Starting phenix.real_space_refine (version: 1.21rc1) on Tue May 16 07:54:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w68_8778/05_2023/5w68_8778.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w68_8778/05_2023/5w68_8778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w68_8778/05_2023/5w68_8778.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w68_8778/05_2023/5w68_8778.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w68_8778/05_2023/5w68_8778.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w68_8778/05_2023/5w68_8778.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.050 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 165 5.16 5 C 24735 2.51 5 N 6750 2.21 5 O 7740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 560": "NH1" <-> "NH2" Residue "A ARG 637": "NH1" <-> "NH2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B ARG 637": "NH1" <-> "NH2" Residue "C ARG 560": "NH1" <-> "NH2" Residue "C ARG 637": "NH1" <-> "NH2" Residue "D ARG 560": "NH1" <-> "NH2" Residue "D ARG 637": "NH1" <-> "NH2" Residue "E ARG 560": "NH1" <-> "NH2" Residue "E ARG 637": "NH1" <-> "NH2" Residue "F ARG 560": "NH1" <-> "NH2" Residue "F ARG 637": "NH1" <-> "NH2" Residue "G ARG 560": "NH1" <-> "NH2" Residue "G ARG 637": "NH1" <-> "NH2" Residue "H ARG 560": "NH1" <-> "NH2" Residue "H ARG 637": "NH1" <-> "NH2" Residue "I ARG 560": "NH1" <-> "NH2" Residue "I ARG 637": "NH1" <-> "NH2" Residue "J ARG 560": "NH1" <-> "NH2" Residue "J ARG 637": "NH1" <-> "NH2" Residue "K ARG 560": "NH1" <-> "NH2" Residue "K ARG 637": "NH1" <-> "NH2" Residue "L ARG 560": "NH1" <-> "NH2" Residue "L ARG 637": "NH1" <-> "NH2" Residue "M ARG 560": "NH1" <-> "NH2" Residue "M ARG 637": "NH1" <-> "NH2" Residue "N ARG 560": "NH1" <-> "NH2" Residue "N ARG 637": "NH1" <-> "NH2" Residue "O ARG 560": "NH1" <-> "NH2" Residue "O ARG 637": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 39390 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2626 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain breaks: 3 Chain: "B" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2626 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain breaks: 3 Chain: "C" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2626 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain breaks: 3 Chain: "D" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2626 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain breaks: 3 Chain: "E" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2626 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain breaks: 3 Chain: "F" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2626 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain breaks: 3 Chain: "G" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2626 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain breaks: 3 Chain: "H" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2626 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain breaks: 3 Chain: "I" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2626 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain breaks: 3 Chain: "J" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2626 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain breaks: 3 Chain: "K" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2626 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain breaks: 3 Chain: "L" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2626 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain breaks: 3 Chain: "M" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2626 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain breaks: 3 Chain: "N" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2626 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain breaks: 3 Chain: "O" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2626 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain breaks: 3 Time building chain proxies: 19.39, per 1000 atoms: 0.49 Number of scatterers: 39390 At special positions: 0 Unit cell: (159, 160.06, 130.38, 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 165 16.00 O 7740 8.00 N 6750 7.00 C 24735 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.54 Conformation dependent library (CDL) restraints added in 6.6 seconds 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9600 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 76 sheets defined 23.4% alpha, 55.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.71 Creating SS restraints... Processing helix chain 'A' and resid 293 through 309 removed outlier: 3.742A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLN A 303 " --> pdb=" O ASP A 299 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR A 307 " --> pdb=" O GLN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 357 removed outlier: 3.571A pdb=" N GLN A 347 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER A 348 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 411 Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 600 through 605 removed outlier: 3.578A pdb=" N LEU A 603 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS A 605 " --> pdb=" O ASN A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 652 removed outlier: 3.716A pdb=" N GLN A 652 " --> pdb=" O TYR A 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 309 removed outlier: 3.742A pdb=" N LEU B 297 " --> pdb=" O LYS B 293 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLN B 303 " --> pdb=" O ASP B 299 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR B 307 " --> pdb=" O GLN B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 357 removed outlier: 3.570A pdb=" N GLN B 347 " --> pdb=" O GLN B 343 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER B 348 " --> pdb=" O ASP B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 411 Processing helix chain 'B' and resid 439 through 444 Processing helix chain 'B' and resid 600 through 605 removed outlier: 3.578A pdb=" N LEU B 603 " --> pdb=" O ILE B 600 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS B 605 " --> pdb=" O ASN B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 652 removed outlier: 3.715A pdb=" N GLN B 652 " --> pdb=" O TYR B 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 309 removed outlier: 3.742A pdb=" N LEU C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLN C 303 " --> pdb=" O ASP C 299 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL C 304 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY C 306 " --> pdb=" O LYS C 302 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR C 307 " --> pdb=" O GLN C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 357 removed outlier: 3.571A pdb=" N GLN C 347 " --> pdb=" O GLN C 343 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER C 348 " --> pdb=" O ASP C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 411 Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 600 through 605 removed outlier: 3.577A pdb=" N LEU C 603 " --> pdb=" O ILE C 600 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS C 605 " --> pdb=" O ASN C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 652 removed outlier: 3.717A pdb=" N GLN C 652 " --> pdb=" O TYR C 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 309 removed outlier: 3.742A pdb=" N LEU D 297 " --> pdb=" O LYS D 293 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLN D 303 " --> pdb=" O ASP D 299 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL D 304 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY D 306 " --> pdb=" O LYS D 302 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR D 307 " --> pdb=" O GLN D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 357 removed outlier: 3.571A pdb=" N GLN D 347 " --> pdb=" O GLN D 343 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER D 348 " --> pdb=" O ASP D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 411 Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 600 through 605 removed outlier: 3.578A pdb=" N LEU D 603 " --> pdb=" O ILE D 600 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS D 605 " --> pdb=" O ASN D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 652 removed outlier: 3.716A pdb=" N GLN D 652 " --> pdb=" O TYR D 648 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 309 removed outlier: 3.742A pdb=" N LEU E 297 " --> pdb=" O LYS E 293 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLN E 303 " --> pdb=" O ASP E 299 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL E 304 " --> pdb=" O VAL E 300 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER E 305 " --> pdb=" O LEU E 301 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY E 306 " --> pdb=" O LYS E 302 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR E 307 " --> pdb=" O GLN E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 357 removed outlier: 3.571A pdb=" N GLN E 347 " --> pdb=" O GLN E 343 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER E 348 " --> pdb=" O ASP E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 411 Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 600 through 605 removed outlier: 3.578A pdb=" N LEU E 603 " --> pdb=" O ILE E 600 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS E 605 " --> pdb=" O ASN E 602 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 652 removed