Starting phenix.real_space_refine (version: dev) on Tue Dec 20 04:43:37 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0c_20993/12_2022/6v0c_20993.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0c_20993/12_2022/6v0c_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_20993/12_2022/6v0c_20993.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0c_20993/12_2022/6v0c_20993.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0c_20993/12_2022/6v0c_20993.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0c_20993/12_2022/6v0c_20993.pdb" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 Convert atoms to be neutral 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: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 20.58, per 1000 atoms: 0.54 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: 14.22 Conformation dependent library (CDL) restraints added in 6.4 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: 3.85 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: 20.74 Time building geometry restraints manager: 15.56 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 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. 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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.580 Check model and map are aligned: 0.650 Convert atoms to be neutral: 0.340 Process input model: 103.320 Find NCS groups from input model: 2.980 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 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 % 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 *********************** 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 : 4.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 912 average time/residue: 0.5263 time to fit residues: 753.1832 Evaluate side-chains 495 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 495 time to evaluate : 4.650 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.5265 ------------------------------------------------------------------------------- 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: 0.6980 chunk 377 optimal weight: 0.7980 chunk 209 optimal weight: 0.5980 chunk 128 optimal weight: 0.6980 chunk 254 optimal weight: 20.0000 chunk 201 optimal weight: 0.3980 chunk 390 optimal weight: 0.5980 chunk 151 optimal weight: 2.9990 chunk 237 optimal weight: 0.1980 chunk 290 optimal weight: 0.7980 chunk 452 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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: 0.8162 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 38616 Z= 0.176 Angle : 0.620 10.124 52404 Z= 0.321 Chirality : 0.047 0.158 6060 Planarity : 0.005 0.055 6822 Dihedral : 5.345 25.255 5358 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 1.22 % 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: -2.73 (0.10), residues: 4980 helix: -3.52 (0.15), residues: 516 sheet: -1.26 (0.12), residues: 1656 loop : -1.81 (0.10), residues: 2808 *********************** 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 621 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 571 time to evaluate : 4.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 20 residues processed: 598 average time/residue: 0.5254 time to fit residues: 514.7917 Evaluate side-chains 445 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 425 time to evaluate : 4.281 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.4150 time to fit residues: 20.4994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 251 optimal weight: 8.9990 chunk 140 optimal weight: 1.9990 chunk 376 optimal weight: 10.0000 chunk 307 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 453 optimal weight: 0.4980 chunk 489 optimal weight: 4.9990 chunk 403 optimal weight: 4.9990 chunk 449 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 363 optimal weight: 0.9980 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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 500 ASN A 558 HIS A 640 HIS A 831 ASN B 158 ASN B 164 HIS ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 500 ASN D 640 HIS D 831 ASN 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 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 640 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2969 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= 0.476 Angle : 0.709 12.427 52404 Z= 0.366 Chirality : 0.050 0.173 6060 Planarity : 0.005 0.049 6822 Dihedral : 5.415 27.517 5358 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 3.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.10), residues: 4980 helix: -2.80 (0.18), residues: 516 sheet: -1.43 (0.12), residues: 1608 loop : -1.80 (0.10), residues: 2856 *********************** 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 593 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 450 time to evaluate : 4.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 143 outliers final: 86 residues processed: 561 average time/residue: 0.4570 time to fit residues: 431.3048 Evaluate side-chains 481 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 395 time to evaluate : 4.798 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 0 residues processed: 86 average time/residue: 0.3321 time to fit residues: 61.3732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.3980 chunk 50 optimal weight: 2.9990 chunk 216 optimal weight: 0.5980 chunk 304 optimal weight: 0.9990 chunk 454 optimal weight: 0.9990 chunk 481 optimal weight: 0.9980 chunk 237 optimal weight: 2.9990 chunk 430 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 409 GLN ** 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** E 551 ASN ** E 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN F 409 GLN F 454 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3184 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= 0.189 Angle : 0.575 9.187 52404 Z= 0.294 Chirality : 0.046 0.189 6060 Planarity : 0.004 0.056 6822 Dihedral : 4.987 23.355 5358 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer Outliers : 1.56 % 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: -2.41 (0.11), residues: 4980 helix: -2.42 (0.20), residues: 522 sheet: -1.28 (0.12), residues: 1524 loop : -1.62 (0.10), residues: 2934 *********************** 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 542 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 478 time to evaluate : 4.631 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 outliers start: 64 outliers final: 22 residues processed: 522 average time/residue: 0.4674 time to fit residues: 409.9728 Evaluate side-chains 438 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 416 time to evaluate : 5.014 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.4237 time to fit residues: 23.1033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 400 optimal weight: 5.9990 chunk 273 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 358 optimal weight: 1.9990 chunk 198 optimal weight: 0.9990 chunk 410 optimal weight: 4.9990 chunk 332 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 245 optimal weight: 0.4980 chunk 432 optimal weight: 4.9990 chunk 121 optimal weight: 0.3980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 591 GLN B 158 ASN C 158 ASN ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN E 47 ASN E 158 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3350 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= 0.203 Angle : 0.566 8.920 52404 Z= 0.289 Chirality : 0.046 0.166 6060 Planarity : 0.004 0.047 6822 Dihedral : 4.842 22.245 5358 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 1.44 % 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: -2.25 (0.11), residues: 4980 helix: -2.12 (0.21), residues: 522 sheet: -1.18 (0.12), residues: 1524 loop : -1.55 (0.10), residues: 2934 *********************** 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 484 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 425 time to evaluate : 4.560 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 outliers start: 59 outliers final: 25 residues processed: 469 average time/residue: 0.4668 time to fit residues: 367.9968 Evaluate side-chains 430 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 405 time to evaluate : 4.492 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.3289 time to fit residues: 21.7904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 282 optimal weight: 0.0870 chunk 118 optimal weight: 0.9980 chunk 481 optimal weight: 3.9990 chunk 399 optimal weight: 1.9990 chunk 223 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 252 optimal weight: 0.0000 overall best weight: 0.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 716 GLN B 158 ASN ** B 454 ASN ** 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 454 ASN ** 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** F 151 GLN F 158 ASN ** F 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 607 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 38616 Z= 0.155 Angle : 0.541 8.239 52404 Z= 0.276 Chirality : 0.045 0.156 6060 Planarity : 0.004 0.047 6822 Dihedral : 4.675 22.542 5358 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer Outliers : 0.95 % 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: -2.02 (0.11), residues: 4980 helix: -2.02 (0.22), residues: 498 sheet: -0.91 (0.12), residues: 1578 loop : -1.46 (0.10), residues: 2904 *********************** 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 493 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 454 time to evaluate : 4.708 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 outliers start: 39 outliers final: 18 residues processed: 484 average time/residue: 0.4729 time to fit residues: 383.8278 Evaluate side-chains 422 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 404 time to evaluate : 4.516 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.3209 time to fit residues: 17.2685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 464 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 274 optimal weight: 1.9990 chunk 351 optimal weight: 7.9990 chunk 272 optimal weight: 1.9990 chunk 405 optimal weight: 5.9990 chunk 269 optimal weight: 6.9990 chunk 479 optimal weight: 0.9990 chunk 300 optimal weight: 0.7980 chunk 292 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN C 309 GLN ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 716 GLN E 158 ASN ** 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** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 38616 Z= 0.228 Angle : 0.563 9.286 52404 Z= 0.287 Chirality : 0.046 0.177 6060 Planarity : 0.004 0.044 6822 Dihedral : 4.691 22.862 5358 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer Outliers : 1.07 % 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: -1.93 (0.11), residues: 4980 helix: -1.88 (0.23), residues: 498 sheet: -0.91 (0.12), residues: 1590 loop : -1.37 (0.10), residues: 2892 *********************** 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 461 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 417 time to evaluate : 4.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 24 residues processed: 444 average time/residue: 0.4632 time to fit residues: 345.4327 Evaluate side-chains 418 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 394 time to evaluate : 4.567 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.3442 time to fit residues: 21.6810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 296 optimal weight: 0.8980 chunk 191 optimal weight: 1.9990 chunk 286 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 92 optimal weight: 30.0000 chunk 305 optimal weight: 6.9990 chunk 327 optimal weight: 3.9990 chunk 237 optimal weight: 0.3980 chunk 44 optimal weight: 0.0060 chunk 377 optimal weight: 2.9990 overall best weight: 1.0600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 861 GLN ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 582 GLN 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 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 ASN F 591 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 38616 Z= 0.221 Angle : 0.565 9.205 52404 Z= 0.287 Chirality : 0.046 0.171 6060 Planarity : 0.004 0.047 6822 Dihedral : 4.689 23.544 5358 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 1.05 % 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: -1.87 (0.11), residues: 4980 helix: -1.79 (0.23), residues: 498 sheet: -0.92 (0.12), residues: 1602 loop : -1.30 (0.11), residues: 2880 *********************** 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 454 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 411 time to evaluate : 4.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 22 residues processed: 441 average time/residue: 0.4857 time to fit residues: 362.4936 Evaluate side-chains 409 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 387 time to evaluate : 4.618 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.3286 time to fit residues: 20.0658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 436 optimal weight: 0.9990 chunk 459 optimal weight: 10.0000 chunk 419 optimal weight: 0.8980 chunk 447 optimal weight: 2.9990 chunk 269 optimal weight: 4.9990 chunk 194 optimal weight: 0.2980 chunk 351 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 404 optimal weight: 0.5980 chunk 423 optimal weight: 9.9990 chunk 445 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 420 GLN ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3816 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= 0.183 Angle : 0.563 9.734 52404 Z= 0.283 Chirality : 0.045 0.180 6060 Planarity : 0.004 0.045 6822 Dihedral : 4.625 24.214 5358 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.11), residues: 4980 helix: -1.74 (0.23), residues: 498 sheet: -0.87 (0.12), residues: 1602 loop : -1.25 (0.11), residues: 2880 *********************** 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 429 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 408 time to evaluate : 4.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 8 residues processed: 424 average time/residue: 0.4775 time to fit residues: 340.3493 Evaluate side-chains 402 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 394 time to evaluate : 4.558 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3423 time to fit residues: 11.5344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 293 optimal weight: 10.0000 chunk 472 optimal weight: 0.9980 chunk 288 optimal weight: 1.9990 chunk 224 optimal weight: 6.9990 chunk 328 optimal weight: 0.0030 chunk 496 optimal weight: 10.0000 chunk 456 optimal weight: 5.9990 chunk 395 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 305 optimal weight: 10.0000 chunk 242 optimal weight: 4.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** C 607 ASN ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3894 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= 0.203 Angle : 0.580 10.379 52404 Z= 0.290 Chirality : 0.046 0.176 6060 Planarity : 0.004 0.043 6822 Dihedral : 4.625 24.525 5358 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer Outliers : 0.22 % 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: -1.74 (0.11), residues: 4980 helix: -1.68 (0.23), residues: 498 sheet: -0.85 (0.12), residues: 1614 loop : -1.20 (0.11), residues: 2868 ********************** 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 415 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 406 time to evaluate : 4.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 410 average time/residue: 0.4743 time to fit residues: 326.2614 Evaluate side-chains 395 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 392 time to evaluate : 4.538 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3233 time to fit residues: 8.0612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 121 optimal weight: 0.0770 chunk 364 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 109 optimal weight: 0.7980 chunk 395 optimal weight: 0.9980 chunk 165 optimal weight: 0.3980 chunk 406 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 GLN ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.164136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.123920 restraints weight = 48882.726| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.52 r_work: 0.3180 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 38616 Z= 0.165 Angle : 0.567 10.849 52404 Z= 0.282 Chirality : 0.045 0.203 6060 Planarity : 0.003 0.043 6822 Dihedral : 4.524 24.381 5358 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.11), residues: 4980 helix: -1.64 (0.23), residues: 498 sheet: -0.79 (0.13), residues: 1602 loop : -1.19 (0.11), residues: 2880 =============================================================================== Job complete usr+sys time: 8151.05 seconds wall clock time: 147 minutes 13.93 seconds (8833.93 seconds total)