Starting phenix.real_space_refine (version: dev) on Sat May 14 16:41:27 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyn_0547/05_2022/6nyn_0547.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyn_0547/05_2022/6nyn_0547.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyn_0547/05_2022/6nyn_0547.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyn_0547/05_2022/6nyn_0547.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyn_0547/05_2022/6nyn_0547.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyn_0547/05_2022/6nyn_0547.pdb" } resolution = 3.5 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= 0.009 sd= 0.074 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 PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 68664 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "B" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "C" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "D" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "E" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "F" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "G" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "H" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "I" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "J" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "K" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "L" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Time building chain proxies: 27.75, per 1000 atoms: 0.40 Number of scatterers: 68664 At special positions: 0 Unit cell: (280.9, 306.34, 124.02, 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 144 16.00 O 13512 8.00 N 12060 7.00 C 42948 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 749 " distance=2.02 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 749 " distance=2.02 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 749 " distance=2.02 Simple disulfide: pdb=" SG CYS G 738 " - pdb=" SG CYS G 749 " distance=2.02 Simple disulfide: pdb=" SG CYS H 738 " - pdb=" SG CYS H 749 " distance=2.02 Simple disulfide: pdb=" SG CYS I 738 " - pdb=" SG CYS I 749 " distance=2.02 Simple disulfide: pdb=" SG CYS J 738 " - pdb=" SG CYS J 749 " distance=2.02 Simple disulfide: pdb=" SG CYS K 738 " - pdb=" SG CYS K 749 " distance=2.02 Simple disulfide: pdb=" SG CYS L 738 " - pdb=" SG CYS L 749 " distance=2.02 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: 20.81 Conformation dependent library (CDL) restraints added in 8.2 seconds 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16080 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 180 sheets defined 4.8% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.16 Creating SS restraints... Processing helix chain 'A' and resid 29 through 38 removed outlier: 3.832A pdb=" N ALA A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 75 removed outlier: 3.560A pdb=" N SER A 74 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 725 Processing helix chain 'A' and resid 744 through 754 removed outlier: 4.297A pdb=" N ALA A 748 " --> pdb=" O ASP A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 765 removed outlier: 3.718A pdb=" N TYR A 765 " --> pdb=" O PRO A 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 38 removed outlier: 3.832A pdb=" N ALA B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 75 removed outlier: 3.560A pdb=" N SER B 74 " --> pdb=" O LEU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 725 Processing helix chain 'B' and resid 744 through 754 removed outlier: 4.297A pdb=" N ALA B 748 " --> pdb=" O ASP B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 removed outlier: 3.717A pdb=" N TYR B 765 " --> pdb=" O PRO B 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 38 removed outlier: 3.832A pdb=" N ALA C 35 " --> pdb=" O GLY C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 75 removed outlier: 3.559A pdb=" N SER C 74 " --> pdb=" O LEU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 725 Processing helix chain 'C' and resid 744 through 754 removed outlier: 4.298A pdb=" N ALA C 748 " --> pdb=" O ASP C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 765 removed outlier: 3.718A pdb=" N TYR C 765 " --> pdb=" O PRO C 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 38 removed outlier: 3.831A pdb=" N ALA D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 75 removed outlier: 3.560A pdb=" N SER D 74 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 725 Processing helix chain 'D' and resid 744 through 754 removed outlier: 4.297A pdb=" N ALA D 748 " --> pdb=" O ASP D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 765 removed outlier: 3.718A pdb=" N TYR D 765 " --> pdb=" O PRO D 762 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 38 removed outlier: 3.832A pdb=" N ALA E 35 " --> pdb=" O GLY E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 75 removed outlier: 3.559A pdb=" N SER E 74 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 721 through 725 Processing helix chain 'E' and resid 744 through 754 removed outlier: 4.298A pdb=" N ALA E 748 " --> pdb=" O ASP E 744 " (cutoff:3.500A) Processing helix chain 'E' and resid 761 through 765 removed outlier: 3.718A pdb=" N TYR E 765 " --> pdb=" O PRO E 762 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 38 removed outlier: 3.832A pdb=" N ALA F 35 " --> pdb=" O GLY F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 75 removed outlier: 3.560A pdb=" N SER F 74 " --> pdb=" O LEU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 721 through 725 Processing helix chain 'F' and resid 744 through 754 removed outlier: 4.297A pdb=" N ALA F 748 " --> pdb=" O ASP F 744 " (cutoff:3.500A) Processing helix chain 'F' and resid 761 through 765 removed outlier: 3.717A pdb=" N TYR F 765 " --> pdb=" O PRO F 762 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 38 removed outlier: 3.831A pdb=" N ALA G 35 " --> pdb=" O GLY G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 75 removed outlier: 3.559A pdb=" N SER G 74 " --> pdb=" O LEU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 721 through 725 Processing helix chain 'G' and resid 744 through 754 removed outlier: 4.298A pdb=" N ALA G 748 " --> pdb=" O ASP G 744 " (cutoff:3.500A) Processing helix chain 'G' and resid 761 through 765 removed outlier: 3.718A pdb=" N TYR G 765 " --> pdb=" O PRO G 762 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 38 removed outlier: 3.832A pdb=" N ALA H 35 " --> pdb=" O GLY H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 75 removed outlier: 3.559A pdb=" N SER H 74 " --> pdb=" O LEU H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 721 through 725 Processing helix chain 'H' and resid 744 through 754 removed outlier: 4.297A pdb=" N ALA H 748 " --> pdb=" O ASP H 744 " (cutoff:3.500A) Processing helix chain 'H' and resid 761 through 765 removed outlier: 3.717A pdb=" N TYR H 765 " --> pdb=" O PRO H 762 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 38 removed outlier: 3.832A pdb=" N ALA I 35 " --> pdb=" O GLY I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 75 removed outlier: 3.559A pdb=" N SER I 74 " --> pdb=" O LEU I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 721 through 725 Processing helix chain 'I' and resid 744 through 754 removed outlier: 4.298A pdb=" N ALA I 748 " --> pdb=" O ASP I 744 " (cutoff:3.500A) Processing helix chain 'I' and resid 761 through 765 removed outlier: 3.717A pdb=" N TYR I 765 " --> pdb=" O PRO I 762 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 38 removed outlier: 3.831A pdb=" N ALA J 35 " --> pdb=" O GLY J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 75 removed outlier: 3.560A pdb=" N SER J 74 " --> pdb=" O LEU J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 721 through 725 Processing helix chain 'J' and resid 744 through 754 removed outlier: 4.297A pdb=" N ALA J 748 " --> pdb=" O ASP J 744 " (cutoff:3.500A) Processing helix chain 'J' and resid 761 through 765 removed outlier: 3.717A pdb=" N TYR J 765 " --> pdb=" O PRO J 762 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 38 removed outlier: 3.832A pdb=" N ALA K 35 " --> pdb=" O GLY K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 75 removed outlier: 3.560A pdb=" N SER K 74 " --> pdb=" O LEU K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 721 through 725 Processing helix chain 'K' and resid 744 through 754 removed outlier: 4.298A pdb=" N ALA K 748 " --> pdb=" O ASP K 744 " (cutoff:3.500A) Processing helix chain 'K' and resid 761 through 765 removed outlier: 3.718A pdb=" N TYR K 765 " --> pdb=" O PRO K 762 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 38 removed outlier: 3.832A pdb=" N ALA L 35 " --> pdb=" O GLY L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 75 removed outlier: 3.560A pdb=" N SER L 74 " --> pdb=" O LEU L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 721 through 725 Processing helix chain 'L' and resid 744 through 754 removed outlier: 4.297A pdb=" N ALA L 748 " --> pdb=" O ASP L 744 " (cutoff:3.500A) Processing helix chain 'L' and resid 761 through 765 removed outlier: 3.717A pdb=" N TYR L 765 " --> pdb=" O PRO L 762 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 53 removed outlier: 9.052A pdb=" N VAL A 48 " --> pdb=" O PRO F 341 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N GLN F 343 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ARG A 50 " --> pdb=" O GLN F 343 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ILE F 345 " --> pdb=" O ARG A 50 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLN A 52 " --> pdb=" O ILE F 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 removed outlier: 6.447A pdb=" N VAL A 101 " --> pdb=" O ASN A 126 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL A 155 " --> pdb=" O THR A 188 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 109 removed outlier: 6.182A pdb=" N GLY A 108 " --> pdb=" O THR A 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 142 removed outlier: 6.808A pdb=" N ASN A 140 " --> pdb=" O GLU A 169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 219 through 226 removed outlier: 7.638A pdb=" N LEU A 220 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N PHE A 254 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLY A 222 " --> pdb=" O PHE A 254 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N HIS A 256 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL A 252 " --> pdb=" O LYS A 274 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS A 276 " --> pdb=" O VAL A 252 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 219 through 226 removed outlier: 7.638A pdb=" N LEU A 220 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N PHE A 254 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLY A 222 " --> pdb=" O PHE A 254 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N HIS A 256 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 9.547A pdb=" N THR A 279 " --> pdb=" O ASN A 253 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASN A 255 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ASP A 281 " --> pdb=" O ASN A 255 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU A 257 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU A 280 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 266 through 270 removed outlier: 7.270A pdb=" N ALA A 267 " --> pdb=" O ASN A 289 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ILE A 291 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE A 269 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU A 288 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR A 381 " --> pdb=" O GLU A 407 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 343 through 345 Processing sheet with id=AA9, first strand: chain 'A' and resid 387 through 388 removed outlier: 6.167A pdb=" N ILE A 413 " --> pdb=" O THR A 451 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 456 through 457 removed outlier: 7.299A pdb=" N ILE A 456 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE A 476 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR A 502 " --> pdb=" O ILE A 518 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE A 569 " --> pdb=" O ARG A 541 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ASN A 543 " --> pdb=" O ILE A 569 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU A 571 " --> pdb=" O ASN A 543 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU A 547 " --> pdb=" O TYR A 573 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ALA A 595 " --> pdb=" O ASP A 570 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE A 572 " --> pdb=" O ALA A 595 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 530 through 531 Processing sheet with id=AB3, first strand: chain 'A' and resid 589 through 590 removed outlier: 3.606A pdb=" N ILE A 590 " --> pdb=" O THR A 614 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A 636 " --> pdb=" O LEU A 613 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 622 through 623 removed outlier: 3.847A pdb=" N TYR A 623 " --> pdb=" O ASN A 643 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE A 642 " --> pdb=" O LYS A 680 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASN A 682 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N TYR A 644 " --> pdb=" O ASN A 682 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE A 679 " --> pdb=" O ALA A 727 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N TYR A 729 " --> pdb=" O ILE A 679 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE A 681 " --> pdb=" O TYR A 729 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 660 through 661 removed outlier: 6.957A pdb=" N ALA A 660 " --> pdb=" O GLY A 702 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 691 through 697 removed outlier: 3.683A pdb=" N THR A 691 " --> pdb=" O TYR A 791 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR A 791 " --> pdb=" O THR A 691 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 695 " --> pdb=" O ILE A 787 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE A 787 " --> pdb=" O LEU A 695 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 771 through 773 Processing sheet with id=AB8, first strand: chain 'B' and resid 101 through 102 removed outlier: 6.447A pdb=" N VAL B 101 " --> pdb=" O ASN B 126 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL B 155 " --> pdb=" O THR B 188 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 108 through 109 removed outlier: 6.182A pdb=" N GLY B 108 " --> pdb=" O THR B 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 140 through 142 removed outlier: 6.809A pdb=" N ASN B 140 " --> pdb=" O GLU B 169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 219 through 226 removed outlier: 7.639A pdb=" N LEU B 220 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N PHE B 254 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLY B 222 " --> pdb=" O PHE B 254 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS B 256 " --> pdb=" O GLY B 222 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL B 252 " --> pdb=" O LYS B 274 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS B 276 " --> pdb=" O VAL B 252 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 219 through 226 removed outlier: 7.639A pdb=" N LEU B 220 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N PHE B 254 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLY B 222 " --> pdb=" O PHE B 254 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS B 256 " --> pdb=" O GLY B 222 " (cutoff:3.500A) removed outlier: 9.547A pdb=" N THR B 279 " --> pdb=" O ASN B 253 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASN B 255 " --> pdb=" O THR B 279 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ASP B 281 " --> pdb=" O ASN B 255 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU B 257 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU B 280 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 266 through 270 removed outlier: 7.269A pdb=" N ALA B 267 " --> pdb=" O ASN B 289 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ILE B 291 " --> pdb=" O ALA B 267 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE B 269 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU B 288 " --> pdb=" O THR B 380 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR B 381 " --> pdb=" O GLU B 407 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 343 through 345 Processing sheet with id=AC6, first strand: chain 'B' and resid 387 through 388 removed outlier: 6.168A pdb=" N ILE B 413 " --> pdb=" O THR B 451 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 456 through 457 removed outlier: 7.299A pdb=" N ILE B 456 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE B 476 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR B 502 " --> pdb=" O ILE B 518 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE B 569 " --> pdb=" O ARG B 541 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ASN B 543 " --> pdb=" O ILE B 569 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU B 571 " --> pdb=" O ASN B 543 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU B 547 " --> pdb=" O TYR B 573 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ALA B 595 " --> pdb=" O ASP B 570 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE B 572 " --> pdb=" O ALA B 595 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 530 through 531 Processing sheet with id=AC9, first strand: chain 'B' and resid 589 through 590 removed outlier: 3.606A pdb=" N ILE B 590 " --> pdb=" O THR B 614 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE B 636 " --> pdb=" O LEU B 613 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 622 through 623 removed outlier: 3.848A pdb=" N TYR B 623 " --> pdb=" O ASN B 643 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE B 642 " --> pdb=" O LYS B 680 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASN B 682 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N TYR B 644 " --> pdb=" O ASN B 682 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE B 679 " --> pdb=" O ALA B 727 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N TYR B 729 " --> pdb=" O ILE B 679 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE B 681 " --> pdb=" O TYR B 729 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 660 through 661 removed outlier: 6.957A pdb=" N ALA B 660 " --> pdb=" O GLY B 702 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 691 through 697 removed outlier: 3.684A pdb=" N THR B 691 " --> pdb=" O TYR B 791 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR B 791 " --> pdb=" O THR B 691 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU B 695 " --> pdb=" O ILE B 787 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ILE B 787 " --> pdb=" O LEU B 695 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 771 through 773 Processing sheet with id=AD5, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.447A pdb=" N VAL C 101 " --> pdb=" O ASN C 126 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL C 155 " --> pdb=" O THR C 188 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 108 through 109 removed outlier: 6.182A pdb=" N GLY C 108 " --> pdb=" O THR C 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 140 through 142 removed outlier: 6.809A pdb=" N ASN C 140 " --> pdb=" O GLU C 169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'C' and resid 219 through 226 removed outlier: 7.639A pdb=" N LEU C 220 " --> pdb=" O VAL C 252 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N PHE C 254 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLY C 222 " --> pdb=" O PHE C 254 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS C 256 " --> pdb=" O GLY C 222 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL C 252 " --> pdb=" O LYS C 274 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS C 276 " --> pdb=" O VAL C 252 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 219 through 226 removed outlier: 7.639A pdb=" N LEU C 220 " --> pdb=" O VAL C 252 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N PHE C 254 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLY C 222 " --> pdb=" O PHE C 254 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS C 256 " --> pdb=" O GLY C 222 " (cutoff:3.500A) removed outlier: 9.549A pdb=" N THR C 279 " --> pdb=" O ASN C 253 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASN C 255 " --> pdb=" O THR C 279 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ASP C 281 " --> pdb=" O ASN C 255 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU C 257 " --> pdb=" O ASP C 281 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU C 280 " --> pdb=" O ASN C 363 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 266 through 270 removed outlier: 7.269A pdb=" N ALA C 267 " --> pdb=" O ASN C 289 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ILE C 291 " --> pdb=" O ALA C 267 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE C 269 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU C 288 " --> pdb=" O THR C 380 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR C 381 " --> pdb=" O GLU C 407 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 343 through 345 Processing sheet with id=AE3, first strand: chain 'C' and resid 387 through 388 removed outlier: 6.167A pdb=" N ILE C 413 " --> pdb=" O THR C 451 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 456 through 457 removed outlier: 7.299A pdb=" N ILE C 456 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE C 476 " --> pdb=" O ILE C 501 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR C 502 " --> pdb=" O ILE C 518 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE C 569 " --> pdb=" O ARG C 541 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASN C 543 " --> pdb=" O ILE C 569 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU C 571 " --> pdb=" O ASN C 543 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU C 547 " --> pdb=" O TYR C 573 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ALA C 595 " --> pdb=" O ASP C 570 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE C 572 " --> pdb=" O ALA C 595 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 530 through 531 Processing sheet with id=AE6, first strand: chain 'C' and resid 589 through 590 removed outlier: 3.607A pdb=" N ILE C 590 " --> pdb=" O THR C 614 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE C 636 " --> pdb=" O LEU C 613 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 622 through 623 removed outlier: 3.847A pdb=" N TYR C 623 " --> pdb=" O ASN C 643 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE C 642 " --> pdb=" O LYS C 680 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASN C 682 " --> pdb=" O ILE C 642 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N TYR C 644 " --> pdb=" O ASN C 682 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE C 679 " --> pdb=" O ALA C 727 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N TYR C 729 " --> pdb=" O ILE C 679 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE C 681 " --> pdb=" O TYR C 729 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 660 through 661 removed outlier: 6.957A pdb=" N ALA C 660 " --> pdb=" O GLY C 702 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 691 through 697 removed outlier: 3.684A pdb=" N THR C 691 " --> pdb=" O TYR C 791 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR C 791 " --> pdb=" O THR C 691 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 695 " --> pdb=" O ILE C 787 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ILE C 787 " --> pdb=" O LEU C 695 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 771 through 773 Processing sheet with id=AF2, first strand: chain 'D' and resid 101 through 102 removed outlier: 6.447A pdb=" N VAL D 101 " --> pdb=" O ASN D 126 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL D 155 " --> pdb=" O THR D 188 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 108 through 109 removed outlier: 6.182A pdb=" N GLY D 108 " --> pdb=" O THR D 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'D' and resid 140 through 142 removed outlier: 6.808A pdb=" N ASN D 140 " --> pdb=" O GLU D 169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'D' and resid 219 through 226 removed outlier: 7.639A pdb=" N LEU D 220 " --> pdb=" O VAL D 252 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N PHE D 254 " --> pdb=" O LEU D 220 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLY D 222 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS D 256 " --> pdb=" O GLY D 222 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL D 252 " --> pdb=" O LYS D 274 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS D 276 " --> pdb=" O VAL D 252 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 219 through 226 removed outlier: 7.639A pdb=" N LEU D 220 " --> pdb=" O VAL D 252 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N PHE D 254 " --> pdb=" O LEU D 220 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLY D 222 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS D 256 " --> pdb=" O GLY D 222 " (cutoff:3.500A) removed outlier: 9.548A pdb=" N THR D 279 " --> pdb=" O ASN D 253 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASN D 255 " --> pdb=" O THR D 279 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ASP D 281 " --> pdb=" O ASN D 255 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU D 257 " --> pdb=" O ASP D 281 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU D 280 " --> pdb=" O ASN D 363 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 266 through 270 removed outlier: 7.270A pdb=" N ALA D 267 " --> pdb=" O ASN D 289 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ILE D 291 " --> pdb=" O ALA D 267 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE D 269 " --> pdb=" O ILE D 291 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU D 288 " --> pdb=" O THR D 380 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR D 381 " --> pdb=" O GLU D 407 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 343 through 345 Processing sheet with id=AF9, first strand: chain 'D' and resid 387 through 388 removed outlier: 6.168A pdb=" N ILE D 413 " --> pdb=" O THR D 451 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 456 through 457 removed outlier: 7.299A pdb=" N ILE D 456 " --> pdb=" O ASP D 477 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE D 476 " --> pdb=" O ILE D 501 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR D 502 " --> pdb=" O ILE D 518 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE D 569 " --> pdb=" O ARG D 541 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASN D 543 " --> pdb=" O ILE D 569 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU D 571 " --> pdb=" O ASN D 543 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU D 547 " --> pdb=" O TYR D 573 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ALA D 595 " --> pdb=" O ASP D 570 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE D 572 " --> pdb=" O ALA D 595 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 530 through 531 Processing sheet with id=AG3, first strand: chain 'D' and resid 589 through 590 removed outlier: 3.607A pdb=" N ILE D 590 " --> pdb=" O THR D 614 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE D 636 " --> pdb=" O LEU D 613 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 622 through 623 removed outlier: 3.848A pdb=" N TYR D 623 " --> pdb=" O ASN D 643 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE D 642 " --> pdb=" O LYS D 680 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASN D 682 " --> pdb=" O ILE D 642 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N TYR D 644 " --> pdb=" O ASN D 682 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE D 679 " --> pdb=" O ALA D 727 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N TYR D 729 " --> pdb=" O ILE D 679 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE D 681 " --> pdb=" O TYR D 729 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 660 through 661 removed outlier: 6.957A pdb=" N ALA D 660 " --> pdb=" O GLY D 702 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'D' and resid 691 through 697 removed outlier: 3.682A pdb=" N THR D 691 " --> pdb=" O TYR D 791 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N TYR D 791 " --> pdb=" O THR D 691 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU D 695 " --> pdb=" O ILE D 787 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE D 787 " --> pdb=" O LEU D 695 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'D' and resid 771 through 773 Processing sheet with id=AG8, first strand: chain 'E' and resid 101 through 102 removed outlier: 6.448A pdb=" N VAL E 101 " --> pdb=" O ASN E 126 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL E 155 " --> pdb=" O THR E 188 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 108 through 109 removed outlier: 6.182A pdb=" N GLY E 108 " --> pdb=" O THR E 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'E' and resid 140 through 142 removed outlier: 6.809A pdb=" N ASN E 140 " --> pdb=" O GLU E 169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'E' and resid 219 through 226 removed outlier: 7.640A pdb=" N LEU E 220 " --> pdb=" O VAL E 252 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N PHE E 254 " --> pdb=" O LEU E 220 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLY E 222 " --> pdb=" O PHE E 254 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS E 256 " --> pdb=" O GLY E 222 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL E 252 " --> pdb=" O LYS E 274 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS E 276 " --> pdb=" O VAL E 252 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 219 through 226 removed outlier: 7.640A pdb=" N LEU E 220 " --> pdb=" O VAL E 252 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N PHE E 254 " --> pdb=" O LEU E 220 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLY E 222 " --> pdb=" O PHE E 254 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS E 256 " --> pdb=" O GLY E 222 " (cutoff:3.500A) removed outlier: 9.548A pdb=" N THR E 279 " --> pdb=" O ASN E 253 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASN E 255 " --> pdb=" O THR E 279 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ASP E 281 " --> pdb=" O ASN E 255 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU E 257 " --> pdb=" O ASP E 281 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU E 280 " --> pdb=" O ASN E 363 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 266 through 270 removed outlier: 7.269A pdb=" N ALA E 267 " --> pdb=" O ASN E 289 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ILE E 291 " --> pdb=" O ALA E 267 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE E 269 " --> pdb=" O ILE E 291 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU E 288 " --> pdb=" O THR E 380 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR E 381 " --> pdb=" O GLU E 407 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 343 through 345 Processing sheet with id=AH6, first strand: chain 'E' and resid 387 through 388 removed outlier: 6.168A pdb=" N ILE E 413 " --> pdb=" O THR E 451 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'E' and resid 456 through 457 removed outlier: 7.299A pdb=" N ILE E 456 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE E 476 " --> pdb=" O ILE E 501 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR E 502 " --> pdb=" O ILE E 518 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE E 569 " --> pdb=" O ARG E 541 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASN E 543 " --> pdb=" O ILE E 569 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU E 571 " --> pdb=" O ASN E 543 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU E 547 " --> pdb=" O TYR E 573 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ALA E 595 " --> pdb=" O ASP E 570 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE E 572 " --> pdb=" O ALA E 595 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'E' and resid 530 through 531 Processing sheet with id=AH9, first strand: chain 'E' and resid 589 through 590 removed outlier: 3.606A pdb=" N ILE E 590 " --> pdb=" O THR E 614 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE E 636 " --> pdb=" O LEU E 613 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'E' and resid 622 through 623 removed outlier: 3.848A pdb=" N TYR E 623 " --> pdb=" O ASN E 643 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE E 642 " --> pdb=" O LYS E 680 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASN E 682 " --> pdb=" O ILE E 642 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N TYR E 644 " --> pdb=" O ASN E 682 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE E 679 " --> pdb=" O ALA E 727 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N TYR E 729 " --> pdb=" O ILE E 679 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE E 681 " --> pdb=" O TYR E 729 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'E' and resid 660 through 661 removed outlier: 6.957A pdb=" N ALA E 660 " --> pdb=" O GLY E 702 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI2 Processing sheet with id=AI3, first strand: chain 'E' and resid 691 through 697 removed outlier: 3.684A pdb=" N THR E 691 " --> pdb=" O TYR E 791 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR E 791 " --> pdb=" O THR E 691 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU E 695 " --> pdb=" O ILE E 787 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ILE E 787 " --> pdb=" O LEU E 695 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'E' and resid 771 through 773 Processing sheet with id=AI5, first strand: chain 'F' and resid 101 through 102 removed outlier: 6.447A pdb=" N VAL F 101 " --> pdb=" O ASN F 126 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL F 155 " --> pdb=" O THR F 188 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'F' and resid 108 through 109 removed outlier: 6.182A pdb=" N GLY F 108 " --> pdb=" O THR F 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'F' and resid 140 through 142 removed outlier: 6.809A pdb=" N ASN F 140 " --> pdb=" O GLU F 169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI7 Processing sheet with id=AI8, first strand: chain 'F' and resid 219 through 226 removed outlier: 7.639A pdb=" N LEU F 220 " --> pdb=" O VAL F 252 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N PHE F 254 " --> pdb=" O LEU F 220 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLY F 222 " --> pdb=" O PHE F 254 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS F 256 " --> pdb=" O GLY F 222 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL F 252 " --> pdb=" O LYS F 274 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS F 276 " --> pdb=" O VAL F 252 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'F' and resid 219 through 226 removed outlier: 7.639A pdb=" N LEU F 220 " --> pdb=" O VAL F 252 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N PHE F 254 " --> pdb=" O LEU F 220 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLY F 222 " --> pdb=" O PHE F 254 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS F 256 " --> pdb=" O GLY F 222 " (cutoff:3.500A) removed outlier: 9.548A pdb=" N THR F 279 " --> pdb=" O ASN F 253 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASN F 255 " --> pdb=" O THR F 279 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ASP F 281 " --> pdb=" O ASN F 255 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU F 257 " --> pdb=" O ASP F 281 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU F 280 " --> pdb=" O ASN F 363 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'F' and resid 266 through 270 removed outlier: 7.269A pdb=" N ALA F 267 " --> pdb=" O ASN F 289 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ILE F 291 " --> pdb=" O ALA F 267 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE F 269 " --> pdb=" O ILE F 291 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU F 288 " --> pdb=" O THR F 380 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR F 381 " --> pdb=" O GLU F 407 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'F' and resid 387 through 388 removed outlier: 6.168A pdb=" N ILE F 413 " --> pdb=" O THR F 451 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'F' and resid 456 through 457 removed outlier: 7.298A pdb=" N ILE F 456 " --> pdb=" O ASP F 477 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE F 476 " --> pdb=" O ILE F 501 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR F 502 " --> pdb=" O ILE F 518 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE F 569 " --> pdb=" O ARG F 541 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASN F 543 " --> pdb=" O ILE F 569 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU F 571 " --> pdb=" O ASN F 543 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU F 547 " --> pdb=" O TYR F 573 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ALA F 595 " --> pdb=" O ASP F 570 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE F 572 " --> pdb=" O ALA F 595 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'F' and resid 530 through 531 Processing sheet with id=AJ5, first strand: chain 'F' and resid 589 through 590 removed outlier: 3.606A pdb=" N ILE F 590 " --> pdb=" O THR F 614 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE F 636 " --> pdb=" O LEU F 613 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'F' and resid 622 through 623 removed outlier: 3.847A pdb=" N TYR F 623 " --> pdb=" O ASN F 643 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE F 642 " --> pdb=" O LYS F 680 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ASN F 682 " --> pdb=" O ILE F 642 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N TYR F 644 " --> pdb=" O ASN F 682 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE F 679 " --> pdb=" O ALA F 727 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N TYR F 729 " --> pdb=" O ILE F 679 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE F 681 " --> pdb=" O TYR F 729 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'F' and resid 660 through 661 removed outlier: 6.958A pdb=" N ALA F 660 " --> pdb=" O GLY F 702 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ7 Processing sheet with id=AJ8, first strand: chain 'F' and resid 691 through 697 removed outlier: 3.684A pdb=" N THR F 691 " --> pdb=" O TYR F 791 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR F 791 " --> pdb=" O THR F 691 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU F 695 " --> pdb=" O ILE F 787 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE F 787 " --> pdb=" O LEU F 695 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'F' and resid 771 through 773 Processing sheet with id=AK1, first strand: chain 'G' and resid 51 through 53 removed outlier: 6.876A pdb=" N GLN G 52 " --> pdb=" O ILE L 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK1 Processing sheet with id=AK2, first strand: chain 'G' and resid 101 through 102 removed outlier: 6.447A pdb=" N VAL G 101 " --> pdb=" O ASN G 126 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL G 155 " --> pdb=" O THR G 188 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'G' and resid 108 through 109 removed outlier: 6.182A pdb=" N GLY G 108 " --> pdb=" O THR G 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK3 Processing sheet with id=AK4, first strand: chain 'G' and resid 140 through 142 removed outlier: 6.808A pdb=" N ASN G 140 " --> pdb=" O GLU G 169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK4 Processing sheet with id=AK5, first strand: chain 'G' and resid 219 through 226 removed outlier: 7.639A pdb=" N LEU G 220 " --> pdb=" O VAL G 252 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N PHE G 254 " --> pdb=" O LEU G 220 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLY G 222 " --> pdb=" O PHE G 254 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS G 256 " --> pdb=" O GLY G 222 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL G 252 " --> pdb=" O LYS G 274 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS G 276 " --> pdb=" O VAL G 252 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'G' and resid 219 through 226 removed outlier: 7.639A pdb=" N LEU G 220 " --> pdb=" O VAL G 252 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N PHE G 254 " --> pdb=" O LEU G 220 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLY G 222 " --> pdb=" O PHE G 254 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS G 256 " --> pdb=" O GLY G 222 " (cutoff:3.500A) removed outlier: 9.548A pdb=" N THR G 279 " --> pdb=" O ASN G 253 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASN G 255 " --> pdb=" O THR G 279 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ASP G 281 " --> pdb=" O ASN G 255 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU G 257 " --> pdb=" O ASP G 281 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU G 280 " --> pdb=" O ASN G 363 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'G' and resid 266 through 270 removed outlier: 7.269A pdb=" N ALA G 267 " --> pdb=" O ASN G 289 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ILE G 291 " --> pdb=" O ALA G 267 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE G 269 " --> pdb=" O ILE G 291 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU G 288 " --> pdb=" O THR G 380 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR G 381 " --> pdb=" O GLU G 407 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'G' and resid 343 through 345 Processing sheet with id=AK9, first strand: chain 'G' and resid 387 through 388 removed outlier: 6.168A pdb=" N ILE G 413 " --> pdb=" O THR G 451 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'G' and resid 456 through 457 removed outlier: 7.299A pdb=" N ILE G 456 " --> pdb=" O ASP G 477 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE G 476 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR G 502 " --> pdb=" O ILE G 518 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE G 569 " --> pdb=" O ARG G 541 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASN G 543 " --> pdb=" O ILE G 569 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU G 571 " --> pdb=" O ASN G 543 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU G 547 " --> pdb=" O TYR G 573 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ALA G 595 " --> pdb=" O ASP G 570 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE G 572 " --> pdb=" O ALA G 595 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'G' and resid 530 through 531 Processing sheet with id=AL3, first strand: chain 'G' and resid 589 through 590 removed outlier: 3.606A pdb=" N ILE G 590 " --> pdb=" O THR G 614 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE G 636 " --> pdb=" O LEU G 613 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'G' and resid 622 through 623 removed outlier: 3.847A pdb=" N TYR G 623 " --> pdb=" O ASN G 643 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE G 642 " --> pdb=" O LYS G 680 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASN G 682 " --> pdb=" O ILE G 642 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N TYR G 644 " --> pdb=" O ASN G 682 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE G 679 " --> pdb=" O ALA G 727 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N TYR G 729 " --> pdb=" O ILE G 679 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE G 681 " --> pdb=" O TYR G 729 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'G' and resid 660 through 661 removed outlier: 6.958A pdb=" N ALA G 660 " --> pdb=" O GLY G 702 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL5 Processing sheet with id=AL6, first strand: chain 'G' and resid 691 through 697 removed outlier: 3.684A pdb=" N THR G 691 " --> pdb=" O TYR G 791 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR G 791 " --> pdb=" O THR G 691 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU G 695 " --> pdb=" O ILE G 787 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE G 787 " --> pdb=" O LEU G 695 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'G' and resid 771 through 773 Processing sheet with id=AL8, first strand: chain 'H' and resid 101 through 102 removed outlier: 6.448A pdb=" N VAL H 101 " --> pdb=" O ASN H 126 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL H 155 " --> pdb=" O THR H 188 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'H' and resid 108 through 109 removed outlier: 6.182A pdb=" N GLY H 108 " --> pdb=" O THR H 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL9 Processing sheet with id=AM1, first strand: chain 'H' and resid 140 through 142 removed outlier: 6.808A pdb=" N ASN H 140 " --> pdb=" O GLU H 169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM1 Processing sheet with id=AM2, first strand: chain 'H' and resid 219 through 226 removed outlier: 7.638A pdb=" N LEU H 220 " --> pdb=" O VAL H 252 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N PHE H 254 " --> pdb=" O LEU H 220 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLY H 222 " --> pdb=" O PHE H 254 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS H 256 " --> pdb=" O GLY H 222 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL H 252 " --> pdb=" O LYS H 274 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS H 276 " --> pdb=" O VAL H 252 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'H' and resid 219 through 226 removed outlier: 7.638A pdb=" N LEU H 220 " --> pdb=" O VAL H 252 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N PHE H 254 " --> pdb=" O LEU H 220 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLY H 222 " --> pdb=" O PHE H 254 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS H 256 " --> pdb=" O GLY H 222 " (cutoff:3.500A) removed outlier: 9.549A pdb=" N THR H 279 " --> pdb=" O ASN H 253 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASN H 255 " --> pdb=" O THR H 279 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ASP H 281 " --> pdb=" O ASN H 255 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU H 257 " --> pdb=" O ASP H 281 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU H 280 " --> pdb=" O ASN H 363 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'H' and resid 266 through 270 removed outlier: 7.270A pdb=" N ALA H 267 " --> pdb=" O ASN H 289 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ILE H 291 " --> pdb=" O ALA H 267 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE H 269 " --> pdb=" O ILE H 291 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU H 288 " --> pdb=" O THR H 380 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR H 381 " --> pdb=" O GLU H 407 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'H' and resid 343 through 345 Processing sheet with id=AM6, first strand: chain 'H' and resid 387 through 388 removed outlier: 6.168A pdb=" N ILE H 413 " --> pdb=" O THR H 451 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'H' and resid 456 through 457 removed outlier: 7.299A pdb=" N ILE H 456 " --> pdb=" O ASP H 477 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE H 476 " --> pdb=" O ILE H 501 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR H 502 " --> pdb=" O ILE H 518 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE H 569 " --> pdb=" O ARG H 541 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASN H 543 " --> pdb=" O ILE H 569 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU H 571 " --> pdb=" O ASN H 543 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU H 547 " --> pdb=" O TYR H 573 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ALA H 595 " --> pdb=" O ASP H 570 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE H 572 " --> pdb=" O ALA H 595 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'H' and resid 530 through 531 Processing sheet with id=AM9, first strand: chain 'H' and resid 589 through 590 removed outlier: 3.606A pdb=" N ILE H 590 " --> pdb=" O THR H 614 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE H 636 " --> pdb=" O LEU H 613 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'H' and resid 622 through 623 removed outlier: 3.847A pdb=" N TYR H 623 " --> pdb=" O ASN H 643 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE H 642 " --> pdb=" O LYS H 680 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASN H 682 " --> pdb=" O ILE H 642 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N TYR H 644 " --> pdb=" O ASN H 682 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE H 679 " --> pdb=" O ALA H 727 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N TYR H 729 " --> pdb=" O ILE H 679 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE H 681 " --> pdb=" O TYR H 729 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'H' and resid 660 through 661 removed outlier: 6.957A pdb=" N ALA H 660 " --> pdb=" O GLY H 702 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN2 Processing sheet with id=AN3, first strand: chain 'H' and resid 691 through 697 removed outlier: 3.684A pdb=" N THR H 691 " --> pdb=" O TYR H 791 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR H 791 " --> pdb=" O THR H 691 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU H 695 " --> pdb=" O ILE H 787 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ILE H 787 " --> pdb=" O LEU H 695 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'H' and resid 771 through 773 Processing sheet with id=AN5, first strand: chain 'I' and resid 101 through 102 removed outlier: 6.447A pdb=" N VAL I 101 " --> pdb=" O ASN I 126 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL I 155 " --> pdb=" O THR I 188 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain 'I' and resid 108 through 109 removed outlier: 6.182A pdb=" N GLY I 108 " --> pdb=" O THR I 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN6 Processing sheet with id=AN7, first strand: chain 'I' and resid 140 through 142 removed outlier: 6.808A pdb=" N ASN I 140 " --> pdb=" O GLU I 169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN7 Processing sheet with id=AN8, first strand: chain 'I' and resid 219 through 226 removed outlier: 7.639A pdb=" N LEU I 220 " --> pdb=" O VAL I 252 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N PHE I 254 " --> pdb=" O LEU I 220 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLY I 222 " --> pdb=" O PHE I 254 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N HIS I 256 " --> pdb=" O GLY I 222 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL I 252 " --> pdb=" O LYS I 274 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS I 276 " --> pdb=" O VAL I 252 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain 'I' and resid 219 through 226 removed outlier: 7.639A pdb=" N LEU I 220 " --> pdb=" O VAL I 252 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N PHE I 254 " --> pdb=" O LEU I 220 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLY I 222 " --> pdb=" O PHE I 254 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N HIS I 256 " --> pdb=" O GLY I 222 " (cutoff:3.500A) removed outlier: 9.548A pdb=" N THR I 279 " --> pdb=" O ASN I 253 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASN I 255 " --> pdb=" O THR I 279 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ASP I 281 " --> pdb=" O ASN I 255 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU I 257 " --> pdb=" O ASP I 281 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU I 280 " --> pdb=" O ASN I 363 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain 'I' and resid 266 through 270 removed outlier: 7.269A pdb=" N ALA I 267 " --> pdb=" O ASN I 289 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ILE I 291 " --> pdb=" O ALA I 267 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE I 269 " --> pdb=" O ILE I 291 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU I 288 " --> pdb=" O THR I 380 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR I 381 " --> pdb=" O GLU I 407 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'I' and resid 343 through 345 Processing sheet with id=AO3, first strand: chain 'I' and resid 387 through 388 removed outlier: 6.167A pdb=" N ILE I 413 " --> pdb=" O THR I 451 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'I' and resid 456 through 457 removed outlier: 7.299A pdb=" N ILE I 456 " --> pdb=" O ASP I 477 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE I 476 " --> pdb=" O ILE I 501 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR I 502 " --> pdb=" O ILE I 518 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE I 569 " --> pdb=" O ARG I 541 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASN I 543 " --> pdb=" O ILE I 569 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU I 571 " --> pdb=" O ASN I 543 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU I 547 " --> pdb=" O TYR I 573 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ALA I 595 " --> pdb=" O ASP I 570 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE I 572 " --> pdb=" O ALA I 595 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'I' and resid 530 through 531 Processing sheet with id=AO6, first strand: chain 'I' and resid 589 through 590 removed outlier: 3.606A pdb=" N ILE I 590 " --> pdb=" O THR I 614 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE I 636 " --> pdb=" O LEU I 613 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'I' and resid 622 through 623 removed outlier: 3.847A pdb=" N TYR I 623 " --> pdb=" O ASN I 643 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE I 642 " --> pdb=" O LYS I 680 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASN I 682 " --> pdb=" O ILE I 642 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N TYR I 644 " --> pdb=" O ASN I 682 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE I 679 " --> pdb=" O ALA I 727 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N TYR I 729 " --> pdb=" O ILE I 679 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE I 681 " --> pdb=" O TYR I 729 " (cutoff:3.500A) Processing sheet with id=AO8, first strand: chain 'I' and resid 660 through 661 removed outlier: 6.958A pdb=" N ALA I 660 " --> pdb=" O GLY I 702 " (cutoff:3.500A) No H-bonds generated for sheet with id=AO8 Processing sheet with id=AO9, first strand: chain 'I' and resid 691 through 697 removed outlier: 3.683A pdb=" N THR I 691 " --> pdb=" O TYR I 791 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TYR I 791 " --> pdb=" O THR I 691 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU I 695 " --> pdb=" O ILE I 787 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE I 787 " --> pdb=" O LEU I 695 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'I' and resid 771 through 773 Processing sheet with id=AP2, first strand: chain 'J' and resid 101 through 102 removed outlier: 6.447A pdb=" N VAL J 101 " --> pdb=" O ASN J 126 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL J 155 " --> pdb=" O THR J 188 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'J' and resid 108 through 109 removed outlier: 6.182A pdb=" N GLY J 108 " --> pdb=" O THR J 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AP3 Processing sheet with id=AP4, first strand: chain 'J' and resid 140 through 142 removed outlier: 6.808A pdb=" N ASN J 140 " --> pdb=" O GLU J 169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AP4 Processing sheet with id=AP5, first strand: chain 'J' and resid 219 through 226 removed outlier: 7.639A pdb=" N LEU J 220 " --> pdb=" O VAL J 252 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N PHE J 254 " --> pdb=" O LEU J 220 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLY J 222 " --> pdb=" O PHE J 254 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS J 256 " --> pdb=" O GLY J 222 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL J 252 " --> pdb=" O LYS J 274 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS J 276 " --> pdb=" O VAL J 252 " (cutoff:3.500A) Processing sheet with id=AP6, first strand: chain 'J' and resid 219 through 226 removed outlier: 7.639A pdb=" N LEU J 220 " --> pdb=" O VAL J 252 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N PHE J 254 " --> pdb=" O LEU J 220 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLY J 222 " --> pdb=" O PHE J 254 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS J 256 " --> pdb=" O GLY J 222 " (cutoff:3.500A) removed outlier: 9.547A pdb=" N THR J 279 " --> pdb=" O ASN J 253 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASN J 255 " --> pdb=" O THR J 279 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ASP J 281 " --> pdb=" O ASN J 255 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU J 257 " --> pdb=" O ASP J 281 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU J 280 " --> pdb=" O ASN J 363 " (cutoff:3.500A) Processing sheet with id=AP7, first strand: chain 'J' and resid 266 through 270 removed outlier: 7.269A pdb=" N ALA J 267 " --> pdb=" O ASN J 289 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ILE J 291 " --> pdb=" O ALA J 267 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE J 269 " --> pdb=" O ILE J 291 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU J 288 " --> pdb=" O THR J 380 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR J 381 " --> pdb=" O GLU J 407 " (cutoff:3.500A) Processing sheet with id=AP8, first strand: chain 'J' and resid 343 through 345 Processing sheet with id=AP9, first strand: chain 'J' and resid 387 through 388 removed outlier: 6.168A pdb=" N ILE J 413 " --> pdb=" O THR J 451 " (cutoff:3.500A) Processing sheet with id=AQ1, first strand: chain 'J' and resid 456 through 457 removed outlier: 7.299A pdb=" N ILE J 456 " --> pdb=" O ASP J 477 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE J 476 " --> pdb=" O ILE J 501 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR J 502 " --> pdb=" O ILE J 518 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE J 569 " --> pdb=" O ARG J 541 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASN J 543 " --> pdb=" O ILE J 569 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU J 571 " --> pdb=" O ASN J 543 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU J 547 " --> pdb=" O TYR J 573 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ALA J 595 " --> pdb=" O ASP J 570 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE J 572 " --> pdb=" O ALA J 595 " (cutoff:3.500A) Processing sheet with id=AQ2, first strand: chain 'J' and resid 530 through 531 Processing sheet with id=AQ3, first strand: chain 'J' and resid 589 through 590 removed outlier: 3.606A pdb=" N ILE J 590 " --> pdb=" O THR J 614 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE J 636 " --> pdb=" O LEU J 613 " (cutoff:3.500A) Processing sheet with id=AQ4, first strand: chain 'J' and resid 622 through 623 removed outlier: 3.848A pdb=" N TYR J 623 " --> pdb=" O ASN J 643 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE J 642 " --> pdb=" O LYS J 680 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASN J 682 " --> pdb=" O ILE J 642 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N TYR J 644 " --> pdb=" O ASN J 682 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE J 679 " --> pdb=" O ALA J 727 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N TYR J 729 " --> pdb=" O ILE J 679 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE J 681 " --> pdb=" O TYR J 729 " (cutoff:3.500A) Processing sheet with id=AQ5, first strand: chain 'J' and resid 660 through 661 removed outlier: 6.958A pdb=" N ALA J 660 " --> pdb=" O GLY J 702 " (cutoff:3.500A) No H-bonds generated for sheet with id=AQ5 Processing sheet with id=AQ6, first strand: chain 'J' and resid 691 through 697 removed outlier: 3.684A pdb=" N THR J 691 " --> pdb=" O TYR J 791 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR J 791 " --> pdb=" O THR J 691 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU J 695 " --> pdb=" O ILE J 787 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE J 787 " --> pdb=" O LEU J 695 " (cutoff:3.500A) Processing sheet with id=AQ7, first strand: chain 'J' and resid 771 through 773 Processing sheet with id=AQ8, first strand: chain 'K' and resid 101 through 102 removed outlier: 6.448A pdb=" N VAL K 101 " --> pdb=" O ASN K 126 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL K 155 " --> pdb=" O THR K 188 " (cutoff:3.500A) Processing sheet with id=AQ9, first strand: chain 'K' and resid 108 through 109 removed outlier: 6.182A pdb=" N GLY K 108 " --> pdb=" O THR K 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AQ9 Processing sheet with id=AR1, first strand: chain 'K' and resid 140 through 142 removed outlier: 6.808A pdb=" N ASN K 140 " --> pdb=" O GLU K 169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AR1 Processing sheet with id=AR2, first strand: chain 'K' and resid 219 through 226 removed outlier: 7.638A pdb=" N LEU K 220 " --> pdb=" O VAL K 252 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N PHE K 254 " --> pdb=" O LEU K 220 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLY K 222 " --> pdb=" O PHE K 254 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS K 256 " --> pdb=" O GLY K 222 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL K 252 " --> pdb=" O LYS K 274 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS K 276 " --> pdb=" O VAL K 252 " (cutoff:3.500A) Processing sheet with id=AR3, first strand: chain 'K' and resid 219 through 226 removed outlier: 7.638A pdb=" N LEU K 220 " --> pdb=" O VAL K 252 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N PHE K 254 " --> pdb=" O LEU K 220 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLY K 222 " --> pdb=" O PHE K 254 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS K 256 " --> pdb=" O GLY K 222 " (cutoff:3.500A) removed outlier: 9.548A pdb=" N THR K 279 " --> pdb=" O ASN K 253 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASN K 255 " --> pdb=" O THR K 279 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ASP K 281 " --> pdb=" O ASN K 255 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU K 257 " --> pdb=" O ASP K 281 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU K 280 " --> pdb=" O ASN K 363 " (cutoff:3.500A) Processing sheet with id=AR4, first strand: chain 'K' and resid 266 through 270 removed outlier: 7.270A pdb=" N ALA K 267 " --> pdb=" O ASN K 289 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ILE K 291 " --> pdb=" O ALA K 267 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE K 269 " --> pdb=" O ILE K 291 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU K 288 " --> pdb=" O THR K 380 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR K 381 " --> pdb=" O GLU K 407 " (cutoff:3.500A) Processing sheet with id=AR5, first strand: chain 'K' and resid 343 through 345 Processing sheet with id=AR6, first strand: chain 'K' and resid 387 through 388 removed outlier: 6.169A pdb=" N ILE K 413 " --> pdb=" O THR K 451 " (cutoff:3.500A) Processing sheet with id=AR7, first strand: chain 'K' and resid 456 through 457 removed outlier: 7.299A pdb=" N ILE K 456 " --> pdb=" O ASP K 477 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE K 476 " --> pdb=" O ILE K 501 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR K 502 " --> pdb=" O ILE K 518 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE K 569 " --> pdb=" O ARG K 541 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASN K 543 " --> pdb=" O ILE K 569 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU K 571 " --> pdb=" O ASN K 543 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU K 547 " --> pdb=" O TYR K 573 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ALA K 595 " --> pdb=" O ASP K 570 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE K 572 " --> pdb=" O ALA K 595 " (cutoff:3.500A) Processing sheet with id=AR8, first strand: chain 'K' and resid 530 through 531 Processing sheet with id=AR9, first strand: chain 'K' and resid 589 through 590 removed outlier: 3.607A pdb=" N ILE K 590 " --> pdb=" O THR K 614 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE K 636 " --> pdb=" O LEU K 613 " (cutoff:3.500A) Processing sheet with id=AS1, first strand: chain 'K' and resid 622 through 623 removed outlier: 3.848A pdb=" N TYR K 623 " --> pdb=" O ASN K 643 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE K 642 " --> pdb=" O LYS K 680 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASN K 682 " --> pdb=" O ILE K 642 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N TYR K 644 " --> pdb=" O ASN K 682 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE K 679 " --> pdb=" O ALA K 727 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N TYR K 729 " --> pdb=" O ILE K 679 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE K 681 " --> pdb=" O TYR K 729 " (cutoff:3.500A) Processing sheet with id=AS2, first strand: chain 'K' and resid 660 through 661 removed outlier: 6.957A pdb=" N ALA K 660 " --> pdb=" O GLY K 702 " (cutoff:3.500A) No H-bonds generated for sheet with id=AS2 Processing sheet with id=AS3, first strand: chain 'K' and resid 691 through 697 removed outlier: 3.684A pdb=" N THR K 691 " --> pdb=" O TYR K 791 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR K 791 " --> pdb=" O THR K 691 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU K 695 " --> pdb=" O ILE K 787 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE K 787 " --> pdb=" O LEU K 695 " (cutoff:3.500A) Processing sheet with id=AS4, first strand: chain 'K' and resid 771 through 773 Processing sheet with id=AS5, first strand: chain 'L' and resid 101 through 102 removed outlier: 6.447A pdb=" N VAL L 101 " --> pdb=" O ASN L 126 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL L 155 " --> pdb=" O THR L 188 " (cutoff:3.500A) Processing sheet with id=AS6, first strand: chain 'L' and resid 108 through 109 removed outlier: 6.182A pdb=" N GLY L 108 " --> pdb=" O THR L 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AS6 Processing sheet with id=AS7, first strand: chain 'L' and resid 140 through 142 removed outlier: 6.809A pdb=" N ASN L 140 " --> pdb=" O GLU L 169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AS7 Processing sheet with id=AS8, first strand: chain 'L' and resid 219 through 226 removed outlier: 7.639A pdb=" N LEU L 220 " --> pdb=" O VAL L 252 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N PHE L 254 " --> pdb=" O LEU L 220 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLY L 222 " --> pdb=" O PHE L 254 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS L 256 " --> pdb=" O GLY L 222 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL L 252 " --> pdb=" O LYS L 274 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS L 276 " --> pdb=" O VAL L 252 " (cutoff:3.500A) Processing sheet with id=AS9, first strand: chain 'L' and resid 219 through 226 removed outlier: 7.639A pdb=" N LEU L 220 " --> pdb=" O VAL L 252 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N PHE L 254 " --> pdb=" O LEU L 220 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLY L 222 " --> pdb=" O PHE L 254 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS L 256 " --> pdb=" O GLY L 222 " (cutoff:3.500A) removed outlier: 9.548A pdb=" N THR L 279 " --> pdb=" O ASN L 253 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASN L 255 " --> pdb=" O THR L 279 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ASP L 281 " --> pdb=" O ASN L 255 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU L 257 " --> pdb=" O ASP L 281 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU L 280 " --> pdb=" O ASN L 363 " (cutoff:3.500A) Processing sheet with id=AT1, first strand: chain 'L' and resid 266 through 270 removed outlier: 7.269A pdb=" N ALA L 267 " --> pdb=" O ASN L 289 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ILE L 291 " --> pdb=" O ALA L 267 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE L 269 " --> pdb=" O ILE L 291 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU L 288 " --> pdb=" O THR L 380 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR L 381 " --> pdb=" O GLU L 407 " (cutoff:3.500A) Processing sheet with id=AT2, first strand: chain 'L' and resid 387 through 388 removed outlier: 6.168A pdb=" N ILE L 413 " --> pdb=" O THR L 451 " (cutoff:3.500A) Processing sheet with id=AT3, first strand: chain 'L' and resid 456 through 457 removed outlier: 7.298A pdb=" N ILE L 456 " --> pdb=" O ASP L 477 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE L 476 " --> pdb=" O ILE L 501 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR L 502 " --> pdb=" O ILE L 518 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE L 569 " --> pdb=" O ARG L 541 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASN L 543 " --> pdb=" O ILE L 569 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU L 571 " --> pdb=" O ASN L 543 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU L 547 " --> pdb=" O TYR L 573 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ALA L 595 " --> pdb=" O ASP L 570 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE L 572 " --> pdb=" O ALA L 595 " (cutoff:3.500A) Processing sheet with id=AT4, first strand: chain 'L' and resid 530 through 531 Processing sheet with id=AT5, first strand: chain 'L' and resid 589 through 590 removed outlier: 3.606A pdb=" N ILE L 590 " --> pdb=" O THR L 614 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE L 636 " --> pdb=" O LEU L 613 " (cutoff:3.500A) Processing sheet with id=AT6, first strand: chain 'L' and resid 622 through 623 removed outlier: 3.847A pdb=" N TYR L 623 " --> pdb=" O ASN L 643 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE L 642 " --> pdb=" O LYS L 680 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASN L 682 " --> pdb=" O ILE L 642 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N TYR L 644 " --> pdb=" O ASN L 682 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE L 679 " --> pdb=" O ALA L 727 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N TYR L 729 " --> pdb=" O ILE L 679 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE L 681 " --> pdb=" O TYR L 729 " (cutoff:3.500A) Processing sheet with id=AT7, first strand: chain 'L' and resid 660 through 661 removed outlier: 6.958A pdb=" N ALA L 660 " --> pdb=" O GLY L 702 " (cutoff:3.500A) No H-bonds generated for sheet with id=AT7 Processing sheet with id=AT8, first strand: chain 'L' and resid 691 through 697 removed outlier: 3.684A pdb=" N THR L 691 " --> pdb=" O TYR L 791 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR L 791 " --> pdb=" O THR L 691 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU L 695 " --> pdb=" O ILE L 787 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ILE L 787 " --> pdb=" O LEU L 695 " (cutoff:3.500A) Processing sheet with id=AT9, first strand: chain 'L' and resid 771 through 773 692 hydrogen bonds defined for protein. 1788 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: 31.12 Time building geometry restraints manager: 23.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 22697 1.34 - 1.46: 12030 1.46 - 1.57: 34849 1.57 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 69840 Sorted by residual: bond pdb=" C ASP B 124 " pdb=" N VAL B 125 " ideal model delta sigma weight residual 1.332 1.312 0.019 9.60e-03 1.09e+04 3.98e+00 bond pdb=" C ASP K 124 " pdb=" N VAL K 125 " ideal model delta sigma weight residual 1.332 1.312 0.019 9.60e-03 1.09e+04 3.98e+00 bond pdb=" C ASP J 124 " pdb=" N VAL J 125 " ideal model delta sigma weight residual 1.332 1.312 0.019 9.60e-03 1.09e+04 3.98e+00 bond pdb=" C ASP G 124 " pdb=" N VAL G 125 " ideal model delta sigma weight residual 1.332 1.312 0.019 9.60e-03 1.09e+04 3.98e+00 bond pdb=" C ASP C 124 " pdb=" N VAL C 125 " ideal model delta sigma weight residual 1.332 1.312 0.019 9.60e-03 1.09e+04 3.97e+00 ... (remaining 69835 not shown) Histogram of bond angle deviations from ideal: 98.88 - 105.92: 888 105.92 - 112.95: 36937 112.95 - 119.98: 23465 119.98 - 127.01: 32654 127.01 - 134.04: 640 Bond angle restraints: 94584 Sorted by residual: angle pdb=" C GLY A 83 " pdb=" N ASN A 84 " pdb=" CA ASN A 84 " ideal model delta sigma weight residual 121.54 130.69 -9.15 1.91e+00 2.74e-01 2.29e+01 angle pdb=" C GLY J 83 " pdb=" N ASN J 84 " pdb=" CA ASN J 84 " ideal model delta sigma weight residual 121.54 130.67 -9.13 1.91e+00 2.74e-01 2.29e+01 angle pdb=" C GLY D 83 " pdb=" N ASN D 84 " pdb=" CA ASN D 84 " ideal model delta sigma weight residual 121.54 130.67 -9.13 1.91e+00 2.74e-01 2.29e+01 angle pdb=" C GLY B 83 " pdb=" N ASN B 84 " pdb=" CA ASN B 84 " ideal model delta sigma weight residual 121.54 130.67 -9.13 1.91e+00 2.74e-01 2.29e+01 angle pdb=" C GLY E 83 " pdb=" N ASN E 84 " pdb=" CA ASN E 84 " ideal model delta sigma weight residual 121.54 130.67 -9.13 1.91e+00 2.74e-01 2.29e+01 ... (remaining 94579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 38580 16.30 - 32.60: 2187 32.60 - 48.90: 345 48.90 - 65.20: 24 65.20 - 81.50: 36 Dihedral angle restraints: 41172 sinusoidal: 15828 harmonic: 25344 Sorted by residual: dihedral pdb=" CB CYS E 738 " pdb=" SG CYS E 738 " pdb=" SG CYS E 749 " pdb=" CB CYS E 749 " ideal model delta sinusoidal sigma weight residual -86.00 -167.50 81.50 1 1.00e+01 1.00e-02 8.18e+01 dihedral pdb=" CB CYS K 738 " pdb=" SG CYS K 738 " pdb=" SG CYS K 749 " pdb=" CB CYS K 749 " ideal model delta sinusoidal sigma weight residual -86.00 -167.49 81.49 1 1.00e+01 1.00e-02 8.18e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 749 " pdb=" CB CYS C 749 " ideal model delta sinusoidal sigma weight residual -86.00 -167.48 81.48 1 1.00e+01 1.00e-02 8.18e+01 ... (remaining 41169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 8320 0.074 - 0.148: 2113 0.148 - 0.222: 151 0.222 - 0.296: 24 0.296 - 0.371: 12 Chirality restraints: 10620 Sorted by residual: chirality pdb=" CB ILE E 713 " pdb=" CA ILE E 713 " pdb=" CG1 ILE E 713 " pdb=" CG2 ILE E 713 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CB ILE J 713 " pdb=" CA ILE J 713 " pdb=" CG1 ILE J 713 " pdb=" CG2 ILE J 713 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CB ILE D 713 " pdb=" CA ILE D 713 " pdb=" CG1 ILE D 713 " pdb=" CG2 ILE D 713 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.39e+00 ... (remaining 10617 not shown) Planarity restraints: 12396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN F 136 " 0.010 2.00e-02 2.50e+03 2.11e-02 4.45e+00 pdb=" C GLN F 136 " -0.036 2.00e-02 2.50e+03 pdb=" O GLN F 136 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE F 137 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 136 " -0.010 2.00e-02 2.50e+03 2.11e-02 4.45e+00 pdb=" C GLN C 136 " 0.036 2.00e-02 2.50e+03 pdb=" O GLN C 136 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE C 137 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN I 136 " -0.010 2.00e-02 2.50e+03 2.11e-02 4.44e+00 pdb=" C GLN I 136 " 0.036 2.00e-02 2.50e+03 pdb=" O GLN I 136 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE I 137 " -0.012 2.00e-02 2.50e+03 ... (remaining 12393 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 16442 2.79 - 3.32: 63660 3.32 - 3.84: 116989 3.84 - 4.37: 135904 4.37 - 4.90: 236104 Nonbonded interactions: 569099 Sorted by model distance: nonbonded pdb=" OG1 THR C 153 " pdb=" OG1 THR C 185 " model vdw 2.259 2.440 nonbonded pdb=" OG1 THR H 153 " pdb=" OG1 THR H 185 " model vdw 2.259 2.440 nonbonded pdb=" OG1 THR K 153 " pdb=" OG1 THR K 185 " model vdw 2.259 2.440 nonbonded pdb=" OG1 THR B 153 " pdb=" OG1 THR B 185 " model vdw 2.259 2.440 nonbonded pdb=" OG1 THR E 153 " pdb=" OG1 THR E 185 " model vdw 2.259 2.440 ... (remaining 569094 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 42948 2.51 5 N 12060 2.21 5 O 13512 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.310 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: 0.040 Extract box with map and model: 15.510 Check model and map are aligned: 0.790 Convert atoms to be neutral: 0.430 Process input model: 142.710 Find NCS groups from input model: 4.160 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 170.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 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 : 0.006 0.056 69840 Z= 0.427 Angle : 1.006 9.710 94584 Z= 0.567 Chirality : 0.061 0.371 10620 Planarity : 0.005 0.044 12396 Dihedral : 10.546 70.922 25056 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer Outliers : 0.97 % 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: -5.19 (0.07), residues: 8952 helix: -4.88 (0.07), residues: 372 sheet: -3.57 (0.10), residues: 2100 loop : -3.58 (0.06), residues: 6480 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 292 time to evaluate : 6.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 0 residues processed: 364 average time/residue: 0.5838 time to fit residues: 376.1806 Evaluate side-chains 168 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 6.032 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.0234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 759 optimal weight: 4.9990 chunk 682 optimal weight: 2.9990 chunk 378 optimal weight: 0.9990 chunk 233 optimal weight: 3.9990 chunk 460 optimal weight: 3.9990 chunk 364 optimal weight: 9.9990 chunk 705 optimal weight: 7.9990 chunk 272 optimal weight: 10.0000 chunk 428 optimal weight: 7.9990 chunk 525 optimal weight: 10.0000 chunk 817 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 HIS A 387 ASN A 469 HIS A 618 ASN ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN A 755 ASN B 256 HIS B 387 ASN B 469 HIS B 618 ASN ** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 ASN B 755 ASN C 256 HIS C 387 ASN C 469 HIS C 618 ASN ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN C 755 ASN D 256 HIS D 387 ASN D 469 HIS D 618 ASN ** D 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 731 ASN D 755 ASN E 256 HIS E 387 ASN E 469 HIS E 618 ASN ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 731 ASN E 755 ASN F 256 HIS F 387 ASN F 469 HIS F 618 ASN ** F 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 731 ASN F 755 ASN G 256 HIS G 387 ASN G 469 HIS G 618 ASN ** G 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 731 ASN G 755 ASN H 256 HIS H 387 ASN H 469 HIS H 618 ASN ** H 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 731 ASN H 755 ASN I 256 HIS I 387 ASN I 469 HIS I 618 ASN ** I 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 731 ASN I 755 ASN J 256 HIS J 387 ASN J 469 HIS J 618 ASN ** J 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 731 ASN J 755 ASN K 256 HIS K 387 ASN K 469 HIS K 618 ASN ** K 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 731 ASN K 755 ASN L 256 HIS L 387 ASN L 469 HIS L 618 ASN ** L 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 731 ASN L 755 ASN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 69840 Z= 0.284 Angle : 0.620 6.988 94584 Z= 0.337 Chirality : 0.048 0.178 10620 Planarity : 0.003 0.041 12396 Dihedral : 6.369 23.729 9516 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.91 % Favored : 85.09 % Rotamer Outliers : 1.27 % 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: -5.09 (0.07), residues: 8952 helix: -3.84 (0.14), residues: 384 sheet: -3.60 (0.10), residues: 2316 loop : -3.49 (0.06), residues: 6252 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 210 time to evaluate : 6.138 Fit side-chains outliers start: 94 outliers final: 75 residues processed: 276 average time/residue: 0.5668 time to fit residues: 285.8690 Evaluate side-chains 248 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 173 time to evaluate : 6.065 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 0 residues processed: 75 average time/residue: 0.4703 time to fit residues: 75.9415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 454 optimal weight: 7.9990 chunk 253 optimal weight: 4.9990 chunk 680 optimal weight: 7.9990 chunk 556 optimal weight: 8.9990 chunk 225 optimal weight: 10.0000 chunk 818 optimal weight: 40.0000 chunk 884 optimal weight: 20.0000 chunk 729 optimal weight: 0.5980 chunk 811 optimal weight: 20.0000 chunk 279 optimal weight: 0.6980 chunk 656 optimal weight: 50.0000 overall best weight: 4.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 543 ASN A 584 ASN ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 ASN B 543 ASN B 584 ASN ** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 GLN B 760 ASN C 543 ASN C 584 ASN ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN C 760 ASN D 543 ASN D 584 ASN ** D 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 ASN E 543 ASN ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 756 GLN E 760 ASN F 289 ASN F 543 ASN ** F 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 756 GLN F 760 ASN G 289 ASN G 543 ASN G 584 ASN ** G 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 ASN H 543 ASN H 584 ASN ** H 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 756 GLN H 760 ASN I 543 ASN I 584 ASN ** I 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 756 GLN I 760 ASN J 543 ASN J 584 ASN ** J 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 289 ASN K 543 ASN ** K 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 756 GLN K 760 ASN L 289 ASN L 543 ASN ** L 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 756 GLN L 760 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 69840 Z= 0.352 Angle : 0.650 7.368 94584 Z= 0.354 Chirality : 0.049 0.157 10620 Planarity : 0.003 0.037 12396 Dihedral : 6.368 25.886 9516 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.41 % Favored : 81.59 % Rotamer Outliers : 1.66 % 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: -5.08 (0.07), residues: 8952 helix: -2.81 (0.20), residues: 384 sheet: -3.59 (0.09), residues: 2508 loop : -3.53 (0.06), residues: 6060 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 192 time to evaluate : 6.177 Fit side-chains outliers start: 123 outliers final: 27 residues processed: 301 average time/residue: 0.5585 time to fit residues: 312.2494 Evaluate side-chains 195 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 168 time to evaluate : 6.113 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.5038 time to fit residues: 33.8994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 808 optimal weight: 2.9990 chunk 615 optimal weight: 9.9990 chunk 424 optimal weight: 20.0000 chunk 90 optimal weight: 8.9990 chunk 390 optimal weight: 9.9990 chunk 549 optimal weight: 2.9990 chunk 821 optimal weight: 30.0000 chunk 869 optimal weight: 0.7980 chunk 429 optimal weight: 6.9990 chunk 778 optimal weight: 20.0000 chunk 234 optimal weight: 8.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 513 ASN ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN A 756 GLN A 760 ASN ** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 ASN C 62 ASN ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN D 513 ASN ** D 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 731 ASN D 756 GLN D 760 ASN E 584 ASN ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 731 ASN F 62 ASN F 584 ASN ** F 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 731 ASN ** G 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 731 ASN G 756 GLN ** H 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 731 ASN I 62 ASN ** I 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 731 ASN J 513 ASN ** J 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 731 ASN J 756 GLN J 760 ASN K 62 ASN K 584 ASN ** K 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 731 ASN L 62 ASN L 584 ASN ** L 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 731 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 69840 Z= 0.352 Angle : 0.666 9.194 94584 Z= 0.355 Chirality : 0.049 0.156 10620 Planarity : 0.003 0.036 12396 Dihedral : 6.306 27.691 9516 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.37 % Favored : 82.63 % Rotamer Outliers : 2.51 % 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: -4.93 (0.07), residues: 8952 helix: -2.67 (0.20), residues: 384 sheet: -3.23 (0.10), residues: 2268 loop : -3.58 (0.06), residues: 6300 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 200 time to evaluate : 6.121 Fit side-chains outliers start: 186 outliers final: 99 residues processed: 353 average time/residue: 0.5453 time to fit residues: 356.5310 Evaluate side-chains 276 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 177 time to evaluate : 6.126 Switching outliers to nearest non-outliers outliers start: 99 outliers final: 0 residues processed: 99 average time/residue: 0.4831 time to fit residues: 100.7111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 724 optimal weight: 20.0000 chunk 493 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 647 optimal weight: 9.9990 chunk 358 optimal weight: 40.0000 chunk 742 optimal weight: 40.0000 chunk 601 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 444 optimal weight: 30.0000 chunk 780 optimal weight: 20.0000 chunk 219 optimal weight: 20.0000 overall best weight: 6.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN ** B 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 GLN ** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 GLN ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 ASN ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 GLN ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 GLN ** F 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 ASN ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 340 GLN G 513 ASN ** G 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 760 ASN H 62 ASN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 340 GLN ** H 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 340 GLN ** I 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 ASN ** J 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 340 GLN ** K 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 340 GLN ** L 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.057 69840 Z= 0.485 Angle : 0.764 9.349 94584 Z= 0.407 Chirality : 0.052 0.174 10620 Planarity : 0.004 0.033 12396 Dihedral : 6.804 30.980 9516 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.05 % Favored : 78.95 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -5.25 (0.07), residues: 8952 helix: -2.50 (0.20), residues: 384 sheet: -3.77 (0.09), residues: 2580 loop : -3.64 (0.07), residues: 5988 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 198 time to evaluate : 6.098 Fit side-chains outliers start: 128 outliers final: 65 residues processed: 313 average time/residue: 0.5509 time to fit residues: 319.2360 Evaluate side-chains 232 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 167 time to evaluate : 6.123 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 0 residues processed: 65 average time/residue: 0.4874 time to fit residues: 68.4518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 292 optimal weight: 2.9990 chunk 783 optimal weight: 9.9990 chunk 171 optimal weight: 1.9990 chunk 510 optimal weight: 0.9990 chunk 214 optimal weight: 20.0000 chunk 870 optimal weight: 8.9990 chunk 722 optimal weight: 6.9990 chunk 403 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 288 optimal weight: 30.0000 chunk 457 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN ** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN ** D 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 340 GLN ** J 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 69840 Z= 0.222 Angle : 0.613 9.302 94584 Z= 0.318 Chirality : 0.047 0.159 10620 Planarity : 0.003 0.033 12396 Dihedral : 5.921 25.888 9516 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.20 % Favored : 85.80 % Rotamer Outliers : 1.40 % 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: -4.79 (0.08), residues: 8952 helix: -2.45 (0.20), residues: 384 sheet: -3.13 (0.10), residues: 2160 loop : -3.50 (0.07), residues: 6408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 187 time to evaluate : 6.132 Fit side-chains outliers start: 104 outliers final: 53 residues processed: 259 average time/residue: 0.5630 time to fit residues: 268.9801 Evaluate side-chains 225 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 172 time to evaluate : 6.180 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.4814 time to fit residues: 56.9920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 839 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 496 optimal weight: 40.0000 chunk 635 optimal weight: 5.9990 chunk 492 optimal weight: 9.9990 chunk 733 optimal weight: 40.0000 chunk 486 optimal weight: 7.9990 chunk 867 optimal weight: 10.0000 chunk 542 optimal weight: 5.9990 chunk 528 optimal weight: 0.0470 chunk 400 optimal weight: 1.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 ASN ** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 628 ASN ** H 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 69840 Z= 0.258 Angle : 0.613 9.646 94584 Z= 0.321 Chirality : 0.047 0.152 10620 Planarity : 0.003 0.031 12396 Dihedral : 5.809 24.930 9516 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.40 % Favored : 82.60 % Rotamer Outliers : 0.85 % 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: -4.79 (0.08), residues: 8952 helix: -2.36 (0.21), residues: 384 sheet: -3.35 (0.10), residues: 2412 loop : -3.38 (0.07), residues: 6156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 184 time to evaluate : 6.109 Fit side-chains outliers start: 63 outliers final: 18 residues processed: 244 average time/residue: 0.5630 time to fit residues: 253.9308 Evaluate side-chains 192 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 174 time to evaluate : 6.051 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.4730 time to fit residues: 24.4212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 536 optimal weight: 4.9990 chunk 346 optimal weight: 40.0000 chunk 518 optimal weight: 9.9990 chunk 261 optimal weight: 20.0000 chunk 170 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 chunk 551 optimal weight: 2.9990 chunk 590 optimal weight: 20.0000 chunk 428 optimal weight: 20.0000 chunk 80 optimal weight: 9.9990 chunk 681 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 ASN ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 628 ASN ** H 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 628 ASN ** L 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.063 69840 Z= 0.539 Angle : 0.797 9.863 94584 Z= 0.427 Chirality : 0.053 0.176 10620 Planarity : 0.004 0.031 12396 Dihedral : 6.866 31.655 9516 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 22.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.26 % Favored : 77.74 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -5.07 (0.08), residues: 8952 helix: -2.34 (0.21), residues: 384 sheet: -3.64 (0.10), residues: 2460 loop : -3.53 (0.07), residues: 6108 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 172 time to evaluate : 6.189 Fit side-chains outliers start: 106 outliers final: 67 residues processed: 259 average time/residue: 0.5721 time to fit residues: 276.6001 Evaluate side-chains 233 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 166 time to evaluate : 6.119 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 0 residues processed: 67 average time/residue: 0.4872 time to fit residues: 70.9170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 789 optimal weight: 3.9990 chunk 831 optimal weight: 10.0000 chunk 758 optimal weight: 4.9990 chunk 808 optimal weight: 40.0000 chunk 830 optimal weight: 8.9990 chunk 486 optimal weight: 7.9990 chunk 352 optimal weight: 7.9990 chunk 634 optimal weight: 4.9990 chunk 248 optimal weight: 0.9990 chunk 730 optimal weight: 6.9990 chunk 764 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 ASN ** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 628 ASN ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 628 ASN ** H 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 628 ASN ** K 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 69840 Z= 0.258 Angle : 0.636 10.708 94584 Z= 0.332 Chirality : 0.047 0.149 10620 Planarity : 0.003 0.028 12396 Dihedral : 6.004 27.779 9516 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.86 % Favored : 84.14 % Rotamer Outliers : 0.27 % 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: -4.78 (0.08), residues: 8952 helix: -2.30 (0.21), residues: 384 sheet: -3.16 (0.10), residues: 2184 loop : -3.50 (0.07), residues: 6384 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 172 time to evaluate : 6.262 Fit side-chains outliers start: 20 outliers final: 11 residues processed: 191 average time/residue: 0.5926 time to fit residues: 210.5121 Evaluate side-chains 183 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 172 time to evaluate : 6.243 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.5052 time to fit residues: 19.0765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 805 optimal weight: 5.9990 chunk 530 optimal weight: 3.9990 chunk 854 optimal weight: 3.9990 chunk 521 optimal weight: 9.9990 chunk 405 optimal weight: 3.9990 chunk 594 optimal weight: 0.0070 chunk 896 optimal weight: 6.9990 chunk 825 optimal weight: 1.9990 chunk 713 optimal weight: 10.0000 chunk 74 optimal weight: 50.0000 chunk 551 optimal weight: 0.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 ASN ** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 628 ASN ** H 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 69840 Z= 0.192 Angle : 0.584 11.820 94584 Z= 0.303 Chirality : 0.046 0.150 10620 Planarity : 0.003 0.026 12396 Dihedral : 5.462 21.603 9516 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.25 % Favored : 84.75 % Rotamer Outliers : 0.15 % 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: -4.51 (0.08), residues: 8952 helix: -2.08 (0.23), residues: 384 sheet: -2.88 (0.11), residues: 1920 loop : -3.36 (0.07), residues: 6648 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 183 time to evaluate : 6.148 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 190 average time/residue: 0.5838 time to fit residues: 206.8767 Evaluate side-chains 174 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 170 time to evaluate : 6.136 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4733 time to fit residues: 11.8122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 437 optimal weight: 0.0980 chunk 567 optimal weight: 10.0000 chunk 760 optimal weight: 0.5980 chunk 218 optimal weight: 7.9990 chunk 658 optimal weight: 40.0000 chunk 105 optimal weight: 3.9990 chunk 198 optimal weight: 10.0000 chunk 715 optimal weight: 2.9990 chunk 299 optimal weight: 50.0000 chunk 734 optimal weight: 20.0000 chunk 90 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 ASN ** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 628 ASN ** H 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 628 ASN ** K 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.089751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.051271 restraints weight = 173777.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.052665 restraints weight = 109486.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.053586 restraints weight = 84528.079| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 69840 Z= 0.164 Angle : 0.559 10.082 94584 Z= 0.290 Chirality : 0.046 0.150 10620 Planarity : 0.002 0.024 12396 Dihedral : 5.179 19.536 9516 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.66 % Favored : 88.34 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.34 (0.08), residues: 8952 helix: -2.04 (0.23), residues: 384 sheet: -2.70 (0.11), residues: 2040 loop : -3.25 (0.07), residues: 6528 =============================================================================== Job complete usr+sys time: 9027.66 seconds wall clock time: 165 minutes 4.30 seconds (9904.30 seconds total)