Starting phenix.real_space_refine on Fri Mar 15 11:09:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyn_0547/03_2024/6nyn_0547.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyn_0547/03_2024/6nyn_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_0547/03_2024/6nyn_0547.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyn_0547/03_2024/6nyn_0547.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyn_0547/03_2024/6nyn_0547.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyn_0547/03_2024/6nyn_0547.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 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 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. 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 25.96, per 1000 atoms: 0.38 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: 19.00 Conformation dependent library (CDL) restraints added in 10.3 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: 6.84 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: 32.30 Time building geometry restraints manager: 21.08 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 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: 2.770 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: 13.800 Check model and map are aligned: 0.750 Set scattering table: 0.450 Process input model: 147.550 Find NCS groups from input model: 4.050 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 172.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 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 % Allowed : 3.24 % Favored : 95.79 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 225 HIS 0.007 0.002 HIS H 469 PHE 0.023 0.003 PHE A 532 TYR 0.026 0.003 TYR L 574 ARG 0.007 0.001 ARG E 228 *********************** 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 : 5.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 VAL cc_start: 0.8720 (t) cc_final: 0.8500 (t) REVERT: A 486 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7175 (mp) REVERT: A 663 MET cc_start: 0.8542 (ttt) cc_final: 0.7820 (tmm) REVERT: B 486 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7170 (tp) REVERT: B 662 MET cc_start: 0.4195 (mtm) cc_final: 0.3972 (mtt) REVERT: B 663 MET cc_start: 0.8707 (ttt) cc_final: 0.8237 (tmm) REVERT: C 109 THR cc_start: 0.8529 (OUTLIER) cc_final: 0.8257 (p) REVERT: C 438 GLU cc_start: 0.7974 (tt0) cc_final: 0.7719 (tt0) REVERT: C 486 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7289 (mp) REVERT: C 663 MET cc_start: 0.8699 (ttt) cc_final: 0.7916 (tmm) REVERT: D 125 VAL cc_start: 0.8796 (t) cc_final: 0.8580 (t) REVERT: D 486 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7098 (mp) REVERT: D 663 MET cc_start: 0.8589 (ttt) cc_final: 0.7879 (tmm) REVERT: E 486 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7158 (tp) REVERT: E 662 MET cc_start: 0.4191 (mtm) cc_final: 0.3968 (mtt) REVERT: E 663 MET cc_start: 0.8706 (ttt) cc_final: 0.8240 (tmm) REVERT: F 109 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8257 (p) REVERT: F 438 GLU cc_start: 0.7976 (tt0) cc_final: 0.7720 (tt0) REVERT: F 486 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7292 (mp) REVERT: F 663 MET cc_start: 0.8700 (ttt) cc_final: 0.7918 (tmm) REVERT: G 125 VAL cc_start: 0.8794 (t) cc_final: 0.8579 (t) REVERT: G 486 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7099 (mp) REVERT: G 663 MET cc_start: 0.8584 (ttt) cc_final: 0.7877 (tmm) REVERT: H 486 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7159 (tp) REVERT: H 662 MET cc_start: 0.4198 (mtm) cc_final: 0.3972 (mtt) REVERT: H 663 MET cc_start: 0.8711 (ttt) cc_final: 0.8241 (tmm) REVERT: I 109 THR cc_start: 0.8534 (OUTLIER) cc_final: 0.8262 (p) REVERT: I 438 GLU cc_start: 0.7971 (tt0) cc_final: 0.7716 (tt0) REVERT: I 486 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7286 (mp) REVERT: I 663 MET cc_start: 0.8705 (ttt) cc_final: 0.7919 (tmm) REVERT: J 125 VAL cc_start: 0.8804 (t) cc_final: 0.8594 (t) REVERT: J 486 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7100 (mp) REVERT: J 663 MET cc_start: 0.8589 (ttt) cc_final: 0.7880 (tmm) REVERT: K 486 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7165 (tp) REVERT: K 662 MET cc_start: 0.4203 (mtm) cc_final: 0.3977 (mtt) REVERT: K 663 MET cc_start: 0.8709 (ttt) cc_final: 0.8241 (tmm) REVERT: L 109 THR cc_start: 0.8530 (OUTLIER) cc_final: 0.8257 (p) REVERT: L 438 GLU cc_start: 0.7974 (tt0) cc_final: 0.7719 (tt0) REVERT: L 486 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7296 (mp) REVERT: L 663 MET cc_start: 0.8697 (ttt) cc_final: 0.7917 (tmm) outliers start: 72 outliers final: 0 residues processed: 364 average time/residue: 0.6052 time to fit residues: 390.3148 Evaluate side-chains 192 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 176 time to evaluate : 5.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 486 LEU Chi-restraints excluded: chain G residue 486 LEU Chi-restraints excluded: chain H residue 486 LEU Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 486 LEU Chi-restraints excluded: chain J residue 486 LEU Chi-restraints excluded: chain K residue 486 LEU Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 486 LEU 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: 2.9990 chunk 364 optimal weight: 8.9990 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: 3.1990 ------------------------------------------------------------------------------- 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: 0.7483 moved from start: 0.1342 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= 0.268 Angle : 0.604 6.974 94584 Z= 0.328 Chirality : 0.047 0.175 10620 Planarity : 0.003 0.040 12396 Dihedral : 6.689 55.726 9544 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.47 % Favored : 85.53 % Rotamer: Outliers : 1.51 % Allowed : 6.08 % Favored : 92.41 % 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: -5.04 (0.07), residues: 8952 helix: -3.78 (0.14), residues: 384 sheet: -3.51 (0.10), residues: 2268 loop : -3.49 (0.06), residues: 6300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 30 HIS 0.003 0.001 HIS B 693 PHE 0.018 0.002 PHE C 488 TYR 0.014 0.002 TYR I 574 ARG 0.005 0.001 ARG G 592 *********************** 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 328 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 216 time to evaluate : 5.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.7754 (mtt) cc_final: 0.7302 (mtt) REVERT: A 124 ASP cc_start: 0.7222 (OUTLIER) cc_final: 0.6844 (p0) REVERT: A 125 VAL cc_start: 0.8717 (t) cc_final: 0.8494 (t) REVERT: A 486 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7496 (mp) REVERT: A 663 MET cc_start: 0.8528 (ttt) cc_final: 0.7903 (tmm) REVERT: B 124 ASP cc_start: 0.7196 (OUTLIER) cc_final: 0.6864 (p0) REVERT: B 125 VAL cc_start: 0.8793 (t) cc_final: 0.8517 (t) REVERT: B 580 PHE cc_start: 0.6694 (t80) cc_final: 0.6434 (t80) REVERT: B 663 MET cc_start: 0.8794 (ttt) cc_final: 0.8283 (tmm) REVERT: B 665 ASN cc_start: 0.9033 (OUTLIER) cc_final: 0.8793 (m-40) REVERT: C 124 ASP cc_start: 0.6904 (OUTLIER) cc_final: 0.6610 (p0) REVERT: C 486 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7537 (mp) REVERT: C 580 PHE cc_start: 0.6693 (t80) cc_final: 0.6308 (t80) REVERT: C 638 ASN cc_start: 0.7740 (t0) cc_final: 0.7533 (t0) REVERT: C 663 MET cc_start: 0.8670 (ttt) cc_final: 0.8215 (tmm) REVERT: D 103 MET cc_start: 0.7769 (mtt) cc_final: 0.7368 (mtt) REVERT: D 124 ASP cc_start: 0.7235 (OUTLIER) cc_final: 0.6928 (p0) REVERT: D 125 VAL cc_start: 0.8765 (t) cc_final: 0.8548 (t) REVERT: D 486 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7433 (mp) REVERT: D 663 MET cc_start: 0.8516 (ttt) cc_final: 0.7872 (tmm) REVERT: E 124 ASP cc_start: 0.7182 (OUTLIER) cc_final: 0.6861 (p0) REVERT: E 125 VAL cc_start: 0.8785 (t) cc_final: 0.8508 (t) REVERT: E 580 PHE cc_start: 0.6685 (t80) cc_final: 0.6425 (t80) REVERT: E 663 MET cc_start: 0.8793 (ttt) cc_final: 0.8283 (tmm) REVERT: E 665 ASN cc_start: 0.9035 (OUTLIER) cc_final: 0.8796 (m-40) REVERT: F 124 ASP cc_start: 0.6900 (OUTLIER) cc_final: 0.6615 (p0) REVERT: F 486 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7541 (mp) REVERT: F 580 PHE cc_start: 0.6688 (t80) cc_final: 0.6307 (t80) REVERT: F 663 MET cc_start: 0.8675 (ttt) cc_final: 0.8206 (tmm) REVERT: G 103 MET cc_start: 0.7767 (mtt) cc_final: 0.7367 (mtt) REVERT: G 124 ASP cc_start: 0.7226 (OUTLIER) cc_final: 0.6919 (p0) REVERT: G 125 VAL cc_start: 0.8764 (t) cc_final: 0.8547 (t) REVERT: G 486 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7434 (mp) REVERT: G 663 MET cc_start: 0.8513 (ttt) cc_final: 0.7873 (tmm) REVERT: H 124 ASP cc_start: 0.7186 (OUTLIER) cc_final: 0.6867 (p0) REVERT: H 125 VAL cc_start: 0.8789 (t) cc_final: 0.8512 (t) REVERT: H 580 PHE cc_start: 0.6694 (t80) cc_final: 0.6433 (t80) REVERT: H 663 MET cc_start: 0.8793 (ttt) cc_final: 0.8281 (tmm) REVERT: H 665 ASN cc_start: 0.9035 (OUTLIER) cc_final: 0.8795 (m-40) REVERT: I 124 ASP cc_start: 0.6907 (OUTLIER) cc_final: 0.6615 (p0) REVERT: I 486 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7529 (mp) REVERT: I 580 PHE cc_start: 0.6697 (t80) cc_final: 0.6313 (t80) REVERT: I 638 ASN cc_start: 0.7744 (t0) cc_final: 0.7534 (t0) REVERT: I 663 MET cc_start: 0.8679 (ttt) cc_final: 0.8221 (tmm) REVERT: J 103 MET cc_start: 0.7771 (mtt) cc_final: 0.7369 (mtt) REVERT: J 124 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.6921 (p0) REVERT: J 125 VAL cc_start: 0.8758 (t) cc_final: 0.8539 (t) REVERT: J 486 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7503 (mp) REVERT: J 663 MET cc_start: 0.8513 (ttt) cc_final: 0.7872 (tmm) REVERT: K 124 ASP cc_start: 0.7183 (OUTLIER) cc_final: 0.6857 (p0) REVERT: K 125 VAL cc_start: 0.8792 (t) cc_final: 0.8519 (t) REVERT: K 580 PHE cc_start: 0.6685 (t80) cc_final: 0.6425 (t80) REVERT: K 663 MET cc_start: 0.8792 (ttt) cc_final: 0.8281 (tmm) REVERT: K 665 ASN cc_start: 0.9032 (OUTLIER) cc_final: 0.8792 (m-40) REVERT: L 124 ASP cc_start: 0.6903 (OUTLIER) cc_final: 0.6618 (p0) REVERT: L 486 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7544 (mp) REVERT: L 580 PHE cc_start: 0.6685 (t80) cc_final: 0.6302 (t80) REVERT: L 663 MET cc_start: 0.8674 (ttt) cc_final: 0.8206 (tmm) outliers start: 112 outliers final: 79 residues processed: 300 average time/residue: 0.5807 time to fit residues: 318.5817 Evaluate side-chains 295 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 192 time to evaluate : 5.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 665 ASN Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain E residue 665 ASN Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 486 LEU Chi-restraints excluded: chain F residue 567 LEU Chi-restraints excluded: chain F residue 613 LEU Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 486 LEU Chi-restraints excluded: chain G residue 545 VAL Chi-restraints excluded: chain G residue 559 VAL Chi-restraints excluded: chain G residue 613 LEU Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 150 ASP Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 613 LEU Chi-restraints excluded: chain H residue 665 ASN Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 150 ASP Chi-restraints excluded: chain I residue 379 LEU Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 486 LEU Chi-restraints excluded: chain I residue 567 LEU Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 486 LEU Chi-restraints excluded: chain J residue 545 VAL Chi-restraints excluded: chain J residue 559 VAL Chi-restraints excluded: chain J residue 613 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 124 ASP Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 150 ASP Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 613 LEU Chi-restraints excluded: chain K residue 665 ASN Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 379 LEU Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 486 LEU Chi-restraints excluded: chain L residue 567 LEU Chi-restraints excluded: chain L residue 613 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 454 optimal weight: 0.2980 chunk 253 optimal weight: 3.9990 chunk 680 optimal weight: 2.9990 chunk 556 optimal weight: 0.0870 chunk 225 optimal weight: 10.0000 chunk 818 optimal weight: 6.9990 chunk 884 optimal weight: 20.0000 chunk 729 optimal weight: 9.9990 chunk 811 optimal weight: 20.0000 chunk 279 optimal weight: 9.9990 chunk 656 optimal weight: 50.0000 overall best weight: 2.8764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN D 584 ASN ** D 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 ASN ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 289 ASN F 543 ASN ** F 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 543 ASN ** G 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 543 ASN ** H 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 543 ASN ** I 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 543 ASN J 584 ASN ** J 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 543 ASN ** K 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 289 ASN L 543 ASN ** L 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 69840 Z= 0.241 Angle : 0.563 6.447 94584 Z= 0.306 Chirality : 0.046 0.158 10620 Planarity : 0.003 0.036 12396 Dihedral : 6.137 56.234 9536 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.88 % Favored : 84.12 % Rotamer: Outliers : 2.47 % Allowed : 6.98 % Favored : 90.55 % 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: -4.83 (0.07), residues: 8952 helix: -2.71 (0.20), residues: 384 sheet: -3.39 (0.10), residues: 2256 loop : -3.40 (0.06), residues: 6312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 30 HIS 0.002 0.001 HIS J 385 PHE 0.015 0.002 PHE L 488 TYR 0.014 0.001 TYR I 574 ARG 0.003 0.001 ARG K 592 *********************** 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 403 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 220 time to evaluate : 5.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.7234 (OUTLIER) cc_final: 0.6727 (p0) REVERT: A 125 VAL cc_start: 0.8795 (t) cc_final: 0.8559 (t) REVERT: A 486 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7548 (mp) REVERT: A 580 PHE cc_start: 0.6856 (t80) cc_final: 0.6641 (t80) REVERT: A 634 ASP cc_start: 0.7159 (OUTLIER) cc_final: 0.6516 (p0) REVERT: A 663 MET cc_start: 0.8547 (ttt) cc_final: 0.7865 (tmm) REVERT: A 761 ASN cc_start: 0.9217 (OUTLIER) cc_final: 0.8847 (p0) REVERT: B 124 ASP cc_start: 0.7338 (OUTLIER) cc_final: 0.6904 (p0) REVERT: B 125 VAL cc_start: 0.8902 (t) cc_final: 0.8594 (t) REVERT: B 580 PHE cc_start: 0.7018 (t80) cc_final: 0.6726 (t80) REVERT: B 663 MET cc_start: 0.8746 (ttt) cc_final: 0.8141 (tmm) REVERT: B 665 ASN cc_start: 0.8913 (OUTLIER) cc_final: 0.8685 (m-40) REVERT: B 761 ASN cc_start: 0.9215 (OUTLIER) cc_final: 0.8890 (p0) REVERT: C 124 ASP cc_start: 0.6958 (OUTLIER) cc_final: 0.6661 (p0) REVERT: C 580 PHE cc_start: 0.6809 (t80) cc_final: 0.6318 (t80) REVERT: C 634 ASP cc_start: 0.6911 (OUTLIER) cc_final: 0.6003 (p0) REVERT: C 663 MET cc_start: 0.8597 (ttt) cc_final: 0.7983 (tmm) REVERT: C 761 ASN cc_start: 0.9205 (OUTLIER) cc_final: 0.8910 (p0) REVERT: D 124 ASP cc_start: 0.7210 (OUTLIER) cc_final: 0.6771 (p0) REVERT: D 125 VAL cc_start: 0.8782 (t) cc_final: 0.8547 (t) REVERT: D 486 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7561 (mp) REVERT: D 580 PHE cc_start: 0.6824 (t80) cc_final: 0.6617 (t80) REVERT: D 634 ASP cc_start: 0.7202 (OUTLIER) cc_final: 0.6571 (p0) REVERT: D 663 MET cc_start: 0.8607 (ttt) cc_final: 0.7930 (tmm) REVERT: D 761 ASN cc_start: 0.9151 (OUTLIER) cc_final: 0.8767 (p0) REVERT: E 124 ASP cc_start: 0.7357 (OUTLIER) cc_final: 0.6926 (p0) REVERT: E 125 VAL cc_start: 0.8900 (t) cc_final: 0.8599 (t) REVERT: E 580 PHE cc_start: 0.7007 (t80) cc_final: 0.6716 (t80) REVERT: E 663 MET cc_start: 0.8745 (ttt) cc_final: 0.8143 (tmm) REVERT: E 665 ASN cc_start: 0.8912 (OUTLIER) cc_final: 0.8701 (m-40) REVERT: E 761 ASN cc_start: 0.9219 (OUTLIER) cc_final: 0.8894 (p0) REVERT: F 124 ASP cc_start: 0.6954 (OUTLIER) cc_final: 0.6677 (p0) REVERT: F 580 PHE cc_start: 0.6787 (t80) cc_final: 0.6284 (t80) REVERT: F 634 ASP cc_start: 0.6933 (OUTLIER) cc_final: 0.6023 (p0) REVERT: F 663 MET cc_start: 0.8596 (ttt) cc_final: 0.7996 (tmm) REVERT: F 761 ASN cc_start: 0.9203 (OUTLIER) cc_final: 0.8908 (p0) REVERT: G 124 ASP cc_start: 0.7207 (OUTLIER) cc_final: 0.6774 (p0) REVERT: G 125 VAL cc_start: 0.8784 (t) cc_final: 0.8549 (t) REVERT: G 486 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7520 (mp) REVERT: G 580 PHE cc_start: 0.6829 (t80) cc_final: 0.6626 (t80) REVERT: G 634 ASP cc_start: 0.7196 (OUTLIER) cc_final: 0.6562 (p0) REVERT: G 663 MET cc_start: 0.8606 (ttt) cc_final: 0.7931 (tmm) REVERT: G 761 ASN cc_start: 0.9155 (OUTLIER) cc_final: 0.8772 (p0) REVERT: H 124 ASP cc_start: 0.7363 (OUTLIER) cc_final: 0.6934 (p0) REVERT: H 125 VAL cc_start: 0.8905 (t) cc_final: 0.8603 (t) REVERT: H 580 PHE cc_start: 0.7016 (t80) cc_final: 0.6724 (t80) REVERT: H 663 MET cc_start: 0.8747 (ttt) cc_final: 0.8141 (tmm) REVERT: H 665 ASN cc_start: 0.8913 (OUTLIER) cc_final: 0.8686 (m-40) REVERT: H 761 ASN cc_start: 0.9220 (OUTLIER) cc_final: 0.8894 (p0) REVERT: I 124 ASP cc_start: 0.6964 (OUTLIER) cc_final: 0.6669 (p0) REVERT: I 580 PHE cc_start: 0.6811 (t80) cc_final: 0.6320 (t80) REVERT: I 634 ASP cc_start: 0.6920 (OUTLIER) cc_final: 0.6008 (p0) REVERT: I 663 MET cc_start: 0.8605 (ttt) cc_final: 0.7986 (tmm) REVERT: I 761 ASN cc_start: 0.9204 (OUTLIER) cc_final: 0.8904 (p0) REVERT: J 124 ASP cc_start: 0.7216 (OUTLIER) cc_final: 0.6779 (p0) REVERT: J 125 VAL cc_start: 0.8778 (t) cc_final: 0.8542 (t) REVERT: J 486 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7525 (mp) REVERT: J 580 PHE cc_start: 0.6827 (t80) cc_final: 0.6623 (t80) REVERT: J 634 ASP cc_start: 0.7198 (OUTLIER) cc_final: 0.6567 (p0) REVERT: J 663 MET cc_start: 0.8607 (ttt) cc_final: 0.7930 (tmm) REVERT: J 761 ASN cc_start: 0.9156 (OUTLIER) cc_final: 0.8774 (p0) REVERT: K 124 ASP cc_start: 0.7351 (OUTLIER) cc_final: 0.6918 (p0) REVERT: K 125 VAL cc_start: 0.8904 (t) cc_final: 0.8605 (t) REVERT: K 580 PHE cc_start: 0.7005 (t80) cc_final: 0.6713 (t80) REVERT: K 663 MET cc_start: 0.8746 (ttt) cc_final: 0.8141 (tmm) REVERT: K 665 ASN cc_start: 0.8909 (OUTLIER) cc_final: 0.8698 (m-40) REVERT: K 761 ASN cc_start: 0.9214 (OUTLIER) cc_final: 0.8888 (p0) REVERT: L 124 ASP cc_start: 0.6957 (OUTLIER) cc_final: 0.6676 (p0) REVERT: L 580 PHE cc_start: 0.6743 (t80) cc_final: 0.6254 (t80) REVERT: L 634 ASP cc_start: 0.6937 (OUTLIER) cc_final: 0.6025 (p0) REVERT: L 663 MET cc_start: 0.8596 (ttt) cc_final: 0.7996 (tmm) REVERT: L 761 ASN cc_start: 0.9207 (OUTLIER) cc_final: 0.8913 (p0) outliers start: 183 outliers final: 74 residues processed: 363 average time/residue: 0.5308 time to fit residues: 359.5061 Evaluate side-chains 324 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 210 time to evaluate : 5.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 761 ASN Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 665 ASN Chi-restraints excluded: chain B residue 761 ASN Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 634 ASP Chi-restraints excluded: chain C residue 761 ASN Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 412 ASN Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 634 ASP Chi-restraints excluded: chain D residue 761 ASN Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 412 ASN Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 665 ASN Chi-restraints excluded: chain E residue 761 ASN Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 567 LEU Chi-restraints excluded: chain F residue 613 LEU Chi-restraints excluded: chain F residue 621 MET Chi-restraints excluded: chain F residue 634 ASP Chi-restraints excluded: chain F residue 761 ASN Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 486 LEU Chi-restraints excluded: chain G residue 559 VAL Chi-restraints excluded: chain G residue 634 ASP Chi-restraints excluded: chain G residue 761 ASN Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 150 ASP Chi-restraints excluded: chain H residue 412 ASN Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 665 ASN Chi-restraints excluded: chain H residue 761 ASN Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 150 ASP Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 567 LEU Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 634 ASP Chi-restraints excluded: chain I residue 761 ASN Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain J residue 412 ASN Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 486 LEU Chi-restraints excluded: chain J residue 559 VAL Chi-restraints excluded: chain J residue 634 ASP Chi-restraints excluded: chain J residue 761 ASN Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 124 ASP Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 150 ASP Chi-restraints excluded: chain K residue 412 ASN Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 665 ASN Chi-restraints excluded: chain K residue 761 ASN Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 567 LEU Chi-restraints excluded: chain L residue 613 LEU Chi-restraints excluded: chain L residue 621 MET Chi-restraints excluded: chain L residue 634 ASP Chi-restraints excluded: chain L residue 761 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 808 optimal weight: 50.0000 chunk 615 optimal weight: 10.0000 chunk 424 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 390 optimal weight: 20.0000 chunk 549 optimal weight: 5.9990 chunk 821 optimal weight: 30.0000 chunk 869 optimal weight: 0.9990 chunk 429 optimal weight: 0.0470 chunk 778 optimal weight: 5.9990 chunk 234 optimal weight: 8.9990 overall best weight: 3.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 ASN ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN B 584 ASN ** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 ASN B 756 GLN B 760 ASN C 584 ASN ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN C 760 ASN ** D 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 731 ASN E 584 ASN ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 731 ASN E 756 GLN E 760 ASN F 584 ASN ** F 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 756 GLN F 760 ASN G 584 ASN ** G 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 731 ASN H 584 ASN ** H 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 731 ASN H 756 GLN H 760 ASN I 584 ASN ** I 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 756 GLN I 760 ASN ** J 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 731 ASN K 584 ASN ** K 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 731 ASN K 756 GLN K 760 ASN L 584 ASN ** L 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 756 GLN L 760 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 69840 Z= 0.302 Angle : 0.618 10.377 94584 Z= 0.328 Chirality : 0.047 0.158 10620 Planarity : 0.003 0.034 12396 Dihedral : 6.049 42.711 9528 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.55 % Favored : 83.45 % Rotamer: Outliers : 3.09 % Allowed : 7.50 % Favored : 89.41 % 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: -4.74 (0.07), residues: 8952 helix: -2.49 (0.20), residues: 384 sheet: -3.17 (0.10), residues: 2196 loop : -3.43 (0.06), residues: 6372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 30 HIS 0.004 0.001 HIS C 262 PHE 0.019 0.002 PHE C 488 TYR 0.015 0.001 TYR L 623 ARG 0.004 0.001 ARG A 402 *********************** 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 445 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 216 time to evaluate : 5.816 Fit side-chains REVERT: A 124 ASP cc_start: 0.7101 (OUTLIER) cc_final: 0.6755 (p0) REVERT: A 125 VAL cc_start: 0.8778 (t) cc_final: 0.8513 (t) REVERT: A 452 PHE cc_start: 0.8118 (OUTLIER) cc_final: 0.7881 (m-80) REVERT: A 634 ASP cc_start: 0.7148 (OUTLIER) cc_final: 0.6465 (p0) REVERT: A 663 MET cc_start: 0.8456 (ttt) cc_final: 0.7765 (tmm) REVERT: A 735 MET cc_start: 0.4704 (mpp) cc_final: 0.4203 (mpp) REVERT: A 761 ASN cc_start: 0.9178 (OUTLIER) cc_final: 0.8806 (p0) REVERT: B 124 ASP cc_start: 0.7329 (OUTLIER) cc_final: 0.6953 (p0) REVERT: B 125 VAL cc_start: 0.8912 (t) cc_final: 0.8615 (t) REVERT: B 438 GLU cc_start: 0.8050 (tt0) cc_final: 0.7414 (tt0) REVERT: B 580 PHE cc_start: 0.7151 (t80) cc_final: 0.6824 (t80) REVERT: B 634 ASP cc_start: 0.6522 (OUTLIER) cc_final: 0.6155 (t0) REVERT: B 663 MET cc_start: 0.8696 (ttt) cc_final: 0.8230 (tmm) REVERT: B 761 ASN cc_start: 0.9226 (OUTLIER) cc_final: 0.8912 (p0) REVERT: C 124 ASP cc_start: 0.6978 (OUTLIER) cc_final: 0.6698 (p0) REVERT: C 438 GLU cc_start: 0.7998 (tt0) cc_final: 0.7673 (tt0) REVERT: C 580 PHE cc_start: 0.6827 (t80) cc_final: 0.6426 (t80) REVERT: C 663 MET cc_start: 0.8510 (ttt) cc_final: 0.7948 (tmm) REVERT: C 761 ASN cc_start: 0.9213 (OUTLIER) cc_final: 0.8942 (p0) REVERT: D 124 ASP cc_start: 0.7161 (OUTLIER) cc_final: 0.6828 (p0) REVERT: D 125 VAL cc_start: 0.8825 (t) cc_final: 0.8568 (t) REVERT: D 452 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7880 (m-80) REVERT: D 634 ASP cc_start: 0.7120 (OUTLIER) cc_final: 0.6368 (p0) REVERT: D 663 MET cc_start: 0.8498 (ttt) cc_final: 0.7789 (tmm) REVERT: D 735 MET cc_start: 0.4697 (mpp) cc_final: 0.4211 (mpp) REVERT: D 761 ASN cc_start: 0.9136 (OUTLIER) cc_final: 0.8745 (p0) REVERT: E 124 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.6949 (p0) REVERT: E 125 VAL cc_start: 0.8908 (t) cc_final: 0.8607 (t) REVERT: E 438 GLU cc_start: 0.8042 (tt0) cc_final: 0.7405 (tt0) REVERT: E 580 PHE cc_start: 0.7138 (t80) cc_final: 0.6809 (t80) REVERT: E 634 ASP cc_start: 0.6512 (OUTLIER) cc_final: 0.6146 (t0) REVERT: E 663 MET cc_start: 0.8694 (ttt) cc_final: 0.8231 (tmm) REVERT: E 761 ASN cc_start: 0.9228 (OUTLIER) cc_final: 0.8916 (p0) REVERT: F 124 ASP cc_start: 0.6972 (OUTLIER) cc_final: 0.6702 (p0) REVERT: F 438 GLU cc_start: 0.8000 (tt0) cc_final: 0.7690 (tt0) REVERT: F 580 PHE cc_start: 0.6854 (t80) cc_final: 0.6555 (t80) REVERT: F 663 MET cc_start: 0.8500 (ttt) cc_final: 0.7942 (tmm) REVERT: F 761 ASN cc_start: 0.9210 (OUTLIER) cc_final: 0.8940 (p0) REVERT: G 124 ASP cc_start: 0.7155 (OUTLIER) cc_final: 0.6823 (p0) REVERT: G 125 VAL cc_start: 0.8821 (t) cc_final: 0.8563 (t) REVERT: G 452 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7883 (m-80) REVERT: G 634 ASP cc_start: 0.7104 (OUTLIER) cc_final: 0.6392 (p0) REVERT: G 663 MET cc_start: 0.8492 (ttt) cc_final: 0.7786 (tmm) REVERT: G 735 MET cc_start: 0.4698 (mpp) cc_final: 0.4211 (mpp) REVERT: G 761 ASN cc_start: 0.9172 (OUTLIER) cc_final: 0.8795 (p0) REVERT: H 124 ASP cc_start: 0.7318 (OUTLIER) cc_final: 0.6934 (p0) REVERT: H 125 VAL cc_start: 0.8909 (t) cc_final: 0.8612 (t) REVERT: H 438 GLU cc_start: 0.8056 (tt0) cc_final: 0.7412 (tt0) REVERT: H 580 PHE cc_start: 0.7148 (t80) cc_final: 0.6818 (t80) REVERT: H 634 ASP cc_start: 0.6517 (OUTLIER) cc_final: 0.6150 (t0) REVERT: H 663 MET cc_start: 0.8698 (ttt) cc_final: 0.8232 (tmm) REVERT: H 761 ASN cc_start: 0.9225 (OUTLIER) cc_final: 0.8897 (p0) REVERT: I 124 ASP cc_start: 0.6977 (OUTLIER) cc_final: 0.6700 (p0) REVERT: I 438 GLU cc_start: 0.7993 (tt0) cc_final: 0.7668 (tt0) REVERT: I 580 PHE cc_start: 0.6828 (t80) cc_final: 0.6428 (t80) REVERT: I 663 MET cc_start: 0.8516 (ttt) cc_final: 0.7950 (tmm) REVERT: I 761 ASN cc_start: 0.9211 (OUTLIER) cc_final: 0.8939 (p0) REVERT: J 124 ASP cc_start: 0.7164 (OUTLIER) cc_final: 0.6836 (p0) REVERT: J 125 VAL cc_start: 0.8821 (t) cc_final: 0.8567 (t) REVERT: J 452 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7879 (m-80) REVERT: J 634 ASP cc_start: 0.7105 (OUTLIER) cc_final: 0.6396 (p0) REVERT: J 663 MET cc_start: 0.8495 (ttt) cc_final: 0.7787 (tmm) REVERT: J 735 MET cc_start: 0.4690 (mpp) cc_final: 0.4204 (mpp) REVERT: J 761 ASN cc_start: 0.9141 (OUTLIER) cc_final: 0.8750 (p0) REVERT: K 124 ASP cc_start: 0.7318 (OUTLIER) cc_final: 0.6945 (p0) REVERT: K 125 VAL cc_start: 0.8908 (t) cc_final: 0.8609 (t) REVERT: K 438 GLU cc_start: 0.8053 (tt0) cc_final: 0.7412 (tt0) REVERT: K 580 PHE cc_start: 0.7140 (t80) cc_final: 0.6812 (t80) REVERT: K 634 ASP cc_start: 0.6520 (OUTLIER) cc_final: 0.6152 (t0) REVERT: K 663 MET cc_start: 0.8697 (ttt) cc_final: 0.8231 (tmm) REVERT: K 761 ASN cc_start: 0.9226 (OUTLIER) cc_final: 0.8914 (p0) REVERT: L 124 ASP cc_start: 0.6976 (OUTLIER) cc_final: 0.6705 (p0) REVERT: L 438 GLU cc_start: 0.7994 (tt0) cc_final: 0.7685 (tt0) REVERT: L 580 PHE cc_start: 0.6815 (t80) cc_final: 0.6413 (t80) REVERT: L 663 MET cc_start: 0.8497 (ttt) cc_final: 0.7941 (tmm) REVERT: L 761 ASN cc_start: 0.9214 (OUTLIER) cc_final: 0.8944 (p0) outliers start: 229 outliers final: 116 residues processed: 407 average time/residue: 0.5481 time to fit residues: 414.4946 Evaluate side-chains 354 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 202 time to evaluate : 5.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 761 ASN Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain B residue 761 ASN Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 496 ASN Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 634 ASP Chi-restraints excluded: chain C residue 761 ASN Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 412 ASN Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 452 PHE Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 634 ASP Chi-restraints excluded: chain D residue 761 ASN Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 354 ASP Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 412 ASN Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 452 PHE Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 634 ASP Chi-restraints excluded: chain E residue 761 ASN Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 496 ASN Chi-restraints excluded: chain F residue 567 LEU Chi-restraints excluded: chain F residue 613 LEU Chi-restraints excluded: chain F residue 621 MET Chi-restraints excluded: chain F residue 634 ASP Chi-restraints excluded: chain F residue 761 ASN Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 452 PHE Chi-restraints excluded: chain G residue 559 VAL Chi-restraints excluded: chain G residue 634 ASP Chi-restraints excluded: chain G residue 761 ASN Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 150 ASP Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 354 ASP Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 412 ASN Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 452 PHE Chi-restraints excluded: chain H residue 559 VAL Chi-restraints excluded: chain H residue 634 ASP Chi-restraints excluded: chain H residue 761 ASN Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 150 ASP Chi-restraints excluded: chain I residue 196 THR Chi-restraints excluded: chain I residue 379 LEU Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 496 ASN Chi-restraints excluded: chain I residue 567 LEU Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 634 ASP Chi-restraints excluded: chain I residue 761 ASN Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain J residue 196 THR Chi-restraints excluded: chain J residue 379 LEU Chi-restraints excluded: chain J residue 412 ASN Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 452 PHE Chi-restraints excluded: chain J residue 559 VAL Chi-restraints excluded: chain J residue 634 ASP Chi-restraints excluded: chain J residue 761 ASN Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 124 ASP Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 150 ASP Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain K residue 379 LEU Chi-restraints excluded: chain K residue 412 ASN Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 452 PHE Chi-restraints excluded: chain K residue 559 VAL Chi-restraints excluded: chain K residue 634 ASP Chi-restraints excluded: chain K residue 761 ASN Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 196 THR Chi-restraints excluded: chain L residue 379 LEU Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 496 ASN Chi-restraints excluded: chain L residue 567 LEU Chi-restraints excluded: chain L residue 613 LEU Chi-restraints excluded: chain L residue 621 MET Chi-restraints excluded: chain L residue 634 ASP Chi-restraints excluded: chain L residue 761 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 724 optimal weight: 10.0000 chunk 493 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 647 optimal weight: 10.0000 chunk 358 optimal weight: 40.0000 chunk 742 optimal weight: 20.0000 chunk 601 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 444 optimal weight: 0.0000 chunk 780 optimal weight: 5.9990 chunk 219 optimal weight: 0.9990 overall best weight: 2.5790 ------------------------------------------------------------------------------- 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 705 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 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 705 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 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 705 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 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 69840 Z= 0.216 Angle : 0.575 9.250 94584 Z= 0.300 Chirality : 0.046 0.156 10620 Planarity : 0.003 0.031 12396 Dihedral : 5.653 41.587 9520 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.18 % Favored : 85.82 % Rotamer: Outliers : 2.82 % Allowed : 9.60 % Favored : 87.57 % 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: -4.57 (0.08), residues: 8952 helix: -2.43 (0.21), residues: 384 sheet: -2.97 (0.11), residues: 2064 loop : -3.35 (0.06), residues: 6504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 225 HIS 0.002 0.001 HIS F 262 PHE 0.013 0.001 PHE L 452 TYR 0.012 0.001 TYR A 574 ARG 0.003 0.000 ARG A 402 *********************** 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 419 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 210 time to evaluate : 5.763 Fit side-chains REVERT: A 124 ASP cc_start: 0.7208 (OUTLIER) cc_final: 0.6691 (p0) REVERT: A 125 VAL cc_start: 0.8718 (t) cc_final: 0.8476 (t) REVERT: A 634 ASP cc_start: 0.7121 (OUTLIER) cc_final: 0.6386 (p0) REVERT: A 663 MET cc_start: 0.8446 (ttt) cc_final: 0.7784 (tmm) REVERT: A 735 MET cc_start: 0.4824 (OUTLIER) cc_final: 0.4284 (mpp) REVERT: A 761 ASN cc_start: 0.9249 (OUTLIER) cc_final: 0.8893 (p0) REVERT: B 124 ASP cc_start: 0.7339 (OUTLIER) cc_final: 0.6899 (p0) REVERT: B 125 VAL cc_start: 0.8891 (t) cc_final: 0.8584 (t) REVERT: B 580 PHE cc_start: 0.7139 (t80) cc_final: 0.6788 (t80) REVERT: B 634 ASP cc_start: 0.6765 (OUTLIER) cc_final: 0.6396 (t0) REVERT: B 663 MET cc_start: 0.8685 (ttt) cc_final: 0.8200 (tmm) REVERT: B 761 ASN cc_start: 0.9222 (OUTLIER) cc_final: 0.8893 (p0) REVERT: C 438 GLU cc_start: 0.7965 (tt0) cc_final: 0.7567 (mt-10) REVERT: C 580 PHE cc_start: 0.6815 (t80) cc_final: 0.6577 (t80) REVERT: C 663 MET cc_start: 0.8563 (ttt) cc_final: 0.8130 (tmm) REVERT: C 735 MET cc_start: 0.4466 (mpp) cc_final: 0.3787 (mpp) REVERT: C 758 MET cc_start: 0.3637 (mpt) cc_final: 0.2454 (mmm) REVERT: C 761 ASN cc_start: 0.9238 (OUTLIER) cc_final: 0.8933 (p0) REVERT: D 124 ASP cc_start: 0.7212 (OUTLIER) cc_final: 0.6727 (p0) REVERT: D 125 VAL cc_start: 0.8748 (t) cc_final: 0.8508 (t) REVERT: D 634 ASP cc_start: 0.7120 (OUTLIER) cc_final: 0.6371 (p0) REVERT: D 663 MET cc_start: 0.8572 (ttt) cc_final: 0.7894 (tmm) REVERT: D 735 MET cc_start: 0.4941 (OUTLIER) cc_final: 0.4474 (mpp) REVERT: D 761 ASN cc_start: 0.9155 (OUTLIER) cc_final: 0.8765 (p0) REVERT: E 124 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.6890 (p0) REVERT: E 125 VAL cc_start: 0.8884 (t) cc_final: 0.8579 (t) REVERT: E 580 PHE cc_start: 0.7127 (t80) cc_final: 0.6773 (t80) REVERT: E 634 ASP cc_start: 0.6767 (OUTLIER) cc_final: 0.6401 (t0) REVERT: E 663 MET cc_start: 0.8683 (ttt) cc_final: 0.8200 (tmm) REVERT: E 761 ASN cc_start: 0.9237 (OUTLIER) cc_final: 0.8903 (p0) REVERT: F 438 GLU cc_start: 0.7959 (tt0) cc_final: 0.7573 (mt-10) REVERT: F 580 PHE cc_start: 0.6881 (t80) cc_final: 0.6602 (t80) REVERT: F 663 MET cc_start: 0.8559 (ttt) cc_final: 0.8130 (tmm) REVERT: F 735 MET cc_start: 0.4452 (mpp) cc_final: 0.3764 (mpp) REVERT: F 758 MET cc_start: 0.3658 (mpt) cc_final: 0.2477 (mmm) REVERT: F 761 ASN cc_start: 0.9238 (OUTLIER) cc_final: 0.8929 (p0) REVERT: G 124 ASP cc_start: 0.7207 (OUTLIER) cc_final: 0.6727 (p0) REVERT: G 125 VAL cc_start: 0.8747 (t) cc_final: 0.8507 (t) REVERT: G 634 ASP cc_start: 0.7114 (OUTLIER) cc_final: 0.6375 (p0) REVERT: G 663 MET cc_start: 0.8506 (ttt) cc_final: 0.7821 (tmm) REVERT: G 735 MET cc_start: 0.4922 (OUTLIER) cc_final: 0.4459 (mpp) REVERT: G 761 ASN cc_start: 0.9157 (OUTLIER) cc_final: 0.8769 (p0) REVERT: H 124 ASP cc_start: 0.7338 (OUTLIER) cc_final: 0.6908 (p0) REVERT: H 125 VAL cc_start: 0.8921 (t) cc_final: 0.8626 (t) REVERT: H 580 PHE cc_start: 0.7133 (t80) cc_final: 0.6780 (t80) REVERT: H 634 ASP cc_start: 0.6753 (OUTLIER) cc_final: 0.6385 (t0) REVERT: H 663 MET cc_start: 0.8686 (ttt) cc_final: 0.8201 (tmm) REVERT: H 761 ASN cc_start: 0.9238 (OUTLIER) cc_final: 0.8905 (p0) REVERT: I 438 GLU cc_start: 0.7962 (tt0) cc_final: 0.7560 (mt-10) REVERT: I 580 PHE cc_start: 0.6815 (t80) cc_final: 0.6579 (t80) REVERT: I 663 MET cc_start: 0.8572 (ttt) cc_final: 0.8136 (tmm) REVERT: I 735 MET cc_start: 0.4477 (mpp) cc_final: 0.3796 (mpp) REVERT: I 758 MET cc_start: 0.3658 (mpt) cc_final: 0.2470 (mmm) REVERT: I 761 ASN cc_start: 0.9236 (OUTLIER) cc_final: 0.8931 (p0) REVERT: J 124 ASP cc_start: 0.7210 (OUTLIER) cc_final: 0.6720 (p0) REVERT: J 125 VAL cc_start: 0.8739 (t) cc_final: 0.8499 (t) REVERT: J 634 ASP cc_start: 0.7114 (OUTLIER) cc_final: 0.6378 (p0) REVERT: J 663 MET cc_start: 0.8567 (ttt) cc_final: 0.7892 (tmm) REVERT: J 735 MET cc_start: 0.4899 (OUTLIER) cc_final: 0.4435 (mpp) REVERT: J 761 ASN cc_start: 0.9157 (OUTLIER) cc_final: 0.8768 (p0) REVERT: K 124 ASP cc_start: 0.7318 (OUTLIER) cc_final: 0.6883 (p0) REVERT: K 125 VAL cc_start: 0.8883 (t) cc_final: 0.8575 (t) REVERT: K 580 PHE cc_start: 0.7126 (t80) cc_final: 0.6775 (t80) REVERT: K 634 ASP cc_start: 0.6784 (OUTLIER) cc_final: 0.6414 (t0) REVERT: K 663 MET cc_start: 0.8685 (ttt) cc_final: 0.8201 (tmm) REVERT: K 761 ASN cc_start: 0.9233 (OUTLIER) cc_final: 0.8900 (p0) REVERT: L 438 GLU cc_start: 0.7956 (tt0) cc_final: 0.7569 (mt-10) REVERT: L 580 PHE cc_start: 0.6880 (t80) cc_final: 0.6594 (t80) REVERT: L 663 MET cc_start: 0.8555 (ttt) cc_final: 0.8126 (tmm) REVERT: L 735 MET cc_start: 0.4453 (mpp) cc_final: 0.3767 (mpp) REVERT: L 758 MET cc_start: 0.3641 (mpt) cc_final: 0.2461 (mmm) REVERT: L 761 ASN cc_start: 0.9242 (OUTLIER) cc_final: 0.8931 (p0) outliers start: 209 outliers final: 112 residues processed: 379 average time/residue: 0.5449 time to fit residues: 383.5434 Evaluate side-chains 351 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 207 time to evaluate : 5.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain A residue 761 ASN Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 513 ASN Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain B residue 761 ASN Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 496 ASN Chi-restraints excluded: chain C residue 513 ASN Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 634 ASP Chi-restraints excluded: chain C residue 761 ASN Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 412 ASN Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 634 ASP Chi-restraints excluded: chain D residue 735 MET Chi-restraints excluded: chain D residue 761 ASN Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 412 ASN Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 513 ASN Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 634 ASP Chi-restraints excluded: chain E residue 761 ASN Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 496 ASN Chi-restraints excluded: chain F residue 513 ASN Chi-restraints excluded: chain F residue 567 LEU Chi-restraints excluded: chain F residue 621 MET Chi-restraints excluded: chain F residue 634 ASP Chi-restraints excluded: chain F residue 761 ASN Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 559 VAL Chi-restraints excluded: chain G residue 634 ASP Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 761 ASN Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 150 ASP Chi-restraints excluded: chain H residue 412 ASN Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 513 ASN Chi-restraints excluded: chain H residue 559 VAL Chi-restraints excluded: chain H residue 634 ASP Chi-restraints excluded: chain H residue 761 ASN Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 150 ASP Chi-restraints excluded: chain I residue 379 LEU Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 496 ASN Chi-restraints excluded: chain I residue 513 ASN Chi-restraints excluded: chain I residue 567 LEU Chi-restraints excluded: chain I residue 634 ASP Chi-restraints excluded: chain I residue 761 ASN Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain J residue 127 MET Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain J residue 196 THR Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 412 ASN Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 559 VAL Chi-restraints excluded: chain J residue 634 ASP Chi-restraints excluded: chain J residue 735 MET Chi-restraints excluded: chain J residue 761 ASN Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 124 ASP Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 150 ASP Chi-restraints excluded: chain K residue 354 ASP Chi-restraints excluded: chain K residue 412 ASN Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 513 ASN Chi-restraints excluded: chain K residue 559 VAL Chi-restraints excluded: chain K residue 634 ASP Chi-restraints excluded: chain K residue 761 ASN Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 379 LEU Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 496 ASN Chi-restraints excluded: chain L residue 513 ASN Chi-restraints excluded: chain L residue 567 LEU Chi-restraints excluded: chain L residue 621 MET Chi-restraints excluded: chain L residue 634 ASP Chi-restraints excluded: chain L residue 761 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 292 optimal weight: 9.9990 chunk 783 optimal weight: 8.9990 chunk 171 optimal weight: 6.9990 chunk 510 optimal weight: 9.9990 chunk 214 optimal weight: 0.0030 chunk 870 optimal weight: 9.9990 chunk 722 optimal weight: 6.9990 chunk 403 optimal weight: 4.9990 chunk 72 optimal weight: 20.0000 chunk 288 optimal weight: 30.0000 chunk 457 optimal weight: 6.9990 overall best weight: 5.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN A 760 ASN B 62 ASN B 340 GLN ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN C 340 GLN ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 ASN ** D 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN ** E 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN F 340 GLN ** F 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 ASN ** G 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 756 GLN G 760 ASN H 62 ASN H 340 GLN ** H 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 ASN I 340 GLN ** I 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 ASN ** J 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 62 ASN K 340 GLN ** K 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 62 ASN L 340 GLN ** L 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 69840 Z= 0.396 Angle : 0.673 9.714 94584 Z= 0.360 Chirality : 0.049 0.161 10620 Planarity : 0.003 0.032 12396 Dihedral : 6.191 43.898 9520 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.12 % Favored : 80.88 % Rotamer: Outliers : 2.85 % Allowed : 10.68 % Favored : 86.47 % 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: -4.85 (0.08), residues: 8952 helix: -2.59 (0.20), residues: 384 sheet: -3.46 (0.10), residues: 2532 loop : -3.35 (0.07), residues: 6036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 30 HIS 0.004 0.001 HIS G 262 PHE 0.024 0.002 PHE I 488 TYR 0.015 0.002 TYR K 765 ARG 0.005 0.001 ARG A 402 *********************** 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 423 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 212 time to evaluate : 5.831 Fit side-chains REVERT: A 124 ASP cc_start: 0.7246 (OUTLIER) cc_final: 0.6868 (p0) REVERT: A 125 VAL cc_start: 0.8810 (t) cc_final: 0.8567 (t) REVERT: A 634 ASP cc_start: 0.7143 (OUTLIER) cc_final: 0.6391 (p0) REVERT: A 663 MET cc_start: 0.8271 (ttt) cc_final: 0.7654 (tmm) REVERT: A 735 MET cc_start: 0.4954 (OUTLIER) cc_final: 0.4481 (mpp) REVERT: A 761 ASN cc_start: 0.9233 (OUTLIER) cc_final: 0.8911 (p0) REVERT: B 124 ASP cc_start: 0.7513 (OUTLIER) cc_final: 0.7130 (p0) REVERT: B 125 VAL cc_start: 0.8889 (t) cc_final: 0.8565 (t) REVERT: B 438 GLU cc_start: 0.8148 (tt0) cc_final: 0.7496 (tt0) REVERT: B 580 PHE cc_start: 0.7343 (t80) cc_final: 0.7005 (t80) REVERT: B 663 MET cc_start: 0.8436 (ttt) cc_final: 0.7943 (tmm) REVERT: B 761 ASN cc_start: 0.9161 (OUTLIER) cc_final: 0.8807 (p0) REVERT: C 407 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7200 (tm-30) REVERT: C 438 GLU cc_start: 0.8130 (tt0) cc_final: 0.7807 (tt0) REVERT: C 580 PHE cc_start: 0.6825 (t80) cc_final: 0.6456 (t80) REVERT: C 663 MET cc_start: 0.8516 (ttt) cc_final: 0.8080 (tmm) REVERT: C 735 MET cc_start: 0.4685 (mpp) cc_final: 0.4135 (mpp) REVERT: C 758 MET cc_start: 0.3945 (mpt) cc_final: 0.2856 (mmm) REVERT: C 761 ASN cc_start: 0.9209 (OUTLIER) cc_final: 0.8887 (p0) REVERT: D 124 ASP cc_start: 0.7257 (OUTLIER) cc_final: 0.6898 (p0) REVERT: D 125 VAL cc_start: 0.8788 (t) cc_final: 0.8535 (t) REVERT: D 634 ASP cc_start: 0.7145 (OUTLIER) cc_final: 0.6372 (p0) REVERT: D 663 MET cc_start: 0.8320 (ttt) cc_final: 0.7675 (tmm) REVERT: D 735 MET cc_start: 0.5088 (OUTLIER) cc_final: 0.4657 (mpp) REVERT: D 761 ASN cc_start: 0.9152 (OUTLIER) cc_final: 0.8797 (p0) REVERT: E 124 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.7142 (p0) REVERT: E 125 VAL cc_start: 0.8890 (t) cc_final: 0.8570 (t) REVERT: E 438 GLU cc_start: 0.8132 (tt0) cc_final: 0.7476 (tt0) REVERT: E 580 PHE cc_start: 0.7332 (t80) cc_final: 0.6996 (t80) REVERT: E 663 MET cc_start: 0.8434 (ttt) cc_final: 0.7945 (tmm) REVERT: E 761 ASN cc_start: 0.9150 (OUTLIER) cc_final: 0.8803 (p0) REVERT: F 407 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7356 (tm-30) REVERT: F 438 GLU cc_start: 0.8078 (tt0) cc_final: 0.7769 (tt0) REVERT: F 580 PHE cc_start: 0.6817 (t80) cc_final: 0.6450 (t80) REVERT: F 663 MET cc_start: 0.8521 (ttt) cc_final: 0.8084 (tmm) REVERT: F 735 MET cc_start: 0.4688 (mpp) cc_final: 0.4133 (mpp) REVERT: F 758 MET cc_start: 0.3965 (mpt) cc_final: 0.2850 (mmm) REVERT: F 761 ASN cc_start: 0.9207 (OUTLIER) cc_final: 0.8885 (p0) REVERT: G 124 ASP cc_start: 0.7252 (OUTLIER) cc_final: 0.6888 (p0) REVERT: G 125 VAL cc_start: 0.8789 (t) cc_final: 0.8537 (t) REVERT: G 634 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6358 (p0) REVERT: G 663 MET cc_start: 0.8315 (ttt) cc_final: 0.7673 (tmm) REVERT: G 735 MET cc_start: 0.5089 (OUTLIER) cc_final: 0.4659 (mpp) REVERT: G 761 ASN cc_start: 0.9160 (OUTLIER) cc_final: 0.8804 (p0) REVERT: H 124 ASP cc_start: 0.7513 (OUTLIER) cc_final: 0.7140 (p0) REVERT: H 125 VAL cc_start: 0.8893 (t) cc_final: 0.8575 (t) REVERT: H 438 GLU cc_start: 0.8148 (tt0) cc_final: 0.7469 (tt0) REVERT: H 580 PHE cc_start: 0.7338 (t80) cc_final: 0.7000 (t80) REVERT: H 663 MET cc_start: 0.8438 (ttt) cc_final: 0.7946 (tmm) REVERT: H 761 ASN cc_start: 0.9167 (OUTLIER) cc_final: 0.8816 (p0) REVERT: I 407 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7200 (tm-30) REVERT: I 438 GLU cc_start: 0.8131 (tt0) cc_final: 0.7806 (tt0) REVERT: I 580 PHE cc_start: 0.6826 (t80) cc_final: 0.6458 (t80) REVERT: I 663 MET cc_start: 0.8526 (ttt) cc_final: 0.8085 (tmm) REVERT: I 735 MET cc_start: 0.4692 (mpp) cc_final: 0.4139 (mpp) REVERT: I 758 MET cc_start: 0.3971 (mpt) cc_final: 0.2881 (mmm) REVERT: I 761 ASN cc_start: 0.9208 (OUTLIER) cc_final: 0.8886 (p0) REVERT: J 124 ASP cc_start: 0.7256 (OUTLIER) cc_final: 0.6904 (p0) REVERT: J 125 VAL cc_start: 0.8783 (t) cc_final: 0.8530 (t) REVERT: J 634 ASP cc_start: 0.7122 (OUTLIER) cc_final: 0.6359 (p0) REVERT: J 663 MET cc_start: 0.8316 (ttt) cc_final: 0.7673 (tmm) REVERT: J 735 MET cc_start: 0.5083 (OUTLIER) cc_final: 0.4654 (mpp) REVERT: J 761 ASN cc_start: 0.9156 (OUTLIER) cc_final: 0.8803 (p0) REVERT: K 124 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.7139 (p0) REVERT: K 125 VAL cc_start: 0.8890 (t) cc_final: 0.8571 (t) REVERT: K 438 GLU cc_start: 0.8142 (tt0) cc_final: 0.7466 (tt0) REVERT: K 580 PHE cc_start: 0.7332 (t80) cc_final: 0.6994 (t80) REVERT: K 663 MET cc_start: 0.8436 (ttt) cc_final: 0.7945 (tmm) REVERT: K 761 ASN cc_start: 0.9149 (OUTLIER) cc_final: 0.8800 (p0) REVERT: L 407 GLU cc_start: 0.7614 (tm-30) cc_final: 0.7353 (tm-30) REVERT: L 438 GLU cc_start: 0.8076 (tt0) cc_final: 0.7767 (tt0) REVERT: L 580 PHE cc_start: 0.6813 (t80) cc_final: 0.6442 (t80) REVERT: L 663 MET cc_start: 0.8519 (ttt) cc_final: 0.8084 (tmm) REVERT: L 735 MET cc_start: 0.4683 (mpp) cc_final: 0.4131 (mpp) REVERT: L 758 MET cc_start: 0.3942 (mpt) cc_final: 0.2831 (mmm) REVERT: L 761 ASN cc_start: 0.9208 (OUTLIER) cc_final: 0.8886 (p0) outliers start: 211 outliers final: 136 residues processed: 377 average time/residue: 0.5382 time to fit residues: 377.1852 Evaluate side-chains 360 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 196 time to evaluate : 5.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain A residue 761 ASN Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain B residue 761 ASN Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 496 ASN Chi-restraints excluded: chain C residue 513 ASN Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 634 ASP Chi-restraints excluded: chain C residue 761 ASN Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 412 ASN Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 634 ASP Chi-restraints excluded: chain D residue 735 MET Chi-restraints excluded: chain D residue 761 ASN Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 412 ASN Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 452 PHE Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 634 ASP Chi-restraints excluded: chain E residue 761 ASN Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 496 ASN Chi-restraints excluded: chain F residue 513 ASN Chi-restraints excluded: chain F residue 567 LEU Chi-restraints excluded: chain F residue 621 MET Chi-restraints excluded: chain F residue 634 ASP Chi-restraints excluded: chain F residue 761 ASN Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 354 ASP Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 559 VAL Chi-restraints excluded: chain G residue 634 ASP Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 761 ASN Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 150 ASP Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 412 ASN Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 452 PHE Chi-restraints excluded: chain H residue 559 VAL Chi-restraints excluded: chain H residue 634 ASP Chi-restraints excluded: chain H residue 761 ASN Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 150 ASP Chi-restraints excluded: chain I residue 196 THR Chi-restraints excluded: chain I residue 379 LEU Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 496 ASN Chi-restraints excluded: chain I residue 513 ASN Chi-restraints excluded: chain I residue 567 LEU Chi-restraints excluded: chain I residue 634 ASP Chi-restraints excluded: chain I residue 761 ASN Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain J residue 127 MET Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain J residue 196 THR Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 354 ASP Chi-restraints excluded: chain J residue 379 LEU Chi-restraints excluded: chain J residue 412 ASN Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 559 VAL Chi-restraints excluded: chain J residue 634 ASP Chi-restraints excluded: chain J residue 735 MET Chi-restraints excluded: chain J residue 761 ASN Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 124 ASP Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 150 ASP Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain K residue 354 ASP Chi-restraints excluded: chain K residue 379 LEU Chi-restraints excluded: chain K residue 412 ASN Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 452 PHE Chi-restraints excluded: chain K residue 559 VAL Chi-restraints excluded: chain K residue 634 ASP Chi-restraints excluded: chain K residue 761 ASN Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 196 THR Chi-restraints excluded: chain L residue 379 LEU Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 496 ASN Chi-restraints excluded: chain L residue 513 ASN Chi-restraints excluded: chain L residue 567 LEU Chi-restraints excluded: chain L residue 621 MET Chi-restraints excluded: chain L residue 634 ASP Chi-restraints excluded: chain L residue 761 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 839 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 496 optimal weight: 30.0000 chunk 635 optimal weight: 1.9990 chunk 492 optimal weight: 8.9990 chunk 733 optimal weight: 8.9990 chunk 486 optimal weight: 7.9990 chunk 867 optimal weight: 7.9990 chunk 542 optimal weight: 5.9990 chunk 528 optimal weight: 0.0170 chunk 400 optimal weight: 3.9990 overall best weight: 3.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 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** D 756 GLN D 760 ASN E 340 GLN ** E 705 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 340 GLN ** G 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 705 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** J 756 GLN J 760 ASN ** K 705 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 69840 Z= 0.283 Angle : 0.611 9.478 94584 Z= 0.322 Chirality : 0.047 0.152 10620 Planarity : 0.003 0.031 12396 Dihedral : 5.891 41.860 9520 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.65 % Favored : 84.35 % Rotamer: Outliers : 3.04 % Allowed : 10.78 % Favored : 86.18 % 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: -4.62 (0.08), residues: 8952 helix: -2.59 (0.20), residues: 384 sheet: -2.96 (0.10), residues: 2208 loop : -3.38 (0.07), residues: 6360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 225 HIS 0.003 0.001 HIS L 262 PHE 0.018 0.002 PHE J 580 TYR 0.011 0.001 TYR D 574 ARG 0.004 0.001 ARG K 402 *********************** 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 430 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 205 time to evaluate : 5.816 Fit side-chains REVERT: A 124 ASP cc_start: 0.7159 (OUTLIER) cc_final: 0.6759 (p0) REVERT: A 125 VAL cc_start: 0.8731 (t) cc_final: 0.8489 (t) REVERT: A 634 ASP cc_start: 0.7118 (OUTLIER) cc_final: 0.6371 (p0) REVERT: A 663 MET cc_start: 0.8275 (ttt) cc_final: 0.7642 (tmm) REVERT: A 735 MET cc_start: 0.4975 (OUTLIER) cc_final: 0.4524 (mpp) REVERT: A 761 ASN cc_start: 0.9243 (OUTLIER) cc_final: 0.8880 (p0) REVERT: B 124 ASP cc_start: 0.7542 (OUTLIER) cc_final: 0.7076 (p0) REVERT: B 125 VAL cc_start: 0.8861 (t) cc_final: 0.8545 (t) REVERT: B 407 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7702 (tm-30) REVERT: B 438 GLU cc_start: 0.8118 (tt0) cc_final: 0.7471 (tt0) REVERT: B 580 PHE cc_start: 0.7181 (t80) cc_final: 0.6854 (t80) REVERT: B 634 ASP cc_start: 0.6870 (OUTLIER) cc_final: 0.6440 (t0) REVERT: B 663 MET cc_start: 0.8446 (ttt) cc_final: 0.7996 (tmm) REVERT: B 761 ASN cc_start: 0.9186 (OUTLIER) cc_final: 0.8862 (p0) REVERT: C 407 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7137 (tm-30) REVERT: C 438 GLU cc_start: 0.8092 (tt0) cc_final: 0.7660 (mt-10) REVERT: C 580 PHE cc_start: 0.6801 (t80) cc_final: 0.6561 (t80) REVERT: C 663 MET cc_start: 0.8488 (ttt) cc_final: 0.8045 (tmm) REVERT: C 735 MET cc_start: 0.4772 (mpp) cc_final: 0.4205 (mpp) REVERT: C 758 MET cc_start: 0.3853 (mpt) cc_final: 0.2756 (mmm) REVERT: C 761 ASN cc_start: 0.9217 (OUTLIER) cc_final: 0.8902 (p0) REVERT: D 103 MET cc_start: 0.7771 (mtt) cc_final: 0.7416 (mtt) REVERT: D 124 ASP cc_start: 0.7291 (OUTLIER) cc_final: 0.6768 (p0) REVERT: D 125 VAL cc_start: 0.8751 (t) cc_final: 0.8518 (t) REVERT: D 634 ASP cc_start: 0.7114 (OUTLIER) cc_final: 0.6351 (p0) REVERT: D 663 MET cc_start: 0.8280 (ttt) cc_final: 0.7870 (tmm) REVERT: D 735 MET cc_start: 0.4973 (OUTLIER) cc_final: 0.4579 (mpp) REVERT: D 761 ASN cc_start: 0.9161 (OUTLIER) cc_final: 0.8813 (p0) REVERT: E 124 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7070 (p0) REVERT: E 125 VAL cc_start: 0.8872 (t) cc_final: 0.8567 (t) REVERT: E 407 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7608 (tm-30) REVERT: E 438 GLU cc_start: 0.8094 (tt0) cc_final: 0.7397 (tt0) REVERT: E 580 PHE cc_start: 0.7235 (t80) cc_final: 0.6929 (t80) REVERT: E 634 ASP cc_start: 0.6866 (OUTLIER) cc_final: 0.6438 (t0) REVERT: E 663 MET cc_start: 0.8443 (ttt) cc_final: 0.7997 (tmm) REVERT: E 761 ASN cc_start: 0.9188 (OUTLIER) cc_final: 0.8837 (p0) REVERT: F 407 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7281 (tm-30) REVERT: F 438 GLU cc_start: 0.8055 (tt0) cc_final: 0.7737 (tt0) REVERT: F 580 PHE cc_start: 0.6797 (t80) cc_final: 0.6559 (t80) REVERT: F 663 MET cc_start: 0.8495 (ttt) cc_final: 0.8048 (tmm) REVERT: F 735 MET cc_start: 0.4776 (mpp) cc_final: 0.4203 (mpp) REVERT: F 758 MET cc_start: 0.3927 (mpt) cc_final: 0.2890 (mmm) REVERT: F 761 ASN cc_start: 0.9216 (OUTLIER) cc_final: 0.8909 (p0) REVERT: G 124 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.6782 (p0) REVERT: G 125 VAL cc_start: 0.8754 (t) cc_final: 0.8511 (t) REVERT: G 634 ASP cc_start: 0.7118 (OUTLIER) cc_final: 0.6359 (p0) REVERT: G 663 MET cc_start: 0.8275 (ttt) cc_final: 0.7867 (tmm) REVERT: G 735 MET cc_start: 0.4975 (OUTLIER) cc_final: 0.4582 (mpp) REVERT: G 761 ASN cc_start: 0.9169 (OUTLIER) cc_final: 0.8819 (p0) REVERT: H 124 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7167 (p0) REVERT: H 125 VAL cc_start: 0.8875 (t) cc_final: 0.8572 (t) REVERT: H 407 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7682 (tm-30) REVERT: H 438 GLU cc_start: 0.8091 (tt0) cc_final: 0.7406 (tt0) REVERT: H 580 PHE cc_start: 0.7170 (t80) cc_final: 0.6841 (t80) REVERT: H 634 ASP cc_start: 0.6867 (OUTLIER) cc_final: 0.6439 (t0) REVERT: H 663 MET cc_start: 0.8448 (ttt) cc_final: 0.7998 (tmm) REVERT: H 761 ASN cc_start: 0.9177 (OUTLIER) cc_final: 0.8825 (p0) REVERT: I 407 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7136 (tm-30) REVERT: I 438 GLU cc_start: 0.8087 (tt0) cc_final: 0.7658 (mt-10) REVERT: I 580 PHE cc_start: 0.6805 (t80) cc_final: 0.6569 (t80) REVERT: I 663 MET cc_start: 0.8499 (ttt) cc_final: 0.8051 (tmm) REVERT: I 735 MET cc_start: 0.4776 (mpp) cc_final: 0.4209 (mpp) REVERT: I 758 MET cc_start: 0.3874 (mpt) cc_final: 0.2771 (mmm) REVERT: I 761 ASN cc_start: 0.9216 (OUTLIER) cc_final: 0.8903 (p0) REVERT: J 103 MET cc_start: 0.7769 (mtt) cc_final: 0.7415 (mtt) REVERT: J 124 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.6778 (p0) REVERT: J 125 VAL cc_start: 0.8747 (t) cc_final: 0.8513 (t) REVERT: J 634 ASP cc_start: 0.7119 (OUTLIER) cc_final: 0.6361 (p0) REVERT: J 663 MET cc_start: 0.8274 (ttt) cc_final: 0.7867 (tmm) REVERT: J 735 MET cc_start: 0.4974 (OUTLIER) cc_final: 0.4580 (mpp) REVERT: J 761 ASN cc_start: 0.9165 (OUTLIER) cc_final: 0.8818 (p0) REVERT: K 124 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7067 (p0) REVERT: K 125 VAL cc_start: 0.8874 (t) cc_final: 0.8570 (t) REVERT: K 407 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7726 (tm-30) REVERT: K 438 GLU cc_start: 0.8060 (tt0) cc_final: 0.7371 (tt0) REVERT: K 580 PHE cc_start: 0.7234 (t80) cc_final: 0.6929 (t80) REVERT: K 634 ASP cc_start: 0.6871 (OUTLIER) cc_final: 0.6441 (t0) REVERT: K 663 MET cc_start: 0.8447 (ttt) cc_final: 0.7999 (tmm) REVERT: K 761 ASN cc_start: 0.9185 (OUTLIER) cc_final: 0.8833 (p0) REVERT: L 407 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7275 (tm-30) REVERT: L 438 GLU cc_start: 0.8053 (tt0) cc_final: 0.7734 (tt0) REVERT: L 580 PHE cc_start: 0.6793 (t80) cc_final: 0.6551 (t80) REVERT: L 663 MET cc_start: 0.8494 (ttt) cc_final: 0.8048 (tmm) REVERT: L 735 MET cc_start: 0.4767 (mpp) cc_final: 0.4199 (mpp) REVERT: L 758 MET cc_start: 0.3904 (mpt) cc_final: 0.2873 (mmm) REVERT: L 761 ASN cc_start: 0.9218 (OUTLIER) cc_final: 0.8911 (p0) outliers start: 225 outliers final: 135 residues processed: 382 average time/residue: 0.5437 time to fit residues: 386.9623 Evaluate side-chains 372 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 205 time to evaluate : 5.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain A residue 761 ASN Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 513 ASN Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain B residue 761 ASN Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 354 ASP Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 496 ASN Chi-restraints excluded: chain C residue 513 ASN Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 634 ASP Chi-restraints excluded: chain C residue 761 ASN Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 412 ASN Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 634 ASP Chi-restraints excluded: chain D residue 735 MET Chi-restraints excluded: chain D residue 761 ASN Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 354 ASP Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 412 ASN Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 513 ASN Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 634 ASP Chi-restraints excluded: chain E residue 761 ASN Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 496 ASN Chi-restraints excluded: chain F residue 513 ASN Chi-restraints excluded: chain F residue 567 LEU Chi-restraints excluded: chain F residue 634 ASP Chi-restraints excluded: chain F residue 761 ASN Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 354 ASP Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 559 VAL Chi-restraints excluded: chain G residue 634 ASP Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 761 ASN Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 127 MET Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 150 ASP Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 354 ASP Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 412 ASN Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 513 ASN Chi-restraints excluded: chain H residue 559 VAL Chi-restraints excluded: chain H residue 634 ASP Chi-restraints excluded: chain H residue 761 ASN Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 150 ASP Chi-restraints excluded: chain I residue 196 THR Chi-restraints excluded: chain I residue 354 ASP Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 449 THR Chi-restraints excluded: chain I residue 496 ASN Chi-restraints excluded: chain I residue 513 ASN Chi-restraints excluded: chain I residue 567 LEU Chi-restraints excluded: chain I residue 634 ASP Chi-restraints excluded: chain I residue 761 ASN Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain J residue 127 MET Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 354 ASP Chi-restraints excluded: chain J residue 379 LEU Chi-restraints excluded: chain J residue 412 ASN Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 559 VAL Chi-restraints excluded: chain J residue 634 ASP Chi-restraints excluded: chain J residue 735 MET Chi-restraints excluded: chain J residue 761 ASN Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 124 ASP Chi-restraints excluded: chain K residue 127 MET Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 150 ASP Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain K residue 354 ASP Chi-restraints excluded: chain K residue 379 LEU Chi-restraints excluded: chain K residue 412 ASN Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 513 ASN Chi-restraints excluded: chain K residue 559 VAL Chi-restraints excluded: chain K residue 634 ASP Chi-restraints excluded: chain K residue 761 ASN Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 196 THR Chi-restraints excluded: chain L residue 354 ASP Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 496 ASN Chi-restraints excluded: chain L residue 513 ASN Chi-restraints excluded: chain L residue 567 LEU Chi-restraints excluded: chain L residue 634 ASP Chi-restraints excluded: chain L residue 761 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 536 optimal weight: 3.9990 chunk 346 optimal weight: 30.0000 chunk 518 optimal weight: 4.9990 chunk 261 optimal weight: 20.0000 chunk 170 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 551 optimal weight: 0.9990 chunk 590 optimal weight: 5.9990 chunk 428 optimal weight: 0.3980 chunk 80 optimal weight: 0.6980 chunk 681 optimal weight: 5.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 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 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 705 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 705 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 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 705 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 69840 Z= 0.191 Angle : 0.560 8.704 94584 Z= 0.293 Chirality : 0.046 0.154 10620 Planarity : 0.003 0.029 12396 Dihedral : 5.426 39.952 9520 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.12 % Favored : 85.88 % Rotamer: Outliers : 2.42 % Allowed : 11.28 % Favored : 86.30 % 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: -4.43 (0.08), residues: 8952 helix: -2.55 (0.21), residues: 384 sheet: -2.72 (0.11), residues: 2004 loop : -3.29 (0.07), residues: 6564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 225 HIS 0.002 0.001 HIS F 276 PHE 0.021 0.001 PHE A 580 TYR 0.012 0.001 TYR D 574 ARG 0.003 0.000 ARG H 402 *********************** 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 380 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 201 time to evaluate : 6.036 Fit side-chains REVERT: A 103 MET cc_start: 0.7614 (mtt) cc_final: 0.7141 (mtt) REVERT: A 124 ASP cc_start: 0.7115 (OUTLIER) cc_final: 0.6579 (p0) REVERT: A 125 VAL cc_start: 0.8695 (t) cc_final: 0.8477 (t) REVERT: A 634 ASP cc_start: 0.7104 (OUTLIER) cc_final: 0.6348 (p0) REVERT: A 663 MET cc_start: 0.8411 (ttt) cc_final: 0.7685 (tmm) REVERT: A 735 MET cc_start: 0.4887 (OUTLIER) cc_final: 0.4355 (mpp) REVERT: A 761 ASN cc_start: 0.9263 (OUTLIER) cc_final: 0.8912 (p0) REVERT: B 124 ASP cc_start: 0.7350 (OUTLIER) cc_final: 0.6867 (p0) REVERT: B 125 VAL cc_start: 0.8850 (t) cc_final: 0.8549 (t) REVERT: B 407 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7379 (tm-30) REVERT: B 580 PHE cc_start: 0.7140 (t80) cc_final: 0.6866 (t80) REVERT: B 663 MET cc_start: 0.8542 (ttt) cc_final: 0.8082 (tmm) REVERT: B 761 ASN cc_start: 0.9197 (OUTLIER) cc_final: 0.8873 (p0) REVERT: C 407 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7033 (tm-30) REVERT: C 438 GLU cc_start: 0.8010 (tt0) cc_final: 0.7626 (mt-10) REVERT: C 663 MET cc_start: 0.8467 (ttt) cc_final: 0.8071 (tmm) REVERT: C 735 MET cc_start: 0.4764 (mpp) cc_final: 0.4184 (mpp) REVERT: C 758 MET cc_start: 0.3812 (mpt) cc_final: 0.2806 (mmm) REVERT: C 761 ASN cc_start: 0.9251 (OUTLIER) cc_final: 0.8856 (p0) REVERT: D 124 ASP cc_start: 0.7118 (OUTLIER) cc_final: 0.6600 (p0) REVERT: D 125 VAL cc_start: 0.8710 (t) cc_final: 0.8482 (t) REVERT: D 634 ASP cc_start: 0.7162 (OUTLIER) cc_final: 0.6410 (p0) REVERT: D 663 MET cc_start: 0.8530 (ttt) cc_final: 0.7802 (tmm) REVERT: D 735 MET cc_start: 0.4938 (OUTLIER) cc_final: 0.4380 (mpp) REVERT: D 761 ASN cc_start: 0.9191 (OUTLIER) cc_final: 0.8832 (p0) REVERT: E 124 ASP cc_start: 0.7338 (OUTLIER) cc_final: 0.6861 (p0) REVERT: E 125 VAL cc_start: 0.8846 (t) cc_final: 0.8542 (t) REVERT: E 407 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7394 (tm-30) REVERT: E 580 PHE cc_start: 0.7123 (t80) cc_final: 0.6849 (t80) REVERT: E 663 MET cc_start: 0.8534 (ttt) cc_final: 0.8065 (tmm) REVERT: E 761 ASN cc_start: 0.9207 (OUTLIER) cc_final: 0.8886 (p0) REVERT: F 407 GLU cc_start: 0.7556 (tm-30) cc_final: 0.7148 (tm-30) REVERT: F 438 GLU cc_start: 0.8006 (tt0) cc_final: 0.7619 (mt-10) REVERT: F 663 MET cc_start: 0.8467 (ttt) cc_final: 0.8070 (tmm) REVERT: F 735 MET cc_start: 0.4763 (mpp) cc_final: 0.4177 (mpp) REVERT: F 758 MET cc_start: 0.3706 (mpt) cc_final: 0.2671 (mmm) REVERT: F 761 ASN cc_start: 0.9251 (OUTLIER) cc_final: 0.8857 (p0) REVERT: G 103 MET cc_start: 0.7686 (mtt) cc_final: 0.7237 (mtt) REVERT: G 124 ASP cc_start: 0.7117 (OUTLIER) cc_final: 0.6620 (p0) REVERT: G 125 VAL cc_start: 0.8715 (t) cc_final: 0.8488 (t) REVERT: G 634 ASP cc_start: 0.7171 (OUTLIER) cc_final: 0.6417 (p0) REVERT: G 663 MET cc_start: 0.8528 (ttt) cc_final: 0.7801 (tmm) REVERT: G 735 MET cc_start: 0.4945 (OUTLIER) cc_final: 0.4385 (mpp) REVERT: G 761 ASN cc_start: 0.9190 (OUTLIER) cc_final: 0.8832 (p0) REVERT: H 124 ASP cc_start: 0.7367 (OUTLIER) cc_final: 0.6879 (p0) REVERT: H 125 VAL cc_start: 0.8849 (t) cc_final: 0.8547 (t) REVERT: H 407 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7399 (tm-30) REVERT: H 580 PHE cc_start: 0.7148 (t80) cc_final: 0.6846 (t80) REVERT: H 663 MET cc_start: 0.8544 (ttt) cc_final: 0.8084 (tmm) REVERT: H 761 ASN cc_start: 0.9207 (OUTLIER) cc_final: 0.8885 (p0) REVERT: I 407 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7032 (tm-30) REVERT: I 438 GLU cc_start: 0.8007 (tt0) cc_final: 0.7620 (mt-10) REVERT: I 663 MET cc_start: 0.8476 (ttt) cc_final: 0.8078 (tmm) REVERT: I 735 MET cc_start: 0.4774 (mpp) cc_final: 0.4193 (mpp) REVERT: I 758 MET cc_start: 0.3833 (mpt) cc_final: 0.2826 (mmm) REVERT: I 761 ASN cc_start: 0.9249 (OUTLIER) cc_final: 0.8853 (p0) REVERT: J 124 ASP cc_start: 0.7116 (OUTLIER) cc_final: 0.6607 (p0) REVERT: J 125 VAL cc_start: 0.8714 (t) cc_final: 0.8484 (t) REVERT: J 634 ASP cc_start: 0.7169 (OUTLIER) cc_final: 0.6418 (p0) REVERT: J 663 MET cc_start: 0.8527 (ttt) cc_final: 0.7800 (tmm) REVERT: J 735 MET cc_start: 0.4940 (OUTLIER) cc_final: 0.4382 (mpp) REVERT: J 761 ASN cc_start: 0.9192 (OUTLIER) cc_final: 0.8834 (p0) REVERT: K 124 ASP cc_start: 0.7350 (OUTLIER) cc_final: 0.6875 (p0) REVERT: K 125 VAL cc_start: 0.8853 (t) cc_final: 0.8549 (t) REVERT: K 407 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7221 (tm-30) REVERT: K 580 PHE cc_start: 0.7126 (t80) cc_final: 0.6855 (t80) REVERT: K 663 MET cc_start: 0.8539 (ttt) cc_final: 0.8069 (tmm) REVERT: K 761 ASN cc_start: 0.9204 (OUTLIER) cc_final: 0.8882 (p0) REVERT: L 407 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7148 (tm-30) REVERT: L 438 GLU cc_start: 0.8006 (tt0) cc_final: 0.7615 (mt-10) REVERT: L 663 MET cc_start: 0.8465 (ttt) cc_final: 0.8069 (tmm) REVERT: L 735 MET cc_start: 0.4759 (mpp) cc_final: 0.4175 (mpp) REVERT: L 758 MET cc_start: 0.3686 (mpt) cc_final: 0.2649 (mmm) REVERT: L 761 ASN cc_start: 0.9254 (OUTLIER) cc_final: 0.8861 (p0) outliers start: 179 outliers final: 119 residues processed: 338 average time/residue: 0.5428 time to fit residues: 341.4292 Evaluate side-chains 343 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 196 time to evaluate : 5.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain A residue 761 ASN Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 513 ASN Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain B residue 761 ASN Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 496 ASN Chi-restraints excluded: chain C residue 513 ASN Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 634 ASP Chi-restraints excluded: chain C residue 761 ASN Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 634 ASP Chi-restraints excluded: chain D residue 735 MET Chi-restraints excluded: chain D residue 761 ASN Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 354 ASP Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 513 ASN Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 634 ASP Chi-restraints excluded: chain E residue 761 ASN Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 496 ASN Chi-restraints excluded: chain F residue 513 ASN Chi-restraints excluded: chain F residue 567 LEU Chi-restraints excluded: chain F residue 634 ASP Chi-restraints excluded: chain F residue 751 MET Chi-restraints excluded: chain F residue 761 ASN Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 354 ASP Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 559 VAL Chi-restraints excluded: chain G residue 634 ASP Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 761 ASN Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 150 ASP Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 354 ASP Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 412 ASN Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 513 ASN Chi-restraints excluded: chain H residue 559 VAL Chi-restraints excluded: chain H residue 634 ASP Chi-restraints excluded: chain H residue 761 ASN Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 150 ASP Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 496 ASN Chi-restraints excluded: chain I residue 513 ASN Chi-restraints excluded: chain I residue 567 LEU Chi-restraints excluded: chain I residue 634 ASP Chi-restraints excluded: chain I residue 761 ASN Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain J residue 127 MET Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 354 ASP Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 559 VAL Chi-restraints excluded: chain J residue 634 ASP Chi-restraints excluded: chain J residue 735 MET Chi-restraints excluded: chain J residue 761 ASN Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 124 ASP Chi-restraints excluded: chain K residue 127 MET Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 150 ASP Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain K residue 354 ASP Chi-restraints excluded: chain K residue 379 LEU Chi-restraints excluded: chain K residue 412 ASN Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 513 ASN Chi-restraints excluded: chain K residue 559 VAL Chi-restraints excluded: chain K residue 634 ASP Chi-restraints excluded: chain K residue 761 ASN Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 496 ASN Chi-restraints excluded: chain L residue 513 ASN Chi-restraints excluded: chain L residue 567 LEU Chi-restraints excluded: chain L residue 634 ASP Chi-restraints excluded: chain L residue 751 MET Chi-restraints excluded: chain L residue 761 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 789 optimal weight: 5.9990 chunk 831 optimal weight: 0.1980 chunk 758 optimal weight: 9.9990 chunk 808 optimal weight: 40.0000 chunk 830 optimal weight: 20.0000 chunk 486 optimal weight: 20.0000 chunk 352 optimal weight: 20.0000 chunk 634 optimal weight: 5.9990 chunk 248 optimal weight: 8.9990 chunk 730 optimal weight: 9.9990 chunk 764 optimal weight: 10.0000 overall best weight: 6.2388 ------------------------------------------------------------------------------- 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 ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN ** 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** E 628 ASN ** E 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 731 ASN ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 628 ASN ** H 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** I 731 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 628 ASN ** K 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 731 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 69840 Z= 0.462 Angle : 0.713 9.235 94584 Z= 0.384 Chirality : 0.051 0.175 10620 Planarity : 0.004 0.029 12396 Dihedral : 6.339 44.300 9520 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.44 % Favored : 79.56 % Rotamer: Outliers : 2.57 % Allowed : 11.45 % Favored : 85.98 % 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: -4.81 (0.08), residues: 8952 helix: -2.64 (0.20), residues: 384 sheet: -3.44 (0.10), residues: 2460 loop : -3.32 (0.07), residues: 6108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 225 HIS 0.006 0.001 HIS A 262 PHE 0.029 0.003 PHE L 488 TYR 0.012 0.002 TYR L 574 ARG 0.006 0.001 ARG G 402 *********************** 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 400 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 210 time to evaluate : 5.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.7357 (OUTLIER) cc_final: 0.6927 (p0) REVERT: A 125 VAL cc_start: 0.8812 (t) cc_final: 0.8567 (t) REVERT: A 634 ASP cc_start: 0.7186 (OUTLIER) cc_final: 0.6406 (p0) REVERT: A 663 MET cc_start: 0.8240 (ttt) cc_final: 0.7890 (tmm) REVERT: A 735 MET cc_start: 0.4962 (OUTLIER) cc_final: 0.4531 (mpp) REVERT: A 761 ASN cc_start: 0.9200 (OUTLIER) cc_final: 0.8868 (p0) REVERT: B 124 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7241 (p0) REVERT: B 125 VAL cc_start: 0.8901 (t) cc_final: 0.8559 (t) REVERT: B 438 GLU cc_start: 0.8172 (tt0) cc_final: 0.7514 (tt0) REVERT: B 580 PHE cc_start: 0.7065 (t80) cc_final: 0.6825 (t80) REVERT: B 663 MET cc_start: 0.8294 (ttt) cc_final: 0.7896 (tmm) REVERT: B 761 ASN cc_start: 0.9149 (OUTLIER) cc_final: 0.8825 (p0) REVERT: C 438 GLU cc_start: 0.8190 (tt0) cc_final: 0.7870 (tt0) REVERT: C 663 MET cc_start: 0.8372 (ttt) cc_final: 0.7940 (tmm) REVERT: C 735 MET cc_start: 0.4922 (mpp) cc_final: 0.4354 (mpp) REVERT: C 761 ASN cc_start: 0.9199 (OUTLIER) cc_final: 0.8892 (p0) REVERT: D 124 ASP cc_start: 0.7345 (OUTLIER) cc_final: 0.6968 (p0) REVERT: D 125 VAL cc_start: 0.8824 (t) cc_final: 0.8568 (t) REVERT: D 634 ASP cc_start: 0.7177 (OUTLIER) cc_final: 0.6406 (p0) REVERT: D 663 MET cc_start: 0.8224 (ttt) cc_final: 0.7858 (tmm) REVERT: D 735 MET cc_start: 0.5045 (OUTLIER) cc_final: 0.4583 (mpp) REVERT: D 761 ASN cc_start: 0.9185 (OUTLIER) cc_final: 0.8826 (p0) REVERT: E 124 ASP cc_start: 0.7533 (OUTLIER) cc_final: 0.7233 (p0) REVERT: E 125 VAL cc_start: 0.8895 (t) cc_final: 0.8551 (t) REVERT: E 580 PHE cc_start: 0.7052 (t80) cc_final: 0.6810 (t80) REVERT: E 663 MET cc_start: 0.8288 (ttt) cc_final: 0.7894 (tmm) REVERT: E 761 ASN cc_start: 0.9190 (OUTLIER) cc_final: 0.8877 (p0) REVERT: F 438 GLU cc_start: 0.8187 (tt0) cc_final: 0.7885 (tt0) REVERT: F 663 MET cc_start: 0.8390 (ttt) cc_final: 0.7952 (tmm) REVERT: F 735 MET cc_start: 0.4941 (mpp) cc_final: 0.4364 (mpp) REVERT: F 761 ASN cc_start: 0.9192 (OUTLIER) cc_final: 0.8878 (p0) REVERT: G 124 ASP cc_start: 0.7331 (OUTLIER) cc_final: 0.6939 (p0) REVERT: G 125 VAL cc_start: 0.8814 (t) cc_final: 0.8565 (t) REVERT: G 634 ASP cc_start: 0.7186 (OUTLIER) cc_final: 0.6410 (p0) REVERT: G 663 MET cc_start: 0.8220 (ttt) cc_final: 0.7856 (tmm) REVERT: G 735 MET cc_start: 0.5046 (OUTLIER) cc_final: 0.4587 (mpp) REVERT: G 761 ASN cc_start: 0.9185 (OUTLIER) cc_final: 0.8826 (p0) REVERT: H 124 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7255 (p0) REVERT: H 125 VAL cc_start: 0.8899 (t) cc_final: 0.8557 (t) REVERT: H 580 PHE cc_start: 0.7057 (t80) cc_final: 0.6810 (t80) REVERT: H 663 MET cc_start: 0.8295 (ttt) cc_final: 0.7897 (tmm) REVERT: H 761 ASN cc_start: 0.9191 (OUTLIER) cc_final: 0.8878 (p0) REVERT: I 438 GLU cc_start: 0.8187 (tt0) cc_final: 0.7865 (tt0) REVERT: I 663 MET cc_start: 0.8382 (ttt) cc_final: 0.7946 (tmm) REVERT: I 735 MET cc_start: 0.4934 (mpp) cc_final: 0.4365 (mpp) REVERT: I 761 ASN cc_start: 0.9198 (OUTLIER) cc_final: 0.8891 (p0) REVERT: J 124 ASP cc_start: 0.7345 (OUTLIER) cc_final: 0.6954 (p0) REVERT: J 125 VAL cc_start: 0.8815 (t) cc_final: 0.8560 (t) REVERT: J 634 ASP cc_start: 0.7187 (OUTLIER) cc_final: 0.6415 (p0) REVERT: J 663 MET cc_start: 0.8216 (ttt) cc_final: 0.7853 (tmm) REVERT: J 735 MET cc_start: 0.5043 (OUTLIER) cc_final: 0.4584 (mpp) REVERT: J 761 ASN cc_start: 0.9185 (OUTLIER) cc_final: 0.8827 (p0) REVERT: K 124 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7241 (p0) REVERT: K 125 VAL cc_start: 0.8908 (t) cc_final: 0.8572 (t) REVERT: K 438 GLU cc_start: 0.8188 (tt0) cc_final: 0.7502 (tt0) REVERT: K 580 PHE cc_start: 0.7055 (t80) cc_final: 0.6815 (t80) REVERT: K 663 MET cc_start: 0.8295 (ttt) cc_final: 0.7899 (tmm) REVERT: K 761 ASN cc_start: 0.9187 (OUTLIER) cc_final: 0.8873 (p0) REVERT: L 438 GLU cc_start: 0.8184 (tt0) cc_final: 0.7881 (tt0) REVERT: L 663 MET cc_start: 0.8386 (ttt) cc_final: 0.7951 (tmm) REVERT: L 735 MET cc_start: 0.4938 (mpp) cc_final: 0.4363 (mpp) REVERT: L 761 ASN cc_start: 0.9194 (OUTLIER) cc_final: 0.8880 (p0) outliers start: 190 outliers final: 137 residues processed: 356 average time/residue: 0.5495 time to fit residues: 362.5131 Evaluate side-chains 354 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 189 time to evaluate : 5.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain A residue 761 ASN Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain B residue 761 ASN Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 496 ASN Chi-restraints excluded: chain C residue 513 ASN Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 634 ASP Chi-restraints excluded: chain C residue 751 MET Chi-restraints excluded: chain C residue 761 ASN Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 412 ASN Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 634 ASP Chi-restraints excluded: chain D residue 735 MET Chi-restraints excluded: chain D residue 761 ASN Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 354 ASP Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 412 ASN Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 634 ASP Chi-restraints excluded: chain E residue 761 ASN Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 496 ASN Chi-restraints excluded: chain F residue 513 ASN Chi-restraints excluded: chain F residue 567 LEU Chi-restraints excluded: chain F residue 634 ASP Chi-restraints excluded: chain F residue 751 MET Chi-restraints excluded: chain F residue 761 ASN Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 354 ASP Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 559 VAL Chi-restraints excluded: chain G residue 634 ASP Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 761 ASN Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 127 MET Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 150 ASP Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 354 ASP Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 412 ASN Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 559 VAL Chi-restraints excluded: chain H residue 634 ASP Chi-restraints excluded: chain H residue 761 ASN Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 150 ASP Chi-restraints excluded: chain I residue 379 LEU Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 449 THR Chi-restraints excluded: chain I residue 496 ASN Chi-restraints excluded: chain I residue 513 ASN Chi-restraints excluded: chain I residue 567 LEU Chi-restraints excluded: chain I residue 634 ASP Chi-restraints excluded: chain I residue 751 MET Chi-restraints excluded: chain I residue 761 ASN Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain J residue 127 MET Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 354 ASP Chi-restraints excluded: chain J residue 379 LEU Chi-restraints excluded: chain J residue 412 ASN Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 559 VAL Chi-restraints excluded: chain J residue 634 ASP Chi-restraints excluded: chain J residue 735 MET Chi-restraints excluded: chain J residue 761 ASN Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 124 ASP Chi-restraints excluded: chain K residue 127 MET Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 150 ASP Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain K residue 354 ASP Chi-restraints excluded: chain K residue 379 LEU Chi-restraints excluded: chain K residue 412 ASN Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 559 VAL Chi-restraints excluded: chain K residue 634 ASP Chi-restraints excluded: chain K residue 761 ASN Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 379 LEU Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 496 ASN Chi-restraints excluded: chain L residue 513 ASN Chi-restraints excluded: chain L residue 567 LEU Chi-restraints excluded: chain L residue 634 ASP Chi-restraints excluded: chain L residue 751 MET Chi-restraints excluded: chain L residue 761 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 805 optimal weight: 6.9990 chunk 530 optimal weight: 4.9990 chunk 854 optimal weight: 0.9980 chunk 521 optimal weight: 10.0000 chunk 405 optimal weight: 5.9990 chunk 594 optimal weight: 0.0030 chunk 896 optimal weight: 5.9990 chunk 825 optimal weight: 0.9990 chunk 713 optimal weight: 4.9990 chunk 74 optimal weight: 20.0000 chunk 551 optimal weight: 1.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- 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 705 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 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 628 ASN ** E 705 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 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 705 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 69840 Z= 0.179 Angle : 0.570 8.745 94584 Z= 0.299 Chirality : 0.046 0.152 10620 Planarity : 0.002 0.027 12396 Dihedral : 5.528 39.623 9520 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.13 % Favored : 87.87 % Rotamer: Outliers : 2.28 % Allowed : 11.86 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.42 (0.08), residues: 8952 helix: -2.59 (0.21), residues: 384 sheet: -2.76 (0.11), residues: 2124 loop : -3.26 (0.07), residues: 6444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 225 HIS 0.002 0.001 HIS K 276 PHE 0.023 0.001 PHE C 580 TYR 0.012 0.001 TYR I 574 ARG 0.003 0.000 ARG E 402 ********************** 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 369 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 200 time to evaluate : 7.872 Fit side-chains REVERT: A 103 MET cc_start: 0.7689 (mtt) cc_final: 0.7271 (mtt) REVERT: A 124 ASP cc_start: 0.7204 (OUTLIER) cc_final: 0.6643 (p0) REVERT: A 125 VAL cc_start: 0.8679 (t) cc_final: 0.8440 (t) REVERT: A 634 ASP cc_start: 0.7117 (OUTLIER) cc_final: 0.6335 (p0) REVERT: A 663 MET cc_start: 0.8364 (ttt) cc_final: 0.7953 (tmm) REVERT: A 735 MET cc_start: 0.4863 (OUTLIER) cc_final: 0.4327 (mpp) REVERT: A 761 ASN cc_start: 0.9251 (OUTLIER) cc_final: 0.8892 (p0) REVERT: B 124 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.6975 (p0) REVERT: B 125 VAL cc_start: 0.8814 (t) cc_final: 0.8508 (t) REVERT: B 407 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7281 (tm-30) REVERT: B 438 GLU cc_start: 0.8028 (tt0) cc_final: 0.7480 (tt0) REVERT: B 663 MET cc_start: 0.8392 (ttt) cc_final: 0.7926 (tmm) REVERT: B 761 ASN cc_start: 0.9202 (OUTLIER) cc_final: 0.8890 (p0) REVERT: C 407 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7079 (tm-30) REVERT: C 438 GLU cc_start: 0.8000 (tt0) cc_final: 0.7591 (mt-10) REVERT: C 663 MET cc_start: 0.8411 (ttt) cc_final: 0.8035 (tmm) REVERT: C 735 MET cc_start: 0.4976 (mpp) cc_final: 0.4425 (mpp) REVERT: C 758 MET cc_start: 0.3656 (mpt) cc_final: 0.2568 (mmm) REVERT: C 761 ASN cc_start: 0.9248 (OUTLIER) cc_final: 0.8842 (p0) REVERT: D 103 MET cc_start: 0.7735 (mtt) cc_final: 0.7434 (mtt) REVERT: D 124 ASP cc_start: 0.7194 (OUTLIER) cc_final: 0.6656 (p0) REVERT: D 125 VAL cc_start: 0.8687 (t) cc_final: 0.8460 (t) REVERT: D 634 ASP cc_start: 0.7117 (OUTLIER) cc_final: 0.6332 (p0) REVERT: D 663 MET cc_start: 0.8483 (ttt) cc_final: 0.8072 (tmm) REVERT: D 735 MET cc_start: 0.4768 (OUTLIER) cc_final: 0.4272 (mpp) REVERT: D 761 ASN cc_start: 0.9188 (OUTLIER) cc_final: 0.8795 (p0) REVERT: E 124 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.7039 (p0) REVERT: E 125 VAL cc_start: 0.8811 (t) cc_final: 0.8504 (t) REVERT: E 407 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7279 (tm-30) REVERT: E 438 GLU cc_start: 0.8033 (tt0) cc_final: 0.7438 (tt0) REVERT: E 663 MET cc_start: 0.8393 (ttt) cc_final: 0.7929 (tmm) REVERT: E 761 ASN cc_start: 0.9228 (OUTLIER) cc_final: 0.8913 (p0) REVERT: F 407 GLU cc_start: 0.7466 (tm-30) cc_final: 0.7016 (tm-30) REVERT: F 438 GLU cc_start: 0.8006 (tt0) cc_final: 0.7603 (mt-10) REVERT: F 663 MET cc_start: 0.8421 (ttt) cc_final: 0.8042 (tmm) REVERT: F 735 MET cc_start: 0.4967 (mpp) cc_final: 0.4420 (mpp) REVERT: F 758 MET cc_start: 0.3639 (mpt) cc_final: 0.2553 (mmm) REVERT: F 761 ASN cc_start: 0.9247 (OUTLIER) cc_final: 0.8843 (p0) REVERT: G 103 MET cc_start: 0.7718 (mtt) cc_final: 0.7298 (mtt) REVERT: G 124 ASP cc_start: 0.7192 (OUTLIER) cc_final: 0.6658 (p0) REVERT: G 125 VAL cc_start: 0.8699 (t) cc_final: 0.8463 (t) REVERT: G 634 ASP cc_start: 0.7121 (OUTLIER) cc_final: 0.6337 (p0) REVERT: G 663 MET cc_start: 0.8437 (ttt) cc_final: 0.8034 (tmm) REVERT: G 735 MET cc_start: 0.4770 (OUTLIER) cc_final: 0.4273 (mpp) REVERT: G 761 ASN cc_start: 0.9189 (OUTLIER) cc_final: 0.8797 (p0) REVERT: H 124 ASP cc_start: 0.7468 (OUTLIER) cc_final: 0.7046 (p0) REVERT: H 125 VAL cc_start: 0.8816 (t) cc_final: 0.8509 (t) REVERT: H 407 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7388 (tm-30) REVERT: H 438 GLU cc_start: 0.8063 (tt0) cc_final: 0.7414 (tt0) REVERT: H 663 MET cc_start: 0.8460 (ttt) cc_final: 0.7983 (tmm) REVERT: H 761 ASN cc_start: 0.9227 (OUTLIER) cc_final: 0.8912 (p0) REVERT: I 407 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7101 (tm-30) REVERT: I 438 GLU cc_start: 0.7997 (tt0) cc_final: 0.7578 (mt-10) REVERT: I 663 MET cc_start: 0.8427 (ttt) cc_final: 0.8053 (tmm) REVERT: I 735 MET cc_start: 0.4985 (mpp) cc_final: 0.4432 (mpp) REVERT: I 758 MET cc_start: 0.3679 (mpt) cc_final: 0.2588 (mmm) REVERT: I 761 ASN cc_start: 0.9227 (OUTLIER) cc_final: 0.8807 (p0) REVERT: J 103 MET cc_start: 0.7731 (mtt) cc_final: 0.7429 (mtt) REVERT: J 124 ASP cc_start: 0.7203 (OUTLIER) cc_final: 0.6643 (p0) REVERT: J 125 VAL cc_start: 0.8675 (t) cc_final: 0.8436 (t) REVERT: J 634 ASP cc_start: 0.7121 (OUTLIER) cc_final: 0.6341 (p0) REVERT: J 663 MET cc_start: 0.8479 (ttt) cc_final: 0.8071 (tmm) REVERT: J 735 MET cc_start: 0.4769 (OUTLIER) cc_final: 0.4272 (mpp) REVERT: J 761 ASN cc_start: 0.9190 (OUTLIER) cc_final: 0.8798 (p0) REVERT: K 124 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.7038 (p0) REVERT: K 125 VAL cc_start: 0.8817 (t) cc_final: 0.8509 (t) REVERT: K 407 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7288 (tm-30) REVERT: K 438 GLU cc_start: 0.8023 (tt0) cc_final: 0.7479 (tt0) REVERT: K 663 MET cc_start: 0.8394 (ttt) cc_final: 0.7929 (tmm) REVERT: K 761 ASN cc_start: 0.9225 (OUTLIER) cc_final: 0.8909 (p0) REVERT: L 407 GLU cc_start: 0.7462 (tm-30) cc_final: 0.7012 (tm-30) REVERT: L 438 GLU cc_start: 0.8003 (tt0) cc_final: 0.7604 (mt-10) REVERT: L 663 MET cc_start: 0.8420 (ttt) cc_final: 0.8041 (tmm) REVERT: L 735 MET cc_start: 0.4964 (mpp) cc_final: 0.4419 (mpp) REVERT: L 758 MET cc_start: 0.3615 (mpt) cc_final: 0.2533 (mmm) REVERT: L 761 ASN cc_start: 0.9250 (OUTLIER) cc_final: 0.8845 (p0) outliers start: 169 outliers final: 126 residues processed: 322 average time/residue: 0.5531 time to fit residues: 332.0289 Evaluate side-chains 346 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 192 time to evaluate : 5.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain A residue 761 ASN Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain B residue 761 ASN Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 496 ASN Chi-restraints excluded: chain C residue 513 ASN Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 634 ASP Chi-restraints excluded: chain C residue 751 MET Chi-restraints excluded: chain C residue 761 ASN Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 412 ASN Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 634 ASP Chi-restraints excluded: chain D residue 735 MET Chi-restraints excluded: chain D residue 761 ASN Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 354 ASP Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 412 ASN Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 634 ASP Chi-restraints excluded: chain E residue 761 ASN Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 496 ASN Chi-restraints excluded: chain F residue 513 ASN Chi-restraints excluded: chain F residue 567 LEU Chi-restraints excluded: chain F residue 634 ASP Chi-restraints excluded: chain F residue 751 MET Chi-restraints excluded: chain F residue 761 ASN Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 354 ASP Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 559 VAL Chi-restraints excluded: chain G residue 634 ASP Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 761 ASN Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 127 MET Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 150 ASP Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 354 ASP Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 559 VAL Chi-restraints excluded: chain H residue 634 ASP Chi-restraints excluded: chain H residue 761 ASN Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 150 ASP Chi-restraints excluded: chain I residue 379 LEU Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 449 THR Chi-restraints excluded: chain I residue 496 ASN Chi-restraints excluded: chain I residue 513 ASN Chi-restraints excluded: chain I residue 567 LEU Chi-restraints excluded: chain I residue 634 ASP Chi-restraints excluded: chain I residue 751 MET Chi-restraints excluded: chain I residue 761 ASN Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain J residue 127 MET Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 354 ASP Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 559 VAL Chi-restraints excluded: chain J residue 634 ASP Chi-restraints excluded: chain J residue 735 MET Chi-restraints excluded: chain J residue 761 ASN Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 124 ASP Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 150 ASP Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain K residue 354 ASP Chi-restraints excluded: chain K residue 379 LEU Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 559 VAL Chi-restraints excluded: chain K residue 634 ASP Chi-restraints excluded: chain K residue 761 ASN Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 379 LEU Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 496 ASN Chi-restraints excluded: chain L residue 513 ASN Chi-restraints excluded: chain L residue 567 LEU Chi-restraints excluded: chain L residue 634 ASP Chi-restraints excluded: chain L residue 751 MET Chi-restraints excluded: chain L residue 761 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 437 optimal weight: 0.0470 chunk 567 optimal weight: 9.9990 chunk 760 optimal weight: 8.9990 chunk 218 optimal weight: 10.0000 chunk 658 optimal weight: 30.0000 chunk 105 optimal weight: 9.9990 chunk 198 optimal weight: 9.9990 chunk 715 optimal weight: 10.0000 chunk 299 optimal weight: 30.0000 chunk 734 optimal weight: 0.0070 chunk 90 optimal weight: 20.0000 overall best weight: 5.8102 ------------------------------------------------------------------------------- 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 ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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** E 628 ASN ** E 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 ASN ** 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** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 628 ASN ** H 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 ** K 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.091884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.051258 restraints weight = 178882.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.052348 restraints weight = 120778.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.052950 restraints weight = 96138.351| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 69840 Z= 0.432 Angle : 0.697 8.429 94584 Z= 0.374 Chirality : 0.050 0.166 10620 Planarity : 0.004 0.028 12396 Dihedral : 6.270 43.833 9520 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.93 % Favored : 79.07 % Rotamer: Outliers : 2.50 % Allowed : 11.84 % Favored : 85.66 % 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: -4.77 (0.08), residues: 8952 helix: -2.57 (0.20), residues: 384 sheet: -3.40 (0.10), residues: 2460 loop : -3.30 (0.07), residues: 6108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 225 HIS 0.005 0.001 HIS A 262 PHE 0.026 0.002 PHE L 488 TYR 0.012 0.002 TYR L 574 ARG 0.006 0.001 ARG A 402 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9532.63 seconds wall clock time: 173 minutes 46.02 seconds (10426.02 seconds total)