86 Processing sheet with id=AC9, first strand: chain 'F' and resid 159 through 162 removed outlier: 3.721A pdb=" N LYS F 159 " --> pdb=" O TYR F 146 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR F 146 " --> pdb=" O LYS F 159 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL F 143 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU F 145 " --> pdb=" O ILE F 252 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN F 178 " --> pdb=" O GLN F 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR F 215 " --> pdb=" O THR F 181 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN F 178 " --> pdb=" O GLN F 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR F 215 " --> pdb=" O THR F 181 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 298 through 300 Processing sheet with id=AD4, first strand: chain 'G' and resid 85 through 86 Processing sheet with id=AD5, first strand: chain 'G' and resid 159 through 162 removed outlier: 3.720A pdb=" N LYS G 159 " --> pdb=" O TYR G 146 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR G 146 " --> pdb=" O LYS G 159 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL G 143 " --> pdb=" O ILE G 254 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU G 145 " --> pdb=" O ILE G 252 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN G 178 " --> pdb=" O GLN G 169 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR G 215 " --> pdb=" O THR G 181 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN G 178 " --> pdb=" O GLN G 169 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR G 215 " --> pdb=" O THR G 181 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 298 through 300 Processing sheet with id=AD9, first strand: chain 'H' and resid 85 through 86 Processing sheet with id=AE1, first strand: chain 'H' and resid 159 through 162 removed outlier: 3.721A pdb=" N LYS H 159 " --> pdb=" O TYR H 146 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR H 146 " --> pdb=" O LYS H 159 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL H 143 " --> pdb=" O ILE H 254 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU H 145 " --> pdb=" O ILE H 252 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN H 178 " --> pdb=" O GLN H 169 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR H 215 " --> pdb=" O THR H 181 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN H 178 " --> pdb=" O GLN H 169 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR H 215 " --> pdb=" O THR H 181 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 298 through 300 Processing sheet with id=AE5, first strand: chain 'I' and resid 85 through 86 Processing sheet with id=AE6, first strand: chain 'I' and resid 159 through 162 removed outlier: 3.720A pdb=" N LYS I 159 " --> pdb=" O TYR I 146 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR I 146 " --> pdb=" O LYS I 159 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL I 143 " --> pdb=" O ILE I 254 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU I 145 " --> pdb=" O ILE I 252 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 166 through 169 removed outlier: 3.761A pdb=" N GLN I 178 " --> pdb=" O GLN I 169 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR I 215 " --> pdb=" O THR I 181 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 166 through 169 removed outlier: 3.761A pdb=" N GLN I 178 " --> pdb=" O GLN I 169 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR I 215 " --> pdb=" O THR I 181 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 298 through 300 Processing sheet with id=AF1, first strand: chain 'J' and resid 85 through 86 Processing sheet with id=AF2, first strand: chain 'J' and resid 159 through 162 removed outlier: 3.721A pdb=" N LYS J 159 " --> pdb=" O TYR J 146 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR J 146 " --> pdb=" O LYS J 159 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL J 143 " --> pdb=" O ILE J 254 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU J 145 " --> pdb=" O ILE J 252 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN J 178 " --> pdb=" O GLN J 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR J 215 " --> pdb=" O THR J 181 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN J 178 " --> pdb=" O GLN J 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR J 215 " --> pdb=" O THR J 181 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 298 through 300 Processing sheet with id=AF6, first strand: chain 'K' and resid 85 through 86 Processing sheet with id=AF7, first strand: chain 'K' and resid 159 through 162 removed outlier: 3.721A pdb=" N LYS K 159 " --> pdb=" O TYR K 146 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR K 146 " --> pdb=" O LYS K 159 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL K 143 " --> pdb=" O ILE K 254 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU K 145 " --> pdb=" O ILE K 252 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN K 178 " --> pdb=" O GLN K 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR K 215 " --> pdb=" O THR K 181 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN K 178 " --> pdb=" O GLN K 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR K 215 " --> pdb=" O THR K 181 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 298 through 300 Processing sheet with id=AG2, first strand: chain 'L' and resid 85 through 86 Processing sheet with id=AG3, first strand: chain 'L' and resid 159 through 162 removed outlier: 3.720A pdb=" N LYS L 159 " --> pdb=" O TYR L 146 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR L 146 " --> pdb=" O LYS L 159 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL L 143 " --> pdb=" O ILE L 254 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU L 145 " --> pdb=" O ILE L 252 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN L 178 " --> pdb=" O GLN L 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR L 215 " --> pdb=" O THR L 181 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN L 178 " --> pdb=" O GLN L 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR L 215 " --> pdb=" O THR L 181 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 298 through 300 2232 hydrogen bonds defined for protein. 6588 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: 18.07 Time building geometry restraints manager: 19.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 13494 1.33 - 1.46: 8674 1.46 - 1.58: 22196 1.58 - 1.71: 0 1.71 - 1.84: 372 Bond restraints: 44736 Sorted by residual: bond pdb=" CA THR I 56 " pdb=" C THR I 56 " ideal model delta sigma weight residual 1.528 1.480 0.048 1.08e-02 8.57e+03 1.94e+01 bond pdb=" CA THR B 56 " pdb=" C THR B 56 " ideal model delta sigma weight residual 1.528 1.480 0.047 1.08e-02 8.57e+03 1.93e+01 bond pdb=" CA THR H 56 " pdb=" C THR H 56 " ideal model delta sigma weight residual 1.528 1.480 0.047 1.08e-02 8.57e+03 1.93e+01 bond pdb=" CA THR J 56 " pdb=" C THR J 56 " ideal model delta sigma weight residual 1.528 1.480 0.047 1.08e-02 8.57e+03 1.90e+01 bond pdb=" CA THR C 56 " pdb=" C THR C 56 " ideal model delta sigma weight residual 1.528 1.481 0.047 1.08e-02 8.57e+03 1.89e+01 ... (remaining 44731 not shown) Histogram of bond angle deviations from ideal: 96.67 - 104.24: 911 104.24 - 111.81: 19022 111.81 - 119.38: 18774 119.38 - 126.96: 21569 126.96 - 134.53: 312 Bond angle restraints: 60588 Sorted by residual: angle pdb=" N ASP D 208 " pdb=" CA ASP D 208 " pdb=" C ASP D 208 " ideal model delta sigma weight residual 111.36 124.14 -12.78 1.09e+00 8.42e-01 1.37e+02 angle pdb=" N ASP A 208 " pdb=" CA ASP A 208 " pdb=" C ASP A 208 " ideal model delta sigma weight residual 111.36 124.13 -12.77 1.09e+00 8.42e-01 1.37e+02 angle pdb=" N ASP B 208 " pdb=" CA ASP B 208 " pdb=" C ASP B 208 " ideal model delta sigma weight residual 111.36 124.13 -12.77 1.09e+00 8.42e-01 1.37e+02 angle pdb=" N ASP E 208 " pdb=" CA ASP E 208 " pdb=" C ASP E 208 " ideal model delta sigma weight residual 111.36 124.11 -12.75 1.09e+00 8.42e-01 1.37e+02 angle pdb=" N ASP J 208 " pdb=" CA ASP J 208 " pdb=" C ASP J 208 " ideal model delta sigma weight residual 111.36 124.10 -12.74 1.09e+00 8.42e-01 1.37e+02 ... (remaining 60583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 23928 17.81 - 35.62: 2364 35.62 - 53.42: 829 53.42 - 71.23: 359 71.23 - 89.04: 84 Dihedral angle restraints: 27564 sinusoidal: 11184 harmonic: 16380 Sorted by residual: dihedral pdb=" C TYR K 37 " pdb=" N TYR K 37 " pdb=" CA TYR K 37 " pdb=" CB TYR K 37 " ideal model delta harmonic sigma weight residual -122.60 -137.73 15.13 0 2.50e+00 1.60e-01 3.66e+01 dihedral pdb=" C TYR I 37 " pdb=" N TYR I 37 " pdb=" CA TYR I 37 " pdb=" CB TYR I 37 " ideal model delta harmonic sigma weight residual -122.60 -137.70 15.10 0 2.50e+00 1.60e-01 3.65e+01 dihedral pdb=" C TYR F 37 " pdb=" N TYR F 37 " pdb=" CA TYR F 37 " pdb=" CB TYR F 37 " ideal model delta harmonic sigma weight residual -122.60 -137.70 15.10 0 2.50e+00 1.60e-01 3.65e+01 ... (remaining 27561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 5578 0.126 - 0.252: 1130 0.252 - 0.378: 96 0.378 - 0.504: 44 0.504 - 0.630: 28 Chirality restraints: 6876 Sorted by residual: chirality pdb=" CA TYR F 37 " pdb=" N TYR F 37 " pdb=" C TYR F 37 " pdb=" CB TYR F 37 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.91e+00 chirality pdb=" CA TYR K 37 " pdb=" N TYR K 37 " pdb=" C TYR K 37 " pdb=" CB TYR K 37 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.87e+00 chirality pdb=" CA TYR I 37 " pdb=" N TYR I 37 " pdb=" C TYR I 37 " pdb=" CB TYR I 37 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.83e+00 ... (remaining 6873 not shown) Planarity restraints: 7932 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU G 398 " -0.056 5.00e-02 4.00e+02 8.46e-02 1.14e+01 pdb=" N PRO G 399 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO G 399 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO G 399 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J 398 " -0.056 5.00e-02 4.00e+02 8.45e-02 1.14e+01 pdb=" N PRO J 399 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO J 399 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO J 399 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 398 " 0.056 5.00e-02 4.00e+02 8.45e-02 1.14e+01 pdb=" N PRO D 399 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO D 399 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 399 " 0.047 5.00e-02 4.00e+02 ... (remaining 7929 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 1395 2.65 - 3.21: 44769 3.21 - 3.78: 70733 3.78 - 4.34: 93193 4.34 - 4.90: 143138 Nonbonded interactions: 353228 Sorted by model distance: nonbonded pdb=" O THR I 6 " pdb=" OG1 THR I 6 " model vdw 2.089 2.440 nonbonded pdb=" O THR H 6 " pdb=" OG1 THR H 6 " model vdw 2.089 2.440 nonbonded pdb=" O THR K 6 " pdb=" OG1 THR K 6 " model vdw 2.089 2.440 nonbonded pdb=" O THR F 6 " pdb=" OG1 THR F 6 " model vdw 2.089 2.440 nonbonded pdb=" O THR G 6 " pdb=" OG1 THR G 6 " model vdw 2.090 2.440 ... (remaining 353223 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.10 max=1.00 mean=0.95 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 16.150 Check model and map are aligned: 0.680 Set scattering table: 0.380 Process input model: 118.050 Find NCS groups from input model: 3.020 Set up NCS constraints: 0.320 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 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 : 0.009 0.051 44736 Z= 0.616 Angle : 1.559 13.408 60588 Z= 1.053 Chirality : 0.108 0.630 6876 Planarity : 0.007 0.085 7932 Dihedral : 18.035 89.041 17052 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.02 % Favored : 93.76 % Rotamer: Outliers : 16.41 % Allowed : 11.87 % Favored : 71.72 % Cbeta Deviations : 1.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.11), residues: 5580 helix: 1.35 (0.10), residues: 2472 sheet: -0.88 (0.19), residues: 648 loop : -2.37 (0.11), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 83 HIS 0.001 0.001 HIS I 216 PHE 0.012 0.002 PHE H 319 TYR 0.018 0.002 TYR L 37 ARG 0.006 0.001 ARG J 266 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2305 residues out of total 4752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 780 poor density : 1525 time to evaluate : 5.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: A 39 ILE cc_start: 0.8854 (tp) cc_final: 0.8571 (pt) REVERT: A 58 TRP cc_start: 0.7793 (m100) cc_final: 0.7249 (m100) REVERT: A 91 TYR cc_start: 0.6758 (t80) cc_final: 0.6489 (t80) REVERT: A 137 LEU cc_start: 0.7764 (tp) cc_final: 0.7460 (tp) REVERT: A 151 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8372 (tt0) REVERT: A 263 SER cc_start: 0.7481 (OUTLIER) cc_final: 0.7242 (m) REVERT: A 268 TYR cc_start: 0.7656 (t80) cc_final: 0.6668 (t80) REVERT: A 273 LEU cc_start: 0.7824 (tp) cc_final: 0.7437 (tt) REVERT: A 284 GLU cc_start: 0.8749 (tt0) cc_final: 0.8442 (tt0) REVERT: A 470 ILE cc_start: 0.6655 (mm) cc_final: 0.5915 (pt) REVERT: A 474 ILE cc_start: 0.4977 (OUTLIER) cc_final: 0.4553 (tp) REVERT: B 52 THR cc_start: 0.8076 (OUTLIER) cc_final: 0.7873 (p) REVERT: B 54 TYR cc_start: 0.6795 (m-10) cc_final: 0.6087 (m-10) REVERT: B 58 TRP cc_start: 0.8203 (m100) cc_final: 0.7833 (m100) REVERT: B 114 GLU cc_start: 0.7049 (tp30) cc_final: 0.6706 (tp30) REVERT: B 124 ASN cc_start: 0.7507 (OUTLIER) cc_final: 0.4893 (m-40) REVERT: B 132 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8233 (tp30) REVERT: B 193 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.7037 (p0) REVERT: B 222 ASP cc_start: 0.6236 (m-30) cc_final: 0.5918 (m-30) REVERT: B 352 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9009 (mm) REVERT: B 353 SER cc_start: 0.9070 (OUTLIER) cc_final: 0.8801 (m) REVERT: B 368 ARG cc_start: 0.0842 (OUTLIER) cc_final: 0.0459 (mmm160) REVERT: B 389 TYR cc_start: 0.7459 (OUTLIER) cc_final: 0.6226 (t80) REVERT: B 412 GLN cc_start: 0.0445 (OUTLIER) cc_final: -0.0570 (pt0) REVERT: B 465 MET cc_start: 0.4105 (mtm) cc_final: 0.2788 (ttt) REVERT: C 91 TYR cc_start: 0.7001 (t80) cc_final: 0.6654 (t80) REVERT: C 235 MET cc_start: 0.7523 (mmm) cc_final: 0.6876 (ptt) REVERT: C 388 VAL cc_start: 0.7633 (m) cc_final: 0.7409 (p) REVERT: C 470 ILE cc_start: 0.6437 (mm) cc_final: 0.5661 (pt) REVERT: C 474 ILE cc_start: 0.4317 (OUTLIER) cc_final: 0.3866 (tp) REVERT: D 58 TRP cc_start: 0.8078 (m100) cc_final: 0.7860 (m100) REVERT: D 59 GLN cc_start: 0.8635 (pp30) cc_final: 0.8407 (pp30) REVERT: D 114 GLU cc_start: 0.7203 (tp30) cc_final: 0.6731 (tp30) REVERT: D 132 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8329 (tp30) REVERT: D 156 ASN cc_start: 0.8393 (t0) cc_final: 0.8118 (m-40) REVERT: D 340 VAL cc_start: 0.8932 (m) cc_final: 0.8624 (t) REVERT: D 446 VAL cc_start: 0.4531 (OUTLIER) cc_final: 0.4303 (p) REVERT: D 465 MET cc_start: 0.3332 (mtm) cc_final: 0.2071 (ttt) REVERT: E 54 TYR cc_start: 0.6579 (m-10) cc_final: 0.6345 (m-10) REVERT: E 58 TRP cc_start: 0.7743 (m100) cc_final: 0.7179 (m100) REVERT: E 88 ILE cc_start: 0.5323 (OUTLIER) cc_final: 0.5003 (tp) REVERT: E 91 TYR cc_start: 0.6674 (t80) cc_final: 0.6469 (t80) REVERT: E 235 MET cc_start: 0.7739 (mmm) cc_final: 0.6941 (ptt) REVERT: E 263 SER cc_start: 0.7290 (OUTLIER) cc_final: 0.7047 (m) REVERT: E 268 TYR cc_start: 0.7685 (t80) cc_final: 0.6634 (t80) REVERT: E 273 LEU cc_start: 0.8195 (tp) cc_final: 0.7671 (tt) REVERT: E 470 ILE cc_start: 0.6932 (mm) cc_final: 0.6218 (pt) REVERT: E 474 ILE cc_start: 0.4801 (OUTLIER) cc_final: 0.4595 (tp) REVERT: F 58 TRP cc_start: 0.8290 (m100) cc_final: 0.7871 (m100) REVERT: F 84 MET cc_start: 0.5740 (ptt) cc_final: 0.5535 (ptt) REVERT: F 114 GLU cc_start: 0.7262 (tp30) cc_final: 0.6580 (tp30) REVERT: F 118 MET cc_start: 0.8275 (mtp) cc_final: 0.7704 (mtp) REVERT: F 124 ASN cc_start: 0.7648 (OUTLIER) cc_final: 0.5745 (m-40) REVERT: F 156 ASN cc_start: 0.8598 (t0) cc_final: 0.8075 (m110) REVERT: F 222 ASP cc_start: 0.6250 (m-30) cc_final: 0.6045 (m-30) REVERT: F 268 TYR cc_start: 0.8306 (t80) cc_final: 0.7947 (t80) REVERT: F 340 VAL cc_start: 0.8867 (m) cc_final: 0.8578 (t) REVERT: F 381 LEU cc_start: 0.7674 (mt) cc_final: 0.7438 (tp) REVERT: F 389 TYR cc_start: 0.7118 (OUTLIER) cc_final: 0.6356 (t80) REVERT: F 392 LEU cc_start: 0.8746 (tp) cc_final: 0.8413 (mm) REVERT: F 412 GLN cc_start: 0.0231 (OUTLIER) cc_final: -0.0354 (mm-40) REVERT: F 446 VAL cc_start: 0.4250 (OUTLIER) cc_final: 0.3984 (p) REVERT: F 465 MET cc_start: 0.3738 (mtm) cc_final: 0.2170 (ttt) REVERT: G 39 ILE cc_start: 0.8859 (tp) cc_final: 0.8540 (pt) REVERT: G 58 TRP cc_start: 0.7790 (m100) cc_final: 0.7211 (m100) REVERT: G 91 TYR cc_start: 0.6661 (t80) cc_final: 0.6452 (t80) REVERT: G 137 LEU cc_start: 0.7717 (tp) cc_final: 0.7348 (tp) REVERT: G 151 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8372 (tt0) REVERT: G 263 SER cc_start: 0.7465 (OUTLIER) cc_final: 0.7264 (m) REVERT: G 268 TYR cc_start: 0.7772 (t80) cc_final: 0.6742 (t80) REVERT: G 273 LEU cc_start: 0.7834 (tp) cc_final: 0.7434 (tt) REVERT: G 284 GLU cc_start: 0.8774 (tt0) cc_final: 0.8449 (tt0) REVERT: G 470 ILE cc_start: 0.6633 (mm) cc_final: 0.5908 (pt) REVERT: G 474 ILE cc_start: 0.4536 (OUTLIER) cc_final: 0.4287 (tp) REVERT: H 54 TYR cc_start: 0.6818 (m-10) cc_final: 0.6117 (m-10) REVERT: H 58 TRP cc_start: 0.8178 (m100) cc_final: 0.7795 (m100) REVERT: H 101 ASP cc_start: 0.6154 (t0) cc_final: 0.5792 (t70) REVERT: H 114 GLU cc_start: 0.7056 (tp30) cc_final: 0.6697 (tp30) REVERT: H 124 ASN cc_start: 0.7500 (OUTLIER) cc_final: 0.4902 (m-40) REVERT: H 132 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8224 (tp30) REVERT: H 193 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.7033 (p0) REVERT: H 222 ASP cc_start: 0.6292 (m-30) cc_final: 0.6026 (m-30) REVERT: H 352 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.9008 (mm) REVERT: H 353 SER cc_start: 0.8982 (OUTLIER) cc_final: 0.8673 (m) REVERT: H 368 ARG cc_start: 0.0880 (OUTLIER) cc_final: 0.0496 (mmm160) REVERT: H 389 TYR cc_start: 0.7456 (OUTLIER) cc_final: 0.6245 (t80) REVERT: H 412 GLN cc_start: 0.0334 (OUTLIER) cc_final: -0.0635 (pt0) REVERT: H 449 TRP cc_start: 0.2726 (m-10) cc_final: 0.2498 (m-10) REVERT: H 465 MET cc_start: 0.4102 (mtm) cc_final: 0.2779 (ttt) REVERT: I 91 TYR cc_start: 0.6987 (t80) cc_final: 0.6607 (t80) REVERT: I 388 VAL cc_start: 0.7629 (m) cc_final: 0.7401 (p) REVERT: I 470 ILE cc_start: 0.6391 (mm) cc_final: 0.5625 (pt) REVERT: I 474 ILE cc_start: 0.4317 (OUTLIER) cc_final: 0.3844 (tp) REVERT: J 58 TRP cc_start: 0.8141 (m100) cc_final: 0.7903 (m100) REVERT: J 59 GLN cc_start: 0.8566 (pp30) cc_final: 0.8319 (pp30) REVERT: J 114 GLU cc_start: 0.7123 (tp30) cc_final: 0.6669 (tp30) REVERT: J 132 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8344 (tp30) REVERT: J 340 VAL cc_start: 0.8921 (m) cc_final: 0.8622 (t) REVERT: J 446 VAL cc_start: 0.3796 (OUTLIER) cc_final: 0.3519 (p) REVERT: J 465 MET cc_start: 0.3374 (mtm) cc_final: 0.2125 (ttt) REVERT: K 54 TYR cc_start: 0.6581 (m-10) cc_final: 0.6350 (m-10) REVERT: K 58 TRP cc_start: 0.7742 (m100) cc_final: 0.7190 (m100) REVERT: K 88 ILE cc_start: 0.5329 (OUTLIER) cc_final: 0.5028 (tp) REVERT: K 91 TYR cc_start: 0.6667 (t80) cc_final: 0.6447 (t80) REVERT: K 235 MET cc_start: 0.7734 (mmm) cc_final: 0.6941 (ptt) REVERT: K 263 SER cc_start: 0.7273 (OUTLIER) cc_final: 0.7031 (m) REVERT: K 268 TYR cc_start: 0.7691 (t80) cc_final: 0.6658 (t80) REVERT: K 273 LEU cc_start: 0.8177 (tp) cc_final: 0.7673 (tt) REVERT: K 470 ILE cc_start: 0.6920 (mm) cc_final: 0.6220 (pt) REVERT: K 474 ILE cc_start: 0.4809 (OUTLIER) cc_final: 0.4594 (tp) REVERT: L 58 TRP cc_start: 0.8286 (m100) cc_final: 0.7868 (m100) REVERT: L 84 MET cc_start: 0.5698 (ptt) cc_final: 0.5215 (ptt) REVERT: L 114 GLU cc_start: 0.7237 (tp30) cc_final: 0.6595 (tp30) REVERT: L 118 MET cc_start: 0.8313 (mtp) cc_final: 0.7419 (mtp) REVERT: L 124 ASN cc_start: 0.7668 (OUTLIER) cc_final: 0.5551 (m-40) REVERT: L 156 ASN cc_start: 0.8599 (t0) cc_final: 0.8074 (m110) REVERT: L 222 ASP cc_start: 0.6052 (m-30) cc_final: 0.5795 (m-30) REVERT: L 268 TYR cc_start: 0.8367 (t80) cc_final: 0.7983 (t80) REVERT: L 340 VAL cc_start: 0.8868 (m) cc_final: 0.8531 (t) REVERT: L 381 LEU cc_start: 0.7700 (mt) cc_final: 0.7471 (tp) REVERT: L 389 TYR cc_start: 0.7071 (OUTLIER) cc_final: 0.6317 (t80) REVERT: L 392 LEU cc_start: 0.8754 (tp) cc_final: 0.8445 (mm) REVERT: L 412 GLN cc_start: 0.0469 (OUTLIER) cc_final: -0.0290 (pt0) REVERT: L 428 THR cc_start: 0.8555 (t) cc_final: 0.8321 (t) REVERT: L 446 VAL cc_start: 0.4305 (OUTLIER) cc_final: 0.4031 (p) REVERT: L 465 MET cc_start: 0.3659 (mtm) cc_final: 0.2131 (ttt) outliers start: 780 outliers final: 155 residues processed: 1990 average time/residue: 0.5740 time to fit residues: 1867.9259 Evaluate side-chains 1005 residues out of total 4752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 813 time to evaluate : 5.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 466 optimal weight: 2.9990 chunk 418 optimal weight: 8.9990 chunk 232 optimal weight: 0.9980 chunk 142 optimal weight: 10.0000 chunk 282 optimal weight: 0.8980 chunk 223 optimal weight: 7.9990 chunk 432 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 263 optimal weight: 4.9990 chunk 322 optimal weight: 10.0000 chunk 501 optimal weight: 0.4980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 124 ASN B 55 GLN B 169 GLN C 55 GLN C 124 ASN C 397 GLN C 472 ASN D 55 GLN D 169 GLN E 55 GLN E 68 ASN E 124 ASN ** E 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 GLN ** F 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 335 GLN G 55 GLN G 124 ASN H 55 GLN H 169 GLN I 55 GLN I 124 ASN I 397 GLN J 55 GLN ** J 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 169 GLN K 55 GLN K 68 ASN K 124 ASN ** K 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN ** L 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 335 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 44736 Z= 0.249 Angle : 0.723 11.586 60588 Z= 0.374 Chirality : 0.045 0.146 6876 Planarity : 0.005 0.052 7932 Dihedral : 5.022 22.708 6204 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.13 % Allowed : 5.05 % Favored : 94.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.11), residues: 5580 helix: 1.24 (0.10), residues: 2544 sheet: -0.94 (0.19), residues: 576 loop : -1.75 (0.12), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 58 HIS 0.005 0.001 HIS J 216 PHE 0.031 0.002 PHE F 131 TYR 0.036 0.002 TYR I 91 ARG 0.007 0.001 ARG D 64 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1031 residues out of total 4752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1025 time to evaluate : 4.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ILE cc_start: 0.8886 (tp) cc_final: 0.8367 (pt) REVERT: A 58 TRP cc_start: 0.8009 (m100) cc_final: 0.7594 (m100) REVERT: A 80 MET cc_start: 0.7433 (mpp) cc_final: 0.7121 (mpp) REVERT: A 151 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8453 (tm-30) REVERT: A 268 TYR cc_start: 0.7791 (t80) cc_final: 0.6658 (t80) REVERT: A 329 PHE cc_start: 0.8451 (m-80) cc_final: 0.8229 (m-80) REVERT: A 373 GLU cc_start: 0.6960 (mt-10) cc_final: 0.6730 (tp30) REVERT: A 465 MET cc_start: 0.4343 (mpp) cc_final: 0.3338 (mpp) REVERT: B 54 TYR cc_start: 0.6239 (m-10) cc_final: 0.5787 (m-10) REVERT: B 132 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8196 (tp30) REVERT: B 222 ASP cc_start: 0.6036 (m-30) cc_final: 0.5710 (m-30) REVERT: B 289 MET cc_start: 0.8147 (ttm) cc_final: 0.7872 (ttm) REVERT: B 449 TRP cc_start: 0.2463 (m-10) cc_final: 0.2185 (m-10) REVERT: C 80 MET cc_start: 0.7868 (mpp) cc_final: 0.7458 (mpp) REVERT: C 108 GLU cc_start: 0.7244 (pt0) cc_final: 0.7011 (tp30) REVERT: C 130 LEU cc_start: 0.8711 (mm) cc_final: 0.8447 (mm) REVERT: C 158 MET cc_start: 0.7496 (tpp) cc_final: 0.7239 (tpp) REVERT: C 396 LEU cc_start: 0.8562 (mt) cc_final: 0.8358 (tp) REVERT: C 465 MET cc_start: 0.3969 (mpp) cc_final: 0.3486 (mmt) REVERT: D 118 MET cc_start: 0.6653 (mtt) cc_final: 0.5999 (mtt) REVERT: D 132 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8292 (tp30) REVERT: D 301 ASN cc_start: 0.8872 (t0) cc_final: 0.8656 (t0) REVERT: E 54 TYR cc_start: 0.7349 (m-10) cc_final: 0.7106 (m-10) REVERT: E 112 MET cc_start: 0.8443 (mtt) cc_final: 0.8156 (mtm) REVERT: E 158 MET cc_start: 0.7637 (tpp) cc_final: 0.7361 (tpp) REVERT: E 268 TYR cc_start: 0.7351 (t80) cc_final: 0.6568 (t80) REVERT: E 381 LEU cc_start: 0.8057 (tp) cc_final: 0.7562 (tp) REVERT: E 467 LYS cc_start: 0.6750 (mttm) cc_final: 0.6533 (tppt) REVERT: E 469 ARG cc_start: 0.4674 (mtt180) cc_final: 0.4412 (mpt-90) REVERT: F 47 SER cc_start: 0.7712 (m) cc_final: 0.7165 (p) REVERT: F 118 MET cc_start: 0.7653 (mtp) cc_final: 0.6664 (mtp) REVERT: F 268 TYR cc_start: 0.8239 (t80) cc_final: 0.7754 (t80) REVERT: F 301 ASN cc_start: 0.8835 (t0) cc_final: 0.8531 (t0) REVERT: F 388 VAL cc_start: 0.8260 (m) cc_final: 0.8027 (p) REVERT: G 39 ILE cc_start: 0.8956 (tp) cc_final: 0.8501 (pt) REVERT: G 58 TRP cc_start: 0.8003 (m100) cc_final: 0.7527 (m100) REVERT: G 80 MET cc_start: 0.7485 (mpp) cc_final: 0.7153 (mpp) REVERT: G 112 MET cc_start: 0.8063 (mtt) cc_final: 0.7837 (mtm) REVERT: G 137 LEU cc_start: 0.7324 (tp) cc_final: 0.7116 (tp) REVERT: G 151 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8409 (tm-30) REVERT: G 158 MET cc_start: 0.7642 (tpp) cc_final: 0.7270 (mmm) REVERT: G 268 TYR cc_start: 0.7821 (t80) cc_final: 0.6687 (t80) REVERT: G 392 LEU cc_start: 0.9010 (tp) cc_final: 0.8767 (tp) REVERT: G 465 MET cc_start: 0.4337 (mpp) cc_final: 0.3374 (mpp) REVERT: G 470 ILE cc_start: 0.5935 (mm) cc_final: 0.5602 (mm) REVERT: H 52 THR cc_start: 0.6460 (p) cc_final: 0.6214 (t) REVERT: H 132 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8206 (tp30) REVERT: H 222 ASP cc_start: 0.6050 (m-30) cc_final: 0.5720 (m-30) REVERT: I 80 MET cc_start: 0.7919 (mpp) cc_final: 0.7481 (mpp) REVERT: I 130 LEU cc_start: 0.8740 (mm) cc_final: 0.8498 (mm) REVERT: I 158 MET cc_start: 0.7496 (tpp) cc_final: 0.7259 (tpp) REVERT: I 465 MET cc_start: 0.3439 (mpp) cc_final: 0.2927 (mmt) REVERT: J 132 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8316 (tp30) REVERT: J 301 ASN cc_start: 0.8854 (t0) cc_final: 0.8627 (t0) REVERT: J 465 MET cc_start: 0.2585 (mtm) cc_final: 0.2373 (mtt) REVERT: K 54 TYR cc_start: 0.7344 (m-10) cc_final: 0.7082 (m-10) REVERT: K 112 MET cc_start: 0.8418 (mtt) cc_final: 0.8144 (mtm) REVERT: K 158 MET cc_start: 0.7639 (tpp) cc_final: 0.7396 (tpp) REVERT: K 268 TYR cc_start: 0.7353 (t80) cc_final: 0.6540 (t80) REVERT: K 381 LEU cc_start: 0.8047 (tp) cc_final: 0.7547 (tp) REVERT: K 469 ARG cc_start: 0.4682 (mtt180) cc_final: 0.4401 (mpt-90) REVERT: L 47 SER cc_start: 0.7725 (m) cc_final: 0.7170 (p) REVERT: L 80 MET cc_start: 0.7255 (tpp) cc_final: 0.7042 (tpp) REVERT: L 118 MET cc_start: 0.7226 (mtp) cc_final: 0.6521 (mtp) REVERT: L 160 LEU cc_start: 0.8391 (pt) cc_final: 0.8170 (pp) REVERT: L 222 ASP cc_start: 0.6251 (m-30) cc_final: 0.6024 (m-30) REVERT: L 301 ASN cc_start: 0.8831 (t0) cc_final: 0.8464 (t0) REVERT: L 388 VAL cc_start: 0.8261 (m) cc_final: 0.8036 (p) REVERT: L 465 MET cc_start: 0.2813 (mtm) cc_final: 0.2583 (mtt) outliers start: 6 outliers final: 0 residues processed: 1030 average time/residue: 0.6193 time to fit residues: 1056.8869 Evaluate side-chains 657 residues out of total 4752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 657 time to evaluate : 5.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 278 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 417 optimal weight: 3.9990 chunk 341 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 502 optimal weight: 1.9990 chunk 542 optimal weight: 7.9990 chunk 447 optimal weight: 4.9990 chunk 497 optimal weight: 4.9990 chunk 171 optimal weight: 8.9990 chunk 402 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN A 124 ASN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 GLN B 283 GLN C 407 GLN C 472 ASN D 169 GLN E 49 ASN ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 472 ASN F 169 GLN F 216 HIS ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 ASN G 124 ASN ** G 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 GLN I 407 GLN J 169 GLN K 49 ASN ** K 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 472 ASN L 169 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 44736 Z= 0.245 Angle : 0.672 9.931 60588 Z= 0.344 Chirality : 0.043 0.158 6876 Planarity : 0.005 0.066 7932 Dihedral : 4.745 23.003 6204 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.02 % Allowed : 4.99 % Favored : 94.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.11), residues: 5580 helix: 1.20 (0.10), residues: 2580 sheet: -0.72 (0.19), residues: 636 loop : -1.73 (0.12), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP J 449 HIS 0.004 0.001 HIS D 216 PHE 0.026 0.002 PHE H 354 TYR 0.039 0.002 TYR I 91 ARG 0.006 0.001 ARG C 323 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 4752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 852 time to evaluate : 5.336 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: A 39 ILE cc_start: 0.8994 (tp) cc_final: 0.8745 (tt) REVERT: A 124 ASN cc_start: 0.8260 (m-40) cc_final: 0.7246 (t0) REVERT: A 151 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8483 (tm-30) REVERT: A 158 MET cc_start: 0.7757 (tpp) cc_final: 0.7390 (tpp) REVERT: A 268 TYR cc_start: 0.7638 (t80) cc_final: 0.7162 (t80) REVERT: B 106 VAL cc_start: 0.7583 (t) cc_final: 0.7358 (t) REVERT: B 132 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8286 (tp30) REVERT: B 289 MET cc_start: 0.8253 (ttm) cc_final: 0.8018 (ttm) REVERT: B 301 ASN cc_start: 0.8974 (t0) cc_final: 0.8753 (t0) REVERT: B 353 SER cc_start: 0.8548 (m) cc_final: 0.8333 (m) REVERT: C 80 MET cc_start: 0.7685 (mpp) cc_final: 0.7424 (mpp) REVERT: C 130 LEU cc_start: 0.8921 (mm) cc_final: 0.8654 (mm) REVERT: C 134 LEU cc_start: 0.8338 (tt) cc_final: 0.8083 (tp) REVERT: D 118 MET cc_start: 0.8021 (mtt) cc_final: 0.7812 (mtp) REVERT: D 132 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8354 (tp30) REVERT: D 216 HIS cc_start: 0.7397 (t-90) cc_final: 0.6934 (t-90) REVERT: D 301 ASN cc_start: 0.8743 (t0) cc_final: 0.8520 (t0) REVERT: D 353 SER cc_start: 0.8268 (m) cc_final: 0.8040 (m) REVERT: E 54 TYR cc_start: 0.7772 (m-10) cc_final: 0.7494 (m-10) REVERT: E 58 TRP cc_start: 0.7780 (m100) cc_final: 0.7480 (m100) REVERT: E 112 MET cc_start: 0.8505 (mtt) cc_final: 0.8295 (mtm) REVERT: E 130 LEU cc_start: 0.8683 (mm) cc_final: 0.8365 (mm) REVERT: E 268 TYR cc_start: 0.7389 (t80) cc_final: 0.6812 (t80) REVERT: E 381 LEU cc_start: 0.7905 (tp) cc_final: 0.7597 (tp) REVERT: E 396 LEU cc_start: 0.8949 (tp) cc_final: 0.8732 (tt) REVERT: E 469 ARG cc_start: 0.5005 (mtt180) cc_final: 0.4699 (mpt-90) REVERT: F 114 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7569 (tp30) REVERT: F 262 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7587 (mt-10) REVERT: F 268 TYR cc_start: 0.8228 (t80) cc_final: 0.7709 (t80) REVERT: F 301 ASN cc_start: 0.8845 (t0) cc_final: 0.8565 (t0) REVERT: G 39 ILE cc_start: 0.9044 (tp) cc_final: 0.8795 (tt) REVERT: G 124 ASN cc_start: 0.8253 (m-40) cc_final: 0.7166 (t0) REVERT: G 151 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8469 (tm-30) REVERT: G 158 MET cc_start: 0.7516 (tpp) cc_final: 0.7073 (mmm) REVERT: G 268 TYR cc_start: 0.7637 (t80) cc_final: 0.7185 (t80) REVERT: H 54 TYR cc_start: 0.5861 (m-10) cc_final: 0.5476 (m-10) REVERT: H 78 PHE cc_start: 0.7816 (m-80) cc_final: 0.7533 (m-80) REVERT: H 130 LEU cc_start: 0.8374 (mt) cc_final: 0.7774 (tt) REVERT: H 132 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8330 (tp30) REVERT: H 301 ASN cc_start: 0.8969 (t0) cc_final: 0.8750 (t0) REVERT: I 80 MET cc_start: 0.7696 (mpp) cc_final: 0.7416 (mpp) REVERT: I 465 MET cc_start: 0.3395 (mpp) cc_final: 0.2827 (mmm) REVERT: J 132 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8369 (tp30) REVERT: J 353 SER cc_start: 0.8267 (m) cc_final: 0.8040 (m) REVERT: K 54 TYR cc_start: 0.7840 (m-10) cc_final: 0.7572 (m-10) REVERT: K 58 TRP cc_start: 0.7790 (m100) cc_final: 0.7475 (m100) REVERT: K 112 MET cc_start: 0.8519 (mtt) cc_final: 0.8266 (mtm) REVERT: K 130 LEU cc_start: 0.8691 (mm) cc_final: 0.8371 (mm) REVERT: K 146 TYR cc_start: 0.6740 (t80) cc_final: 0.6310 (t80) REVERT: K 268 TYR cc_start: 0.7378 (t80) cc_final: 0.6751 (t80) REVERT: K 357 MET cc_start: 0.7167 (tpp) cc_final: 0.6900 (tpt) REVERT: K 396 LEU cc_start: 0.8965 (tp) cc_final: 0.8733 (tt) REVERT: K 465 MET cc_start: 0.4556 (mpp) cc_final: 0.4283 (mpp) REVERT: K 469 ARG cc_start: 0.5027 (mtt180) cc_final: 0.4708 (mpt-90) REVERT: L 122 GLU cc_start: 0.9142 (pt0) cc_final: 0.8748 (tt0) REVERT: L 160 LEU cc_start: 0.8605 (pt) cc_final: 0.8359 (pp) REVERT: L 268 TYR cc_start: 0.8350 (t80) cc_final: 0.7972 (t80) REVERT: L 301 ASN cc_start: 0.8841 (t0) cc_final: 0.8519 (t0) outliers start: 1 outliers final: 0 residues processed: 853 average time/residue: 0.5607 time to fit residues: 788.2562 Evaluate side-chains 596 residues out of total 4752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 596 time to evaluate : 5.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 496 optimal weight: 0.0980 chunk 377 optimal weight: 0.0470 chunk 260 optimal weight: 0.5980 chunk 55 optimal weight: 7.9990 chunk 239 optimal weight: 6.9990 chunk 337 optimal weight: 9.9990 chunk 503 optimal weight: 9.9990 chunk 533 optimal weight: 1.9990 chunk 263 optimal weight: 5.9990 chunk 477 optimal weight: 7.9990 chunk 143 optimal weight: 0.9990 overall best weight: 0.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 ASN B 169 GLN C 335 GLN D 169 GLN D 335 GLN E 335 GLN ** E 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 GLN G 335 GLN ** G 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 472 ASN H 169 GLN I 335 GLN J 169 GLN J 335 GLN ** K 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.5815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 44736 Z= 0.171 Angle : 0.611 8.135 60588 Z= 0.312 Chirality : 0.042 0.164 6876 Planarity : 0.004 0.045 7932 Dihedral : 4.362 22.453 6204 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.11 % Allowed : 3.41 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.11), residues: 5580 helix: 1.43 (0.10), residues: 2580 sheet: -0.79 (0.18), residues: 696 loop : -1.67 (0.13), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 83 HIS 0.005 0.001 HIS D 216 PHE 0.023 0.002 PHE L 354 TYR 0.036 0.002 TYR I 91 ARG 0.004 0.000 ARG G 402 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 4752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 880 time to evaluate : 4.989 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: A 39 ILE cc_start: 0.8958 (tp) cc_final: 0.8749 (tt) REVERT: A 41 SER cc_start: 0.8451 (p) cc_final: 0.8205 (p) REVERT: A 59 GLN cc_start: 0.7982 (pp30) cc_final: 0.7760 (pp30) REVERT: A 124 ASN cc_start: 0.8432 (m-40) cc_final: 0.7557 (t0) REVERT: A 151 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8454 (tm-30) REVERT: A 268 TYR cc_start: 0.7448 (t80) cc_final: 0.7154 (t80) REVERT: A 470 ILE cc_start: 0.5920 (mm) cc_final: 0.5625 (mm) REVERT: B 106 VAL cc_start: 0.7515 (t) cc_final: 0.7314 (t) REVERT: B 114 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7772 (tp30) REVERT: B 132 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8249 (tp30) REVERT: B 291 MET cc_start: 0.7980 (mmp) cc_final: 0.7382 (ttp) REVERT: B 301 ASN cc_start: 0.8837 (t0) cc_final: 0.8609 (t0) REVERT: B 376 TYR cc_start: 0.6848 (t80) cc_final: 0.6595 (t80) REVERT: C 80 MET cc_start: 0.7624 (mpp) cc_final: 0.7397 (mpp) REVERT: C 158 MET cc_start: 0.7021 (mmm) cc_final: 0.6555 (tpp) REVERT: C 279 LEU cc_start: 0.9238 (tp) cc_final: 0.9021 (tt) REVERT: C 465 MET cc_start: 0.3503 (mpp) cc_final: 0.2878 (mmm) REVERT: C 470 ILE cc_start: 0.5835 (mm) cc_final: 0.5481 (mm) REVERT: D 37 TYR cc_start: 0.7514 (m-80) cc_final: 0.7220 (m-10) REVERT: D 132 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8234 (tp30) REVERT: D 216 HIS cc_start: 0.7207 (t-90) cc_final: 0.6787 (t-90) REVERT: D 301 ASN cc_start: 0.8803 (t0) cc_final: 0.8558 (t0) REVERT: D 353 SER cc_start: 0.7986 (m) cc_final: 0.7386 (t) REVERT: E 58 TRP cc_start: 0.7620 (m100) cc_final: 0.6116 (m100) REVERT: E 130 LEU cc_start: 0.8685 (mm) cc_final: 0.8413 (mm) REVERT: E 268 TYR cc_start: 0.7314 (t80) cc_final: 0.6954 (t80) REVERT: E 465 MET cc_start: 0.4191 (mpp) cc_final: 0.3905 (mmt) REVERT: E 469 ARG cc_start: 0.5079 (mtt180) cc_final: 0.4673 (mpt-90) REVERT: F 47 SER cc_start: 0.7612 (m) cc_final: 0.7004 (p) REVERT: F 169 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7678 (tm-30) REVERT: F 268 TYR cc_start: 0.8269 (t80) cc_final: 0.7750 (t80) REVERT: F 291 MET cc_start: 0.8138 (mmp) cc_final: 0.7717 (mmm) REVERT: F 301 ASN cc_start: 0.8762 (t0) cc_final: 0.8488 (t0) REVERT: F 428 THR cc_start: 0.8162 (t) cc_final: 0.7827 (t) REVERT: G 39 ILE cc_start: 0.9057 (tp) cc_final: 0.8771 (tt) REVERT: G 41 SER cc_start: 0.8524 (p) cc_final: 0.8223 (p) REVERT: G 124 ASN cc_start: 0.8327 (m-40) cc_final: 0.7434 (t0) REVERT: G 151 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8458 (tm-30) REVERT: G 268 TYR cc_start: 0.7440 (t80) cc_final: 0.7135 (t80) REVERT: G 273 LEU cc_start: 0.8156 (tp) cc_final: 0.7718 (tp) REVERT: G 351 ARG cc_start: 0.6552 (ttm170) cc_final: 0.6152 (ttm110) REVERT: H 83 TRP cc_start: 0.5764 (p90) cc_final: 0.5429 (p90) REVERT: H 132 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8425 (tp30) REVERT: I 58 TRP cc_start: 0.7921 (m100) cc_final: 0.6810 (m100) REVERT: I 80 MET cc_start: 0.7618 (mpp) cc_final: 0.7366 (mpp) REVERT: I 158 MET cc_start: 0.6995 (mmm) cc_final: 0.6582 (tpp) REVERT: I 465 MET cc_start: 0.3329 (mpp) cc_final: 0.2903 (mmt) REVERT: J 37 TYR cc_start: 0.7515 (m-80) cc_final: 0.7186 (m-10) REVERT: J 132 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8279 (tp30) REVERT: J 301 ASN cc_start: 0.8815 (t0) cc_final: 0.8528 (t0) REVERT: J 472 ASN cc_start: 0.7321 (t0) cc_final: 0.7064 (p0) REVERT: K 54 TYR cc_start: 0.7533 (m-10) cc_final: 0.7281 (m-10) REVERT: K 58 TRP cc_start: 0.7584 (m100) cc_final: 0.6029 (m100) REVERT: K 61 VAL cc_start: 0.8552 (t) cc_final: 0.8271 (t) REVERT: K 130 LEU cc_start: 0.8674 (mm) cc_final: 0.8421 (mm) REVERT: K 279 LEU cc_start: 0.9140 (tp) cc_final: 0.8928 (tt) REVERT: K 465 MET cc_start: 0.4066 (mpp) cc_final: 0.3760 (mmt) REVERT: K 469 ARG cc_start: 0.5143 (mtt180) cc_final: 0.4721 (mpt-90) REVERT: L 47 SER cc_start: 0.7628 (m) cc_final: 0.6980 (p) REVERT: L 268 TYR cc_start: 0.8266 (t80) cc_final: 0.7739 (t80) REVERT: L 291 MET cc_start: 0.7937 (mmp) cc_final: 0.7493 (mmm) REVERT: L 301 ASN cc_start: 0.8809 (t0) cc_final: 0.8472 (t0) REVERT: L 428 THR cc_start: 0.8382 (t) cc_final: 0.8114 (t) outliers start: 5 outliers final: 0 residues processed: 885 average time/residue: 0.5569 time to fit residues: 822.8569 Evaluate side-chains 608 residues out of total 4752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 607 time to evaluate : 5.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 444 optimal weight: 7.9990 chunk 302 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 397 optimal weight: 10.0000 chunk 220 optimal weight: 0.0370 chunk 455 optimal weight: 0.9990 chunk 368 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 272 optimal weight: 10.0000 chunk 478 optimal weight: 20.0000 chunk 134 optimal weight: 6.9990 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 GLN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN ** D 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 GLN ** E 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 GLN ** G 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 178 GLN ** G 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 ASN ** J 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 169 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.6111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 44736 Z= 0.285 Angle : 0.672 7.426 60588 Z= 0.346 Chirality : 0.043 0.156 6876 Planarity : 0.005 0.057 7932 Dihedral : 4.659 22.176 6204 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.04 % Allowed : 3.79 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.11), residues: 5580 helix: 0.97 (0.10), residues: 2640 sheet: -0.76 (0.20), residues: 648 loop : -1.55 (0.13), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 58 HIS 0.004 0.001 HIS G 216 PHE 0.026 0.002 PHE B 131 TYR 0.024 0.002 TYR H 126 ARG 0.007 0.001 ARG K 64 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 4752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 767 time to evaluate : 4.909 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: A 39 ILE cc_start: 0.9080 (tp) cc_final: 0.8777 (tt) REVERT: A 58 TRP cc_start: 0.7259 (m-10) cc_final: 0.6809 (m100) REVERT: A 59 GLN cc_start: 0.8220 (pp30) cc_final: 0.7936 (pp30) REVERT: A 124 ASN cc_start: 0.8700 (m-40) cc_final: 0.7993 (t0) REVERT: A 151 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8386 (tt0) REVERT: A 268 TYR cc_start: 0.7734 (t80) cc_final: 0.7358 (t80) REVERT: A 273 LEU cc_start: 0.8115 (tp) cc_final: 0.7843 (tp) REVERT: B 106 VAL cc_start: 0.7480 (t) cc_final: 0.7211 (t) REVERT: B 118 MET cc_start: 0.6796 (mtt) cc_final: 0.6564 (mtt) REVERT: B 132 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8365 (tp30) REVERT: B 179 MET cc_start: 0.7845 (ptp) cc_final: 0.7581 (ptp) REVERT: B 291 MET cc_start: 0.8593 (mmp) cc_final: 0.8015 (mmm) REVERT: B 353 SER cc_start: 0.8540 (m) cc_final: 0.8156 (m) REVERT: C 80 MET cc_start: 0.7599 (mpp) cc_final: 0.7288 (mpp) REVERT: C 108 GLU cc_start: 0.7559 (pt0) cc_final: 0.7295 (tp30) REVERT: C 158 MET cc_start: 0.6825 (mmm) cc_final: 0.6535 (tpp) REVERT: D 37 TYR cc_start: 0.7627 (m-80) cc_final: 0.7387 (m-80) REVERT: D 118 MET cc_start: 0.7797 (mtt) cc_final: 0.7583 (mtp) REVERT: D 216 HIS cc_start: 0.7546 (t-90) cc_final: 0.7041 (t-170) REVERT: D 256 MET cc_start: 0.7133 (tmm) cc_final: 0.6806 (tpp) REVERT: D 291 MET cc_start: 0.8063 (mmp) cc_final: 0.7170 (ttt) REVERT: E 58 TRP cc_start: 0.7924 (m100) cc_final: 0.7599 (m-10) REVERT: E 130 LEU cc_start: 0.8695 (mm) cc_final: 0.8494 (mm) REVERT: F 37 TYR cc_start: 0.7580 (m-80) cc_final: 0.7375 (m-10) REVERT: F 235 MET cc_start: 0.7456 (ptp) cc_final: 0.6941 (ptt) REVERT: F 260 ASP cc_start: 0.5967 (p0) cc_final: 0.5605 (p0) REVERT: F 291 MET cc_start: 0.8645 (mmp) cc_final: 0.8020 (mmm) REVERT: F 301 ASN cc_start: 0.8806 (t0) cc_final: 0.8525 (t0) REVERT: F 460 ASP cc_start: 0.5167 (t70) cc_final: 0.4935 (m-30) REVERT: G 39 ILE cc_start: 0.9133 (tp) cc_final: 0.8777 (tt) REVERT: G 58 TRP cc_start: 0.7153 (m-10) cc_final: 0.6922 (m100) REVERT: G 59 GLN cc_start: 0.8238 (pp30) cc_final: 0.7947 (pp30) REVERT: G 124 ASN cc_start: 0.8661 (m-40) cc_final: 0.7995 (t0) REVERT: G 151 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8359 (tt0) REVERT: G 268 TYR cc_start: 0.7737 (t80) cc_final: 0.7267 (t80) REVERT: G 273 LEU cc_start: 0.8065 (tp) cc_final: 0.7698 (tp) REVERT: H 78 PHE cc_start: 0.8199 (m-80) cc_final: 0.7759 (m-10) REVERT: H 106 VAL cc_start: 0.7500 (t) cc_final: 0.7290 (t) REVERT: H 179 MET cc_start: 0.7817 (ptp) cc_final: 0.7574 (ptp) REVERT: H 353 SER cc_start: 0.8649 (m) cc_final: 0.8344 (m) REVERT: I 42 LEU cc_start: 0.8860 (tt) cc_final: 0.8595 (tt) REVERT: I 112 MET cc_start: 0.8083 (mtt) cc_final: 0.7853 (mtm) REVERT: I 134 LEU cc_start: 0.8521 (pp) cc_final: 0.8137 (pp) REVERT: J 132 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8422 (tp30) REVERT: J 291 MET cc_start: 0.7969 (mmp) cc_final: 0.7010 (ttt) REVERT: J 353 SER cc_start: 0.8366 (m) cc_final: 0.8074 (m) REVERT: K 58 TRP cc_start: 0.7903 (m100) cc_final: 0.7141 (m-10) REVERT: K 275 ASP cc_start: 0.8606 (m-30) cc_final: 0.8321 (m-30) REVERT: L 37 TYR cc_start: 0.7549 (m-80) cc_final: 0.7305 (m-10) REVERT: L 78 PHE cc_start: 0.8605 (m-80) cc_final: 0.8400 (m-80) REVERT: L 169 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7646 (tm-30) REVERT: L 291 MET cc_start: 0.8456 (mmp) cc_final: 0.7906 (mmm) outliers start: 2 outliers final: 0 residues processed: 769 average time/residue: 0.5318 time to fit residues: 688.1909 Evaluate side-chains 568 residues out of total 4752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 567 time to evaluate : 5.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 179 optimal weight: 0.9990 chunk 480 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 313 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 534 optimal weight: 3.9990 chunk 443 optimal weight: 0.6980 chunk 247 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 chunk 280 optimal weight: 0.0470 overall best weight: 1.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 GLN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 GLN E 32 GLN ** E 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 GLN F 283 GLN G 55 GLN G 68 ASN G 175 ASN ** G 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 283 GLN H 397 GLN ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 169 GLN J 472 ASN ** K 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 283 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.6421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 44736 Z= 0.188 Angle : 0.614 8.227 60588 Z= 0.314 Chirality : 0.042 0.199 6876 Planarity : 0.004 0.056 7932 Dihedral : 4.352 21.614 6204 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.06 % Allowed : 2.59 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.11), residues: 5580 helix: 1.11 (0.10), residues: 2640 sheet: -0.71 (0.18), residues: 768 loop : -1.64 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 58 HIS 0.005 0.001 HIS F 216 PHE 0.030 0.002 PHE D 131 TYR 0.042 0.002 TYR I 91 ARG 0.007 0.000 ARG C 64 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 4752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 783 time to evaluate : 4.982 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: A 39 ILE cc_start: 0.9040 (tp) cc_final: 0.8728 (tt) REVERT: A 58 TRP cc_start: 0.6907 (m-10) cc_final: 0.6473 (m100) REVERT: A 64 ARG cc_start: 0.8130 (ttp80) cc_final: 0.7642 (ttp-110) REVERT: A 68 ASN cc_start: 0.8792 (t0) cc_final: 0.8560 (t0) REVERT: A 124 ASN cc_start: 0.8745 (m-40) cc_final: 0.7939 (t0) REVERT: A 137 LEU cc_start: 0.7510 (tp) cc_final: 0.7246 (tp) REVERT: A 151 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8448 (tt0) REVERT: A 273 LEU cc_start: 0.8154 (tp) cc_final: 0.7754 (tp) REVERT: A 465 MET cc_start: 0.3820 (mmt) cc_final: 0.3229 (mmt) REVERT: A 470 ILE cc_start: 0.5751 (mm) cc_final: 0.5507 (mm) REVERT: B 106 VAL cc_start: 0.7521 (t) cc_final: 0.7285 (t) REVERT: B 132 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8493 (tp30) REVERT: B 291 MET cc_start: 0.8096 (mmp) cc_final: 0.7425 (ttp) REVERT: B 376 TYR cc_start: 0.6694 (t80) cc_final: 0.6352 (t80) REVERT: C 108 GLU cc_start: 0.7542 (pt0) cc_final: 0.7216 (tp30) REVERT: C 208 ASP cc_start: 0.8029 (m-30) cc_final: 0.7705 (p0) REVERT: C 470 ILE cc_start: 0.5292 (mm) cc_final: 0.5015 (mm) REVERT: D 37 TYR cc_start: 0.7436 (m-80) cc_final: 0.7224 (m-10) REVERT: D 108 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7205 (pm20) REVERT: D 216 HIS cc_start: 0.7483 (t-90) cc_final: 0.6895 (t-170) REVERT: D 291 MET cc_start: 0.7962 (mmp) cc_final: 0.6782 (ttt) REVERT: D 301 ASN cc_start: 0.8794 (t0) cc_final: 0.8573 (t0) REVERT: D 376 TYR cc_start: 0.6867 (t80) cc_final: 0.6339 (t80) REVERT: D 449 TRP cc_start: 0.2951 (m-10) cc_final: 0.2679 (m-10) REVERT: E 58 TRP cc_start: 0.7530 (m100) cc_final: 0.7242 (m100) REVERT: E 470 ILE cc_start: 0.5659 (mm) cc_final: 0.5382 (mm) REVERT: F 37 TYR cc_start: 0.7412 (m-80) cc_final: 0.7108 (m-10) REVERT: F 260 ASP cc_start: 0.5974 (p0) cc_final: 0.5561 (p0) REVERT: F 291 MET cc_start: 0.8223 (mmp) cc_final: 0.7558 (mmm) REVERT: F 301 ASN cc_start: 0.8858 (t0) cc_final: 0.8526 (t0) REVERT: G 39 ILE cc_start: 0.9006 (tp) cc_final: 0.8720 (tt) REVERT: G 68 ASN cc_start: 0.8740 (t0) cc_final: 0.8398 (t0) REVERT: G 124 ASN cc_start: 0.8706 (m-40) cc_final: 0.7949 (t0) REVERT: G 137 LEU cc_start: 0.7543 (tp) cc_final: 0.7342 (tp) REVERT: G 151 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8433 (tt0) REVERT: G 268 TYR cc_start: 0.7654 (t80) cc_final: 0.7374 (t80) REVERT: G 273 LEU cc_start: 0.8086 (tp) cc_final: 0.7703 (tp) REVERT: G 465 MET cc_start: 0.3591 (mmt) cc_final: 0.2840 (mmt) REVERT: H 54 TYR cc_start: 0.7023 (m-10) cc_final: 0.6806 (m-10) REVERT: H 130 LEU cc_start: 0.8746 (mt) cc_final: 0.8463 (mt) REVERT: H 283 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8395 (tp-100) REVERT: H 397 GLN cc_start: 0.6670 (OUTLIER) cc_final: 0.6041 (mm-40) REVERT: I 42 LEU cc_start: 0.8647 (tt) cc_final: 0.8359 (tt) REVERT: I 84 MET cc_start: 0.7248 (ptm) cc_final: 0.6876 (ptm) REVERT: I 208 ASP cc_start: 0.8089 (m-30) cc_final: 0.7719 (p0) REVERT: J 132 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8355 (tp30) REVERT: J 291 MET cc_start: 0.7842 (mmp) cc_final: 0.6860 (ttt) REVERT: J 301 ASN cc_start: 0.8789 (t0) cc_final: 0.8552 (t0) REVERT: J 353 SER cc_start: 0.8240 (m) cc_final: 0.7973 (m) REVERT: J 472 ASN cc_start: 0.7437 (t0) cc_final: 0.6877 (m-40) REVERT: K 279 LEU cc_start: 0.9156 (tp) cc_final: 0.8935 (tt) REVERT: K 470 ILE cc_start: 0.5614 (mm) cc_final: 0.5282 (mm) REVERT: L 37 TYR cc_start: 0.7438 (m-80) cc_final: 0.7077 (m-80) REVERT: L 268 TYR cc_start: 0.8061 (t80) cc_final: 0.7805 (t80) REVERT: L 291 MET cc_start: 0.8178 (mmp) cc_final: 0.7578 (mmm) REVERT: L 301 ASN cc_start: 0.8832 (t0) cc_final: 0.8453 (t0) outliers start: 3 outliers final: 0 residues processed: 786 average time/residue: 0.5422 time to fit residues: 717.0627 Evaluate side-chains 550 residues out of total 4752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 547 time to evaluate : 5.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 514 optimal weight: 9.9990 chunk 60 optimal weight: 0.0770 chunk 304 optimal weight: 0.7980 chunk 390 optimal weight: 7.9990 chunk 302 optimal weight: 1.9990 chunk 449 optimal weight: 9.9990 chunk 298 optimal weight: 10.0000 chunk 532 optimal weight: 8.9990 chunk 332 optimal weight: 20.0000 chunk 324 optimal weight: 0.8980 chunk 245 optimal weight: 6.9990 overall best weight: 2.