outlier: 3.716A pdb=" N GLN E 652 " --> pdb=" O TYR E 648 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 309 removed outlier: 3.742A pdb=" N LEU F 297 " --> pdb=" O LYS F 293 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLN F 303 " --> pdb=" O ASP F 299 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL F 304 " --> pdb=" O VAL F 300 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER F 305 " --> pdb=" O LEU F 301 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY F 306 " --> pdb=" O LYS F 302 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR F 307 " --> pdb=" O GLN F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 357 removed outlier: 3.572A pdb=" N GLN F 347 " --> pdb=" O GLN F 343 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER F 348 " --> pdb=" O ASP F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 411 Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 600 through 605 removed outlier: 3.577A pdb=" N LEU F 603 " --> pdb=" O ILE F 600 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS F 605 " --> pdb=" O ASN F 602 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 652 removed outlier: 3.716A pdb=" N GLN F 652 " --> pdb=" O TYR F 648 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 309 removed outlier: 3.742A pdb=" N LEU G 297 " --> pdb=" O LYS G 293 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLN G 303 " --> pdb=" O ASP G 299 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL G 304 " --> pdb=" O VAL G 300 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER G 305 " --> pdb=" O LEU G 301 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY G 306 " --> pdb=" O LYS G 302 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR G 307 " --> pdb=" O GLN G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 357 removed outlier: 3.571A pdb=" N GLN G 347 " --> pdb=" O GLN G 343 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER G 348 " --> pdb=" O ASP G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 401 through 411 Processing helix chain 'G' and resid 439 through 444 Processing helix chain 'G' and resid 600 through 605 removed outlier: 3.578A pdb=" N LEU G 603 " --> pdb=" O ILE G 600 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS G 605 " --> pdb=" O ASN G 602 " (cutoff:3.500A) Processing helix chain 'G' and resid 627 through 652 removed outlier: 3.716A pdb=" N GLN G 652 " --> pdb=" O TYR G 648 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 309 removed outlier: 3.743A pdb=" N LEU H 297 " --> pdb=" O LYS H 293 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLN H 303 " --> pdb=" O ASP H 299 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL H 304 " --> pdb=" O VAL H 300 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER H 305 " --> pdb=" O LEU H 301 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY H 306 " --> pdb=" O LYS H 302 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR H 307 " --> pdb=" O GLN H 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 342 through 357 removed outlier: 3.570A pdb=" N GLN H 347 " --> pdb=" O GLN H 343 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER H 348 " --> pdb=" O ASP H 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 401 through 411 Processing helix chain 'H' and resid 439 through 444 Processing helix chain 'H' and resid 600 through 605 removed outlier: 3.578A pdb=" N LEU H 603 " --> pdb=" O ILE H 600 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS H 605 " --> pdb=" O ASN H 602 " (cutoff:3.500A) Processing helix chain 'H' and resid 627 through 652 removed outlier: 3.716A pdb=" N GLN H 652 " --> pdb=" O TYR H 648 " (cutoff:3.500A) Processing helix chain 'I' and resid 293 through 309 removed outlier: 3.743A pdb=" N LEU I 297 " --> pdb=" O LYS I 293 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLN I 303 " --> pdb=" O ASP I 299 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL I 304 " --> pdb=" O VAL I 300 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER I 305 " --> pdb=" O LEU I 301 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY I 306 " --> pdb=" O LYS I 302 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR I 307 " --> pdb=" O GLN I 303 " (cutoff:3.500A) Processing helix chain 'I' and resid 342 through 357 removed outlier: 3.571A pdb=" N GLN I 347 " --> pdb=" O GLN I 343 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER I 348 " --> pdb=" O ASP I 344 " (cutoff:3.500A) Processing helix chain 'I' and resid 401 through 411 Processing helix chain 'I' and resid 439 through 444 Processing helix chain 'I' and resid 600 through 605 removed outlier: 3.578A pdb=" N LEU I 603 " --> pdb=" O ILE I 600 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS I 605 " --> pdb=" O ASN I 602 " (cutoff:3.500A) Processing helix chain 'I' and resid 627 through 652 removed outlier: 3.716A pdb=" N GLN I 652 " --> pdb=" O TYR I 648 " (cutoff:3.500A) Processing helix chain 'J' and resid 293 through 309 removed outlier: 3.743A pdb=" N LEU J 297 " --> pdb=" O LYS J 293 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLN J 303 " --> pdb=" O ASP J 299 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL J 304 " --> pdb=" O VAL J 300 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER J 305 " --> pdb=" O LEU J 301 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY J 306 " --> pdb=" O LYS J 302 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR J 307 " --> pdb=" O GLN J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 342 through 357 removed outlier: 3.571A pdb=" N GLN J 347 " --> pdb=" O GLN J 343 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER J 348 " --> pdb=" O ASP J 344 " (cutoff:3.500A) Processing helix chain 'J' and resid 401 through 411 Processing helix chain 'J' and resid 439 through 444 Processing helix chain 'J' and resid 600 through 605 removed outlier: 3.578A pdb=" N LEU J 603 " --> pdb=" O ILE J 600 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS J 605 " --> pdb=" O ASN J 602 " (cutoff:3.500A) Processing helix chain 'J' and resid 627 through 652 removed outlier: 3.716A pdb=" N GLN J 652 " --> pdb=" O TYR J 648 " (cutoff:3.500A) Processing helix chain 'K' and resid 293 through 309 removed outlier: 3.742A pdb=" N LEU K 297 " --> pdb=" O LYS K 293 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLN K 303 " --> pdb=" O ASP K 299 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL K 304 " --> pdb=" O VAL K 300 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER K 305 " --> pdb=" O LEU K 301 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY K 306 " --> pdb=" O LYS K 302 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR K 307 " --> pdb=" O GLN K 303 " (cutoff:3.500A) Processing helix chain 'K' and resid 342 through 357 removed outlier: 3.571A pdb=" N GLN K 347 " --> pdb=" O GLN K 343 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER K 348 " --> pdb=" O ASP K 344 " (cutoff:3.500A) Processing helix chain 'K' and resid 401 through 411 Processing helix chain 'K' and resid 439 through 444 Processing helix chain 'K' and resid 600 through 605 removed outlier: 3.578A pdb=" N LEU K 603 " --> pdb=" O ILE K 600 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS K 605 " --> pdb=" O ASN K 602 " (cutoff:3.500A) Processing helix chain 'K' and resid 627 through 652 removed outlier: 3.716A pdb=" N GLN K 652 " --> pdb=" O TYR K 648 " (cutoff:3.500A) Processing helix chain 'L' and resid 293 through 309 removed outlier: 3.743A pdb=" N LEU L 297 " --> pdb=" O LYS L 293 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLN L 303 " --> pdb=" O ASP L 299 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL L 304 " --> pdb=" O VAL L 300 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER L 305 " --> pdb=" O LEU L 301 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY L 306 " --> pdb=" O LYS L 302 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR L 307 " --> pdb=" O GLN L 303 " (cutoff:3.500A) Processing helix chain 'L' and resid 342 through 357 removed outlier: 3.571A pdb=" N GLN L 347 " --> pdb=" O GLN L 343 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER L 348 " --> pdb=" O ASP L 344 " (cutoff:3.500A) Processing helix chain 'L' and resid 401 through 411 Processing helix chain 'L' and resid 439 through 444 Processing helix chain 'L' and resid 600 through 605 removed outlier: 3.578A pdb=" N LEU L 603 " --> pdb=" O ILE L 600 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS L 605 " --> pdb=" O ASN L 602 " (cutoff:3.500A) Processing helix chain 'L' and resid 627 through 652 removed outlier: 3.716A pdb=" N GLN L 652 " --> pdb=" O TYR L 648 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 309 removed outlier: 3.743A pdb=" N LEU M 297 " --> pdb=" O LYS M 293 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLN M 303 " --> pdb=" O ASP M 299 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL M 304 " --> pdb=" O VAL M 300 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER M 305 " --> pdb=" O LEU M 301 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY M 306 " --> pdb=" O LYS M 302 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR M 307 " --> pdb=" O GLN M 303 " (cutoff:3.500A) Processing helix chain 'M' and resid 342 through 357 removed outlier: 3.571A pdb=" N GLN M 347 " --> pdb=" O GLN M 343 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER M 348 " --> pdb=" O ASP M 344 " (cutoff:3.500A) Processing helix chain 'M' and resid 401 through 411 Processing helix chain 'M' and resid 439 through 444 Processing helix chain 'M' and resid 600 through 605 removed outlier: 3.578A pdb=" N LEU M 603 " --> pdb=" O ILE M 600 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS M 605 " --> pdb=" O ASN M 602 " (cutoff:3.500A) Processing helix chain 'M' and resid 627 through 652 removed outlier: 3.716A pdb=" N GLN M 652 " --> pdb=" O TYR M 648 " (cutoff:3.500A) Processing helix chain 'N' and resid 293 through 309 removed outlier: 3.743A pdb=" N LEU N 297 " --> pdb=" O LYS N 293 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLN N 303 " --> pdb=" O ASP N 299 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL N 304 " --> pdb=" O VAL N 300 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER N 305 " --> pdb=" O LEU N 301 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY N 306 " --> pdb=" O LYS N 302 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR N 307 " --> pdb=" O GLN N 303 " (cutoff:3.500A) Processing helix chain 'N' and resid 342 through 357 removed outlier: 3.571A pdb=" N GLN N 347 " --> pdb=" O GLN N 343 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER N 348 " --> pdb=" O ASP N 344 " (cutoff:3.500A) Processing helix chain 'N' and resid 401 through 411 Processing helix chain 'N' and resid 439 through 444 Processing helix chain 'N' and resid 600 through 605 removed outlier: 3.577A pdb=" N LEU N 603 " --> pdb=" O ILE N 600 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS N 605 " --> pdb=" O ASN N 602 " (cutoff:3.500A) Processing helix chain 'N' and resid 627 through 652 removed outlier: 3.716A pdb=" N GLN N 652 " --> pdb=" O TYR N 648 " (cutoff:3.500A) Processing helix chain 'O' and resid 293 through 309 removed outlier: 3.743A pdb=" N LEU O 297 " --> pdb=" O LYS O 293 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLN O 303 " --> pdb=" O ASP O 299 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL O 304 " --> pdb=" O VAL O 300 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER O 305 " --> pdb=" O LEU O 301 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY O 306 " --> pdb=" O LYS O 302 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR O 307 " --> pdb=" O GLN O 303 " (cutoff:3.500A) Processing helix chain 'O' and resid 342 through 357 removed outlier: 3.571A pdb=" N GLN O 347 " --> pdb=" O GLN O 343 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER O 348 " --> pdb=" O ASP O 344 " (cutoff:3.500A) Processing helix chain 'O' and resid 401 through 411 Processing helix chain 'O' and resid 439 through 444 Processing helix chain 'O' and resid 600 through 605 removed outlier: 3.577A pdb=" N LEU O 603 " --> pdb=" O ILE O 600 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS O 605 " --> pdb=" O ASN O 602 " (cutoff:3.500A) Processing helix chain 'O' and resid 627 through 652 removed outlier: 3.716A pdb=" N GLN O 652 " --> pdb=" O TYR O 648 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 284 through 288 Processing sheet with id=AA2, first strand: chain 'A' and resid 608 through 609 removed outlier: 3.826A pdb=" N SER A 587 " --> pdb=" O ALA A 608 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS O 467 " --> pdb=" O LYS A 590 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN O 468 " --> pdb=" O ASN O 377 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN O 377 " --> pdb=" O ASN O 468 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN O 362 " --> pdb=" O LEU O 625 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU A 576 " --> pdb=" O THR O 481 " (cutoff:3.500A) removed outlier: 12.230A pdb=" N LEU O 483 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 15.547A pdb=" N ILE A 574 " --> pdb=" O LEU O 483 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'O' and resid 608 through 609 removed outlier: 3.826A pdb=" N SER O 587 " --> pdb=" O ALA O 608 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS N 467 " --> pdb=" O LYS O 590 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN N 468 " --> pdb=" O ASN N 377 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN N 377 " --> pdb=" O ASN N 468 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN N 362 " --> pdb=" O LEU N 625 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU O 576 " --> pdb=" O THR N 481 " (cutoff:3.500A) removed outlier: 12.224A pdb=" N LEU N 483 " --> pdb=" O ILE O 574 " (cutoff:3.500A) removed outlier: 15.540A pdb=" N ILE O 574 " --> pdb=" O LEU N 483 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'N' and resid 608 through 609 removed outlier: 3.827A pdb=" N SER N 587 " --> pdb=" O ALA N 608 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS M 467 " --> pdb=" O LYS N 590 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN M 468 " --> pdb=" O ASN M 377 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN M 377 " --> pdb=" O ASN M 468 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN M 362 " --> pdb=" O LEU M 625 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU N 576 " --> pdb=" O THR M 481 " (cutoff:3.500A) removed outlier: 12.229A pdb=" N LEU M 483 " --> pdb=" O ILE N 574 " (cutoff:3.500A) removed outlier: 15.546A pdb=" N ILE N 574 " --> pdb=" O LEU M 483 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 608 through 609 removed outlier: 3.826A pdb=" N SER M 587 " --> pdb=" O ALA M 608 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS L 467 " --> pdb=" O LYS M 590 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN L 468 " --> pdb=" O ASN L 377 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN L 377 " --> pdb=" O ASN L 468 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN L 362 " --> pdb=" O LEU L 625 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU M 576 " --> pdb=" O THR L 481 " (cutoff:3.500A) removed outlier: 12.228A pdb=" N LEU L 483 " --> pdb=" O ILE M 574 " (cutoff:3.500A) removed outlier: 15.545A pdb=" N ILE M 574 " --> pdb=" O LEU L 483 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 608 through 609 removed outlier: 3.826A pdb=" N SER L 587 " --> pdb=" O ALA L 608 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS K 467 " --> pdb=" O LYS L 590 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN K 468 " --> pdb=" O ASN K 377 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN K 377 " --> pdb=" O ASN K 468 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN K 362 " --> pdb=" O LEU K 625 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU L 576 " --> pdb=" O THR K 481 " (cutoff:3.500A) removed outlier: 12.233A pdb=" N LEU K 483 " --> pdb=" O ILE L 574 " (cutoff:3.500A) removed outlier: 15.548A pdb=" N ILE L 574 " --> pdb=" O LEU K 483 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 608 through 609 removed outlier: 3.826A pdb=" N SER K 587 " --> pdb=" O ALA K 608 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS J 467 " --> pdb=" O LYS K 590 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN J 468 " --> pdb=" O ASN J 377 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN J 377 " --> pdb=" O ASN J 468 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN J 362 " --> pdb=" O LEU J 625 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU K 576 " --> pdb=" O THR J 481 " (cutoff:3.500A) removed outlier: 12.226A pdb=" N LEU J 483 " --> pdb=" O ILE K 574 " (cutoff:3.500A) removed outlier: 15.542A pdb=" N ILE K 574 " --> pdb=" O LEU J 483 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 608 through 609 removed outlier: 3.826A pdb=" N SER J 587 " --> pdb=" O ALA J 608 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS I 467 " --> pdb=" O LYS J 590 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN I 468 " --> pdb=" O ASN I 377 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN I 377 " --> pdb=" O ASN I 468 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN I 362 " --> pdb=" O LEU I 625 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU J 576 " --> pdb=" O THR I 481 " (cutoff:3.500A) removed outlier: 12.220A pdb=" N LEU I 483 " --> pdb=" O ILE J 574 " (cutoff:3.500A) removed outlier: 15.532A pdb=" N ILE J 574 " --> pdb=" O LEU I 483 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 608 through 609 removed outlier: 3.826A pdb=" N SER I 587 " --> pdb=" O ALA I 608 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS H 467 " --> pdb=" O LYS I 590 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN H 468 " --> pdb=" O ASN H 377 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN H 377 " --> pdb=" O ASN H 468 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN H 362 " --> pdb=" O LEU H 625 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU I 576 " --> pdb=" O THR H 481 " (cutoff:3.500A) removed outlier: 12.248A pdb=" N LEU H 483 " --> pdb=" O ILE I 574 " (cutoff:3.500A) removed outlier: 15.567A pdb=" N ILE I 574 " --> pdb=" O LEU H 483 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 608 through 609 removed outlier: 3.826A pdb=" N SER H 587 " --> pdb=" O ALA H 608 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS G 467 " --> pdb=" O LYS H 590 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN G 468 " --> pdb=" O ASN G 377 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN G 377 " --> pdb=" O ASN G 468 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN G 362 " --> pdb=" O LEU G 625 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU H 576 " --> pdb=" O THR G 481 " (cutoff:3.500A) removed outlier: 12.239A pdb=" N LEU G 483 " --> pdb=" O ILE H 574 " (cutoff:3.500A) removed outlier: 15.550A pdb=" N ILE H 574 " --> pdb=" O LEU G 483 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 608 through 609 removed outlier: 3.826A pdb=" N SER G 587 " --> pdb=" O ALA G 608 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS F 467 " --> pdb=" O LYS G 590 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN F 468 " --> pdb=" O ASN F 377 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN F 377 " --> pdb=" O ASN F 468 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN F 362 " --> pdb=" O LEU F 625 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU G 576 " --> pdb=" O THR F 481 " (cutoff:3.500A) removed outlier: 12.249A pdb=" N LEU F 483 " --> pdb=" O ILE G 574 " (cutoff:3.500A) removed outlier: 15.569A pdb=" N ILE G 574 " --> pdb=" O LEU F 483 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 608 through 609 removed outlier: 3.827A pdb=" N SER F 587 " --> pdb=" O ALA F 608 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS E 467 " --> pdb=" O LYS F 590 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN E 468 " --> pdb=" O ASN E 377 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN E 377 " --> pdb=" O ASN E 468 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN E 362 " --> pdb=" O LEU E 625 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU F 576 " --> pdb=" O THR E 481 " (cutoff:3.500A) removed outlier: 12.224A pdb=" N LEU E 483 " --> pdb=" O ILE F 574 " (cutoff:3.500A) removed outlier: 15.541A pdb=" N ILE F 574 " --> pdb=" O LEU E 483 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 608 through 609 removed outlier: 3.827A pdb=" N SER E 587 " --> pdb=" O ALA E 608 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS D 467 " --> pdb=" O LYS E 590 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN D 468 " --> pdb=" O ASN D 377 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN D 377 " --> pdb=" O ASN D 468 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN D 362 " --> pdb=" O LEU D 625 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU E 576 " --> pdb=" O THR D 481 " (cutoff:3.500A) removed outlier: 12.250A pdb=" N LEU D 483 " --> pdb=" O ILE E 574 " (cutoff:3.500A) removed outlier: 15.568A pdb=" N ILE E 574 " --> pdb=" O LEU D 483 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 608 through 609 removed outlier: 3.826A pdb=" N SER D 587 " --> pdb=" O ALA D 608 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS C 467 " --> pdb=" O LYS D 590 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN C 468 " --> pdb=" O ASN C 377 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN C 377 " --> pdb=" O ASN C 468 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN C 362 " --> pdb=" O LEU C 625 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU D 576 " --> pdb=" O THR C 481 " (cutoff:3.500A) removed outlier: 12.216A pdb=" N LEU C 483 " --> pdb=" O ILE D 574 " (cutoff:3.500A) removed outlier: 15.530A pdb=" N ILE D 574 " --> pdb=" O LEU C 483 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 608 through 609 removed outlier: 3.826A pdb=" N SER C 587 " --> pdb=" O ALA C 608 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 467 " --> pdb=" O LYS C 590 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN B 468 " --> pdb=" O ASN B 377 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN B 377 " --> pdb=" O ASN B 468 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN B 362 " --> pdb=" O LEU B 625 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU C 576 " --> pdb=" O THR B 481 " (cutoff:3.500A) removed outlier: 12.237A pdb=" N LEU B 483 " --> pdb=" O ILE C 574 " (cutoff:3.500A) removed outlier: 15.555A pdb=" N ILE C 574 " --> pdb=" O LEU B 483 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 608 through 609 removed outlier: 3.827A pdb=" N SER B 587 " --> pdb=" O ALA B 608 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A 467 " --> pdb=" O LYS B 590 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN A 468 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN A 377 " --> pdb=" O ASN A 468 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN A 362 " --> pdb=" O LEU A 625 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU B 576 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 12.224A pdb=" N LEU A 483 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 15.540A pdb=" N ILE B 574 " --> pdb=" O LEU A 483 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 574 through 583 removed outlier: 15.547A pdb=" N ILE A 574 " --> pdb=" O LEU O 483 " (cutoff:3.500A) removed outlier: 12.230A pdb=" N LEU O 483 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU A 576 " --> pdb=" O THR O 481 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN O 362 " --> pdb=" O LEU O 625 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLU O 612 " --> pdb=" O ASP O 582 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ASP O 582 " --> pdb=" O GLU O 612 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG O 614 " --> pdb=" O MET O 580 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N MET O 580 " --> pdb=" O ARG O 614 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU O 616 " --> pdb=" O GLY O 578 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY O 578 " --> pdb=" O LEU O 616 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL O 618 " --> pdb=" O LEU O 576 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE O 574 " --> pdb=" O ILE O 620 " (cutoff:3.500A) removed outlier: 15.540A pdb=" N ILE O 574 " --> pdb=" O LEU N 483 " (cutoff:3.500A) removed outlier: 12.224A pdb=" N LEU N 483 " --> pdb=" O ILE O 574 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU O 576 " --> pdb=" O THR N 481 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN N 362 " --> pdb=" O LEU N 625 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLU N 612 " --> pdb=" O ASP N 582 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASP N 582 " --> pdb=" O GLU N 612 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG N 614 " --> pdb=" O MET N 580 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N MET N 580 " --> pdb=" O ARG N 614 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU N 616 " --> pdb=" O GLY N 578 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY N 578 " --> pdb=" O LEU N 616 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL N 618 " --> pdb=" O LEU N 576 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE N 574 " --> pdb=" O ILE N 620 " (cutoff:3.500A) removed outlier: 15.546A pdb=" N ILE N 574 " --> pdb=" O LEU M 483 " (cutoff:3.500A) removed outlier: 12.229A pdb=" N LEU M 483 " --> pdb=" O ILE N 574 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU N 576 " --> pdb=" O THR M 481 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN M 362 " --> pdb=" O LEU M 625 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N GLU M 612 " --> pdb=" O ASP M 582 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASP M 582 " --> pdb=" O GLU M 612 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG M 614 " --> pdb=" O MET M 580 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N MET M 580 " --> pdb=" O ARG M 614 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU M 616 " --> pdb=" O GLY M 578 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLY M 578 " --> pdb=" O LEU M 616 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL M 618 " --> pdb=" O LEU M 576 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE M 574 " --> pdb=" O ILE M 620 " (cutoff:3.500A) removed outlier: 15.545A pdb=" N ILE M 574 " --> pdb=" O LEU L 483 " (cutoff:3.500A) removed outlier: 12.228A pdb=" N LEU L 483 " --> pdb=" O ILE M 574 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU M 576 " --> pdb=" O THR L 481 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN L 362 " --> pdb=" O LEU L 625 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLU L 612 " --> pdb=" O ASP L 582 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ASP L 582 " --> pdb=" O GLU L 612 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG L 614 " --> pdb=" O MET L 580 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N MET L 580 " --> pdb=" O ARG L 614 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU L 616 " --> pdb=" O GLY L 578 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY L 578 " --> pdb=" O LEU L 616 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL L 618 " --> pdb=" O LEU L 576 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE L 574 " --> pdb=" O ILE L 620 " (cutoff:3.500A) removed outlier: 15.548A pdb=" N ILE L 574 " --> pdb=" O LEU K 483 " (cutoff:3.500A) removed outlier: 12.233A pdb=" N LEU K 483 " --> pdb=" O ILE L 574 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU L 576 " --> pdb=" O THR K 481 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN K 362 " --> pdb=" O LEU K 625 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLU K 612 " --> pdb=" O ASP K 582 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASP K 582 " --> pdb=" O GLU K 612 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG K 614 " --> pdb=" O MET K 580 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N MET K 580 " --> pdb=" O ARG K 614 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU K 616 " --> pdb=" O GLY K 578 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY K 578 " --> pdb=" O LEU K 616 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL K 618 " --> pdb=" O LEU K 576 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE K 574 " --> pdb=" O ILE K 620 " (cutoff:3.500A) removed outlier: 15.542A pdb=" N ILE K 574 " --> pdb=" O LEU J 483 " (cutoff:3.500A) removed outlier: 12.226A pdb=" N LEU J 483 " --> pdb=" O ILE K 574 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU K 576 " --> pdb=" O THR J 481 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN J 362 " --> pdb=" O LEU J 625 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLU J 612 " --> pdb=" O ASP J 582 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASP J 582 " --> pdb=" O GLU J 612 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG J 614 " --> pdb=" O MET J 580 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N MET J 580 " --> pdb=" O ARG J 614 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU J 616 " --> pdb=" O GLY J 578 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY J 578 " --> pdb=" O LEU J 616 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL J 618 " --> pdb=" O LEU J 576 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE J 574 " --> pdb=" O ILE J 620 " (cutoff:3.500A) removed outlier: 15.532A pdb=" N ILE J 574 " --> pdb=" O LEU I 483 " (cutoff:3.500A) removed outlier: 12.220A pdb=" N LEU I 483 " --> pdb=" O ILE J 574 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU J 576 " --> pdb=" O THR I 481 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN I 362 " --> pdb=" O LEU I 625 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLU I 612 " --> pdb=" O ASP I 582 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASP I 582 " --> pdb=" O GLU I 612 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG I 614 " --> pdb=" O MET I 580 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N MET I 580 " --> pdb=" O ARG I 614 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU I 616 " --> pdb=" O GLY I 578 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY I 578 " --> pdb=" O LEU I 616 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL I 618 " --> pdb=" O LEU I 576 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE I 574 " --> pdb=" O ILE I 620 " (cutoff:3.500A) removed outlier: 15.567A pdb=" N ILE I 574 " --> pdb=" O LEU H 483 " (cutoff:3.500A) removed outlier: 12.248A pdb=" N LEU H 483 " --> pdb=" O ILE I 574 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU I 576 " --> pdb=" O THR H 481 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN H 362 " --> pdb=" O LEU H 625 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLU H 612 " --> pdb=" O ASP H 582 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ASP H 582 " --> pdb=" O GLU H 612 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG H 614 " --> pdb=" O MET H 580 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N MET H 580 " --> pdb=" O ARG H 614 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU H 616 " --> pdb=" O GLY H 578 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY H 578 " --> pdb=" O LEU H 616 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL H 618 " --> pdb=" O LEU H 576 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE H 574 " --> pdb=" O ILE H 620 " (cutoff:3.500A) removed outlier: 15.550A pdb=" N ILE H 574 " --> pdb=" O LEU G 483 " (cutoff:3.500A) removed outlier: 12.239A pdb=" N LEU G 483 " --> pdb=" O ILE H 574 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU H 576 " --> pdb=" O THR G 481 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN G 362 " --> pdb=" O LEU G 625 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLU G 612 " --> pdb=" O ASP G 582 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASP G 582 " --> pdb=" O GLU G 612 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG G 614 " --> pdb=" O MET G 580 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N MET G 580 " --> pdb=" O ARG G 614 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU G 616 " --> pdb=" O GLY G 578 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLY G 578 " --> pdb=" O LEU G 616 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL G 618 " --> pdb=" O LEU G 576 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE G 574 " --> pdb=" O ILE G 620 " (cutoff:3.500A) removed outlier: 15.569A pdb=" N ILE G 574 " --> pdb=" O LEU F 483 " (cutoff:3.500A) removed outlier: 12.249A pdb=" N LEU F 483 " --> pdb=" O ILE G 574 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU G 576 " --> pdb=" O THR F 481 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN F 362 " --> pdb=" O LEU F 625 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N GLU F 612 " --> pdb=" O ASP F 582 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASP F 582 " --> pdb=" O GLU F 612 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG F 614 " --> pdb=" O MET F 580 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N MET F 580 " --> pdb=" O ARG F 614 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU F 616 " --> pdb=" O GLY F 578 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY F 578 " --> pdb=" O LEU F 616 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL F 618 " --> pdb=" O LEU F 576 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 15.541A pdb=" N ILE F 574 " --> pdb=" O LEU E 483 " (cutoff:3.500A) removed outlier: 12.224A pdb=" N LEU E 483 " --> pdb=" O ILE F 574 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU F 576 " --> pdb=" O THR E 481 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN E 362 " --> pdb=" O LEU E 625 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLU E 612 " --> pdb=" O ASP E 582 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASP E 582 " --> pdb=" O GLU E 612 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG E 614 " --> pdb=" O MET E 580 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N MET E 580 " --> pdb=" O ARG E 614 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU E 616 " --> pdb=" O GLY E 578 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY E 578 " --> pdb=" O LEU E 616 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL E 618 " --> pdb=" O LEU E 576 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 15.568A pdb=" N ILE E 574 " --> pdb=" O LEU D 483 " (cutoff:3.500A) removed outlier: 12.250A pdb=" N LEU D 483 " --> pdb=" O ILE E 574 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU E 576 " --> pdb=" O THR D 481 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN D 362 " --> pdb=" O LEU D 625 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLU D 612 " --> pdb=" O ASP D 582 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ASP D 582 " --> pdb=" O GLU D 612 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG D 614 " --> pdb=" O MET D 580 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N MET D 580 " --> pdb=" O ARG D 614 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU D 616 " --> pdb=" O GLY D 578 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY D 578 " --> pdb=" O LEU D 616 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL D 618 " --> pdb=" O LEU D 576 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 15.530A pdb=" N ILE D 574 " --> pdb=" O LEU C 483 " (cutoff:3.500A) removed outlier: 12.216A pdb=" N LEU C 483 " --> pdb=" O ILE D 574 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU D 576 " --> pdb=" O THR C 481 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN C 362 " --> pdb=" O LEU C 625 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLU C 612 " --> pdb=" O ASP C 582 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ASP C 582 " --> pdb=" O GLU C 612 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG C 614 " --> pdb=" O MET C 580 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N MET C 580 " --> pdb=" O ARG C 614 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU C 616 " --> pdb=" O GLY C 578 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLY C 578 " --> pdb=" O LEU C 616 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL C 618 " --> pdb=" O LEU C 576 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 15.555A pdb=" N ILE C 574 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 12.237A pdb=" N LEU B 483 " --> pdb=" O ILE C 574 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU C 576 " --> pdb=" O THR B 481 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN B 362 " --> pdb=" O LEU B 625 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLU B 612 " --> pdb=" O ASP B 582 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ASP B 582 " --> pdb=" O GLU B 612 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG B 614 " --> pdb=" O MET B 580 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N MET B 580 " --> pdb=" O ARG B 614 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU B 616 " --> pdb=" O GLY B 578 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY B 578 " --> pdb=" O LEU B 616 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL B 618 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 15.540A pdb=" N ILE B 574 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 12.224A pdb=" N LEU A 483 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU B 576 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN A 362 " --> pdb=" O LEU A 625 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N GLU A 612 " --> pdb=" O ASP A 582 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASP A 582 " --> pdb=" O GLU A 612 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG A 614 " --> pdb=" O MET A 580 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N MET A 580 " --> pdb=" O ARG A 614 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU A 616 " --> pdb=" O GLY A 578 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY A 578 " --> pdb=" O LEU A 616 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL A 618 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 515 through 519 removed outlier: 3.671A pdb=" N ASP A 495 " --> pdb=" O PHE B 557 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 556 " --> pdb=" O GLU B 548 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 523 through 525 Processing sheet with id=AC2, first strand: chain 'A' and resid 523 through 525 Processing sheet with id=AC3, first strand: chain 'A' and resid 546 through 548 removed outlier: 3.772A pdb=" N VAL A 556 " --> pdb=" O GLU A 548 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP O 495 " --> pdb=" O PHE A 557 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 284 through 288 Processing sheet with id=AC5, first strand: chain 'B' and resid 515 through 519 removed outlier: 3.680A pdb=" N ASP B 495 " --> pdb=" O PHE C 557 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL C 556 " --> pdb=" O GLU C 548 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 523 through 525 Processing sheet with id=AC7, first strand: chain 'B' and resid 523 through 525 Processing sheet with id=AC8, first strand: chain 'C' and resid 284 through 288 Processing sheet with id=AC9, first strand: chain 'C' and resid 515 through 519 removed outlier: 3.663A pdb=" N ASP C 495 " --> pdb=" O PHE D 557 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL D 556 " --> pdb=" O GLU D 548 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 523 through 525 Processing sheet with id=AD2, first strand: chain 'C' and resid 523 through 525 Processing sheet with id=AD3, first strand: chain 'D' and resid 284 through 288 Processing sheet with id=AD4, first strand: chain 'D' and resid 515 through 519 removed outlier: 3.695A pdb=" N ASP D 495 " --> pdb=" O PHE E 557 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL E 556 " --> pdb=" O GLU E 548 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 523 through 525 Processing sheet with id=AD6, first strand: chain 'D' and resid 523 through 525 Processing sheet with id=AD7, first strand: chain 'E' and resid 284 through 288 Processing sheet with id=AD8, first strand: chain 'E' and resid 515 through 519 removed outlier: 3.660A pdb=" N ASP E 495 " --> pdb=" O PHE F 557 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL F 556 " --> pdb=" O GLU F 548 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 523 through 525 Processing sheet with id=AE1, first strand: chain 'E' and resid 523 through 525 Processing sheet with id=AE2, first strand: chain 'F' and resid 284 through 288 Processing sheet with id=AE3, first strand: chain 'F' and resid 515 through 519 removed outlier: 3.635A pdb=" N ASP F 495 " --> pdb=" O PHE G 557 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL G 556 " --> pdb=" O GLU G 548 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 523 through 525 Processing sheet with id=AE5, first strand: chain 'F' and resid 523 through 525 Processing sheet with id=AE6, first strand: chain 'G' and resid 284 through 288 Processing sheet with id=AE7, first strand: chain 'G' and resid 515 through 519 removed outlier: 3.748A pdb=" N ASP G 495 " --> pdb=" O PHE H 557 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL H 556 " --> pdb=" O GLU H 548 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 523 through 525 Processing sheet with id=AE9, first strand: chain 'G' and resid 523 through 525 Processing sheet with id=AF1, first strand: chain 'H' and resid 284 through 288 Processing sheet with id=AF2, first strand: chain 'H' and resid 515 through 519 removed outlier: 3.684A pdb=" N ASP H 495 " --> pdb=" O PHE I 557 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL I 556 " --> pdb=" O GLU I 548 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 523 through 525 Processing sheet with id=AF4, first strand: chain 'H' and resid 523 through 525 Processing sheet with id=AF5, first strand: chain 'I' and resid 284 through 288 Processing sheet with id=AF6, first strand: chain 'I' and resid 515 through 519 removed outlier: 3.669A pdb=" N ASP I 495 " --> pdb=" O PHE J 557 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL J 556 " --> pdb=" O GLU J 548 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 523 through 525 Processing sheet with id=AF8, first strand: chain 'I' and resid 523 through 525 Processing sheet with id=AF9, first strand: chain 'J' and resid 284 through 288 Processing sheet with id=AG1, first strand: chain 'J' and resid 515 through 519 removed outlier: 3.670A pdb=" N ASP J 495 " --> pdb=" O PHE K 557 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL K 556 " --> pdb=" O GLU K 548 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 523 through 525 Processing sheet with id=AG3, first strand: chain 'J' and resid 523 through 525 Processing sheet with id=AG4, first strand: chain 'K' and resid 284 through 288 Processing sheet with id=AG5, first strand: chain 'K' and resid 515 through 519 removed outlier: 3.681A pdb=" N ASP K 495 " --> pdb=" O PHE L 557 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL L 556 " --> pdb=" O GLU L 548 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 523 through 525 Processing sheet with id=AG7, first strand: chain 'K' and resid 523 through 525 Processing sheet with id=AG8, first strand: chain 'L' and resid 284 through 288 Processing sheet with id=AG9, first strand: chain 'L' and resid 515 through 519 removed outlier: 3.671A pdb=" N ASP L 495 " --> pdb=" O PHE M 557 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL M 556 " --> pdb=" O GLU M 548 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 523 through 525 Processing sheet with id=AH2, first strand: chain 'L' and resid 523 through 525 Processing sheet with id=AH3, first strand: chain 'M' and resid 284 through 288 Processing sheet with id=AH4, first strand: chain 'M' and resid 515 through 519 removed outlier: 3.676A pdb=" N ASP M 495 " --> pdb=" O PHE N 557 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL N 556 " --> pdb=" O GLU N 548 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'M' and resid 523 through 525 Processing sheet with id=AH6, first strand: chain 'M' and resid 523 through 525 Processing sheet with id=AH7, first strand: chain 'N' and resid 284 through 288 Processing sheet with id=AH8, first strand: chain 'N' and resid 515 through 519 removed outlier: 3.673A pdb=" N ASP N 495 " --> pdb=" O PHE O 557 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL O 556 " --> pdb=" O GLU O 548 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'N' and resid 523 through 525 Processing sheet with id=AI1, first strand: chain 'N' and resid 523 through 525 Processing sheet with id=AI2, first strand: chain 'O' and resid 284 through 288 Processing sheet with id=AI3, first strand: chain 'O' and resid 523 through 525 Processing sheet with id=AI4, first strand: chain 'O' and resid 523 through 525 2370 hydrogen bonds defined for protein. 6345 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: 21.08 Time building geometry restraints manager: 15.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 12562 1.33 - 1.45: 4156 1.45 - 1.57: 22792 1.57 - 1.69: 0 1.69 - 1.80: 330 Bond restraints: 39840 Sorted by residual: bond pdb=" C ASN E 430 " pdb=" N PRO E 431 " ideal model delta sigma weight residual 1.329 1.380 -0.051 1.25e-02 6.40e+03 1.67e+01 bond pdb=" C ASN L 430 " pdb=" N PRO L 431 " ideal model delta sigma weight residual 1.329 1.380 -0.051 1.25e-02 6.40e+03 1.66e+01 bond pdb=" C ASN K 430 " pdb=" N PRO K 431 " ideal model delta sigma weight residual 1.329 1.380 -0.051 1.25e-02 6.40e+03 1.65e+01 bond pdb=" C ASN G 430 " pdb=" N PRO G 431 " ideal model delta sigma weight residual 1.329 1.380 -0.051 1.25e-02 6.40e+03 1.64e+01 bond pdb=" C ASN J 430 " pdb=" N PRO J 431 " ideal model delta sigma weight residual 1.329 1.380 -0.051 1.25e-02 6.40e+03 1.63e+01 ... (remaining 39835 not shown) Histogram of bond angle deviations from ideal: 99.61 - 106.48: 1108 106.48 - 113.36: 22771 113.36 - 120.23: 12925 120.23 - 127.10: 16831 127.10 - 133.97: 260 Bond angle restraints: 53895 Sorted by residual: angle pdb=" N PRO O 592 " pdb=" CA PRO O 592 " pdb=" C PRO O 592 " ideal model delta sigma weight residual 113.47 119.10 -5.63 1.43e+00 4.89e-01 1.55e+01 angle pdb=" N PRO C 592 " pdb=" CA PRO C 592 " pdb=" C PRO C 592 " ideal model delta sigma weight residual 113.47 119.08 -5.61 1.43e+00 4.89e-01 1.54e+01 angle pdb=" N PRO G 592 " pdb=" CA PRO G 592 " pdb=" C PRO G 592 " ideal model delta sigma weight residual 113.47 119.07 -5.60 1.43e+00 4.89e-01 1.54e+01 angle pdb=" N PRO D 592 " pdb=" CA PRO D 592 " pdb=" C PRO D 592 " ideal model delta sigma weight residual 113.47 119.07 -5.60 1.43e+00 4.89e-01 1.53e+01 angle pdb=" N PRO H 592 " pdb=" CA PRO H 592 " pdb=" C PRO H 592 " ideal model delta sigma weight residual 113.47 119.06 -5.59 1.43e+00 4.89e-01 1.53e+01 ... (remaining 53890 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 23370 16.16 - 32.31: 805 32.31 - 48.47: 140 48.47 - 64.63: 0 64.63 - 80.79: 75 Dihedral angle restraints: 24390 sinusoidal: 9525 harmonic: 14865 Sorted by residual: dihedral pdb=" CA VAL A 591 " pdb=" C VAL A 591 " pdb=" N PRO A 592 " pdb=" CA PRO A 592 " ideal model delta harmonic sigma weight residual -180.00 -153.45 -26.55 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA VAL J 591 " pdb=" C VAL J 591 " pdb=" N PRO J 592 " pdb=" CA PRO J 592 " ideal model delta harmonic sigma weight residual 180.00 -153.45 -26.55 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA VAL L 591 " pdb=" C VAL L 591 " pdb=" N PRO L 592 " pdb=" CA PRO L 592 " ideal model delta harmonic sigma weight residual -180.00 -153.46 -26.54 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 24387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 4793 0.057 - 0.114: 1272 0.114 - 0.171: 340 0.171 - 0.228: 45 0.228 - 0.285: 30 Chirality restraints: 6480 Sorted by residual: chirality pdb=" CB ILE J 400 " pdb=" CA ILE J 400 " pdb=" CG1 ILE J 400 " pdb=" CG2 ILE J 400 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB ILE B 400 " pdb=" CA ILE B 400 " pdb=" CG1 ILE B 400 " pdb=" CG2 ILE B 400 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CB ILE H 400 " pdb=" CA ILE H 400 " pdb=" CG1 ILE H 400 " pdb=" CG2 ILE H 400 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 6477 not shown) Planarity restraints: 6990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 549 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" C GLY A 549 " 0.039 2.00e-02 2.50e+03 pdb=" O GLY A 549 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN A 550 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 549 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.16e+00 pdb=" C GLY C 549 " 0.039 2.00e-02 2.50e+03 pdb=" O GLY C 549 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN C 550 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 549 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.15e+00 pdb=" C GLY B 549 " 0.039 2.00e-02 2.50e+03 pdb=" O GLY B 549 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN B 550 " -0.013 2.00e-02 2.50e+03 ... (remaining 6987 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3838 2.75 - 3.28: 35257 3.28 - 3.82: 60712 3.82 - 4.36: 68437 4.36 - 4.90: 130206 Nonbonded interactions: 298450 Sorted by model distance: nonbonded pdb=" OG SER G 327 " pdb=" OG1 THR H 307 " model vdw 2.206 2.440 nonbonded pdb=" OG SER I 327 " pdb=" OG1 THR J 307 " model vdw 2.231 2.440 nonbonded pdb=" OG SER K 327 " pdb=" OG1 THR L 307 " model vdw 2.233 2.440 nonbonded pdb=" OG SER D 327 " pdb=" OG1 THR E 307 " model vdw 2.234 2.440 nonbonded pdb=" OG SER J 327 " pdb=" OG1 THR K 307 " model vdw 2.235 2.440 ... (remaining 298445 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' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 9.040 Check model and map are aligned: 0.570 Set scattering table: 0.340 Process input model: 102.900 Find NCS groups from input model: 2.770 Set up NCS constraints: 0.270 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 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 0.052 39840 Z= 0.374 Angle : 0.890 9.589 53895 Z= 0.479 Chirality : 0.059 0.285 6480 Planarity : 0.006 0.048 6990 Dihedral : 10.333 80.787 14790 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer Outliers : 0.69 % 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: -5.31 (0.10), residues: 5130 helix: -3.94 (0.07), residues: 1245 sheet: -2.88 (0.10), residues: 2505 loop : -3.56 (0.14), residues: 1380 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1167 residues out of total 4350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1137 time to evaluate : 5.258 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 outliers start: 30 outliers final: 15 residues processed: 1167 average time/residue: 0.6139 time to fit residues: 1105.7184 Evaluate side-chains 602 residues out of total 4350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 587 time to evaluate : 4.881 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3374 time to fit residues: 16.4132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 443 optimal weight: 0.7980 chunk 397 optimal weight: 10.0000 chunk 220 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 268 optimal weight: 6.9990 chunk 212 optimal weight: 10.0000 chunk 411 optimal weight: 2.9990 chunk 159 optimal weight: 0.0050 chunk 250 optimal weight: 3.9990 chunk 306 optimal weight: 5.9990 chunk 476 optimal weight: 6.9990 overall best weight: 2.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 ASN A 364 HIS A 430 ASN ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN B 364 HIS B 430 ASN ** B 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN C 364 HIS C 430 ASN ** C 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 ASN D 364 HIS D 430 ASN ** D 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 335 ASN E 364 HIS E 430 ASN ** E 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 335 ASN F 364 HIS F 430 ASN ** F 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 335 ASN G 364 HIS G 430 ASN ** G 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 335 ASN H 364 HIS H 430 ASN ** H 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 335 ASN I 364 HIS I 430 ASN ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 335 ASN J 364 HIS J 430 ASN ** J 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 335 ASN K 364 HIS K 430 ASN ** K 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 335 ASN L 364 HIS L 430 ASN ** L 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 335 ASN M 364 HIS M 430 ASN ** M 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 335 ASN N 364 HIS N 430 ASN ** N 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 335 ASN O 364 HIS O 430 ASN ** O 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 652 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 39840 Z= 0.267 Angle : 0.675 8.581 53895 Z= 0.351 Chirality : 0.049 0.176 6480 Planarity : 0.005 0.041 6990 Dihedral : 5.498 25.399 5415 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer Outliers : 2.80 % 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: -3.98 (0.10), residues: 5130 helix: -1.54 (0.12), residues: 1155 sheet: -2.54 (0.10), residues: 2475 loop : -3.17 (0.13), residues: 1500 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 4350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 652 time to evaluate : 4.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 122 outliers final: 61 residues processed: 755 average time/residue: 0.5627 time to fit residues: 668.2803 Evaluate side-chains 566 residues out of total 4350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 505 time to evaluate : 4.921 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 0.3419 time to fit residues: 46.4280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 264 optimal weight: 0.0770 chunk 147 optimal weight: 3.9990 chunk 396 optimal weight: 0.9990 chunk 324 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 477 optimal weight: 0.9980 chunk 515 optimal weight: 6.9990 chunk 425 optimal weight: 6.9990 chunk 473 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 383 optimal weight: 20.0000 overall best weight: 1.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 ASN ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN ** B 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN C 430 ASN ** C 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 ASN ** D 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 430 ASN ** E 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 542 GLN F 430 ASN ** F 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 652 GLN H 430 ASN ** H 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 652 GLN ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 652 GLN ** J 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 652 GLN K 430 ASN ** K 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 652 GLN L 430 ASN ** L 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 652 GLN M 430 ASN ** M 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 652 GLN N 430 ASN ** N 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 652 GLN O 430 ASN ** O 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 652 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 39840 Z= 0.164 Angle : 0.587 9.157 53895 Z= 0.303 Chirality : 0.047 0.167 6480 Planarity : 0.004 0.038 6990 Dihedral : 4.865 20.764 5415 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.11), residues: 5130 helix: -0.44 (0.15), residues: 1155 sheet: -2.25 (0.10), residues: 2535 loop : -2.87 (0.14), residues: 1440 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 4350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 679 time to evaluate : 5.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 94 outliers final: 46 residues processed: 759 average time/residue: 0.5522 time to fit residues: 668.2563 Evaluate side-chains 558 residues out of total 4350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 512 time to evaluate : 5.237 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.3518 time to fit residues: 37.6253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 471 optimal weight: 2.9990 chunk 359 optimal weight: 0.9990 chunk 247 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 227 optimal weight: 6.9990 chunk 320 optimal weight: 0.9980 chunk 479 optimal weight: 6.9990 chunk 507 optimal weight: 9.9990 chunk 250 optimal weight: 0.9990 chunk 454 optimal weight: 10.0000 chunk 136 optimal weight: 9.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN ** B 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 GLN B 615 ASN ** C 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 ASN ** D 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 430 ASN ** F 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 430 ASN ** G 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 430 ASN ** H 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 430 ASN ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 430 ASN ** J 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 430 ASN ** K 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 430 ASN ** N 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 430 ASN ** O 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 39840 Z= 0.204 Angle : 0.593 10.903 53895 Z= 0.302 Chirality : 0.047 0.162 6480 Planarity : 0.004 0.036 6990 Dihedral : 4.779 20.577 5415 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer Outliers : 1.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.11), residues: 5130 helix: 0.02 (0.16), residues: 1155 sheet: -2.18 (0.10), residues: 2595 loop : -2.81 (0.15), residues: 1380 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 4350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 559 time to evaluate : 4.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 25 residues processed: 607 average time/residue: 0.5719 time to fit residues: 543.2170 Evaluate side-chains 529 residues out of total 4350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 504 time to evaluate : 5.206 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.3783 time to fit residues: 24.2241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 422 optimal weight: 7.9990 chunk 288 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 377 optimal weight: 8.9990 chunk 209 optimal weight: 10.0000 chunk 433 optimal weight: 9.9990 chunk 350 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 259 optimal weight: 9.9990 chunk 455 optimal weight: 10.0000 chunk 128 optimal weight: 0.1980 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN ** B 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 GLN B 615 ASN ** C 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 ASN ** D 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 430 ASN ** F 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 430 ASN ** H 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 430 ASN ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 430 ASN ** K 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 430 ASN ** N 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 430 ASN ** O 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.055 39840 Z= 0.390 Angle : 0.669 10.649 53895 Z= 0.344 Chirality : 0.048 0.177 6480 Planarity : 0.005 0.040 6990 Dihedral : 5.182 22.810 5415 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.19 % Favored : 91.62 % Rotamer Outliers : 2.39 % 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: -3.11 (0.11), residues: 5130 helix: -0.17 (0.15), residues: 1245 sheet: -2.26 (0.10), residues: 2580 loop : -2.94 (0.15), residues: 1305 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 4350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 537 time to evaluate : 4.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 104 outliers final: 77 residues processed: 619 average time/residue: 0.5789 time to fit residues: 566.8449 Evaluate side-chains 575 residues out of total 4350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 498 time to evaluate : 4.806 Switching outliers to nearest non-outliers outliers start: 77 outliers final: 0 residues processed: 77 average time/residue: 0.3527 time to fit residues: 58.0446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 170 optimal weight: 4.9990 chunk 456 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 297 optimal weight: 8.9990 chunk 125 optimal weight: 3.9990 chunk 507 optimal weight: 2.9990 chunk 421 optimal weight: 2.9990 chunk 235 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 168 optimal weight: 9.9990 chunk 266 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 ASN ** C 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 430 ASN ** K 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 430 ASN ** O 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 39840 Z= 0.290 Angle : 0.649 12.098 53895 Z= 0.324 Chirality : 0.047 0.185 6480 Planarity : 0.004 0.040 6990 Dihedral : 4.991 21.718 5415 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.21 % Favored : 92.50 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.12), residues: 5130 helix: 0.08 (0.15), residues: 1245 sheet: -2.18 (0.10), residues: 2580 loop : -2.90 (0.15), residues: 1305 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 4350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 536 time to evaluate : 4.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 29 residues processed: 591 average time/residue: 0.5682 time to fit residues: 530.8304 Evaluate side-chains 533 residues out of total 4350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 504 time to evaluate : 4.799 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.3565 time to fit residues: 25.9255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 489 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 289 optimal weight: 10.0000 chunk 370 optimal weight: 5.9990 chunk 287 optimal weight: 5.9990 chunk 427 optimal weight: 3.9990 chunk 283 optimal weight: 1.9990 chunk 506 optimal weight: 6.9990 chunk 316 optimal weight: 4.9990 chunk 308 optimal weight: 10.0000 chunk 233 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 39840 Z= 0.326 Angle : 0.679 12.073 53895 Z= 0.338 Chirality : 0.048 0.190 6480 Planarity : 0.004 0.043 6990 Dihedral : 5.054 22.171 5415 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.84 % Favored : 91.87 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.12), residues: 5130 helix: 0.17 (0.15), residues: 1245 sheet: -2.19 (0.10), residues: 2595 loop : -2.89 (0.15), residues: 1290 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 4350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 527 time to evaluate : 5.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 21 residues processed: 570 average time/residue: 0.5762 time to fit residues: 520.4641 Evaluate side-chains 527 residues out of total 4350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 506 time to evaluate : 4.945 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.3648 time to fit residues: 20.8980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 313 optimal weight: 0.9980 chunk 202 optimal weight: 0.0020 chunk 302 optimal weight: 2.9990 chunk 152 optimal weight: 0.0060 chunk 99 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 321 optimal weight: 6.9990 chunk 344 optimal weight: 5.9990 chunk 250 optimal weight: 0.6980 chunk 47 optimal weight: 8.9990 chunk 397 optimal weight: 20.0000 overall best weight: 0.9406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN ** B 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 485 ASN ** D 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 39840 Z= 0.165 Angle : 0.645 13.768 53895 Z= 0.312 Chirality : 0.047 0.162 6480 Planarity : 0.004 0.047 6990 Dihedral : 4.652 18.666 5415 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.36 % Favored : 94.35 % Rotamer Outliers : 0.41 % 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: -2.62 (0.12), residues: 5130 helix: 0.41 (0.16), residues: 1245 sheet: -2.02 (0.10), residues: 2595 loop : -2.76 (0.15), residues: 1290 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 4350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 576 time to evaluate : 5.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 4 residues processed: 587 average time/residue: 0.5752 time to fit residues: 534.2463 Evaluate side-chains 521 residues out of total 4350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 517 time to evaluate : 4.973 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3485 time to fit residues: 9.4998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 460 optimal weight: 3.9990 chunk 484 optimal weight: 0.9990 chunk 442 optimal weight: 5.9990 chunk 471 optimal weight: 9.9990 chunk 283 optimal weight: 0.9980 chunk 205 optimal weight: 1.9990 chunk 370 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 426 optimal weight: 7.9990 chunk 445 optimal weight: 0.6980 chunk 469 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: