Starting phenix.real_space_refine on Sat Mar 23 17:08:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0c_20993/03_2024/6v0c_20993.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0c_20993/03_2024/6v0c_20993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0c_20993/03_2024/6v0c_20993.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0c_20993/03_2024/6v0c_20993.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0c_20993/03_2024/6v0c_20993.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0c_20993/03_2024/6v0c_20993.pdb" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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 72 5.16 5 C 24042 2.51 5 N 6522 2.21 5 O 7284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 67": "NH1" <-> "NH2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ARG 456": "NH1" <-> "NH2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 547": "NH1" <-> "NH2" Residue "A ARG 564": "NH1" <-> "NH2" Residue "A PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 672": "NH1" <-> "NH2" Residue "A ARG 691": "NH1" <-> "NH2" Residue "A ARG 743": "NH1" <-> "NH2" Residue "A ARG 797": "NH1" <-> "NH2" Residue "A ARG 869": "NH1" <-> "NH2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 86": "NH1" <-> "NH2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B ARG 456": "NH1" <-> "NH2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 547": "NH1" <-> "NH2" Residue "B ARG 564": "NH1" <-> "NH2" Residue "B PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 672": "NH1" <-> "NH2" Residue "B ARG 691": "NH1" <-> "NH2" Residue "B ARG 743": "NH1" <-> "NH2" Residue "B ARG 797": "NH1" <-> "NH2" Residue "B ARG 869": "NH1" <-> "NH2" Residue "C ARG 67": "NH1" <-> "NH2" Residue "C ARG 86": "NH1" <-> "NH2" Residue "C ARG 220": "NH1" <-> "NH2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "C ARG 456": "NH1" <-> "NH2" Residue "C ARG 547": "NH1" <-> "NH2" Residue "C ARG 564": "NH1" <-> "NH2" Residue "C PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 672": "NH1" <-> "NH2" Residue "C ARG 691": "NH1" <-> "NH2" Residue "C ARG 743": "NH1" <-> "NH2" Residue "C ARG 797": "NH1" <-> "NH2" Residue "C ARG 869": "NH1" <-> "NH2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D ARG 220": "NH1" <-> "NH2" Residue "D ARG 336": "NH1" <-> "NH2" Residue "D ARG 456": "NH1" <-> "NH2" Residue "D TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 547": "NH1" <-> "NH2" Residue "D ARG 564": "NH1" <-> "NH2" Residue "D PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 672": "NH1" <-> "NH2" Residue "D ARG 691": "NH1" <-> "NH2" Residue "D ARG 743": "NH1" <-> "NH2" Residue "D ARG 797": "NH1" <-> "NH2" Residue "D ARG 869": "NH1" <-> "NH2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 86": "NH1" <-> "NH2" Residue "E ARG 220": "NH1" <-> "NH2" Residue "E ARG 336": "NH1" <-> "NH2" Residue "E ARG 456": "NH1" <-> "NH2" Residue "E TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 547": "NH1" <-> "NH2" Residue "E ARG 564": "NH1" <-> "NH2" Residue "E PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 672": "NH1" <-> "NH2" Residue "E ARG 691": "NH1" <-> "NH2" Residue "E ARG 743": "NH1" <-> "NH2" Residue "E ARG 797": "NH1" <-> "NH2" Residue "E ARG 869": "NH1" <-> "NH2" Residue "F ARG 67": "NH1" <-> "NH2" Residue "F ARG 86": "NH1" <-> "NH2" Residue "F ARG 220": "NH1" <-> "NH2" Residue "F ARG 336": "NH1" <-> "NH2" Residue "F ARG 456": "NH1" <-> "NH2" Residue "F TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 547": "NH1" <-> "NH2" Residue "F ARG 564": "NH1" <-> "NH2" Residue "F PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 672": "NH1" <-> "NH2" Residue "F ARG 691": "NH1" <-> "NH2" Residue "F ARG 743": "NH1" <-> "NH2" Residue "F ARG 797": "NH1" <-> "NH2" Residue "F ARG 869": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 37920 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 6320 Classifications: {'peptide': 832} Link IDs: {'PTRANS': 43, 'TRANS': 788} Chain: "B" Number of atoms: 6320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 6320 Classifications: {'peptide': 832} Link IDs: {'PTRANS': 43, 'TRANS': 788} Chain: "C" Number of atoms: 6320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 6320 Classifications: {'peptide': 832} Link IDs: {'PTRANS': 43, 'TRANS': 788} Chain: "D" Number of atoms: 6320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 6320 Classifications: {'peptide': 832} Link IDs: {'PTRANS': 43, 'TRANS': 788} Chain: "E" Number of atoms: 6320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 6320 Classifications: {'peptide': 832} Link IDs: {'PTRANS': 43, 'TRANS': 788} Chain: "F" Number of atoms: 6320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 6320 Classifications: {'peptide': 832} Link IDs: {'PTRANS': 43, 'TRANS': 788} Time building chain proxies: 19.04, per 1000 atoms: 0.50 Number of scatterers: 37920 At special positions: 0 Unit cell: (113.97, 111.35, 235.8, 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 72 16.00 O 7284 8.00 N 6522 7.00 C 24042 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: 12.94 Conformation dependent library (CDL) restraints added in 7.0 seconds 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8964 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 66 sheets defined 13.2% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.90 Creating SS restraints... Processing helix chain 'A' and resid 95 through 102 Processing helix chain 'A' and resid 116 through 122 Processing helix chain 'A' and resid 209 through 212 Processing helix chain 'A' and resid 243 through 248 removed outlier: 4.343A pdb=" N VAL A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 243 through 248' Processing helix chain 'A' and resid 274 through 278 removed outlier: 3.639A pdb=" N GLN A 278 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 335 Processing helix chain 'A' and resid 354 through 361 removed outlier: 4.056A pdb=" N LEU A 358 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.191A pdb=" N LEU A 386 " --> pdb=" O GLU A 383 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU A 389 " --> pdb=" O LEU A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 removed outlier: 3.863A pdb=" N VAL A 445 " --> pdb=" O HIS A 441 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LYS A 446 " --> pdb=" O ARG A 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 441 through 446' Processing helix chain 'A' and resid 472 through 479 removed outlier: 3.617A pdb=" N ILE A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 506 removed outlier: 3.665A pdb=" N ALA A 504 " --> pdb=" O ASN A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 567 removed outlier: 3.715A pdb=" N LEU A 567 " --> pdb=" O ARG A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 600 Processing helix chain 'A' and resid 611 through 617 removed outlier: 3.677A pdb=" N GLN A 615 " --> pdb=" O ALA A 611 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS A 617 " --> pdb=" O ALA A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 631 Processing helix chain 'A' and resid 711 through 715 Processing helix chain 'A' and resid 798 through 802 removed outlier: 3.652A pdb=" N VAL A 802 " --> pdb=" O GLN A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 835 Processing helix chain 'B' and resid 95 through 102 Processing helix chain 'B' and resid 116 through 122 Processing helix chain 'B' and resid 209 through 212 Processing helix chain 'B' and resid 243 through 248 removed outlier: 4.343A pdb=" N VAL B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 243 through 248' Processing helix chain 'B' and resid 274 through 278 removed outlier: 3.640A pdb=" N GLN B 278 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 335 Processing helix chain 'B' and resid 354 through 361 removed outlier: 4.055A pdb=" N LEU B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY B 361 " --> pdb=" O ALA B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.191A pdb=" N LEU B 386 " --> pdb=" O GLU B 383 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU B 389 " --> pdb=" O LEU B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 446 removed outlier: 3.863A pdb=" N VAL B 445 " --> pdb=" O HIS B 441 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LYS B 446 " --> pdb=" O ARG B 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 441 through 446' Processing helix chain 'B' and resid 472 through 479 removed outlier: 3.618A pdb=" N ILE B 477 " --> pdb=" O ALA B 473 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN B 478 " --> pdb=" O SER B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 506 removed outlier: 3.665A pdb=" N ALA B 504 " --> pdb=" O ASN B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 567 removed outlier: 3.715A pdb=" N LEU B 567 " --> pdb=" O ARG B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 600 Processing helix chain 'B' and resid 611 through 617 removed outlier: 3.676A pdb=" N GLN B 615 " --> pdb=" O ALA B 611 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS B 617 " --> pdb=" O ALA B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 631 Processing helix chain 'B' and resid 711 through 715 Processing helix chain 'B' and resid 798 through 802 removed outlier: 3.652A pdb=" N VAL B 802 " --> pdb=" O GLN B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 835 Processing helix chain 'C' and resid 95 through 102 Processing helix chain 'C' and resid 116 through 122 Processing helix chain 'C' and resid 243 through 248 removed outlier: 4.353A pdb=" N VAL C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 243 through 248' Processing helix chain 'C' and resid 354 through 361 removed outlier: 4.249A pdb=" N LEU C 358 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY C 361 " --> pdb=" O ALA C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.198A pdb=" N LEU C 386 " --> pdb=" O GLU C 383 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU C 389 " --> pdb=" O LEU C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 446 removed outlier: 3.816A pdb=" N VAL C 445 " --> pdb=" O HIS C 441 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LYS C 446 " --> pdb=" O ARG C 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 441 through 446' Processing helix chain 'C' and resid 472 through 479 Processing helix chain 'C' and resid 500 through 506 removed outlier: 3.583A pdb=" N ALA C 504 " --> pdb=" O ASN C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 567 removed outlier: 3.639A pdb=" N LEU C 567 " --> pdb=" O ARG C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 600 Processing helix chain 'C' and resid 611 through 617 removed outlier: 3.627A pdb=" N GLN C 615 " --> pdb=" O ALA C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 631 Processing helix chain 'C' and resid 711 through 715 removed outlier: 3.504A pdb=" N ILE C 714 " --> pdb=" O LEU C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 802 removed outlier: 3.672A pdb=" N VAL C 802 " --> pdb=" O GLN C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 835 Processing helix chain 'D' and resid 95 through 102 Processing helix chain 'D' and resid 116 through 122 Processing helix chain 'D' and resid 209 through 212 Processing helix chain 'D' and resid 243 through 248 removed outlier: 4.343A pdb=" N VAL D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 243 through 248' Processing helix chain 'D' and resid 274 through 278 removed outlier: 3.640A pdb=" N GLN D 278 " --> pdb=" O ALA D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 335 Processing helix chain 'D' and resid 354 through 361 removed outlier: 4.055A pdb=" N LEU D 358 " --> pdb=" O ASN D 354 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY D 361 " --> pdb=" O ALA D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 389 removed outlier: 4.192A pdb=" N LEU D 386 " --> pdb=" O GLU D 383 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU D 389 " --> pdb=" O LEU D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 446 removed outlier: 3.863A pdb=" N VAL D 445 " --> pdb=" O HIS D 441 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LYS D 446 " --> pdb=" O ARG D 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 441 through 446' Processing helix chain 'D' and resid 472 through 479 removed outlier: 3.618A pdb=" N ILE D 477 " --> pdb=" O ALA D 473 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN D 478 " --> pdb=" O SER D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 506 removed outlier: 3.665A pdb=" N ALA D 504 " --> pdb=" O ASN D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 567 removed outlier: 3.715A pdb=" N LEU D 567 " --> pdb=" O ARG D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 600 Processing helix chain 'D' and resid 611 through 617 removed outlier: 3.677A pdb=" N GLN D 615 " --> pdb=" O ALA D 611 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS D 617 " --> pdb=" O ALA D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 631 Processing helix chain 'D' and resid 711 through 715 Processing helix chain 'D' and resid 798 through 802 removed outlier: 3.652A pdb=" N VAL D 802 " --> pdb=" O GLN D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 830 through 835 Processing helix chain 'E' and resid 95 through 102 Processing helix chain 'E' and resid 116 through 122 Processing helix chain 'E' and resid 209 through 212 Processing helix chain 'E' and resid 243 through 248 removed outlier: 4.343A pdb=" N VAL E 247 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN E 248 " --> pdb=" O ALA E 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 243 through 248' Processing helix chain 'E' and resid 274 through 278 removed outlier: 3.641A pdb=" N GLN E 278 " --> pdb=" O ALA E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 335 Processing helix chain 'E' and resid 354 through 361 removed outlier: 4.056A pdb=" N LEU E 358 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY E 361 " --> pdb=" O ALA E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 389 removed outlier: 4.191A pdb=" N LEU E 386 " --> pdb=" O GLU E 383 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU E 389 " --> pdb=" O LEU E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 446 removed outlier: 3.863A pdb=" N VAL E 445 " --> pdb=" O HIS E 441 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LYS E 446 " --> pdb=" O ARG E 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 441 through 446' Processing helix chain 'E' and resid 472 through 479 removed outlier: 3.618A pdb=" N ILE E 477 " --> pdb=" O ALA E 473 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN E 478 " --> pdb=" O SER E 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 500 through 506 removed outlier: 3.665A pdb=" N ALA E 504 " --> pdb=" O ASN E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 563 through 567 removed outlier: 3.715A pdb=" N LEU E 567 " --> pdb=" O ARG E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 594 through 600 Processing helix chain 'E' and resid 611 through 617 removed outlier: 3.676A pdb=" N GLN E 615 " --> pdb=" O ALA E 611 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS E 617 " --> pdb=" O ALA E 613 " (cutoff:3.500A) Processing helix chain 'E' and resid 626 through 631 Processing helix chain 'E' and resid 711 through 715 Processing helix chain 'E' and resid 798 through 802 removed outlier: 3.652A pdb=" N VAL E 802 " --> pdb=" O GLN E 799 " (cutoff:3.500A) Processing helix chain 'E' and resid 830 through 835 Processing helix chain 'F' and resid 95 through 102 Processing helix chain 'F' and resid 116 through 122 Processing helix chain 'F' and resid 209 through 212 Processing helix chain 'F' and resid 243 through 248 removed outlier: 4.343A pdb=" N VAL F 247 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN F 248 " --> pdb=" O ALA F 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 243 through 248' Processing helix chain 'F' and resid 274 through 278 removed outlier: 3.640A pdb=" N GLN F 278 " --> pdb=" O ALA F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 335 Processing helix chain 'F' and resid 354 through 361 removed outlier: 4.056A pdb=" N LEU F 358 " --> pdb=" O ASN F 354 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY F 361 " --> pdb=" O ALA F 357 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 389 removed outlier: 4.192A pdb=" N LEU F 386 " --> pdb=" O GLU F 383 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU F 389 " --> pdb=" O LEU F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 446 removed outlier: 3.863A pdb=" N VAL F 445 " --> pdb=" O HIS F 441 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LYS F 446 " --> pdb=" O ARG F 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 441 through 446' Processing helix chain 'F' and resid 472 through 479 removed outlier: 3.617A pdb=" N ILE F 477 " --> pdb=" O ALA F 473 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN F 478 " --> pdb=" O SER F 474 " (cutoff:3.500A) Processing helix chain 'F' and resid 500 through 506 removed outlier: 3.665A pdb=" N ALA F 504 " --> pdb=" O ASN F 500 " (cutoff:3.500A) Processing helix chain 'F' and resid 563 through 567 removed outlier: 3.715A pdb=" N LEU F 567 " --> pdb=" O ARG F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 594 through 600 Processing helix chain 'F' and resid 611 through 617 removed outlier: 3.677A pdb=" N GLN F 615 " --> pdb=" O ALA F 611 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS F 617 " --> pdb=" O ALA F 613 " (cutoff:3.500A) Processing helix chain 'F' and resid 626 through 631 Processing helix chain 'F' and resid 711 through 715 Processing helix chain 'F' and resid 798 through 802 removed outlier: 3.652A pdb=" N VAL F 802 " --> pdb=" O GLN F 799 " (cutoff:3.500A) Processing helix chain 'F' and resid 830 through 835 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 removed outlier: 6.097A pdb=" N VAL A 66 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL A 76 " --> pdb=" O SER A 93 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N SER A 93 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR A 50 " --> pdb=" O PHE A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 111 removed outlier: 3.708A pdb=" N TYR A 131 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 161 through 167 removed outlier: 6.152A pdb=" N LEU A 206 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL A 189 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHE A 181 " --> pdb=" O PRO A 185 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY A 187 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE A 221 " --> pdb=" O TYR A 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 228 through 229 Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 239 Processing sheet with id=AA6, first strand: chain 'A' and resid 340 through 344 removed outlier: 6.165A pdb=" N LEU A 300 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N LEU A 310 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR A 326 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 281 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N PHE A 377 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS A 284 " --> pdb=" O PHE A 377 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 449 through 453 removed outlier: 8.359A pdb=" N ILE A 483 " --> pdb=" O PRO A 410 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE A 412 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU A 411 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR A 434 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ARG A 424 " --> pdb=" O THR A 432 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N THR A 432 " --> pdb=" O ARG A 424 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR A 495 " --> pdb=" O THR A 396 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 458 through 460 Processing sheet with id=AA9, first strand: chain 'A' and resid 517 through 521 removed outlier: 3.780A pdb=" N VAL A 517 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N HIS A 558 " --> pdb=" O VAL A 543 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N VAL A 543 " --> pdb=" O HIS A 558 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 533 through 535 removed outlier: 9.241A pdb=" N TYR A 624 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N PHE A 573 " --> pdb=" O TYR A 624 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 695 through 699 removed outlier: 4.600A pdb=" N TYR A 718 " --> pdb=" O VAL A 699 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE A 653 " --> pdb=" O ILE A 660 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS A 678 " --> pdb=" O GLN A 664 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU A 666 " --> pdb=" O GLN A 676 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLN A 676 " --> pdb=" O LEU A 666 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LEU A 668 " --> pdb=" O GLU A 674 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N GLU A 674 " --> pdb=" O LEU A 668 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N PHE A 732 " --> pdb=" O GLN A 636 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N THR A 638 " --> pdb=" O PHE A 732 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 749 through 754 removed outlier: 7.138A pdb=" N MET A 789 " --> pdb=" O MET A 779 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N MET A 779 " --> pdb=" O MET A 789 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA A 791 " --> pdb=" O THR A 777 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLU A 772 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE A 768 " --> pdb=" O GLU A 772 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 841 " --> pdb=" O VAL A 807 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE A 808 " --> pdb=" O GLN A 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.096A pdb=" N VAL B 66 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL B 76 " --> pdb=" O SER B 93 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N SER B 93 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR B 50 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 107 through 111 removed outlier: 3.708A pdb=" N TYR B 131 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 161 through 167 removed outlier: 6.152A pdb=" N LEU B 206 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL B 189 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHE B 181 " --> pdb=" O PRO B 185 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY B 187 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N PHE B 221 " --> pdb=" O TYR B 271 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 228 through 229 Processing sheet with id=AB8, first strand: chain 'B' and resid 340 through 344 removed outlier: 6.165A pdb=" N LEU B 300 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LEU B 310 " --> pdb=" O THR B 326 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR B 326 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B 281 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N PHE B 377 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS B 284 " --> pdb=" O PHE B 377 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 449 through 453 removed outlier: 8.359A pdb=" N ILE B 483 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ILE B 412 " --> pdb=" O ILE B 483 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU B 411 " --> pdb=" O VAL B 418 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR B 434 " --> pdb=" O ILE B 422 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ARG B 424 " --> pdb=" O THR B 432 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N THR B 432 " --> pdb=" O ARG B 424 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR B 495 " --> pdb=" O THR B 396 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 458 through 460 Processing sheet with id=AC2, first strand: chain 'B' and resid 517 through 521 removed outlier: 3.778A pdb=" N VAL B 517 " --> pdb=" O LEU B 557 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N HIS B 558 " --> pdb=" O VAL B 543 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N VAL B 543 " --> pdb=" O HIS B 558 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 533 through 535 removed outlier: 9.242A pdb=" N TYR B 624 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N PHE B 573 " --> pdb=" O TYR B 624 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 580 through 581 Processing sheet with id=AC5, first strand: chain 'B' and resid 695 through 699 removed outlier: 4.599A pdb=" N TYR B 718 " --> pdb=" O VAL B 699 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE B 653 " --> pdb=" O ILE B 660 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS B 678 " --> pdb=" O GLN B 664 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU B 666 " --> pdb=" O GLN B 676 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLN B 676 " --> pdb=" O LEU B 666 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LEU B 668 " --> pdb=" O GLU B 674 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N GLU B 674 " --> pdb=" O LEU B 668 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N PHE B 732 " --> pdb=" O GLN B 636 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N THR B 638 " --> pdb=" O PHE B 732 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 749 through 754 removed outlier: 7.139A pdb=" N MET B 789 " --> pdb=" O MET B 779 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N MET B 779 " --> pdb=" O MET B 789 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA B 791 " --> pdb=" O THR B 777 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLU B 772 " --> pdb=" O PHE B 768 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE B 768 " --> pdb=" O GLU B 772 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA B 841 " --> pdb=" O VAL B 807 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE B 808 " --> pdb=" O GLN B 861 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 65 through 68 removed outlier: 6.100A pdb=" N VAL C 66 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N VAL C 76 " --> pdb=" O SER C 93 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N SER C 93 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR C 50 " --> pdb=" O PHE C 145 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 107 through 111 removed outlier: 3.741A pdb=" N TYR C 131 " --> pdb=" O VAL C 111 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 161 through 167 removed outlier: 6.096A pdb=" N LEU C 206 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N VAL C 189 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL C 179 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N PHE C 221 " --> pdb=" O TYR C 271 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 228 through 229 Processing sheet with id=AD2, first strand: chain 'C' and resid 340 through 344 removed outlier: 4.660A pdb=" N THR C 298 " --> pdb=" O LEU C 310 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR C 302 " --> pdb=" O GLU C 306 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLU C 306 " --> pdb=" O TYR C 302 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LEU C 310 " --> pdb=" O THR C 326 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR C 326 " --> pdb=" O LEU C 310 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N PHE C 377 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LYS C 284 " --> pdb=" O PHE C 377 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 449 through 453 removed outlier: 6.963A pdb=" N LEU C 411 " --> pdb=" O VAL C 418 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR C 434 " --> pdb=" O ILE C 422 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ARG C 424 " --> pdb=" O THR C 432 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR C 432 " --> pdb=" O ARG C 424 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR C 495 " --> pdb=" O THR C 396 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 458 through 460 Processing sheet with id=AD5, first strand: chain 'C' and resid 517 through 521 removed outlier: 3.851A pdb=" N VAL C 517 " --> pdb=" O LEU C 557 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASP C 554 " --> pdb=" O VAL C 546 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL C 546 " --> pdb=" O ASP C 554 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASP C 556 " --> pdb=" O ILE C 544 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL C 533 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 9.220A pdb=" N TYR C 624 " --> pdb=" O SER C 571 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N PHE C 573 " --> pdb=" O TYR C 624 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 695 through 699 removed outlier: 4.495A pdb=" N TYR C 718 " --> pdb=" O VAL C 699 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE C 653 " --> pdb=" O ILE C 660 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LYS C 678 " --> pdb=" O GLN C 664 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU C 666 " --> pdb=" O GLN C 676 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLN C 676 " --> pdb=" O LEU C 666 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU C 668 " --> pdb=" O GLU C 674 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU C 674 " --> pdb=" O LEU C 668 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N PHE C 732 " --> pdb=" O GLN C 636 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N THR C 638 " --> pdb=" O PHE C 732 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 749 through 754 removed outlier: 7.041A pdb=" N MET C 789 " --> pdb=" O MET C 779 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N MET C 779 " --> pdb=" O MET C 789 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA C 791 " --> pdb=" O THR C 777 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N GLU C 772 " --> pdb=" O PHE C 768 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE C 768 " --> pdb=" O GLU C 772 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N PHE C 808 " --> pdb=" O GLN C 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 65 through 68 removed outlier: 6.097A pdb=" N VAL D 66 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL D 76 " --> pdb=" O SER D 93 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N SER D 93 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR D 50 " --> pdb=" O PHE D 145 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 107 through 111 removed outlier: 3.708A pdb=" N TYR D 131 " --> pdb=" O VAL D 111 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 161 through 167 removed outlier: 6.153A pdb=" N LEU D 206 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL D 189 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHE D 181 " --> pdb=" O PRO D 185 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY D 187 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N PHE D 221 " --> pdb=" O TYR D 271 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 228 through 229 Processing sheet with id=AE3, first strand: chain 'D' and resid 340 through 344 removed outlier: 6.166A pdb=" N LEU D 300 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LEU D 310 " --> pdb=" O THR D 326 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR D 326 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL D 281 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N PHE D 377 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS D 284 " --> pdb=" O PHE D 377 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 449 through 453 removed outlier: 8.359A pdb=" N ILE D 483 " --> pdb=" O PRO D 410 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE D 412 " --> pdb=" O ILE D 483 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU D 411 " --> pdb=" O VAL D 418 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR D 434 " --> pdb=" O ILE D 422 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ARG D 424 " --> pdb=" O THR D 432 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N THR D 432 " --> pdb=" O ARG D 424 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR D 495 " --> pdb=" O THR D 396 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 458 through 460 Processing sheet with id=AE6, first strand: chain 'D' and resid 517 through 521 removed outlier: 3.779A pdb=" N VAL D 517 " --> pdb=" O LEU D 557 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N HIS D 558 " --> pdb=" O VAL D 543 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N VAL D 543 " --> pdb=" O HIS D 558 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 533 through 535 removed outlier: 9.241A pdb=" N TYR D 624 " --> pdb=" O SER D 571 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N PHE D 573 " --> pdb=" O TYR D 624 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 695 through 699 removed outlier: 4.600A pdb=" N TYR D 718 " --> pdb=" O VAL D 699 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE D 653 " --> pdb=" O ILE D 660 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS D 678 " --> pdb=" O GLN D 664 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU D 666 " --> pdb=" O GLN D 676 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLN D 676 " --> pdb=" O LEU D 666 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LEU D 668 " --> pdb=" O GLU D 674 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N GLU D 674 " --> pdb=" O LEU D 668 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N PHE D 732 " --> pdb=" O GLN D 636 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N THR D 638 " --> pdb=" O PHE D 732 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 749 through 754 removed outlier: 7.138A pdb=" N MET D 789 " --> pdb=" O MET D 779 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N MET D 779 " --> pdb=" O MET D 789 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA D 791 " --> pdb=" O THR D 777 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLU D 772 " --> pdb=" O PHE D 768 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE D 768 " --> pdb=" O GLU D 772 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA D 841 " --> pdb=" O VAL D 807 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE D 808 " --> pdb=" O GLN D 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 65 through 68 removed outlier: 6.096A pdb=" N VAL E 66 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL E 76 " --> pdb=" O SER E 93 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N SER E 93 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR E 50 " --> pdb=" O PHE E 145 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 107 through 111 removed outlier: 3.708A pdb=" N TYR E 131 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 161 through 167 removed outlier: 6.152A pdb=" N LEU E 206 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL E 189 " --> pdb=" O LEU E 206 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHE E 181 " --> pdb=" O PRO E 185 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY E 187 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N PHE E 221 " --> pdb=" O TYR E 271 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 228 through 229 Processing sheet with id=AF5, first strand: chain 'E' and resid 340 through 344 removed outlier: 6.165A pdb=" N LEU E 300 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N LEU E 310 " --> pdb=" O THR E 326 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR E 326 " --> pdb=" O LEU E 310 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL E 281 " --> pdb=" O VAL E 327 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N PHE E 377 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS E 284 " --> pdb=" O PHE E 377 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 449 through 453 removed outlier: 8.359A pdb=" N ILE E 483 " --> pdb=" O PRO E 410 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE E 412 " --> pdb=" O ILE E 483 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU E 411 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR E 434 " --> pdb=" O ILE E 422 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ARG E 424 " --> pdb=" O THR E 432 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N THR E 432 " --> pdb=" O ARG E 424 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR E 495 " --> pdb=" O THR E 396 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 458 through 460 Processing sheet with id=AF8, first strand: chain 'E' and resid 517 through 521 removed outlier: 3.778A pdb=" N VAL E 517 " --> pdb=" O LEU E 557 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N HIS E 558 " --> pdb=" O VAL E 543 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N VAL E 543 " --> pdb=" O HIS E 558 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 533 through 535 removed outlier: 9.241A pdb=" N TYR E 624 " --> pdb=" O SER E 571 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N PHE E 573 " --> pdb=" O TYR E 624 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 695 through 699 removed outlier: 4.599A pdb=" N TYR E 718 " --> pdb=" O VAL E 699 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE E 653 " --> pdb=" O ILE E 660 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS E 678 " --> pdb=" O GLN E 664 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU E 666 " --> pdb=" O GLN E 676 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLN E 676 " --> pdb=" O LEU E 666 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LEU E 668 " --> pdb=" O GLU E 674 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N GLU E 674 " --> pdb=" O LEU E 668 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N PHE E 732 " --> pdb=" O GLN E 636 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N THR E 638 " --> pdb=" O PHE E 732 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 749 through 754 removed outlier: 7.139A pdb=" N MET E 789 " --> pdb=" O MET E 779 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N MET E 779 " --> pdb=" O MET E 789 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA E 791 " --> pdb=" O THR E 777 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLU E 772 " --> pdb=" O PHE E 768 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE E 768 " --> pdb=" O GLU E 772 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA E 841 " --> pdb=" O VAL E 807 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE E 808 " --> pdb=" O GLN E 861 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 65 through 68 removed outlier: 6.097A pdb=" N VAL F 66 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL F 76 " --> pdb=" O SER F 93 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N SER F 93 " --> pdb=" O VAL F 76 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR F 50 " --> pdb=" O PHE F 145 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 107 through 111 removed outlier: 3.708A pdb=" N TYR F 131 " --> pdb=" O VAL F 111 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 161 through 167 removed outlier: 6.153A pdb=" N LEU F 206 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL F 189 " --> pdb=" O LEU F 206 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHE F 181 " --> pdb=" O PRO F 185 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY F 187 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE F 221 " --> pdb=" O TYR F 271 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 340 through 344 removed outlier: 6.165A pdb=" N LEU F 300 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LEU F 310 " --> pdb=" O THR F 326 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR F 326 " --> pdb=" O LEU F 310 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL F 281 " --> pdb=" O VAL F 327 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N PHE F 377 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS F 284 " --> pdb=" O PHE F 377 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 449 through 453 removed outlier: 8.360A pdb=" N ILE F 483 " --> pdb=" O PRO F 410 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE F 412 " --> pdb=" O ILE F 483 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU F 411 " --> pdb=" O VAL F 418 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR F 434 " --> pdb=" O ILE F 422 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ARG F 424 " --> pdb=" O THR F 432 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N THR F 432 " --> pdb=" O ARG F 424 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR F 495 " --> pdb=" O THR F 396 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 458 through 460 Processing sheet with id=AG9, first strand: chain 'F' and resid 517 through 521 removed outlier: 3.779A pdb=" N VAL F 517 " --> pdb=" O LEU F 557 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N HIS F 558 " --> pdb=" O VAL F 543 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N VAL F 543 " --> pdb=" O HIS F 558 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 533 through 535 removed outlier: 9.241A pdb=" N TYR F 624 " --> pdb=" O SER F 571 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N PHE F 573 " --> pdb=" O TYR F 624 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 695 through 699 removed outlier: 4.600A pdb=" N TYR F 718 " --> pdb=" O VAL F 699 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE F 653 " --> pdb=" O ILE F 660 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS F 678 " --> pdb=" O GLN F 664 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU F 666 " --> pdb=" O GLN F 676 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLN F 676 " --> pdb=" O LEU F 666 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LEU F 668 " --> pdb=" O GLU F 674 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N GLU F 674 " --> pdb=" O LEU F 668 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N PHE F 732 " --> pdb=" O GLN F 636 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N THR F 638 " --> pdb=" O PHE F 732 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 749 through 754 removed outlier: 7.138A pdb=" N MET F 789 " --> pdb=" O MET F 779 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N MET F 779 " --> pdb=" O MET F 789 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA F 791 " --> pdb=" O THR F 777 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLU F 772 " --> pdb=" O PHE F 768 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE F 768 " --> pdb=" O GLU F 772 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA F 841 " --> pdb=" O VAL F 807 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE F 808 " --> pdb=" O GLN F 861 " (cutoff:3.500A) 1082 hydrogen bonds defined for protein. 2655 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: 19.44 Time building geometry restraints manager: 14.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10679 1.33 - 1.45: 5659 1.45 - 1.57: 22134 1.57 - 1.69: 0 1.69 - 1.81: 144 Bond restraints: 38616 Sorted by residual: bond pdb=" N THR C 829 " pdb=" CA THR C 829 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.14e+00 bond pdb=" N THR D 829 " pdb=" CA THR D 829 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.30e+00 bond pdb=" N THR F 829 " pdb=" CA THR F 829 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.26e+00 bond pdb=" N THR A 829 " pdb=" CA THR A 829 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.21e+00 bond pdb=" N THR B 829 " pdb=" CA THR B 829 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.20e+00 ... (remaining 38611 not shown) Histogram of bond angle deviations from ideal: 97.85 - 105.80: 970 105.80 - 113.76: 22288 113.76 - 121.71: 19444 121.71 - 129.66: 9546 129.66 - 137.61: 156 Bond angle restraints: 52404 Sorted by residual: angle pdb=" CA LEU C 583 " pdb=" CB LEU C 583 " pdb=" CG LEU C 583 " ideal model delta sigma weight residual 116.30 137.61 -21.31 3.50e+00 8.16e-02 3.71e+01 angle pdb=" N VAL C 331 " pdb=" CA VAL C 331 " pdb=" CB VAL C 331 " ideal model delta sigma weight residual 112.07 104.66 7.41 1.52e+00 4.33e-01 2.38e+01 angle pdb=" N VAL B 331 " pdb=" CA VAL B 331 " pdb=" CB VAL B 331 " ideal model delta sigma weight residual 112.07 105.37 6.70 1.52e+00 4.33e-01 1.94e+01 angle pdb=" N VAL D 331 " pdb=" CA VAL D 331 " pdb=" CB VAL D 331 " ideal model delta sigma weight residual 112.07 105.37 6.70 1.52e+00 4.33e-01 1.94e+01 angle pdb=" N VAL E 331 " pdb=" CA VAL E 331 " pdb=" CB VAL E 331 " ideal model delta sigma weight residual 112.07 105.39 6.68 1.52e+00 4.33e-01 1.93e+01 ... (remaining 52399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.32: 22016 15.32 - 30.64: 948 30.64 - 45.96: 238 45.96 - 61.28: 6 61.28 - 76.59: 48 Dihedral angle restraints: 23256 sinusoidal: 9180 harmonic: 14076 Sorted by residual: dihedral pdb=" CA ALA C 471 " pdb=" C ALA C 471 " pdb=" N SER C 472 " pdb=" CA SER C 472 " ideal model delta harmonic sigma weight residual 180.00 146.58 33.42 0 5.00e+00 4.00e-02 4.47e+01 dihedral pdb=" CA THR C 846 " pdb=" C THR C 846 " pdb=" N PRO C 847 " pdb=" CA PRO C 847 " ideal model delta harmonic sigma weight residual 180.00 151.65 28.35 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA ALA F 471 " pdb=" C ALA F 471 " pdb=" N SER F 472 " pdb=" CA SER F 472 " ideal model delta harmonic sigma weight residual 180.00 151.87 28.13 0 5.00e+00 4.00e-02 3.17e+01 ... (remaining 23253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3729 0.045 - 0.090: 1559 0.090 - 0.135: 615 0.135 - 0.180: 137 0.180 - 0.225: 20 Chirality restraints: 6060 Sorted by residual: chirality pdb=" CG LEU C 583 " pdb=" CB LEU C 583 " pdb=" CD1 LEU C 583 " pdb=" CD2 LEU C 583 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB ILE B 622 " pdb=" CA ILE B 622 " pdb=" CG1 ILE B 622 " pdb=" CG2 ILE B 622 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB ILE E 622 " pdb=" CA ILE E 622 " pdb=" CG1 ILE E 622 " pdb=" CG2 ILE E 622 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 6057 not shown) Planarity restraints: 6822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 328 " 0.049 5.00e-02 4.00e+02 7.39e-02 8.75e+00 pdb=" N PRO C 329 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO C 329 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 329 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 328 " -0.044 5.00e-02 4.00e+02 6.70e-02 7.17e+00 pdb=" N PRO E 329 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO E 329 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 329 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 328 " -0.044 5.00e-02 4.00e+02 6.69e-02 7.16e+00 pdb=" N PRO A 329 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 329 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 329 " -0.037 5.00e-02 4.00e+02 ... (remaining 6819 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 9787 2.80 - 3.33: 30923 3.33 - 3.85: 59320 3.85 - 4.38: 67536 4.38 - 4.90: 120220 Nonbonded interactions: 287786 Sorted by model distance: nonbonded pdb=" NH1 ARG F 536 " pdb=" OD2 ASP F 606 " model vdw 2.280 2.520 nonbonded pdb=" NH1 ARG E 536 " pdb=" OD2 ASP E 606 " model vdw 2.280 2.520 nonbonded pdb=" NH1 ARG B 536 " pdb=" OD2 ASP B 606 " model vdw 2.280 2.520 nonbonded pdb=" NH1 ARG A 536 " pdb=" OD2 ASP A 606 " model vdw 2.280 2.520 nonbonded pdb=" NH1 ARG D 536 " pdb=" OD2 ASP D 606 " model vdw 2.280 2.520 ... (remaining 287781 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 6.440 Check model and map are aligned: 0.550 Set scattering table: 0.300 Process input model: 102.550 Find NCS groups from input model: 2.750 Set up NCS constraints: 0.220 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 38616 Z= 0.449 Angle : 0.937 21.314 52404 Z= 0.493 Chirality : 0.057 0.225 6060 Planarity : 0.007 0.074 6822 Dihedral : 10.081 76.594 14292 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.09), residues: 4980 helix: -4.39 (0.09), residues: 468 sheet: -1.44 (0.11), residues: 1632 loop : -2.30 (0.09), residues: 2880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 222 HIS 0.008 0.002 HIS C 558 PHE 0.037 0.004 PHE C 605 TYR 0.017 0.003 TYR F 814 ARG 0.012 0.001 ARG C 536 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 912 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 912 time to evaluate : 4.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.6655 (mtp) cc_final: 0.6411 (mtm) REVERT: A 240 LEU cc_start: 0.7503 (tt) cc_final: 0.7065 (tp) REVERT: A 456 ARG cc_start: 0.7472 (mtm110) cc_final: 0.7148 (mmm160) REVERT: A 704 SER cc_start: 0.9242 (m) cc_final: 0.9017 (t) REVERT: B 456 ARG cc_start: 0.7766 (mtm110) cc_final: 0.7479 (mmm160) REVERT: B 627 GLU cc_start: 0.7253 (tm-30) cc_final: 0.6946 (tm-30) REVERT: B 704 SER cc_start: 0.9306 (m) cc_final: 0.8967 (t) REVERT: B 766 VAL cc_start: 0.8629 (t) cc_final: 0.8334 (t) REVERT: C 240 LEU cc_start: 0.7438 (tt) cc_final: 0.7173 (tp) REVERT: C 537 LYS cc_start: 0.8000 (mttt) cc_final: 0.7791 (mttt) REVERT: C 604 SER cc_start: 0.8062 (t) cc_final: 0.7836 (m) REVERT: C 704 SER cc_start: 0.9096 (m) cc_final: 0.8846 (t) REVERT: C 827 THR cc_start: 0.8003 (p) cc_final: 0.7738 (p) REVERT: D 240 LEU cc_start: 0.7461 (tt) cc_final: 0.7009 (tp) REVERT: D 456 ARG cc_start: 0.7429 (mtm110) cc_final: 0.7126 (mmm160) REVERT: D 704 SER cc_start: 0.9273 (m) cc_final: 0.9062 (t) REVERT: E 456 ARG cc_start: 0.7714 (mtm110) cc_final: 0.7476 (mmm160) REVERT: E 488 LYS cc_start: 0.7596 (tttp) cc_final: 0.7368 (tttm) REVERT: E 597 ARG cc_start: 0.7568 (ttt180) cc_final: 0.7364 (ttt180) REVERT: E 704 SER cc_start: 0.9289 (m) cc_final: 0.8999 (t) REVERT: E 766 VAL cc_start: 0.8644 (t) cc_final: 0.8353 (t) REVERT: F 240 LEU cc_start: 0.7460 (tt) cc_final: 0.7158 (tp) REVERT: F 314 ASP cc_start: 0.8090 (m-30) cc_final: 0.7710 (m-30) REVERT: F 491 MET cc_start: 0.8700 (tpp) cc_final: 0.8498 (tpp) REVERT: F 704 SER cc_start: 0.9121 (m) cc_final: 0.8874 (t) outliers start: 0 outliers final: 0 residues processed: 912 average time/residue: 0.5355 time to fit residues: 763.4978 Evaluate side-chains 503 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 503 time to evaluate : 4.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 420 optimal weight: 6.9990 chunk 377 optimal weight: 2.9990 chunk 209 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 254 optimal weight: 20.0000 chunk 201 optimal weight: 0.0980 chunk 390 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 237 optimal weight: 0.1980 chunk 290 optimal weight: 2.9990 chunk 452 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN A 316 ASN A 345 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 GLN A 687 GLN A 804 ASN B 151 GLN B 158 ASN B 164 HIS B 316 ASN B 345 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 ASN B 804 ASN C 69 GLN C 151 GLN C 174 ASN C 345 ASN C 409 GLN ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 ASN C 591 GLN C 804 ASN D 151 GLN D 316 ASN D 345 ASN ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN D 735 GLN D 804 ASN E 151 GLN E 158 ASN E 164 HIS E 316 ASN E 345 ASN E 388 HIS ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 551 ASN E 584 ASN E 804 ASN F 151 GLN F 158 ASN F 345 ASN ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 ASN F 591 GLN F 804 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 38616 Z= 0.207 Angle : 0.635 10.225 52404 Z= 0.330 Chirality : 0.047 0.164 6060 Planarity : 0.005 0.055 6822 Dihedral : 5.420 25.540 5358 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.27 % Allowed : 10.98 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.10), residues: 4980 helix: -3.51 (0.15), residues: 516 sheet: -1.26 (0.12), residues: 1650 loop : -1.92 (0.10), residues: 2814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 109 HIS 0.003 0.001 HIS E 388 PHE 0.016 0.002 PHE B 364 TYR 0.020 0.001 TYR E 535 ARG 0.008 0.000 ARG E 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 548 time to evaluate : 4.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 TRP cc_start: 0.8345 (p-90) cc_final: 0.8115 (p-90) REVERT: A 240 LEU cc_start: 0.7574 (tt) cc_final: 0.7201 (tp) REVERT: A 301 MET cc_start: 0.8635 (mmm) cc_final: 0.8377 (mmm) REVERT: A 456 ARG cc_start: 0.7599 (mtm110) cc_final: 0.7217 (mmm160) REVERT: B 456 ARG cc_start: 0.7822 (mtm110) cc_final: 0.7538 (mmm160) REVERT: B 570 ASN cc_start: 0.8310 (m-40) cc_final: 0.7954 (p0) REVERT: B 756 GLU cc_start: 0.8058 (pm20) cc_final: 0.7567 (pm20) REVERT: C 109 TRP cc_start: 0.8240 (p-90) cc_final: 0.7980 (p-90) REVERT: C 240 LEU cc_start: 0.7671 (tt) cc_final: 0.7328 (tp) REVERT: C 570 ASN cc_start: 0.8097 (m-40) cc_final: 0.7865 (p0) REVERT: C 867 GLU cc_start: 0.7768 (pm20) cc_final: 0.7487 (pm20) REVERT: D 109 TRP cc_start: 0.8359 (p-90) cc_final: 0.8068 (p-90) REVERT: D 145 PHE cc_start: 0.7047 (m-80) cc_final: 0.6533 (m-80) REVERT: D 243 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.6275 (mm) REVERT: D 301 MET cc_start: 0.8628 (mmm) cc_final: 0.8334 (mmm) REVERT: D 456 ARG cc_start: 0.7563 (mtm110) cc_final: 0.7241 (mmm160) REVERT: D 500 ASN cc_start: 0.8962 (p0) cc_final: 0.8664 (p0) REVERT: D 503 LYS cc_start: 0.8399 (mtpp) cc_final: 0.8069 (mtpp) REVERT: D 570 ASN cc_start: 0.8234 (m-40) cc_final: 0.8028 (m-40) REVERT: D 736 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6892 (mp0) REVERT: E 456 ARG cc_start: 0.7784 (mtm110) cc_final: 0.7541 (mmm160) REVERT: E 570 ASN cc_start: 0.8364 (m-40) cc_final: 0.7917 (p0) REVERT: E 627 GLU cc_start: 0.7696 (tp30) cc_final: 0.7277 (tp30) REVERT: E 756 GLU cc_start: 0.8134 (pm20) cc_final: 0.7632 (pm20) REVERT: E 831 ASN cc_start: 0.8051 (t0) cc_final: 0.7732 (t0) REVERT: F 109 TRP cc_start: 0.8249 (p-90) cc_final: 0.7998 (p-90) REVERT: F 153 LYS cc_start: 0.7201 (tptt) cc_final: 0.6995 (mmtt) REVERT: F 243 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6415 (mm) outliers start: 52 outliers final: 27 residues processed: 577 average time/residue: 0.5019 time to fit residues: 468.5785 Evaluate side-chains 453 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 423 time to evaluate : 4.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 792 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain D residue 54 MET Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 736 GLU Chi-restraints excluded: chain D residue 792 MET Chi-restraints excluded: chain D residue 859 LEU Chi-restraints excluded: chain D residue 863 SER Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 660 ILE Chi-restraints excluded: chain E residue 727 ASN Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 792 MET Chi-restraints excluded: chain F residue 830 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 251 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 376 optimal weight: 9.9990 chunk 307 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 453 optimal weight: 0.4980 chunk 489 optimal weight: 4.9990 chunk 403 optimal weight: 5.9990 chunk 449 optimal weight: 4.9990 chunk 154 optimal weight: 5.9990 chunk 363 optimal weight: 0.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 HIS B 158 ASN B 164 HIS B 409 GLN B 640 HIS ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 558 HIS C 591 GLN C 607 ASN C 640 HIS D 409 GLN D 558 HIS D 640 HIS E 158 ASN E 164 HIS ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 551 ASN E 640 HIS F 158 ASN ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 HIS F 584 ASN F 607 ASN F 640 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 38616 Z= 0.562 Angle : 0.769 14.439 52404 Z= 0.395 Chirality : 0.053 0.181 6060 Planarity : 0.005 0.053 6822 Dihedral : 5.622 29.019 5358 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.90 % Allowed : 11.84 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.10), residues: 4980 helix: -2.68 (0.19), residues: 468 sheet: -1.45 (0.12), residues: 1608 loop : -1.74 (0.10), residues: 2904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 871 HIS 0.007 0.001 HIS C 414 PHE 0.028 0.003 PHE C 364 TYR 0.024 0.003 TYR F 535 ARG 0.009 0.001 ARG C 536 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 453 time to evaluate : 4.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ASN cc_start: 0.8781 (OUTLIER) cc_final: 0.8393 (p0) REVERT: A 240 LEU cc_start: 0.7767 (tt) cc_final: 0.7333 (tp) REVERT: A 301 MET cc_start: 0.8813 (mmm) cc_final: 0.8454 (mmm) REVERT: A 309 GLN cc_start: 0.8335 (tp-100) cc_final: 0.8112 (tp40) REVERT: A 456 ARG cc_start: 0.7730 (mtm110) cc_final: 0.7173 (mmm160) REVERT: A 477 ILE cc_start: 0.7541 (OUTLIER) cc_final: 0.7106 (pp) REVERT: B 109 TRP cc_start: 0.8358 (p-90) cc_final: 0.8032 (p-90) REVERT: B 456 ARG cc_start: 0.7989 (mtm110) cc_final: 0.7603 (mmm160) REVERT: B 477 ILE cc_start: 0.6965 (OUTLIER) cc_final: 0.6604 (pt) REVERT: B 570 ASN cc_start: 0.8292 (m-40) cc_final: 0.7931 (p0) REVERT: B 704 SER cc_start: 0.9407 (m) cc_final: 0.9068 (p) REVERT: B 756 GLU cc_start: 0.8316 (pm20) cc_final: 0.7800 (pm20) REVERT: C 240 LEU cc_start: 0.7713 (tt) cc_final: 0.7404 (tp) REVERT: C 476 TRP cc_start: 0.6980 (t60) cc_final: 0.6779 (t60) REVERT: C 606 ASP cc_start: 0.8139 (t0) cc_final: 0.7915 (t0) REVERT: D 145 PHE cc_start: 0.7017 (m-80) cc_final: 0.6466 (m-80) REVERT: D 195 ASN cc_start: 0.8750 (OUTLIER) cc_final: 0.8324 (p0) REVERT: D 309 GLN cc_start: 0.8370 (tp-100) cc_final: 0.8157 (tp40) REVERT: D 456 ARG cc_start: 0.7630 (mtm110) cc_final: 0.7056 (mmm160) REVERT: D 477 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.7137 (pp) REVERT: D 503 LYS cc_start: 0.8473 (mtpp) cc_final: 0.8234 (mtpp) REVERT: D 860 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8693 (mt) REVERT: E 109 TRP cc_start: 0.8348 (p-90) cc_final: 0.8061 (p-90) REVERT: E 456 ARG cc_start: 0.7817 (mtm110) cc_final: 0.7489 (mmm160) REVERT: E 477 ILE cc_start: 0.7056 (OUTLIER) cc_final: 0.6700 (pt) REVERT: E 570 ASN cc_start: 0.8369 (m-40) cc_final: 0.7905 (p0) REVERT: E 756 GLU cc_start: 0.8325 (pm20) cc_final: 0.7708 (pm20) REVERT: F 109 TRP cc_start: 0.8433 (p-90) cc_final: 0.8184 (p-90) REVERT: F 477 ILE cc_start: 0.7453 (OUTLIER) cc_final: 0.7171 (pp) REVERT: F 491 MET cc_start: 0.8846 (tpp) cc_final: 0.8538 (mmp) REVERT: F 672 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.6635 (mtp85) outliers start: 160 outliers final: 98 residues processed: 573 average time/residue: 0.4611 time to fit residues: 441.9463 Evaluate side-chains 497 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 390 time to evaluate : 4.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 792 MET Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 646 LYS Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 727 ASN Chi-restraints excluded: chain C residue 742 SER Chi-restraints excluded: chain C residue 746 ASP Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 783 THR Chi-restraints excluded: chain C residue 792 MET Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain D residue 54 MET Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 704 SER Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain D residue 792 MET Chi-restraints excluded: chain D residue 846 THR Chi-restraints excluded: chain D residue 860 LEU Chi-restraints excluded: chain D residue 863 SER Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain E residue 481 ILE Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 545 THR Chi-restraints excluded: chain E residue 568 THR Chi-restraints excluded: chain E residue 660 ILE Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 704 SER Chi-restraints excluded: chain E residue 715 LEU Chi-restraints excluded: chain E residue 727 ASN Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 777 THR Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 477 ILE Chi-restraints excluded: chain F residue 481 ILE Chi-restraints excluded: chain F residue 505 LEU Chi-restraints excluded: chain F residue 545 THR Chi-restraints excluded: chain F residue 568 THR Chi-restraints excluded: chain F residue 665 THR Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 672 ARG Chi-restraints excluded: chain F residue 715 LEU Chi-restraints excluded: chain F residue 742 SER Chi-restraints excluded: chain F residue 777 THR Chi-restraints excluded: chain F residue 783 THR Chi-restraints excluded: chain F residue 792 MET Chi-restraints excluded: chain F residue 807 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 447 optimal weight: 1.9990 chunk 340 optimal weight: 20.0000 chunk 235 optimal weight: 3.9990 chunk 50 optimal weight: 0.4980 chunk 216 optimal weight: 0.0270 chunk 304 optimal weight: 0.9990 chunk 454 optimal weight: 0.9990 chunk 481 optimal weight: 0.7980 chunk 237 optimal weight: 2.9990 chunk 430 optimal weight: 0.0470 chunk 129 optimal weight: 0.7980 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 ASN B 158 ASN ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 ASN ** D 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 ASN E 158 ASN E 409 GLN ** E 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN F 409 GLN ** F 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 38616 Z= 0.149 Angle : 0.572 9.081 52404 Z= 0.292 Chirality : 0.046 0.212 6060 Planarity : 0.004 0.060 6822 Dihedral : 5.002 22.448 5358 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.49 % Allowed : 14.35 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.11), residues: 4980 helix: -2.37 (0.20), residues: 522 sheet: -1.28 (0.12), residues: 1560 loop : -1.64 (0.10), residues: 2898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 109 HIS 0.005 0.001 HIS B 441 PHE 0.016 0.002 PHE D 253 TYR 0.011 0.001 TYR F 563 ARG 0.004 0.000 ARG C 442 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 461 time to evaluate : 4.446 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: A 243 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6091 (mm) REVERT: A 301 MET cc_start: 0.8796 (mmm) cc_final: 0.8564 (mmm) REVERT: A 456 ARG cc_start: 0.7686 (mtm110) cc_final: 0.7194 (mmm160) REVERT: A 477 ILE cc_start: 0.7300 (OUTLIER) cc_final: 0.6800 (pp) REVERT: B 456 ARG cc_start: 0.7939 (mtm110) cc_final: 0.7635 (mmm160) REVERT: B 477 ILE cc_start: 0.6962 (OUTLIER) cc_final: 0.6670 (pp) REVERT: B 505 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8409 (mt) REVERT: B 570 ASN cc_start: 0.8243 (m-40) cc_final: 0.7914 (p0) REVERT: B 704 SER cc_start: 0.9297 (m) cc_final: 0.8976 (p) REVERT: B 756 GLU cc_start: 0.8237 (pm20) cc_final: 0.7703 (pm20) REVERT: C 109 TRP cc_start: 0.8243 (p-90) cc_final: 0.8007 (p-90) REVERT: C 135 MET cc_start: 0.7145 (mtt) cc_final: 0.6825 (mtt) REVERT: C 243 LEU cc_start: 0.7292 (OUTLIER) cc_final: 0.6363 (mm) REVERT: D 145 PHE cc_start: 0.7029 (m-80) cc_final: 0.6470 (m-80) REVERT: D 456 ARG cc_start: 0.7743 (mtm110) cc_final: 0.7201 (mmm160) REVERT: D 477 ILE cc_start: 0.7302 (OUTLIER) cc_final: 0.6803 (pp) REVERT: E 135 MET cc_start: 0.6685 (mtt) cc_final: 0.6471 (mtt) REVERT: E 456 ARG cc_start: 0.7887 (mtm110) cc_final: 0.7580 (mmm160) REVERT: E 477 ILE cc_start: 0.6965 (OUTLIER) cc_final: 0.6610 (pp) REVERT: E 505 LEU cc_start: 0.8769 (mm) cc_final: 0.8363 (mt) REVERT: E 570 ASN cc_start: 0.8322 (m-40) cc_final: 0.7895 (p0) REVERT: E 756 GLU cc_start: 0.8280 (pm20) cc_final: 0.7671 (pm20) REVERT: F 153 LYS cc_start: 0.7392 (tptt) cc_final: 0.7122 (tptp) REVERT: F 195 ASN cc_start: 0.8332 (OUTLIER) cc_final: 0.7953 (p0) REVERT: F 258 GLU cc_start: 0.7735 (pm20) cc_final: 0.7530 (pm20) REVERT: F 477 ILE cc_start: 0.7274 (OUTLIER) cc_final: 0.6959 (pp) outliers start: 102 outliers final: 51 residues processed: 530 average time/residue: 0.4699 time to fit residues: 413.3698 Evaluate side-chains 473 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 413 time to evaluate : 4.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 792 MET Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 646 LYS Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 783 THR Chi-restraints excluded: chain C residue 792 MET Chi-restraints excluded: chain D residue 54 MET Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 441 HIS Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain D residue 792 MET Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 441 HIS Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain E residue 660 ILE Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 792 MET Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain E residue 860 LEU Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 477 ILE Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 783 THR Chi-restraints excluded: chain F residue 807 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 400 optimal weight: 2.9990 chunk 273 optimal weight: 0.0670 chunk 6 optimal weight: 2.9990 chunk 358 optimal weight: 1.9990 chunk 198 optimal weight: 0.0370 chunk 410 optimal weight: 4.9990 chunk 332 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 245 optimal weight: 0.9990 chunk 432 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN B 158 ASN C 151 GLN ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN F 151 GLN F 158 ASN ** F 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 38616 Z= 0.249 Angle : 0.583 9.976 52404 Z= 0.296 Chirality : 0.046 0.170 6060 Planarity : 0.004 0.048 6822 Dihedral : 4.913 22.850 5358 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.03 % Allowed : 14.81 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.11), residues: 4980 helix: -2.08 (0.20), residues: 558 sheet: -1.25 (0.12), residues: 1530 loop : -1.63 (0.10), residues: 2892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 109 HIS 0.006 0.001 HIS F 441 PHE 0.015 0.002 PHE D 253 TYR 0.021 0.001 TYR B 131 ARG 0.004 0.000 ARG C 536 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 429 time to evaluate : 4.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.8252 (p0) REVERT: A 243 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6084 (mm) REVERT: A 301 MET cc_start: 0.8830 (mmm) cc_final: 0.8627 (mmm) REVERT: A 456 ARG cc_start: 0.7808 (mtm110) cc_final: 0.7003 (tpt170) REVERT: A 477 ILE cc_start: 0.7353 (OUTLIER) cc_final: 0.6857 (pp) REVERT: B 109 TRP cc_start: 0.8325 (p-90) cc_final: 0.7947 (p-90) REVERT: B 456 ARG cc_start: 0.7819 (mtm110) cc_final: 0.7526 (mmm160) REVERT: B 477 ILE cc_start: 0.6990 (OUTLIER) cc_final: 0.6723 (pp) REVERT: B 570 ASN cc_start: 0.8257 (m-40) cc_final: 0.7933 (p0) REVERT: B 704 SER cc_start: 0.9303 (m) cc_final: 0.8995 (p) REVERT: B 756 GLU cc_start: 0.8325 (pm20) cc_final: 0.7836 (pm20) REVERT: C 109 TRP cc_start: 0.8267 (p-90) cc_final: 0.8056 (p-90) REVERT: C 135 MET cc_start: 0.7009 (mtt) cc_final: 0.6736 (mtt) REVERT: C 243 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6229 (mm) REVERT: C 336 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8320 (mtp85) REVERT: D 145 PHE cc_start: 0.7049 (m-80) cc_final: 0.6477 (m-80) REVERT: D 195 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8349 (p0) REVERT: D 243 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6004 (mm) REVERT: D 456 ARG cc_start: 0.7733 (mtm110) cc_final: 0.7133 (tpt170) REVERT: D 477 ILE cc_start: 0.7359 (OUTLIER) cc_final: 0.6883 (pp) REVERT: E 117 LEU cc_start: 0.8011 (tt) cc_final: 0.7798 (tt) REVERT: E 135 MET cc_start: 0.6757 (mtt) cc_final: 0.6535 (mtt) REVERT: E 411 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8372 (tt) REVERT: E 456 ARG cc_start: 0.7766 (mtm110) cc_final: 0.7538 (mmm160) REVERT: E 477 ILE cc_start: 0.6967 (OUTLIER) cc_final: 0.6572 (pt) REVERT: E 503 LYS cc_start: 0.8340 (mttt) cc_final: 0.8138 (mtpp) REVERT: E 505 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8418 (mt) REVERT: E 570 ASN cc_start: 0.8336 (m-40) cc_final: 0.7914 (p0) REVERT: E 756 GLU cc_start: 0.8379 (pm20) cc_final: 0.7753 (pm20) REVERT: F 109 TRP cc_start: 0.8287 (p-90) cc_final: 0.8070 (p-90) REVERT: F 195 ASN cc_start: 0.8268 (OUTLIER) cc_final: 0.7950 (p0) REVERT: F 243 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6147 (mm) REVERT: F 477 ILE cc_start: 0.7349 (OUTLIER) cc_final: 0.7022 (pp) outliers start: 124 outliers final: 77 residues processed: 518 average time/residue: 0.4605 time to fit residues: 400.2146 Evaluate side-chains 486 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 394 time to evaluate : 4.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 792 MET Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 646 LYS Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 727 ASN Chi-restraints excluded: chain C residue 783 THR Chi-restraints excluded: chain C residue 792 MET Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain D residue 54 MET Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain D residue 792 MET Chi-restraints excluded: chain D residue 846 THR Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain E residue 660 ILE Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain E residue 727 ASN Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 742 SER Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 296 ASP Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 477 ILE Chi-restraints excluded: chain F residue 505 LEU Chi-restraints excluded: chain F residue 590 VAL Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 742 SER Chi-restraints excluded: chain F residue 746 ASP Chi-restraints excluded: chain F residue 783 THR Chi-restraints excluded: chain F residue 792 MET Chi-restraints excluded: chain F residue 807 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 161 optimal weight: 0.8980 chunk 433 optimal weight: 9.9990 chunk 95 optimal weight: 0.0970 chunk 282 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 481 optimal weight: 2.9990 chunk 399 optimal weight: 0.2980 chunk 223 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 252 optimal weight: 0.0870 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 500 ASN D 591 GLN ** E 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN ** F 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 38616 Z= 0.145 Angle : 0.537 8.598 52404 Z= 0.272 Chirality : 0.045 0.160 6060 Planarity : 0.003 0.050 6822 Dihedral : 4.677 22.772 5358 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.12 % Allowed : 15.42 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.11), residues: 4980 helix: -2.02 (0.21), residues: 570 sheet: -0.95 (0.12), residues: 1578 loop : -1.60 (0.10), residues: 2832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 109 HIS 0.013 0.001 HIS E 441 PHE 0.014 0.001 PHE D 253 TYR 0.012 0.001 TYR F 535 ARG 0.014 0.000 ARG B 103 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 453 time to evaluate : 4.360 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: A 243 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6014 (mm) REVERT: A 301 MET cc_start: 0.8772 (mmm) cc_final: 0.8515 (mmm) REVERT: A 456 ARG cc_start: 0.7790 (mtm110) cc_final: 0.7037 (tpt170) REVERT: A 477 ILE cc_start: 0.7272 (OUTLIER) cc_final: 0.6762 (pp) REVERT: B 239 LYS cc_start: 0.6482 (mttt) cc_final: 0.6175 (mtpt) REVERT: B 456 ARG cc_start: 0.7781 (mtm110) cc_final: 0.7516 (mmm160) REVERT: B 477 ILE cc_start: 0.6893 (OUTLIER) cc_final: 0.6403 (pp) REVERT: B 505 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8324 (mt) REVERT: B 535 TYR cc_start: 0.6573 (t80) cc_final: 0.6004 (t80) REVERT: B 570 ASN cc_start: 0.8247 (m-40) cc_final: 0.7933 (p0) REVERT: B 627 GLU cc_start: 0.7799 (tp30) cc_final: 0.7448 (tp30) REVERT: B 704 SER cc_start: 0.9266 (m) cc_final: 0.8992 (p) REVERT: B 756 GLU cc_start: 0.8334 (pm20) cc_final: 0.7817 (pm20) REVERT: C 243 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6186 (mm) REVERT: D 145 PHE cc_start: 0.7098 (m-80) cc_final: 0.6513 (m-80) REVERT: D 243 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.5949 (mm) REVERT: D 456 ARG cc_start: 0.7690 (mtm110) cc_final: 0.7135 (tpt170) REVERT: D 477 ILE cc_start: 0.7290 (OUTLIER) cc_final: 0.6786 (pp) REVERT: E 135 MET cc_start: 0.7136 (mtt) cc_final: 0.6899 (mtt) REVERT: E 240 LEU cc_start: 0.7717 (tt) cc_final: 0.7460 (tp) REVERT: E 456 ARG cc_start: 0.7740 (mtm110) cc_final: 0.7097 (tpt90) REVERT: E 477 ILE cc_start: 0.6978 (OUTLIER) cc_final: 0.6549 (pp) REVERT: E 505 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8354 (mt) REVERT: E 535 TYR cc_start: 0.6652 (t80) cc_final: 0.6046 (t80) REVERT: E 570 ASN cc_start: 0.8318 (m-40) cc_final: 0.7910 (p0) REVERT: E 756 GLU cc_start: 0.8262 (pm20) cc_final: 0.7661 (pm20) REVERT: F 195 ASN cc_start: 0.8232 (OUTLIER) cc_final: 0.7760 (p0) REVERT: F 243 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6228 (mm) REVERT: F 477 ILE cc_start: 0.7285 (OUTLIER) cc_final: 0.7004 (pp) outliers start: 128 outliers final: 76 residues processed: 547 average time/residue: 0.4424 time to fit residues: 409.7555 Evaluate side-chains 507 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 419 time to evaluate : 4.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 792 MET Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 646 LYS Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 783 THR Chi-restraints excluded: chain C residue 792 MET Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 792 MET Chi-restraints excluded: chain D residue 846 THR Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain E residue 660 ILE Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 477 ILE Chi-restraints excluded: chain F residue 505 LEU Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 590 VAL Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 746 ASP Chi-restraints excluded: chain F residue 783 THR Chi-restraints excluded: chain F residue 792 MET Chi-restraints excluded: chain F residue 807 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 464 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 274 optimal weight: 0.9980 chunk 351 optimal weight: 0.4980 chunk 272 optimal weight: 2.9990 chunk 405 optimal weight: 9.9990 chunk 269 optimal weight: 0.3980 chunk 479 optimal weight: 4.9990 chunk 300 optimal weight: 0.9980 chunk 292 optimal weight: 0.8980 chunk 221 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 GLN ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN E 388 HIS ** E 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN F 345 ASN ** F 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 38616 Z= 0.181 Angle : 0.549 10.340 52404 Z= 0.278 Chirality : 0.045 0.178 6060 Planarity : 0.003 0.046 6822 Dihedral : 4.612 23.415 5358 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.12 % Allowed : 16.23 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.11), residues: 4980 helix: -1.91 (0.21), residues: 570 sheet: -0.86 (0.13), residues: 1578 loop : -1.51 (0.11), residues: 2832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 109 HIS 0.007 0.001 HIS B 441 PHE 0.014 0.001 PHE D 253 TYR 0.020 0.001 TYR E 131 ARG 0.008 0.000 ARG B 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 433 time to evaluate : 3.399 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: A 162 MET cc_start: 0.8020 (tpt) cc_final: 0.7644 (tpp) REVERT: A 195 ASN cc_start: 0.8667 (OUTLIER) cc_final: 0.8189 (p0) REVERT: A 206 LEU cc_start: 0.8625 (tp) cc_final: 0.8395 (mp) REVERT: A 243 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6027 (mm) REVERT: A 301 MET cc_start: 0.8771 (mmm) cc_final: 0.8540 (mmm) REVERT: A 456 ARG cc_start: 0.7757 (mtm110) cc_final: 0.7210 (tpt170) REVERT: A 475 GLU cc_start: 0.6338 (mt-10) cc_final: 0.6118 (mt-10) REVERT: A 477 ILE cc_start: 0.7277 (OUTLIER) cc_final: 0.6805 (pp) REVERT: A 789 MET cc_start: 0.7920 (mtm) cc_final: 0.7403 (mmm) REVERT: B 135 MET cc_start: 0.6820 (mtt) cc_final: 0.6618 (mtt) REVERT: B 239 LYS cc_start: 0.6457 (mttt) cc_final: 0.6179 (mtpt) REVERT: B 456 ARG cc_start: 0.7800 (mtm110) cc_final: 0.7117 (tpt90) REVERT: B 477 ILE cc_start: 0.6896 (OUTLIER) cc_final: 0.6403 (pp) REVERT: B 505 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8343 (mt) REVERT: B 535 TYR cc_start: 0.6676 (t80) cc_final: 0.6091 (t80) REVERT: B 570 ASN cc_start: 0.8252 (m-40) cc_final: 0.7939 (p0) REVERT: B 627 GLU cc_start: 0.7808 (tp30) cc_final: 0.7396 (tp30) REVERT: B 704 SER cc_start: 0.9305 (m) cc_final: 0.9021 (p) REVERT: B 756 GLU cc_start: 0.8349 (pm20) cc_final: 0.7838 (pm20) REVERT: C 243 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6244 (mm) REVERT: C 336 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8405 (mtp85) REVERT: D 145 PHE cc_start: 0.7093 (m-80) cc_final: 0.6511 (m-80) REVERT: D 195 ASN cc_start: 0.8757 (OUTLIER) cc_final: 0.8306 (p0) REVERT: D 206 LEU cc_start: 0.8760 (tp) cc_final: 0.8546 (mt) REVERT: D 243 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.5953 (mm) REVERT: D 456 ARG cc_start: 0.7706 (mtm110) cc_final: 0.7128 (tpt170) REVERT: D 477 ILE cc_start: 0.7289 (OUTLIER) cc_final: 0.6790 (pp) REVERT: E 240 LEU cc_start: 0.7670 (tt) cc_final: 0.7413 (tp) REVERT: E 411 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8324 (tt) REVERT: E 456 ARG cc_start: 0.7756 (mtm110) cc_final: 0.7551 (mmm160) REVERT: E 477 ILE cc_start: 0.6969 (OUTLIER) cc_final: 0.6528 (pp) REVERT: E 505 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8391 (mt) REVERT: E 535 TYR cc_start: 0.6789 (t80) cc_final: 0.6216 (t80) REVERT: E 570 ASN cc_start: 0.8317 (m-40) cc_final: 0.7912 (p0) REVERT: E 756 GLU cc_start: 0.8325 (pm20) cc_final: 0.7745 (pm20) REVERT: F 195 ASN cc_start: 0.8177 (OUTLIER) cc_final: 0.7641 (p0) REVERT: F 243 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6100 (mm) REVERT: F 477 ILE cc_start: 0.7289 (OUTLIER) cc_final: 0.6993 (pp) outliers start: 128 outliers final: 85 residues processed: 523 average time/residue: 0.4465 time to fit residues: 394.7315 Evaluate side-chains 511 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 410 time to evaluate : 4.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 792 MET Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 646 LYS Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 746 ASP Chi-restraints excluded: chain C residue 783 THR Chi-restraints excluded: chain C residue 792 MET Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 792 MET Chi-restraints excluded: chain D residue 846 THR Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain E residue 660 ILE Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 477 ILE Chi-restraints excluded: chain F residue 501 LEU Chi-restraints excluded: chain F residue 505 LEU Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 590 VAL Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 746 ASP Chi-restraints excluded: chain F residue 783 THR Chi-restraints excluded: chain F residue 792 MET Chi-restraints excluded: chain F residue 807 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 296 optimal weight: 0.0010 chunk 191 optimal weight: 1.9990 chunk 286 optimal weight: 0.8980 chunk 144 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 92 optimal weight: 20.0000 chunk 305 optimal weight: 7.9990 chunk 327 optimal weight: 0.9990 chunk 237 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 377 optimal weight: 2.9990 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 GLN A 716 GLN B 158 ASN ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 861 GLN C 158 ASN ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN ** E 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 861 GLN F 158 ASN ** F 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 38616 Z= 0.209 Angle : 0.562 9.303 52404 Z= 0.283 Chirality : 0.045 0.171 6060 Planarity : 0.003 0.045 6822 Dihedral : 4.615 23.816 5358 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.39 % Allowed : 16.42 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.11), residues: 4980 helix: -1.81 (0.21), residues: 570 sheet: -0.84 (0.13), residues: 1578 loop : -1.46 (0.11), residues: 2832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP C 109 HIS 0.008 0.001 HIS B 441 PHE 0.014 0.001 PHE D 253 TYR 0.033 0.001 TYR A 744 ARG 0.007 0.000 ARG B 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 418 time to evaluate : 4.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 MET cc_start: 0.8048 (tpt) cc_final: 0.7649 (tpp) REVERT: A 195 ASN cc_start: 0.8699 (OUTLIER) cc_final: 0.8263 (p0) REVERT: A 206 LEU cc_start: 0.8608 (tp) cc_final: 0.8390 (mp) REVERT: A 243 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.6045 (mm) REVERT: A 301 MET cc_start: 0.8810 (mmm) cc_final: 0.8590 (mmm) REVERT: A 456 ARG cc_start: 0.7761 (mtm110) cc_final: 0.7190 (tpt170) REVERT: A 475 GLU cc_start: 0.6381 (mt-10) cc_final: 0.6124 (mt-10) REVERT: A 477 ILE cc_start: 0.7287 (OUTLIER) cc_final: 0.6778 (pp) REVERT: A 744 TYR cc_start: 0.8660 (m-10) cc_final: 0.8458 (m-10) REVERT: A 789 MET cc_start: 0.7919 (mtm) cc_final: 0.7542 (mmm) REVERT: B 456 ARG cc_start: 0.7819 (mtm110) cc_final: 0.7123 (tpt90) REVERT: B 477 ILE cc_start: 0.6911 (OUTLIER) cc_final: 0.6411 (pp) REVERT: B 505 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8360 (mt) REVERT: B 535 TYR cc_start: 0.6726 (t80) cc_final: 0.6132 (t80) REVERT: B 570 ASN cc_start: 0.8255 (m-40) cc_final: 0.7940 (p0) REVERT: B 704 SER cc_start: 0.9310 (m) cc_final: 0.9013 (p) REVERT: B 756 GLU cc_start: 0.8376 (pm20) cc_final: 0.7863 (pm20) REVERT: C 243 LEU cc_start: 0.6981 (OUTLIER) cc_final: 0.6013 (mm) REVERT: C 336 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8358 (mtp85) REVERT: D 145 PHE cc_start: 0.7104 (m-80) cc_final: 0.6520 (m-80) REVERT: D 195 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8319 (p0) REVERT: D 243 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6088 (mm) REVERT: D 456 ARG cc_start: 0.7688 (mtm110) cc_final: 0.7121 (tpt170) REVERT: D 477 ILE cc_start: 0.7304 (OUTLIER) cc_final: 0.6813 (pp) REVERT: E 240 LEU cc_start: 0.7669 (tt) cc_final: 0.7400 (tp) REVERT: E 456 ARG cc_start: 0.7761 (mtm110) cc_final: 0.7096 (tpt90) REVERT: E 477 ILE cc_start: 0.6972 (OUTLIER) cc_final: 0.6505 (pp) REVERT: E 505 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8422 (mt) REVERT: E 570 ASN cc_start: 0.8328 (m-40) cc_final: 0.7919 (p0) REVERT: E 756 GLU cc_start: 0.8361 (pm20) cc_final: 0.7773 (pm20) REVERT: F 195 ASN cc_start: 0.8323 (OUTLIER) cc_final: 0.7816 (p0) REVERT: F 243 LEU cc_start: 0.7061 (OUTLIER) cc_final: 0.6068 (mm) REVERT: F 477 ILE cc_start: 0.7299 (OUTLIER) cc_final: 0.7014 (pp) outliers start: 139 outliers final: 98 residues processed: 514 average time/residue: 0.4355 time to fit residues: 379.0967 Evaluate side-chains 509 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 396 time to evaluate : 4.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 792 MET Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 646 LYS Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 742 SER Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 746 ASP Chi-restraints excluded: chain C residue 792 MET Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 792 MET Chi-restraints excluded: chain D residue 846 THR Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 568 THR Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain E residue 660 ILE Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 783 THR Chi-restraints excluded: chain E residue 792 MET Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 477 ILE Chi-restraints excluded: chain F residue 501 LEU Chi-restraints excluded: chain F residue 505 LEU Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 590 VAL Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 742 SER Chi-restraints excluded: chain F residue 746 ASP Chi-restraints excluded: chain F residue 783 THR Chi-restraints excluded: chain F residue 792 MET Chi-restraints excluded: chain F residue 807 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 436 optimal weight: 3.9990 chunk 459 optimal weight: 4.9990 chunk 419 optimal weight: 3.9990 chunk 447 optimal weight: 0.9990 chunk 269 optimal weight: 3.9990 chunk 194 optimal weight: 0.0030 chunk 351 optimal weight: 0.0470 chunk 137 optimal weight: 1.9990 chunk 404 optimal weight: 1.9990 chunk 423 optimal weight: 10.0000 chunk 445 optimal weight: 7.9990 overall best weight: 1.0094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN B 158 ASN ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 831 ASN E 47 ASN ** E 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN ** F 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 38616 Z= 0.214 Angle : 0.572 11.565 52404 Z= 0.287 Chirality : 0.046 0.175 6060 Planarity : 0.003 0.043 6822 Dihedral : 4.628 24.077 5358 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.32 % Allowed : 16.74 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.11), residues: 4980 helix: -1.77 (0.22), residues: 570 sheet: -0.82 (0.13), residues: 1578 loop : -1.42 (0.11), residues: 2832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP F 109 HIS 0.008 0.001 HIS B 441 PHE 0.019 0.002 PHE A 468 TYR 0.037 0.001 TYR B 744 ARG 0.006 0.000 ARG B 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 396 time to evaluate : 4.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 MET cc_start: 0.8103 (tpt) cc_final: 0.7688 (tpp) REVERT: A 195 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8270 (p0) REVERT: A 206 LEU cc_start: 0.8604 (tp) cc_final: 0.8391 (mp) REVERT: A 243 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.6096 (mm) REVERT: A 301 MET cc_start: 0.8812 (mmm) cc_final: 0.8592 (mmm) REVERT: A 456 ARG cc_start: 0.7772 (mtm110) cc_final: 0.7196 (tpt170) REVERT: A 475 GLU cc_start: 0.6393 (mt-10) cc_final: 0.6128 (mt-10) REVERT: A 477 ILE cc_start: 0.7281 (OUTLIER) cc_final: 0.6766 (pp) REVERT: A 789 MET cc_start: 0.7965 (mtm) cc_final: 0.7589 (mmm) REVERT: B 239 LYS cc_start: 0.6456 (mttt) cc_final: 0.6183 (mtpt) REVERT: B 456 ARG cc_start: 0.7821 (mtm110) cc_final: 0.7128 (tpt90) REVERT: B 477 ILE cc_start: 0.6916 (OUTLIER) cc_final: 0.6412 (pp) REVERT: B 505 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8360 (mt) REVERT: B 535 TYR cc_start: 0.6776 (t80) cc_final: 0.6104 (t80) REVERT: B 570 ASN cc_start: 0.8255 (m-40) cc_final: 0.7934 (p0) REVERT: B 627 GLU cc_start: 0.7834 (tp30) cc_final: 0.7374 (tp30) REVERT: B 704 SER cc_start: 0.9316 (m) cc_final: 0.9009 (p) REVERT: B 756 GLU cc_start: 0.8326 (pm20) cc_final: 0.7717 (pm20) REVERT: C 243 LEU cc_start: 0.7005 (OUTLIER) cc_final: 0.6053 (mm) REVERT: C 336 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8350 (mtp85) REVERT: D 145 PHE cc_start: 0.7106 (m-80) cc_final: 0.6513 (m-80) REVERT: D 195 ASN cc_start: 0.8787 (OUTLIER) cc_final: 0.8326 (p0) REVERT: D 243 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6014 (mm) REVERT: D 456 ARG cc_start: 0.7706 (mtm110) cc_final: 0.7122 (tpt170) REVERT: D 477 ILE cc_start: 0.7273 (OUTLIER) cc_final: 0.6775 (pp) REVERT: E 240 LEU cc_start: 0.7660 (tt) cc_final: 0.7402 (tp) REVERT: E 456 ARG cc_start: 0.7766 (mtm110) cc_final: 0.7092 (tpt90) REVERT: E 477 ILE cc_start: 0.6972 (OUTLIER) cc_final: 0.6497 (pp) REVERT: E 505 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8418 (mt) REVERT: E 570 ASN cc_start: 0.8325 (m-40) cc_final: 0.7914 (p0) REVERT: E 756 GLU cc_start: 0.8334 (pm20) cc_final: 0.7749 (pm20) REVERT: F 195 ASN cc_start: 0.8258 (OUTLIER) cc_final: 0.7742 (p0) REVERT: F 243 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6077 (mm) REVERT: F 477 ILE cc_start: 0.7299 (OUTLIER) cc_final: 0.7015 (pp) outliers start: 136 outliers final: 99 residues processed: 491 average time/residue: 0.4381 time to fit residues: 362.8085 Evaluate side-chains 503 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 389 time to evaluate : 4.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 792 MET Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 646 LYS Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 742 SER Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 746 ASP Chi-restraints excluded: chain C residue 792 MET Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 792 MET Chi-restraints excluded: chain D residue 846 THR Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 509 LEU Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 568 THR Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain E residue 660 ILE Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 783 THR Chi-restraints excluded: chain E residue 792 MET Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain F residue 158 ASN Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 296 ASP Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 477 ILE Chi-restraints excluded: chain F residue 501 LEU Chi-restraints excluded: chain F residue 505 LEU Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 590 VAL Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 742 SER Chi-restraints excluded: chain F residue 746 ASP Chi-restraints excluded: chain F residue 783 THR Chi-restraints excluded: chain F residue 792 MET Chi-restraints excluded: chain F residue 807 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 293 optimal weight: 7.9990 chunk 472 optimal weight: 0.8980 chunk 288 optimal weight: 0.9980 chunk 224 optimal weight: 3.9990 chunk 328 optimal weight: 0.0370 chunk 496 optimal weight: 3.9990 chunk 456 optimal weight: 4.9990 chunk 395 optimal weight: 0.9980 chunk 41 optimal weight: 0.0010 chunk 305 optimal weight: 7.9990 chunk 242 optimal weight: 0.9980 overall best weight: 0.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 831 ASN ** E 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN ** F 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 38616 Z= 0.164 Angle : 0.562 10.139 52404 Z= 0.280 Chirality : 0.045 0.166 6060 Planarity : 0.003 0.043 6822 Dihedral : 4.553 24.416 5358 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.71 % Allowed : 17.20 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.11), residues: 4980 helix: -1.64 (0.23), residues: 498 sheet: -0.78 (0.13), residues: 1590 loop : -1.23 (0.11), residues: 2892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 109 HIS 0.006 0.001 HIS B 441 PHE 0.015 0.001 PHE B 833 TYR 0.028 0.001 TYR A 744 ARG 0.006 0.000 ARG B 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 416 time to evaluate : 3.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 PHE cc_start: 0.6869 (m-80) cc_final: 0.6216 (m-80) REVERT: A 162 MET cc_start: 0.8014 (tpt) cc_final: 0.7685 (tpp) REVERT: A 195 ASN cc_start: 0.8652 (OUTLIER) cc_final: 0.8199 (p0) REVERT: A 206 LEU cc_start: 0.8592 (tp) cc_final: 0.8362 (mp) REVERT: A 243 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6036 (mm) REVERT: A 301 MET cc_start: 0.8806 (mmm) cc_final: 0.8567 (mmm) REVERT: A 456 ARG cc_start: 0.7767 (mtm110) cc_final: 0.7202 (tpt170) REVERT: A 477 ILE cc_start: 0.7215 (OUTLIER) cc_final: 0.6732 (pp) REVERT: A 789 MET cc_start: 0.7920 (mtm) cc_final: 0.7562 (mmm) REVERT: B 239 LYS cc_start: 0.6453 (mttt) cc_final: 0.6173 (mtpt) REVERT: B 456 ARG cc_start: 0.7811 (mtm110) cc_final: 0.7127 (tpt90) REVERT: B 477 ILE cc_start: 0.6868 (OUTLIER) cc_final: 0.6334 (pp) REVERT: B 505 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8353 (mt) REVERT: B 570 ASN cc_start: 0.8252 (m-40) cc_final: 0.7953 (p0) REVERT: B 627 GLU cc_start: 0.7819 (tp30) cc_final: 0.7350 (tp30) REVERT: B 704 SER cc_start: 0.9319 (m) cc_final: 0.9017 (p) REVERT: B 756 GLU cc_start: 0.8291 (pm20) cc_final: 0.7695 (pm20) REVERT: C 243 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6032 (mm) REVERT: C 336 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8357 (mtp85) REVERT: D 145 PHE cc_start: 0.7082 (m-80) cc_final: 0.6490 (m-80) REVERT: D 195 ASN cc_start: 0.8767 (OUTLIER) cc_final: 0.8316 (p0) REVERT: D 243 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6046 (mm) REVERT: D 456 ARG cc_start: 0.7699 (mtm110) cc_final: 0.7122 (tpt170) REVERT: D 477 ILE cc_start: 0.7205 (OUTLIER) cc_final: 0.6696 (pp) REVERT: E 240 LEU cc_start: 0.7652 (tt) cc_final: 0.7395 (tp) REVERT: E 477 ILE cc_start: 0.6923 (OUTLIER) cc_final: 0.6425 (pp) REVERT: E 505 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8354 (mt) REVERT: E 570 ASN cc_start: 0.8317 (m-40) cc_final: 0.7911 (p0) REVERT: E 756 GLU cc_start: 0.8346 (pm20) cc_final: 0.7724 (pm20) REVERT: F 195 ASN cc_start: 0.8209 (OUTLIER) cc_final: 0.7629 (p0) REVERT: F 243 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6056 (mm) REVERT: F 477 ILE cc_start: 0.7255 (OUTLIER) cc_final: 0.6959 (pp) outliers start: 111 outliers final: 88 residues processed: 489 average time/residue: 0.4595 time to fit residues: 377.8033 Evaluate side-chains 500 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 397 time to evaluate : 4.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 792 MET Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 646 LYS Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 742 SER Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 746 ASP Chi-restraints excluded: chain C residue 792 MET Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 792 MET Chi-restraints excluded: chain D residue 846 THR Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain E residue 660 ILE Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 792 MET Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 477 ILE Chi-restraints excluded: chain F residue 501 LEU Chi-restraints excluded: chain F residue 505 LEU Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 590 VAL Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 783 THR Chi-restraints excluded: chain F residue 792 MET Chi-restraints excluded: chain F residue 807 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 313 optimal weight: 2.9990 chunk 420 optimal weight: 7.9990 chunk 121 optimal weight: 0.9990 chunk 364 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 109 optimal weight: 0.6980 chunk 395 optimal weight: 1.9990 chunk 165 optimal weight: 0.5980 chunk 406 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 831 ASN ** E 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN ** F 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.171807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.132958 restraints weight = 48166.422| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.68 r_work: 0.3127 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 38616 Z= 0.185 Angle : 0.565 9.175 52404 Z= 0.281 Chirality : 0.045 0.202 6060 Planarity : 0.003 0.043 6822 Dihedral : 4.520 24.217 5358 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.98 % Allowed : 17.30 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.11), residues: 4980 helix: -1.59 (0.23), residues: 498 sheet: -0.76 (0.13), residues: 1578 loop : -1.23 (0.11), residues: 2904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP F 109 HIS 0.007 0.001 HIS B 441 PHE 0.018 0.001 PHE A 468 TYR 0.028 0.001 TYR B 744 ARG 0.007 0.000 ARG F 442 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8497.94 seconds wall clock time: 153 minutes 28.68 seconds (9208.68 seconds total)