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 GLN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 GLN ** E 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 GLN G 178 GLN ** G 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 283 GLN H 397 GLN ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 ASN ** J 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 GLN ** K 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 169 GLN L 283 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.6646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 44736 Z= 0.220 Angle : 0.627 9.373 60588 Z= 0.321 Chirality : 0.042 0.245 6876 Planarity : 0.004 0.047 7932 Dihedral : 4.373 20.584 6204 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.11), residues: 5580 helix: 1.08 (0.10), residues: 2640 sheet: -0.66 (0.18), residues: 768 loop : -1.69 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP J 449 HIS 0.004 0.001 HIS H 216 PHE 0.023 0.002 PHE D 131 TYR 0.028 0.002 TYR I 91 ARG 0.010 0.000 ARG G 64 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 4752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 729 time to evaluate : 5.218 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: A 39 ILE cc_start: 0.8952 (tp) cc_final: 0.8688 (tt) REVERT: A 80 MET cc_start: 0.7486 (mpp) cc_final: 0.7252 (mpp) REVERT: A 124 ASN cc_start: 0.8735 (m-40) cc_final: 0.7957 (t0) REVERT: A 151 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8433 (tt0) REVERT: A 273 LEU cc_start: 0.8192 (tp) cc_final: 0.7804 (tp) REVERT: A 465 MET cc_start: 0.3876 (mmt) cc_final: 0.3404 (mmt) REVERT: A 470 ILE cc_start: 0.5771 (mm) cc_final: 0.5538 (mm) REVERT: B 132 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8513 (tp30) REVERT: B 260 ASP cc_start: 0.5797 (p0) cc_final: 0.5472 (p0) REVERT: B 291 MET cc_start: 0.8182 (mmp) cc_final: 0.7440 (ttp) REVERT: B 301 ASN cc_start: 0.8911 (t0) cc_final: 0.8629 (t0) REVERT: C 80 MET cc_start: 0.7707 (mpp) cc_final: 0.7358 (mpp) REVERT: C 208 ASP cc_start: 0.8146 (m-30) cc_final: 0.7749 (p0) REVERT: C 351 ARG cc_start: 0.7178 (ttm170) cc_final: 0.6757 (ttm170) REVERT: C 465 MET cc_start: 0.3665 (mpp) cc_final: 0.3323 (mpp) REVERT: C 470 ILE cc_start: 0.5476 (mm) cc_final: 0.5093 (mm) REVERT: D 114 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7546 (tp30) REVERT: D 216 HIS cc_start: 0.7507 (t-90) cc_final: 0.6934 (t-170) REVERT: D 291 MET cc_start: 0.7982 (mmp) cc_final: 0.6869 (ttt) REVERT: E 58 TRP cc_start: 0.7968 (m100) cc_final: 0.7229 (m100) REVERT: E 227 LEU cc_start: 0.8080 (mp) cc_final: 0.7809 (tp) REVERT: E 470 ILE cc_start: 0.5589 (mm) cc_final: 0.5323 (mm) REVERT: F 37 TYR cc_start: 0.7462 (m-80) cc_final: 0.7129 (m-10) REVERT: F 260 ASP cc_start: 0.5990 (p0) cc_final: 0.5597 (p0) REVERT: F 291 MET cc_start: 0.8425 (mmp) cc_final: 0.7834 (mmm) REVERT: F 301 ASN cc_start: 0.8844 (t0) cc_final: 0.8540 (t0) REVERT: G 39 ILE cc_start: 0.9088 (tp) cc_final: 0.8777 (tt) REVERT: G 68 ASN cc_start: 0.8796 (t0) cc_final: 0.8571 (t0) REVERT: G 124 ASN cc_start: 0.8726 (m-40) cc_final: 0.7900 (t0) REVERT: G 151 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8426 (tt0) REVERT: G 273 LEU cc_start: 0.8153 (tp) cc_final: 0.7762 (tp) REVERT: G 357 MET cc_start: 0.6847 (tpt) cc_final: 0.6530 (tpt) REVERT: G 465 MET cc_start: 0.3870 (mmt) cc_final: 0.3286 (mmt) REVERT: H 260 ASP cc_start: 0.5825 (p0) cc_final: 0.5531 (p0) REVERT: H 301 ASN cc_start: 0.8968 (t0) cc_final: 0.8758 (t0) REVERT: I 208 ASP cc_start: 0.8196 (m-30) cc_final: 0.7746 (p0) REVERT: J 132 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8417 (tp30) REVERT: J 291 MET cc_start: 0.7938 (mmp) cc_final: 0.6957 (ttt) REVERT: J 353 SER cc_start: 0.8349 (m) cc_final: 0.8111 (m) REVERT: J 376 TYR cc_start: 0.6818 (t80) cc_final: 0.6355 (t80) REVERT: J 402 ARG cc_start: 0.7672 (tpp80) cc_final: 0.7197 (ttm-80) REVERT: J 455 MET cc_start: 0.2624 (tpp) cc_final: 0.2382 (tpp) REVERT: K 227 LEU cc_start: 0.8142 (mp) cc_final: 0.7896 (tp) REVERT: K 465 MET cc_start: 0.3408 (mmt) cc_final: 0.3019 (mpp) REVERT: L 37 TYR cc_start: 0.7468 (m-80) cc_final: 0.7155 (m-10) REVERT: L 121 ILE cc_start: 0.8231 (mm) cc_final: 0.7955 (mm) REVERT: L 235 MET cc_start: 0.7450 (ptp) cc_final: 0.6534 (ptt) REVERT: L 260 ASP cc_start: 0.5737 (p0) cc_final: 0.5261 (p0) REVERT: L 268 TYR cc_start: 0.8111 (t80) cc_final: 0.7821 (t80) REVERT: L 291 MET cc_start: 0.8430 (mmp) cc_final: 0.7827 (mmm) outliers start: 0 outliers final: 0 residues processed: 729 average time/residue: 0.5292 time to fit residues: 650.0258 Evaluate side-chains 528 residues out of total 4752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 4.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 329 optimal weight: 1.9990 chunk 212 optimal weight: 9.9990 chunk 317 optimal weight: 0.0060 chunk 160 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 chunk 338 optimal weight: 2.9990 chunk 362 optimal weight: 9.9990 chunk 263 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 418 optimal weight: 8.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 ASN ** F 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 GLN H 335 GLN ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 472 ASN ** K 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.6913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 44736 Z= 0.172 Angle : 0.610 11.915 60588 Z= 0.308 Chirality : 0.042 0.187 6876 Planarity : 0.004 0.042 7932 Dihedral : 4.146 20.267 6204 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.02 % Allowed : 1.12 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.11), residues: 5580 helix: 1.18 (0.10), residues: 2640 sheet: -0.55 (0.18), residues: 768 loop : -1.75 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP J 449 HIS 0.004 0.001 HIS H 216 PHE 0.019 0.001 PHE D 131 TYR 0.025 0.001 TYR L 54 ARG 0.009 0.000 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 4752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 750 time to evaluate : 4.964 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: A 39 ILE cc_start: 0.8903 (tp) cc_final: 0.8489 (tt) REVERT: A 41 SER cc_start: 0.8451 (p) cc_final: 0.8228 (p) REVERT: A 80 MET cc_start: 0.7501 (mpp) cc_final: 0.7268 (mpp) REVERT: A 112 MET cc_start: 0.8433 (mtm) cc_final: 0.8188 (mtm) REVERT: A 124 ASN cc_start: 0.8719 (m-40) cc_final: 0.7867 (t0) REVERT: A 151 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8454 (tt0) REVERT: A 273 LEU cc_start: 0.8113 (tp) cc_final: 0.7705 (tp) REVERT: A 465 MET------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 483 optimal weight: 20.0000 chunk 509 optimal weight: 0.0000 chunk 465 optimal weight: 0.0470 chunk 495 optimal weight: 0.9980 chunk 298 optimal weight: 5.9990 chunk 215 optimal weight: 7.9990 chunk 389 optimal weight: 2.9990 chunk 152 optimal weight: 0.0970 chunk 448 optimal weight: 7.9990 chunk 468 optimal weight: 9.9990 chunk 494 optimal weight: 2.9990 overall best weight: 0.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 ASN A 178 GLN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 GLN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN G 178 GLN ** G 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.7100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 44736 Z= 0.173 Angle : 0.609 8.534 60588 Z= 0.307 Chirality : 0.041 0.171 6876 Planarity : 0.004 0.043 7932 Dihedral : 4.060 19.063 6204 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.02 % Allowed : 0.74 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.11), residues: 5580 helix: 1.19 (0.10), residues: 2640 sheet: -0.73 (0.16), residues: 888 loop : -1.72 (0.14), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP J 449 HIS 0.004 0.001 HIS H 216 PHE 0.016 0.001 PHE C 354 TYR 0.026 0.001 TYR F 272 ARG 0.009 0.000 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 4752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 719 time to evaluate : 5.445 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: A 39 ILE cc_start: 0.8864 (tp) cc_final: 0.8561 (tt) REVERT: A 80 MET cc_start: 0.7500 (mpp) cc_final: 0.7253 (mpp) REVERT: A 112 MET cc_start: 0.8414 (mtm) cc_final: 0.8159 (mtm) REVERT: A 124 ASN cc_start: 0.8705 (m-40) cc_final: 0.7849 (t0) REVERT: A 151 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8465 (tt0) REVERT: A 273 LEU cc_start: 0.8190 (tp) cc_final: 0.7753 (tp) REVERT: A 465 MET cc_start: 0.3955 (mmt) cc_final: 0.3433 (mmt) REVERT: B 114 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7953 (pp20) REVERT: B 132 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8274 (tp30) REVERT: B 235 MET cc_start: 0.7086 (ptp) cc_final: 0.6842 (ptt) REVERT: B 260 ASP cc_start: 0.5865 (p0) cc_final: 0.5521 (p0) REVERT: B 291 MET cc_start: 0.8009 (mmp) cc_final: 0.7149 (ttt) REVERT: B 301 ASN cc_start: 0.8923 (t0) cc_final: 0.8664 (t0) REVERT: B 376 TYR cc_start: 0.6474 (t80) cc_final: 0.6060 (t80) REVERT: C 58 TRP cc_start: 0.7770 (m100) cc_final: 0.7352 (m100) REVERT: C 134 LEU cc_start: 0.8606 (pp) cc_final: 0.7953 (pp) REVERT: C 146 TYR cc_start: 0.6951 (t80) cc_final: 0.6687 (t80) REVERT: C 208 ASP cc_start: 0.8210 (m-30) cc_final: 0.7798 (p0) REVERT: C 279 LEU cc_start: 0.8885 (tp) cc_final: 0.8596 (tt) REVERT: C 313 LYS cc_start: 0.8649 (tmmt) cc_final: 0.8286 (ttmt) REVERT: C 465 MET cc_start: 0.3654 (mpp) cc_final: 0.3107 (mpp) REVERT: C 470 ILE cc_start: 0.5136 (mm) cc_final: 0.4751 (mm) REVERT: D 114 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7649 (tp30) REVERT: D 291 MET cc_start: 0.7764 (mmp) cc_final: 0.6763 (ttt) REVERT: D 301 ASN cc_start: 0.8788 (t0) cc_final: 0.8567 (t0) REVERT: D 376 TYR cc_start: 0.6727 (t80) cc_final: 0.6240 (t80) REVERT: E 58 TRP cc_start: 0.7826 (m100) cc_final: 0.7152 (m100) REVERT: E 74 MET cc_start: 0.8190 (tpp) cc_final: 0.7395 (tpp) REVERT: E 134 LEU cc_start: 0.7913 (tp) cc_final: 0.7482 (tt) REVERT: E 465 MET cc_start: 0.3874 (mpp) cc_final: 0.2863 (mpp) REVERT: F 37 TYR cc_start: 0.7459 (m-10) cc_final: 0.6847 (m-10) REVERT: F 291 MET cc_start: 0.8266 (mmp) cc_final: 0.7726 (mmm) REVERT: F 301 ASN cc_start: 0.8754 (t0) cc_final: 0.8466 (t0) REVERT: F 472 ASN cc_start: 0.6246 (m-40) cc_final: 0.5944 (p0) REVERT: G 39 ILE cc_start: 0.8847 (tp) cc_final: 0.8505 (tt) REVERT: G 124 ASN cc_start: 0.8648 (m-40) cc_final: 0.7816 (t0) REVERT: G 151 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8411 (tt0) REVERT: G 273 LEU cc_start: 0.8037 (tp) cc_final: 0.7691 (tp) REVERT: G 465 MET cc_start: 0.3937 (mmt) cc_final: 0.3496 (mmt) REVERT: H 235 MET cc_start: 0.7100 (ptp) cc_final: 0.6865 (ptt) REVERT: H 260 ASP cc_start: 0.5911 (p0) cc_final: 0.5526 (p0) REVERT: H 408 LEU cc_start: 0.8028 (mp) cc_final: 0.6789 (tp) REVERT: I 173 PHE cc_start: 0.8003 (t80) cc_final: 0.7802 (t80) REVERT: I 208 ASP cc_start: 0.8182 (m-30) cc_final: 0.7784 (p0) REVERT: J 132 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8267 (tp30) REVERT: J 291 MET cc_start: 0.7821 (mmp) cc_final: 0.6830 (ttt) REVERT: J 353 SER cc_start: 0.8249 (m) cc_final: 0.7507 (t) REVERT: J 376 TYR cc_start: 0.6861 (t80) cc_final: 0.6386 (t80) REVERT: J 465 MET cc_start: 0.3530 (mtt) c------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 325 optimal weight: 0.9990 chunk 524 optimal weight: 7.9990 chunk 319 optimal weight: 8.9990 chunk 248 optimal weight: 4.9990 chunk 364 optimal weight: 10.0000 chunk 549 optimal weight: 0.9990 chunk 506 optimal weight: 0.3980 chunk 437 optimal weight: 30.0000 chunk 45 optimal weight: 1.9990 chunk 338 optimal weight: 9.9990 chunk 268 optimal weight: 9.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 ASN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** G 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 472 ASN ** K 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.7182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 44736 Z= 0.208 Angle : 0.629 10.323 60588 Z= 0.320 Chirality : 0.042 0.189 6876 Planarity : 0.004 0.042 7932 Dihedral : 4.141 19.228 6204 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.04 % Allowed : 0.25 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.11), residues: 5580 helix: 1.11 (0.10), residues: 2640 sheet: -0.67 (0.17), residues: 888 loop : -1.72 (0.14), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP J 449 HIS 0.003 0.001 HIS J 216 PHE 0.020 0.002 PHE L 131 TYR 0.023 0.002 TYR F 91 ARG 0.009 0.000 ARG A 64 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 4752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 681 time to evaluate : 4.719 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: A 39 ILE cc_start: 0.8938 (tp) cc_final: 0.8641 (tt) REVERT: A 80 MET cc_start: 0.7836 (mpp) cc_final: 0.7479 (mpp) REVERT: A 112 MET cc_start: 0.8421 (mtm) cc_final: 0.8215 (mtm) REVERT: A 124 ASN cc_start: 0.8734 (m-40) cc_final: 0.7882 (t0) REVERT: A 151 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8463 (tt0) REVERT: A 273 LEU cc_start: 0.8177 (tp) cc_final: 0.7803 (tp) REVERT: A 465 MET cc_start: 0.3934 (mmt) cc_final: 0.3407 (mmt) REVERT: B 132 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8328 (tp30) REVERT: B 291 MET cc_start: 0.8154 (mmp) cc_final: 0.7223 (ttt) REVERT: B 301 ASN cc_start: 0.8835 (t0) cc_final: 0.8555 (t0) REVERT: B 376 TYR cc_start: 0.6428 (t80) cc_final: 0.5913 (t80) REVERT: C 58 TRP cc_start: 0.7947 (m100) cc_final: 0.7413 (m100) REVERT: C 208 ASP cc_start: 0.8219 (m-30) cc_final: 0.7802 (p0) REVERT: C 465 MET cc_start: 0.3534 (mpp) cc_final: 0.3113 (mpp) REVERT: C 470 ILE cc_start: 0.4969 (mm) cc_final: 0.4606 (mm) REVERT: D 114 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7677 (tp30) REVERT: D 291 MET cc_start: 0.7906 (mmp) cc_final: 0.6804 (ttt) REVERT: D 376 TYR cc_start: 0.6750 (t80) cc_final: 0.6300 (t80) REVERT: E 58 TRP cc_start: 0.8018 (m100) cc_final: 0.7330 (m100) REVERT: E 74 MET cc_start: 0.8225 (tpp) cc_final: 0.7401 (tpp) REVERT: E 357 MET cc_start: 0.6723 (tpt) cc_final: 0.6451 (tpt) REVERT: E 465 MET cc_start: 0.3378 (mpp) cc_final: 0.2784 (mpp) REVERT: F 37 TYR cc_start: 0.7463 (m-10) cc_final: 0.6900 (m-10) REVERT: F 268 TYR cc_start: 0.7870 (t80) cc_final: 0.7557 (t80) REVERT: F 291 MET cc_start: 0.8374 (mmp) cc_final: 0.7569 (mmm) REVERT: G 39 ILE cc_start: 0.8904 (tp) cc_final: 0.8585 (tt) REVERT: G 124 ASN cc_start: 0.8683 (m-40) cc_final: 0.7839 (t0) REVERT: G 151 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8429 (tt0) REVERT: G 273 LEU cc_start: 0.8038 (tp) cc_final: 0.7639 (tp) REVERT: G 465 MET cc_start: 0.4013 (mmt) cc_final: 0.3562 (mmt) REVERT: H 78 PHE cc_start: 0.8337 (m-80) cc_final: 0.8022 (m-10) REVERT: H 121 ILE cc_start: 0.7601 (mm) cc_final: 0.7350 (mm) REVERT: H 408 LEU cc_start: 0.8040 (mp) cc_final: 0.6795 (tp) REVERT: I 58 TRP cc_start: 0.7267 (m100) cc_final: 0.6294 (m100) REVERT: I 208 ASP cc_start: 0.8277 (m-30) cc_final: 0.7822 (p0) REVERT: I 313 LYS cc_start: 0.8798 (tmmt) cc_final: 0.8366 (ttmt) REVERT: J 132 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8423 (tp30) REVERT: J 291 MET cc_start: 0.7922 (mmp) cc_final: 0.6847 (ttt) REVERT: J 353 SER cc_start: 0.8311 (m) cc_final: 0.7758 (t) REVERT: J 376 TYR cc_start: 0.6814 (t80) cc_final: 0.6390 (t80) REVERT: J 465 MET cc_start: 0.3423 (mtt) cc_final: 0.3018 (mtm) REVERT: K 61 VAL cc_start: 0.8845 (t) cc_final: 0.8417 (t) REVERT: K 112 MET cc_start: 0.8065 (mtm) cc_final: 0.7851 (mtm) REVERT: K 470 ILE cc_start: 0.5207 (mm) cc_final: 0.4936 (mm) REVERT: L 37 TYR cc_start: 0.7511 (m-10) cc_final: 0.6856 (m-10) REVERT: L 112 MET cc_start: 0.6174 (ptp) cc_final: 0.5094 (tpp) REVERT: L 251 TYR cc_start: 0.7418 (m-80) cc_final: 0.6962 (m-80) REVERT: L 260 ASP cc_start: 0.5526 (p0) cc_final: 0.5125 (p0) REVERT: L 291 MET cc_start: 0.8287 (mmp) cc_final: 0.7494 (ttt) REVERT: L 455 MET cc_start: 0.3771 (tpp) cc_final: 0.3315 (tpt) outliers start: 2 outliers final: 0 residues processed: 682 average time/residue: 0.4542 time to fit residues: 532.5845 Evaluate side-chains 516 residues out of total 4752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 516 time to evaluate : 3.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 347 optimal weight: 0.6980 chunk 466 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 403 optimal weight: 0.6980 chunk 64 optimal weight: 10.0000 chunk 121 optimal weight: 0.4980 chunk 438 optimal weight: 0.8980 chunk 183 optimal weight: 30.0000 chunk 450 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 178 GLN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 GLN G 68 ASN G 178 GLN ** G 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 335 GLN ** K 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 178 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.146222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.136641 restraints weight = 99178.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 75)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.135658 restraints weight = 106214.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.134697 restraints weight = 91764.180| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3839 r_free = 0.3839 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3740 r_free = 0.3740 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 603 | |-----------------------------------------------------------------------------| r_final: 0.3740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.7396 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: