Starting phenix.real_space_refine on Tue Apr 16 14:05:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w68_8778/04_2024/5w68_8778.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w68_8778/04_2024/5w68_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_8778/04_2024/5w68_8778.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w68_8778/04_2024/5w68_8778.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w68_8778/04_2024/5w68_8778.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w68_8778/04_2024/5w68_8778.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 20.00, per 1000 atoms: 0.51 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: 13.22 Conformation dependent library (CDL) restraints added in 7.0 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: 5.84 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: 17.58 Time building geometry restraints manager: 14.46 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: 1.280 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: 7.160 Check model and map are aligned: 0.610 Set scattering table: 0.350 Process input model: 100.510 Find NCS groups from input model: 2.870 Set up NCS constraints: 0.280 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.730 ------------------------------------------------------------------------------- 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 % Allowed : 4.34 % Favored : 94.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.31 (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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 459 HIS 0.003 0.001 HIS F 659 PHE 0.025 0.002 PHE G 489 TYR 0.020 0.002 TYR M 648 ARG 0.008 0.001 ARG C 643 *********************** 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 : 4.645 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: A 302 LYS cc_start: 0.8875 (mmmt) cc_final: 0.8370 (tptp) REVERT: A 346 MET cc_start: 0.8663 (tpp) cc_final: 0.8424 (mmm) REVERT: A 350 GLN cc_start: 0.8939 (tt0) cc_final: 0.8682 (tm-30) REVERT: A 359 ARG cc_start: 0.7769 (tpt-90) cc_final: 0.7567 (tpt-90) REVERT: A 392 MET cc_start: 0.7226 (mpt) cc_final: 0.6996 (mpp) REVERT: A 462 LEU cc_start: 0.9066 (tp) cc_final: 0.8844 (tp) REVERT: A 540 ILE cc_start: 0.8744 (tt) cc_final: 0.8483 (mp) REVERT: A 541 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7341 (tm-30) REVERT: A 649 ARG cc_start: 0.8429 (mmt180) cc_final: 0.8214 (mmm-85) REVERT: B 291 TYR cc_start: 0.9246 (m-80) cc_final: 0.9037 (m-80) REVERT: B 302 LYS cc_start: 0.9028 (mmmt) cc_final: 0.8352 (tptt) REVERT: B 346 MET cc_start: 0.8878 (tpp) cc_final: 0.8444 (mmm) REVERT: B 350 GLN cc_start: 0.8991 (tt0) cc_final: 0.8663 (tm-30) REVERT: B 359 ARG cc_start: 0.8000 (tpt-90) cc_final: 0.7774 (tpt-90) REVERT: B 392 MET cc_start: 0.7303 (mpt) cc_final: 0.7006 (mpp) REVERT: B 447 PHE cc_start: 0.8480 (t80) cc_final: 0.7966 (t80) REVERT: B 462 LEU cc_start: 0.8992 (tp) cc_final: 0.8504 (tt) REVERT: B 540 ILE cc_start: 0.8667 (tt) cc_final: 0.8407 (mp) REVERT: B 541 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7016 (tm-30) REVERT: B 639 TYR cc_start: 0.8300 (t80) cc_final: 0.7916 (t80) REVERT: B 643 ARG cc_start: 0.8390 (ttt180) cc_final: 0.7924 (ttt-90) REVERT: B 649 ARG cc_start: 0.8676 (mmt180) cc_final: 0.8366 (mmm-85) REVERT: C 346 MET cc_start: 0.8502 (tpp) cc_final: 0.8241 (mmm) REVERT: C 392 MET cc_start: 0.7510 (mpt) cc_final: 0.7221 (mpp) REVERT: C 462 LEU cc_start: 0.9134 (tp) cc_final: 0.8675 (tt) REVERT: C 540 ILE cc_start: 0.8693 (tt) cc_final: 0.8451 (mp) REVERT: C 541 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7496 (tm-30) REVERT: C 639 TYR cc_start: 0.8459 (t80) cc_final: 0.8243 (t80) REVERT: C 649 ARG cc_start: 0.8552 (mmt180) cc_final: 0.8237 (mmm-85) REVERT: D 291 TYR cc_start: 0.9264 (m-80) cc_final: 0.9047 (m-80) REVERT: D 346 MET cc_start: 0.8818 (tpp) cc_final: 0.8440 (mmm) REVERT: D 350 GLN cc_start: 0.8911 (tt0) cc_final: 0.8471 (tm-30) REVERT: D 392 MET cc_start: 0.7149 (mpt) cc_final: 0.6835 (mpp) REVERT: D 447 PHE cc_start: 0.8521 (t80) cc_final: 0.8310 (t80) REVERT: D 460 MET cc_start: 0.7891 (ttp) cc_final: 0.7545 (ttm) REVERT: D 462 LEU cc_start: 0.8904 (tp) cc_final: 0.8424 (tt) REVERT: D 487 GLU cc_start: 0.7897 (pt0) cc_final: 0.7663 (pt0) REVERT: D 519 LYS cc_start: 0.8850 (mttm) cc_final: 0.8607 (mmtm) REVERT: D 523 MET cc_start: 0.7033 (ttm) cc_final: 0.6602 (mtp) REVERT: D 540 ILE cc_start: 0.8739 (tt) cc_final: 0.8499 (mp) REVERT: D 541 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7045 (tm-30) REVERT: D 649 ARG cc_start: 0.8490 (mmt180) cc_final: 0.8275 (mmm-85) REVERT: E 291 TYR cc_start: 0.9340 (m-80) cc_final: 0.9138 (m-80) REVERT: E 346 MET cc_start: 0.8576 (tpp) cc_final: 0.8297 (mmm) REVERT: E 350 GLN cc_start: 0.8833 (tt0) cc_final: 0.8486 (tm-30) REVERT: E 392 MET cc_start: 0.7255 (mpt) cc_final: 0.6964 (mpp) REVERT: E 462 LEU cc_start: 0.9028 (tp) cc_final: 0.8510 (tt) REVERT: E 541 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7326 (tm-30) REVERT: E 612 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7729 (tm-30) REVERT: E 649 ARG cc_start: 0.8584 (mmt180) cc_final: 0.8276 (mmm-85) REVERT: F 346 MET cc_start: 0.8639 (tpp) cc_final: 0.8332 (mmm) REVERT: F 350 GLN cc_start: 0.9033 (tt0) cc_final: 0.8731 (tm-30) REVERT: F 392 MET cc_start: 0.7343 (mpt) cc_final: 0.7117 (mpp) REVERT: F 462 LEU cc_start: 0.9055 (tp) cc_final: 0.8561 (tt) REVERT: F 540 ILE cc_start: 0.8743 (tt) cc_final: 0.8518 (mp) REVERT: F 643 ARG cc_start: 0.8373 (ttt180) cc_final: 0.8085 (tpt-90) REVERT: G 346 MET cc_start: 0.8724 (tpp) cc_final: 0.8331 (mmm) REVERT: G 350 GLN cc_start: 0.8948 (tt0) cc_final: 0.8588 (tm-30) REVERT: G 359 ARG cc_start: 0.8065 (tpt-90) cc_final: 0.7823 (tpt-90) REVERT: G 392 MET cc_start: 0.7279 (mpt) cc_final: 0.7052 (mpp) REVERT: G 462 LEU cc_start: 0.8983 (tp) cc_final: 0.8677 (tp) REVERT: G 541 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7166 (tm-30) REVERT: G 643 ARG cc_start: 0.8281 (ttt180) cc_final: 0.8057 (ttt-90) REVERT: G 649 ARG cc_start: 0.8586 (mmt180) cc_final: 0.8231 (mmm-85) REVERT: H 291 TYR cc_start: 0.9316 (m-80) cc_final: 0.9042 (m-80) REVERT: H 302 LYS cc_start: 0.8989 (mmmt) cc_final: 0.8369 (tptt) REVERT: H 346 MET cc_start: 0.8681 (tpp) cc_final: 0.8380 (mmm) REVERT: H 350 GLN cc_start: 0.8977 (tt0) cc_final: 0.8758 (tm-30) REVERT: H 392 MET cc_start: 0.7124 (mpt) cc_final: 0.6915 (mpp) REVERT: H 541 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7201 (tm-30) REVERT: I 302 LYS cc_start: 0.8924 (mmmt) cc_final: 0.8227 (tptt) REVERT: I 346 MET cc_start: 0.8575 (tpp) cc_final: 0.8238 (mmm) REVERT: I 350 GLN cc_start: 0.8968 (tt0) cc_final: 0.8762 (tm-30) REVERT: I 460 MET cc_start: 0.8036 (ttp) cc_final: 0.7638 (ttm) REVERT: I 462 LEU cc_start: 0.9051 (tp) cc_final: 0.8478 (mp) REVERT: I 541 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7487 (tm-30) REVERT: J 291 TYR cc_start: 0.9278 (m-80) cc_final: 0.9053 (m-80) REVERT: J 346 MET cc_start: 0.8763 (tpp) cc_final: 0.8419 (mmm) REVERT: J 350 GLN cc_start: 0.9008 (tt0) cc_final: 0.8668 (tm-30) REVERT: J 392 MET cc_start: 0.7244 (mpt) cc_final: 0.6923 (mpp) REVERT: J 462 LEU cc_start: 0.8964 (tp) cc_final: 0.8652 (tp) REVERT: J 487 GLU cc_start: 0.7850 (pt0) cc_final: 0.7616 (pt0) REVERT: J 491 MET cc_start: 0.7497 (ttt) cc_final: 0.7241 (ttm) REVERT: J 541 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7253 (tm-30) REVERT: J 643 ARG cc_start: 0.8394 (ttt180) cc_final: 0.8019 (tpt-90) REVERT: J 649 ARG cc_start: 0.8611 (mmt180) cc_final: 0.8313 (mmm-85) REVERT: K 291 TYR cc_start: 0.9260 (m-80) cc_final: 0.9042 (m-80) REVERT: K 346 MET cc_start: 0.8704 (tpp) cc_final: 0.8486 (mmm) REVERT: K 350 GLN cc_start: 0.8997 (tt0) cc_final: 0.8677 (tm-30) REVERT: K 357 ASP cc_start: 0.7202 (t0) cc_final: 0.6984 (t0) REVERT: K 392 MET cc_start: 0.7265 (mpt) cc_final: 0.6779 (mpp) REVERT: K 541 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7084 (tm-30) REVERT: K 639 TYR cc_start: 0.8437 (t80) cc_final: 0.7920 (t80) REVERT: K 643 ARG cc_start: 0.8479 (ttt180) cc_final: 0.8188 (ttt-90) REVERT: L 291 TYR cc_start: 0.9265 (m-80) cc_final: 0.9007 (m-80) REVERT: L 346 MET cc_start: 0.8568 (tpp) cc_final: 0.8225 (mmm) REVERT: L 350 GLN cc_start: 0.8980 (tt0) cc_final: 0.8631 (tm-30) REVERT: L 541 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7359 (tm-30) REVERT: L 639 TYR cc_start: 0.8251 (t80) cc_final: 0.7825 (t80) REVERT: L 643 ARG cc_start: 0.8367 (ttt180) cc_final: 0.7876 (ttt-90) REVERT: M 291 TYR cc_start: 0.9291 (m-80) cc_final: 0.9089 (m-80) REVERT: M 346 MET cc_start: 0.8787 (tpp) cc_final: 0.8493 (mmm) REVERT: M 350 GLN cc_start: 0.8886 (tt0) cc_final: 0.8667 (tm-30) REVERT: M 392 MET cc_start: 0.7443 (mpt) cc_final: 0.7155 (mpp) REVERT: M 462 LEU cc_start: 0.8988 (tp) cc_final: 0.8541 (tt) REVERT: M 541 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7413 (tm-30) REVERT: N 346 MET cc_start: 0.8657 (tpp) cc_final: 0.8393 (mmm) REVERT: N 350 GLN cc_start: 0.8932 (tt0) cc_final: 0.8636 (tm-30) REVERT: N 392 MET cc_start: 0.7469 (mpt) cc_final: 0.7257 (mpp) REVERT: N 541 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7324 (tm-30) REVERT: O 291 TYR cc_start: 0.9300 (m-80) cc_final: 0.9016 (m-80) REVERT: O 346 MET cc_start: 0.8633 (tpp) cc_final: 0.8398 (mmm) REVERT: O 350 GLN cc_start: 0.8963 (tt0) cc_final: 0.8683 (tm-30) REVERT: O 460 MET cc_start: 0.7921 (ttp) cc_final: 0.7520 (ttm) REVERT: O 462 LEU cc_start: 0.9050 (tp) cc_final: 0.8503 (mp) REVERT: O 541 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7480 (tm-30) REVERT: O 649 ARG cc_start: 0.8420 (mmt180) cc_final: 0.8204 (mmm-85) outliers start: 30 outliers final: 15 residues processed: 1167 average time/residue: 0.6199 time to fit residues: 1112.3996 Evaluate side-chains 650 residues out of total 4350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 635 time to evaluate : 4.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain I residue 477 THR Chi-restraints excluded: chain J residue 477 THR Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain L residue 477 THR Chi-restraints excluded: chain M residue 477 THR Chi-restraints excluded: chain N residue 477 THR Chi-restraints excluded: chain O residue 477 THR 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: 8.9990 chunk 135 optimal weight: 3.9990 chunk 268 optimal weight: 6.9990 chunk 212 optimal weight: 10.0000 chunk 411 optimal weight: 10.0000 chunk 159 optimal weight: 0.0050 chunk 250 optimal weight: 8.9990 chunk 306 optimal weight: 0.4980 chunk 476 optimal weight: 4.9990 overall best weight: 2.0598 ------------------------------------------------------------------------------- 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: 0.7659 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 39840 Z= 0.234 Angle : 0.634 8.748 53895 Z= 0.333 Chirality : 0.048 0.170 6480 Planarity : 0.005 0.041 6990 Dihedral : 5.643 34.486 5430 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 2.99 % Allowed : 13.29 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.10), residues: 5130 helix: -1.51 (0.13), residues: 1155 sheet: -2.54 (0.10), residues: 2535 loop : -3.07 (0.13), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP O 384 HIS 0.003 0.001 HIS N 364 PHE 0.020 0.002 PHE L 447 TYR 0.022 0.001 TYR O 639 ARG 0.007 0.001 ARG L 626 *********************** 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 832 residues out of total 4350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 702 time to evaluate : 4.844 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: A 302 LYS cc_start: 0.8799 (mmmt) cc_final: 0.8356 (tptt) REVERT: A 332 LYS cc_start: 0.9003 (ttmm) cc_final: 0.8687 (tmtt) REVERT: A 333 HIS cc_start: 0.8389 (m90) cc_final: 0.8085 (m90) REVERT: A 346 MET cc_start: 0.8676 (tpp) cc_final: 0.8352 (mmm) REVERT: A 350 GLN cc_start: 0.9028 (tt0) cc_final: 0.8693 (pp30) REVERT: A 392 MET cc_start: 0.7731 (mpt) cc_final: 0.7318 (mpp) REVERT: A 462 LEU cc_start: 0.9056 (tp) cc_final: 0.8739 (tp) REVERT: A 541 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7230 (tm-30) REVERT: A 639 TYR cc_start: 0.8136 (t80) cc_final: 0.7877 (t80) REVERT: A 649 ARG cc_start: 0.8518 (mmt180) cc_final: 0.8206 (mmm-85) REVERT: B 346 MET cc_start: 0.8873 (tpp) cc_final: 0.8389 (tpp) REVERT: B 350 GLN cc_start: 0.9099 (tt0) cc_final: 0.8677 (pp30) REVERT: B 392 MET cc_start: 0.7558 (mpt) cc_final: 0.7076 (mpp) REVERT: B 447 PHE cc_start: 0.8386 (t80) cc_final: 0.7885 (t80) REVERT: B 462 LEU cc_start: 0.8944 (tp) cc_final: 0.8685 (tp) REVERT: B 553 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7133 (tm) REVERT: B 639 TYR cc_start: 0.8123 (t80) cc_final: 0.7845 (t80) REVERT: B 649 ARG cc_start: 0.8738 (mmt180) cc_final: 0.8368 (mmm-85) REVERT: C 332 LYS cc_start: 0.9059 (ttmm) cc_final: 0.8820 (tmtt) REVERT: C 333 HIS cc_start: 0.8406 (m-70) cc_final: 0.7529 (m-70) REVERT: C 392 MET cc_start: 0.7768 (mpt) cc_final: 0.7328 (mpp) REVERT: C 462 LEU cc_start: 0.9084 (tp) cc_final: 0.8868 (tp) REVERT: C 468 ASN cc_start: 0.8150 (OUTLIER) cc_final: 0.7329 (p0) REVERT: C 626 ARG cc_start: 0.7549 (mtm-85) cc_final: 0.6344 (mmm-85) REVERT: C 639 TYR cc_start: 0.8140 (t80) cc_final: 0.7897 (t80) REVERT: C 649 ARG cc_start: 0.8692 (mmt180) cc_final: 0.8283 (mmm-85) REVERT: D 333 HIS cc_start: 0.8627 (m90) cc_final: 0.7821 (m-70) REVERT: D 346 MET cc_start: 0.8727 (tpp) cc_final: 0.8421 (tpp) REVERT: D 350 GLN cc_start: 0.9005 (tt0) cc_final: 0.8582 (pp30) REVERT: D 359 ARG cc_start: 0.7851 (tpt-90) cc_final: 0.7515 (tpt-90) REVERT: D 392 MET cc_start: 0.7571 (mpt) cc_final: 0.6973 (mpp) REVERT: D 447 PHE cc_start: 0.8488 (t80) cc_final: 0.7967 (t80) REVERT: D 460 MET cc_start: 0.7877 (ttp) cc_final: 0.7576 (ttm) REVERT: D 462 LEU cc_start: 0.8917 (tp) cc_final: 0.8636 (tp) REVERT: D 487 GLU cc_start: 0.7807 (pt0) cc_final: 0.7524 (pt0) REVERT: D 540 ILE cc_start: 0.8525 (tt) cc_final: 0.8304 (mp) REVERT: D 541 GLU cc_start: 0.7373 (mt-10) cc_final: 0.6910 (tm-30) REVERT: D 639 TYR cc_start: 0.8051 (t80) cc_final: 0.7794 (t80) REVERT: D 649 ARG cc_start: 0.8487 (mmt180) cc_final: 0.8183 (mmm-85) REVERT: E 346 MET cc_start: 0.8803 (tpp) cc_final: 0.8492 (mmm) REVERT: E 350 GLN cc_start: 0.8922 (tt0) cc_final: 0.8491 (pp30) REVERT: E 354 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8146 (mt-10) REVERT: E 359 ARG cc_start: 0.7861 (tpt-90) cc_final: 0.7556 (tpt-90) REVERT: E 392 MET cc_start: 0.7739 (mpt) cc_final: 0.7348 (mpp) REVERT: E 442 GLN cc_start: 0.9308 (pp30) cc_final: 0.8980 (pp30) REVERT: E 460 MET cc_start: 0.7058 (ttm) cc_final: 0.6543 (ttm) REVERT: E 612 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7489 (tm-30) REVERT: E 639 TYR cc_start: 0.8052 (t80) cc_final: 0.7775 (t80) REVERT: E 649 ARG cc_start: 0.8580 (mmt180) cc_final: 0.8243 (mmm-85) REVERT: F 346 MET cc_start: 0.8678 (tpp) cc_final: 0.8459 (tpp) REVERT: F 350 GLN cc_start: 0.9038 (tt0) cc_final: 0.8589 (pp30) REVERT: F 359 ARG cc_start: 0.7816 (tpt-90) cc_final: 0.7455 (tpt-90) REVERT: F 392 MET cc_start: 0.7596 (mpt) cc_final: 0.7059 (mpp) REVERT: F 447 PHE cc_start: 0.8522 (t80) cc_final: 0.8263 (t80) REVERT: F 462 LEU cc_start: 0.8999 (tp) cc_final: 0.8731 (tp) REVERT: F 540 ILE cc_start: 0.8689 (tt) cc_final: 0.8441 (mp) REVERT: F 652 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.7053 (mt0) REVERT: G 332 LYS cc_start: 0.8784 (tmtt) cc_final: 0.8287 (ttmm) REVERT: G 350 GLN cc_start: 0.9023 (tt0) cc_final: 0.8576 (pp30) REVERT: G 359 ARG cc_start: 0.8029 (tpt-90) cc_final: 0.7757 (tpt-90) REVERT: G 392 MET cc_start: 0.7754 (mpt) cc_final: 0.7266 (mpp) REVERT: G 462 LEU cc_start: 0.9051 (tp) cc_final: 0.8705 (tp) REVERT: G 468 ASN cc_start: 0.7980 (OUTLIER) cc_final: 0.7432 (p0) REVERT: G 553 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7223 (tp) REVERT: G 649 ARG cc_start: 0.8636 (mmt180) cc_final: 0.8265 (mmm-85) REVERT: H 346 MET cc_start: 0.8642 (tpp) cc_final: 0.8280 (tpp) REVERT: H 350 GLN cc_start: 0.9131 (tt0) cc_final: 0.8710 (pp30) REVERT: H 580 MET cc_start: 0.8562 (mpp) cc_final: 0.8230 (mpp) REVERT: H 614 ARG cc_start: 0.8300 (tmm-80) cc_final: 0.7994 (mtp-110) REVERT: I 332 LYS cc_start: 0.9101 (ttmt) cc_final: 0.8679 (tmtt) REVERT: I 346 MET cc_start: 0.8604 (tpp) cc_final: 0.8328 (mmm) REVERT: I 350 GLN cc_start: 0.9093 (tt0) cc_final: 0.8674 (pp30) REVERT: I 359 ARG cc_start: 0.7777 (tpt-90) cc_final: 0.7356 (tpt-90) REVERT: I 366 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7154 (pm20) REVERT: I 460 MET cc_start: 0.8008 (ttp) cc_final: 0.7545 (ttm) REVERT: I 462 LEU cc_start: 0.9036 (tp) cc_final: 0.8586 (mp) REVERT: I 553 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7394 (tp) REVERT: I 639 TYR cc_start: 0.8028 (t80) cc_final: 0.7759 (t80) REVERT: J 332 LYS cc_start: 0.8957 (ttmm) cc_final: 0.8713 (tmtt) REVERT: J 350 GLN cc_start: 0.9018 (tt0) cc_final: 0.8566 (pp30) REVERT: J 359 ARG cc_start: 0.7910 (tpt-90) cc_final: 0.7672 (tpt-90) REVERT: J 392 MET cc_start: 0.7543 (mpt) cc_final: 0.7134 (mpp) REVERT: J 462 LEU cc_start: 0.8981 (tp) cc_final: 0.8687 (tp) REVERT: J 487 GLU cc_start: 0.7816 (pt0) cc_final: 0.7544 (pt0) REVERT: J 649 ARG cc_start: 0.8760 (mmt180) cc_final: 0.8385 (mmm-85) REVERT: K 346 MET cc_start: 0.8749 (tpp) cc_final: 0.8476 (mmm) REVERT: K 350 GLN cc_start: 0.9012 (tt0) cc_final: 0.8564 (pp30) REVERT: K 392 MET cc_start: 0.7486 (mpt) cc_final: 0.7038 (mpp) REVERT: K 462 LEU cc_start: 0.9051 (tp) cc_final: 0.8778 (tp) REVERT: K 516 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7848 (mm-30) REVERT: K 523 MET cc_start: 0.6885 (ttt) cc_final: 0.6623 (ttt) REVERT: K 554 ASP cc_start: 0.7649 (t0) cc_final: 0.7415 (m-30) REVERT: K 639 TYR cc_start: 0.8200 (t80) cc_final: 0.7421 (t80) REVERT: K 643 ARG cc_start: 0.8239 (ttt180) cc_final: 0.8007 (ttt-90) REVERT: L 346 MET cc_start: 0.8589 (tpp) cc_final: 0.8231 (mmm) REVERT: L 350 GLN cc_start: 0.9059 (tt0) cc_final: 0.8553 (pp30) REVERT: L 392 MET cc_start: 0.6914 (mpp) cc_final: 0.6673 (mpp) REVERT: L 442 GLN cc_start: 0.9355 (pp30) cc_final: 0.8999 (pp30) REVERT: L 468 ASN cc_start: 0.8010 (OUTLIER) cc_final: 0.7374 (p0) REVERT: L 516 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7818 (mm-30) REVERT: L 639 TYR cc_start: 0.7968 (t80) cc_final: 0.7684 (t80) REVERT: M 332 LYS cc_start: 0.9036 (ttmt) cc_final: 0.8809 (tmtt) REVERT: M 346 MET cc_start: 0.8822 (tpp) cc_final: 0.8552 (mmm) REVERT: M 350 GLN cc_start: 0.8931 (tt0) cc_final: 0.8694 (pp30) REVERT: M 462 LEU cc_start: 0.9001 (tp) cc_final: 0.8707 (tp) REVERT: M 626 ARG cc_start: 0.7439 (mtm-85) cc_final: 0.6334 (mmm160) REVERT: N 346 MET cc_start: 0.8659 (tpp) cc_final: 0.8414 (mmm) REVERT: N 350 GLN cc_start: 0.9021 (tt0) cc_final: 0.8701 (pp30) REVERT: N 354 GLU cc_start: 0.8442 (mt-10) cc_final: 0.7931 (mt-10) REVERT: N 392 MET cc_start: 0.7823 (mpt) cc_final: 0.7373 (mpp) REVERT: N 460 MET cc_start: 0.7221 (ttm) cc_final: 0.6888 (ttm) REVERT: N 553 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7185 (tp) REVERT: O 291 TYR cc_start: 0.9173 (m-80) cc_final: 0.8943 (m-80) REVERT: O 346 MET cc_start: 0.8662 (tpp) cc_final: 0.8387 (mmm) REVERT: O 350 GLN cc_start: 0.9027 (tt0) cc_final: 0.8659 (pp30) REVERT: O 359 ARG cc_start: 0.7830 (tpt-90) cc_final: 0.7576 (tpt-90) REVERT: O 460 MET cc_start: 0.7940 (ttp) cc_final: 0.7577 (ttm) REVERT: O 462 LEU cc_start: 0.9059 (tp) cc_final: 0.8820 (tp) REVERT: O 649 ARG cc_start: 0.8337 (mmt180) cc_final: 0.8108 (mmm-85) outliers start: 130 outliers final: 67 residues processed: 811 average time/residue: 0.5636 time to fit residues: 718.3988 Evaluate side-chains 636 residues out of total 4350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 558 time to evaluate : 4.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain C residue 468 ASN Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 575 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 652 GLN Chi-restraints excluded: chain F residue 664 ILE Chi-restraints excluded: chain G residue 353 ILE Chi-restraints excluded: chain G residue 468 ASN Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 496 VAL Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 553 LEU Chi-restraints excluded: chain G residue 575 VAL Chi-restraints excluded: chain H residue 366 GLU Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 480 ILE Chi-restraints excluded: chain H residue 575 VAL Chi-restraints excluded: chain H residue 593 LEU Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 477 THR Chi-restraints excluded: chain I residue 540 ILE Chi-restraints excluded: chain I residue 553 LEU Chi-restraints excluded: chain I residue 593 LEU Chi-restraints excluded: chain J residue 477 THR Chi-restraints excluded: chain J residue 480 ILE Chi-restraints excluded: chain J residue 482 THR Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 516 GLU Chi-restraints excluded: chain K residue 593 LEU Chi-restraints excluded: chain K residue 664 ILE Chi-restraints excluded: chain L residue 402 ILE Chi-restraints excluded: chain L residue 468 ASN Chi-restraints excluded: chain L residue 477 THR Chi-restraints excluded: chain L residue 516 GLU Chi-restraints excluded: chain L residue 575 VAL Chi-restraints excluded: chain L residue 593 LEU Chi-restraints excluded: chain M residue 477 THR Chi-restraints excluded: chain M residue 540 ILE Chi-restraints excluded: chain M residue 573 LEU Chi-restraints excluded: chain M residue 574 ILE Chi-restraints excluded: chain M residue 593 LEU Chi-restraints excluded: chain M residue 664 ILE Chi-restraints excluded: chain N residue 477 THR Chi-restraints excluded: chain N residue 496 VAL Chi-restraints excluded: chain N residue 553 LEU Chi-restraints excluded: chain N residue 575 VAL Chi-restraints excluded: chain N residue 664 ILE Chi-restraints excluded: chain O residue 353 ILE Chi-restraints excluded: chain O residue 366 GLU Chi-restraints excluded: chain O residue 402 ILE Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 540 ILE Chi-restraints excluded: chain O residue 575 VAL Chi-restraints excluded: chain O residue 664 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 264 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 396 optimal weight: 6.9990 chunk 324 optimal weight: 7.9990 chunk 131 optimal weight: 9.9990 chunk 477 optimal weight: 4.9990 chunk 515 optimal weight: 7.9990 chunk 425 optimal weight: 1.9990 chunk 473 optimal weight: 6.9990 chunk 162 optimal weight: 0.9990 chunk 383 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 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** 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 430 ASN ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 652 GLN J 430 ASN ** 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** O 430 ASN ** O 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 652 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 39840 Z= 0.276 Angle : 0.608 9.193 53895 Z= 0.316 Chirality : 0.047 0.159 6480 Planarity : 0.004 0.064 6990 Dihedral : 5.397 39.010 5430 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 4.00 % Allowed : 14.99 % Favored : 81.01 % 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: -3.29 (0.11), residues: 5130 helix: -0.44 (0.15), residues: 1155 sheet: -2.32 (0.10), residues: 2475 loop : -2.88 (0.14), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 384 HIS 0.004 0.001 HIS D 364 PHE 0.017 0.002 PHE D 619 TYR 0.015 0.001 TYR F 291 ARG 0.007 0.001 ARG J 560 *********************** 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 792 residues out of total 4350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 618 time to evaluate : 4.413 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: A 302 LYS cc_start: 0.8858 (mmmt) cc_final: 0.8363 (tptt) REVERT: A 332 LYS cc_start: 0.8936 (ttmm) cc_final: 0.8668 (tmtt) REVERT: A 333 HIS cc_start: 0.8514 (m90) cc_final: 0.8214 (m90) REVERT: A 346 MET cc_start: 0.8684 (tpp) cc_final: 0.8405 (mmm) REVERT: A 392 MET cc_start: 0.7805 (mpt) cc_final: 0.7368 (mpp) REVERT: A 462 LEU cc_start: 0.9017 (tp) cc_final: 0.8748 (tp) REVERT: A 541 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7225 (tm-30) REVERT: A 649 ARG cc_start: 0.8550 (mmt180) cc_final: 0.8167 (mmm-85) REVERT: B 346 MET cc_start: 0.8831 (tpp) cc_final: 0.8321 (tpp) REVERT: B 350 GLN cc_start: 0.9139 (tt0) cc_final: 0.8663 (pp30) REVERT: B 359 ARG cc_start: 0.7886 (tpt-90) cc_final: 0.7470 (tpt-90) REVERT: B 392 MET cc_start: 0.7546 (mpt) cc_final: 0.6946 (mpp) REVERT: B 462 LEU cc_start: 0.8937 (tp) cc_final: 0.8459 (mp) REVERT: B 540 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8296 (mp) REVERT: B 649 ARG cc_start: 0.8789 (mmt180) cc_final: 0.8387 (mmm-85) REVERT: C 346 MET cc_start: 0.8690 (tpp) cc_final: 0.8314 (mmm) REVERT: C 392 MET cc_start: 0.7856 (mpt) cc_final: 0.7475 (mpp) REVERT: C 468 ASN cc_start: 0.8114 (OUTLIER) cc_final: 0.7327 (p0) REVERT: C 639 TYR cc_start: 0.8009 (t80) cc_final: 0.7755 (t80) REVERT: C 649 ARG cc_start: 0.8742 (mmt180) cc_final: 0.8345 (mmm-85) REVERT: D 332 LYS cc_start: 0.8762 (tmtt) cc_final: 0.8295 (ttmm) REVERT: D 346 MET cc_start: 0.8733 (tpp) cc_final: 0.8460 (tpp) REVERT: D 392 MET cc_start: 0.7633 (mpt) cc_final: 0.7034 (mpp) REVERT: D 460 MET cc_start: 0.7778 (ttp) cc_final: 0.7461 (ttm) REVERT: D 487 GLU cc_start: 0.7833 (pt0) cc_final: 0.7514 (pt0) REVERT: D 541 GLU cc_start: 0.7319 (mt-10) cc_final: 0.7077 (tm-30) REVERT: D 649 ARG cc_start: 0.8489 (mmt180) cc_final: 0.8158 (mmm-85) REVERT: E 346 MET cc_start: 0.8867 (tpp) cc_final: 0.8484 (mmm) REVERT: E 366 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7472 (pt0) REVERT: E 392 MET cc_start: 0.7909 (mpt) cc_final: 0.7462 (mpp) REVERT: E 462 LEU cc_start: 0.8963 (tp) cc_final: 0.8418 (mp) REVERT: E 540 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8014 (pt) REVERT: E 612 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7474 (tm-30) REVERT: E 649 ARG cc_start: 0.8571 (mmt180) cc_final: 0.8212 (mmm-85) REVERT: F 299 ASP cc_start: 0.8097 (m-30) cc_final: 0.7785 (m-30) REVERT: F 346 MET cc_start: 0.8711 (tpp) cc_final: 0.8465 (tpp) REVERT: F 350 GLN cc_start: 0.9079 (tt0) cc_final: 0.8666 (pp30) REVERT: F 359 ARG cc_start: 0.7813 (tpt-90) cc_final: 0.7566 (tpt-90) REVERT: F 392 MET cc_start: 0.7708 (mpt) cc_final: 0.7185 (mpp) REVERT: F 462 LEU cc_start: 0.8976 (tp) cc_final: 0.8470 (mp) REVERT: F 540 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8039 (pt) REVERT: G 332 LYS cc_start: 0.8887 (tmtt) cc_final: 0.8574 (tmtt) REVERT: G 359 ARG cc_start: 0.8049 (tpt-90) cc_final: 0.7782 (tpt-90) REVERT: G 392 MET cc_start: 0.7772 (mpt) cc_final: 0.7306 (mpp) REVERT: G 462 LEU cc_start: 0.8969 (tp) cc_final: 0.8488 (mp) REVERT: G 468 ASN cc_start: 0.7942 (OUTLIER) cc_final: 0.7363 (p0) REVERT: G 639 TYR cc_start: 0.7904 (t80) cc_final: 0.7702 (t80) REVERT: G 649 ARG cc_start: 0.8855 (mmt180) cc_final: 0.8341 (mmm160) REVERT: H 328 ILE cc_start: 0.9114 (mm) cc_final: 0.8887 (mm) REVERT: H 346 MET cc_start: 0.8663 (tpp) cc_final: 0.8309 (tpp) REVERT: H 350 GLN cc_start: 0.9142 (tt0) cc_final: 0.8893 (pp30) REVERT: H 554 ASP cc_start: 0.7683 (t0) cc_final: 0.7368 (m-30) REVERT: H 580 MET cc_start: 0.8460 (mpp) cc_final: 0.8128 (mpp) REVERT: I 332 LYS cc_start: 0.9084 (ttmt) cc_final: 0.8832 (tmtt) REVERT: I 346 MET cc_start: 0.8678 (tpp) cc_final: 0.8286 (mmm) REVERT: I 350 GLN cc_start: 0.9135 (tt0) cc_final: 0.8609 (pp30) REVERT: I 366 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7311 (pm20) REVERT: I 371 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7584 (tm-30) REVERT: I 460 MET cc_start: 0.7958 (ttp) cc_final: 0.7494 (ttm) REVERT: I 462 LEU cc_start: 0.9024 (tp) cc_final: 0.8554 (mp) REVERT: J 332 LYS cc_start: 0.8916 (ttmm) cc_final: 0.8714 (tmtt) REVERT: J 346 MET cc_start: 0.8842 (tpp) cc_final: 0.8335 (mmm) REVERT: J 350 GLN cc_start: 0.9058 (tt0) cc_final: 0.8475 (pp30) REVERT: J 392 MET cc_start: 0.7631 (mpt) cc_final: 0.7162 (mpp) REVERT: J 462 LEU cc_start: 0.8978 (tp) cc_final: 0.8679 (tp) REVERT: J 487 GLU cc_start: 0.7824 (pt0) cc_final: 0.7539 (pt0) REVERT: J 612 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7491 (tm-30) REVERT: J 626 ARG cc_start: 0.7481 (mtm-85) cc_final: 0.7239 (mtm-85) REVERT: J 649 ARG cc_start: 0.8747 (mmt180) cc_final: 0.8362 (mmm-85) REVERT: K 346 MET cc_start: 0.8753 (tpp) cc_final: 0.8468 (tpp) REVERT: K 350 GLN cc_start: 0.9084 (tt0) cc_final: 0.8482 (pp30) REVERT: K 392 MET cc_start: 0.7558 (mpt) cc_final: 0.7106 (mpp) REVERT: K 462 LEU cc_start: 0.8930 (tp) cc_final: 0.8423 (mp) REVERT: K 554 ASP cc_start: 0.7740 (t0) cc_final: 0.7517 (m-30) REVERT: K 610 LYS cc_start: 0.8596 (ttmm) cc_final: 0.8272 (ttmm) REVERT: K 639 TYR cc_start: 0.8063 (t80) cc_final: 0.7654 (t80) REVERT: L 346 MET cc_start: 0.8560 (tpp) cc_final: 0.8279 (mmm) REVERT: L 350 GLN cc_start: 0.9052 (tt0) cc_final: 0.8258 (pp30) REVERT: L 354 GLU cc_start: 0.8601 (mt-10) cc_final: 0.7973 (pt0) REVERT: L 359 ARG cc_start: 0.7887 (tpt-90) cc_final: 0.7652 (tpt-90) REVERT: L 392 MET cc_start: 0.7240 (mpp) cc_final: 0.6973 (mpp) REVERT: L 442 GLN cc_start: 0.9321 (pp30) cc_final: 0.9036 (pp30) REVERT: L 468 ASN cc_start: 0.7815 (OUTLIER) cc_final: 0.7220 (p0) REVERT: L 516 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7888 (mm-30) REVERT: L 639 TYR cc_start: 0.7904 (t80) cc_final: 0.7692 (t80) REVERT: M 346 MET cc_start: 0.8763 (tpp) cc_final: 0.8518 (mmm) REVERT: M 350 GLN cc_start: 0.8973 (tt0) cc_final: 0.8715 (pp30) REVERT: M 460 MET cc_start: 0.7180 (ttm) cc_final: 0.6589 (ttm) REVERT: M 462 LEU cc_start: 0.8963 (tp) cc_final: 0.8361 (mp) REVERT: M 468 ASN cc_start: 0.8060 (OUTLIER) cc_final: 0.7547 (p0) REVERT: M 523 MET cc_start: 0.6955 (ttm) cc_final: 0.6746 (ttm) REVERT: N 350 GLN cc_start: 0.9081 (tt0) cc_final: 0.8212 (pp30) REVERT: N 354 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7692 (pt0) REVERT: N 392 MET cc_start: 0.7829 (mpt) cc_final: 0.7349 (mpp) REVERT: N 460 MET cc_start: 0.7231 (ttm) cc_final: 0.6859 (ttm) REVERT: O 346 MET cc_start: 0.8662 (tpp) cc_final: 0.8440 (mmm) REVERT: O 350 GLN cc_start: 0.9063 (tt0) cc_final: 0.8596 (pp30) REVERT: O 460 MET cc_start: 0.7967 (ttp) cc_final: 0.7500 (ttm) REVERT: O 462 LEU cc_start: 0.9022 (tp) cc_final: 0.8543 (mp) REVERT: O 649 ARG cc_start: 0.8584 (mmt180) cc_final: 0.8303 (mmm-85) outliers start: 174 outliers final: 114 residues processed: 766 average time/residue: 0.5512 time to fit residues: 671.1320 Evaluate side-chains 649 residues out of total 4350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 525 time to evaluate : 4.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 468 ASN Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 468 ASN Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 468 ASN Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 482 THR Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 550 GLN Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 468 ASN Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 540 ILE Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 575 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain G residue 353 ILE Chi-restraints excluded: chain G residue 366 GLU Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 468 ASN Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 482 THR Chi-restraints excluded: chain G residue 496 VAL Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 575 VAL Chi-restraints excluded: chain H residue 366 GLU Chi-restraints excluded: chain H residue 468 ASN Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 550 GLN Chi-restraints excluded: chain H residue 575 VAL Chi-restraints excluded: chain H residue 593 LEU Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 433 THR Chi-restraints excluded: chain I residue 468 ASN Chi-restraints excluded: chain I residue 477 THR Chi-restraints excluded: chain I residue 496 VAL Chi-restraints excluded: chain I residue 540 ILE Chi-restraints excluded: chain I residue 575 VAL Chi-restraints excluded: chain I residue 593 LEU Chi-restraints excluded: chain J residue 366 GLU Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain J residue 468 ASN Chi-restraints excluded: chain J residue 477 THR Chi-restraints excluded: chain J residue 480 ILE Chi-restraints excluded: chain J residue 482 THR Chi-restraints excluded: chain J residue 550 GLN Chi-restraints excluded: chain J residue 553 LEU Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 468 ASN Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 482 THR Chi-restraints excluded: chain K residue 575 VAL Chi-restraints excluded: chain K residue 576 LEU Chi-restraints excluded: chain K residue 593 LEU Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain L residue 468 ASN Chi-restraints excluded: chain L residue 477 THR Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 516 GLU Chi-restraints excluded: chain L residue 575 VAL Chi-restraints excluded: chain L residue 593 LEU Chi-restraints excluded: chain M residue 366 GLU Chi-restraints excluded: chain M residue 433 THR Chi-restraints excluded: chain M residue 468 ASN Chi-restraints excluded: chain M residue 477 THR Chi-restraints excluded: chain M residue 496 VAL Chi-restraints excluded: chain M residue 540 ILE Chi-restraints excluded: chain M residue 573 LEU Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 593 LEU Chi-restraints excluded: chain N residue 366 GLU Chi-restraints excluded: chain N residue 433 THR Chi-restraints excluded: chain N residue 468 ASN Chi-restraints excluded: chain N residue 477 THR Chi-restraints excluded: chain N residue 482 THR Chi-restraints excluded: chain N residue 496 VAL Chi-restraints excluded: chain N residue 575 VAL Chi-restraints excluded: chain N residue 579 LEU Chi-restraints excluded: chain O residue 353 ILE Chi-restraints excluded: chain O residue 366 GLU Chi-restraints excluded: chain O residue 433 THR Chi-restraints excluded: chain O residue 468 ASN Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 482 THR Chi-restraints excluded: chain O residue 540 ILE Chi-restraints excluded: chain O residue 575 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 471 optimal weight: 8.9990 chunk 359 optimal weight: 10.0000 chunk 247 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 227 optimal weight: 5.9990 chunk 320 optimal weight: 1.9990 chunk 479 optimal weight: 5.9990 chunk 507 optimal weight: 1.9990 chunk 250 optimal weight: 1.9990 chunk 454 optimal weight: 8.9990 chunk 136 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 ASN ** D 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 ASN ** E 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 430 ASN ** G 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 615 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** M 615 ASN ** N 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 615 ASN O 430 ASN ** O 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 602 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 39840 Z= 0.336 Angle : 0.637 10.557 53895 Z= 0.328 Chirality : 0.047 0.166 6480 Planarity : 0.004 0.041 6990 Dihedral : 5.494 41.224 5430 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 4.21 % Allowed : 16.21 % Favored : 79.59 % 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: -3.09 (0.11), residues: 5130 helix: 0.01 (0.16), residues: 1140 sheet: -2.30 (0.10), residues: 2505 loop : -2.79 (0.14), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 384 HIS 0.005 0.001 HIS D 364 PHE 0.023 0.002 PHE H 619 TYR 0.022 0.001 TYR J 639 ARG 0.008 0.001 ARG M 626 *********************** 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 746 residues out of total 4350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 563 time to evaluate : 4.516 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: A 302 LYS cc_start: 0.8890 (mmmt) cc_final: 0.8306 (tptt) REVERT: A 332 LYS cc_start: 0.8990 (ttmm) cc_final: 0.8744 (tmtt) REVERT: A 333 HIS cc_start: 0.8604 (m90) cc_final: 0.8334 (m90) REVERT: A 350 GLN cc_start: 0.9096 (OUTLIER) cc_final: 0.8849 (tm-30) REVERT: A 392 MET cc_start: 0.7941 (mpt) cc_final: 0.7621 (mpt) REVERT: A 462 LEU cc_start: 0.9022 (tp) cc_final: 0.8498 (mp) REVERT: A 649 ARG cc_start: 0.8624 (mmt180) cc_final: 0.8046 (mmm160) REVERT: B 346 MET cc_start: 0.8880 (tpp) cc_final: 0.8358 (tpp) REVERT: B 350 GLN cc_start: 0.9144 (tt0) cc_final: 0.8708 (pp30) REVERT: B 392 MET cc_start: 0.7654 (mpt) cc_final: 0.6908 (mpp) REVERT: B 462 LEU cc_start: 0.8937 (tp) cc_final: 0.8737 (tp) REVERT: B 649 ARG cc_start: 0.8776 (mmt180) cc_final: 0.8330 (mmm-85) REVERT: C 462 LEU cc_start: 0.9034 (tp) cc_final: 0.8460 (mp) REVERT: C 468 ASN cc_start: 0.8102 (OUTLIER) cc_final: 0.7333 (p0) REVERT: C 540 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8068 (pt) REVERT: C 629 MET cc_start: 0.6385 (tmm) cc_final: 0.6063 (tmm) REVERT: C 649 ARG cc_start: 0.8727 (mmt180) cc_final: 0.8304 (mmm-85) REVERT: D 332 LYS cc_start: 0.8754 (tmtt) cc_final: 0.8457 (ttmt) REVERT: D 346 MET cc_start: 0.8703 (tpp) cc_final: 0.8395 (tpp) REVERT: D 350 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8764 (tm-30) REVERT: D 392 MET cc_start: 0.7682 (mpt) cc_final: 0.7018 (mpp) REVERT: D 460 MET cc_start: 0.7849 (ttp) cc_final: 0.7253 (ttm) REVERT: D 462 LEU cc_start: 0.8878 (tp) cc_final: 0.8368 (mp) REVERT: D 487 GLU cc_start: 0.7769 (pt0) cc_final: 0.7449 (pt0) REVERT: D 540 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8136 (pt) REVERT: D 610 LYS cc_start: 0.8573 (ttmm) cc_final: 0.8340 (tttm) REVERT: D 649 ARG cc_start: 0.8604 (mmt180) cc_final: 0.8134 (mmm-85) REVERT: E 346 MET cc_start: 0.8831 (tpp) cc_final: 0.8393 (tpp) REVERT: E 350 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8731 (tm-30) REVERT: E 359 ARG cc_start: 0.7914 (tpt-90) cc_final: 0.7654 (tpt-90) REVERT: E 366 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7558 (pt0) REVERT: E 392 MET cc_start: 0.7874 (mpt) cc_final: 0.7585 (mpt) REVERT: E 462 LEU cc_start: 0.8944 (tp) cc_final: 0.8398 (mp) REVERT: E 540 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8036 (pt) REVERT: E 612 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7569 (tm-30) REVERT: E 614 ARG cc_start: 0.8363 (tmm-80) cc_final: 0.7976 (mtp-110) REVERT: E 649 ARG cc_start: 0.8643 (mmt180) cc_final: 0.8232 (mmm-85) REVERT: F 299 ASP cc_start: 0.8172 (m-30) cc_final: 0.7828 (m-30) REVERT: F 346 MET cc_start: 0.8764 (tpp) cc_final: 0.8481 (tpp) REVERT: F 350 GLN cc_start: 0.9161 (tt0) cc_final: 0.8689 (pp30) REVERT: F 354 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8100 (mt-10) REVERT: F 359 ARG cc_start: 0.7774 (tpt-90) cc_final: 0.7561 (tpt-90) REVERT: F 460 MET cc_start: 0.6798 (ttm) cc_final: 0.6314 (ttm) REVERT: F 462 LEU cc_start: 0.8951 (tp) cc_final: 0.8448 (mp) REVERT: F 540 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8043 (pt) REVERT: G 332 LYS cc_start: 0.8913 (tmtt) cc_final: 0.8613 (tmtt) REVERT: G 338 ILE cc_start: 0.9368 (mm) cc_final: 0.9166 (mm) REVERT: G 359 ARG cc_start: 0.8071 (tpt-90) cc_final: 0.7578 (tpt-90) REVERT: G 392 MET cc_start: 0.7895 (mpt) cc_final: 0.7404 (mpp) REVERT: G 462 LEU cc_start: 0.8978 (tp) cc_final: 0.8488 (mp) REVERT: G 468 ASN cc_start: 0.7918 (OUTLIER) cc_final: 0.7366 (p0) REVERT: G 649 ARG cc_start: 0.8808 (mmt180) cc_final: 0.8337 (mmm-85) REVERT: H 346 MET cc_start: 0.8647 (tpp) cc_final: 0.8198 (tpp) REVERT: H 350 GLN cc_start: 0.9227 (tt0) cc_final: 0.8873 (tm-30) REVERT: I 346 MET cc_start: 0.8853 (tpp) cc_final: 0.8376 (mmm) REVERT: I 350 GLN cc_start: 0.9150 (tt0) cc_final: 0.8634 (pp30) REVERT: I 366 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7246 (pm20) REVERT: I 371 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7761 (tm-30) REVERT: I 460 MET cc_start: 0.8056 (ttp) cc_final: 0.7554 (ttm) REVERT: I 462 LEU cc_start: 0.9029 (tp) cc_final: 0.8523 (mp) REVERT: J 350 GLN cc_start: 0.9107 (tt0) cc_final: 0.8478 (pp30) REVERT: J 359 ARG cc_start: 0.7902 (tpt-90) cc_final: 0.7600 (tpt-90) REVERT: J 366 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7426 (pt0) REVERT: J 392 MET cc_start: 0.7776 (mpt) cc_final: 0.7364 (mpt) REVERT: J 460 MET cc_start: 0.6844 (ttm) cc_final: 0.6585 (ttm) REVERT: J 462 LEU cc_start: 0.8993 (tp) cc_final: 0.8504 (mp) REVERT: J 487 GLU cc_start: 0.7794 (pt0) cc_final: 0.7496 (pt0) REVERT: J 541 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7492 (mp0) REVERT: J 612 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7594 (tm-30) REVERT: J 649 ARG cc_start: 0.8909 (mmt180) cc_final: 0.8453 (mmm-85) REVERT: K 346 MET cc_start: 0.8717 (tpp) cc_final: 0.8289 (tpp) REVERT: K 350 GLN cc_start: 0.9111 (tt0) cc_final: 0.8516 (pp30) REVERT: K 392 MET cc_start: 0.7645 (mpt) cc_final: 0.7195 (mpp) REVERT: K 462 LEU cc_start: 0.8913 (tp) cc_final: 0.8395 (mp) REVERT: L 346 MET cc_start: 0.8558 (tpp) cc_final: 0.8259 (mmm) REVERT: L 350 GLN cc_start: 0.9074 (tt0) cc_final: 0.8685 (pp30) REVERT: L 359 ARG cc_start: 0.7882 (tpt-90) cc_final: 0.7596 (tpt-90) REVERT: L 392 MET cc_start: 0.7384 (mpp) cc_final: 0.7141 (mpp) REVERT: L 468 ASN cc_start: 0.7776 (OUTLIER) cc_final: 0.7205 (p0) REVERT: M 332 LYS cc_start: 0.8816 (tmtt) cc_final: 0.8395 (ttmt) REVERT: M 346 MET cc_start: 0.8791 (tpp) cc_final: 0.8433 (tpp) REVERT: M 350 GLN cc_start: 0.9011 (tt0) cc_final: 0.8743 (pp30) REVERT: M 460 MET cc_start: 0.7280 (ttm) cc_final: 0.7064 (ttm) REVERT: M 462 LEU cc_start: 0.8960 (tp) cc_final: 0.8672 (tp) REVERT: M 540 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8315 (pt) REVERT: M 629 MET cc_start: 0.5346 (tmm) cc_final: 0.4742 (tmm) REVERT: N 332 LYS cc_start: 0.8977 (tmtt) cc_final: 0.8494 (ttmt) REVERT: N 346 MET cc_start: 0.8747 (tpp) cc_final: 0.8267 (mmm) REVERT: N 350 GLN cc_start: 0.9078 (tt0) cc_final: 0.8255 (pp30) REVERT: N 354 GLU cc_start: 0.8457 (mt-10) cc_final: 0.7714 (pt0) REVERT: N 392 MET cc_start: 0.7966 (mpt) cc_final: 0.7425 (mpp) REVERT: N 460 MET cc_start: 0.7060 (ttm) cc_final: 0.6675 (ttm) REVERT: O 346 MET cc_start: 0.8664 (tpp) cc_final: 0.8349 (mmm) REVERT: O 350 GLN cc_start: 0.9068 (tt0) cc_final: 0.8578 (pp30) REVERT: O 460 MET cc_start: 0.8037 (ttp) cc_final: 0.7445 (ttm) REVERT: O 462 LEU cc_start: 0.8999 (tp) cc_final: 0.8540 (mp) REVERT: O 610 LYS cc_start: 0.8583 (ttmm) cc_final: 0.8207 (tttm) REVERT: O 626 ARG cc_start: 0.7631 (mtm-85) cc_final: 0.6371 (mmm160) REVERT: O 649 ARG cc_start: 0.8617 (mmt180) cc_final: 0.8285 (mmm-85) outliers start: 183 outliers final: 132 residues processed: 720 average time/residue: 0.5654 time to fit residues: 649.4405 Evaluate side-chains 650 residues out of total 4350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 504 time to evaluate : 4.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 468 ASN Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 468 ASN Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 350 GLN Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 448 SER Chi-restraints excluded: chain E residue 468 ASN Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 482 THR Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 550 GLN Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 468 ASN Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 540 ILE Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 575 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 468 ASN Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 482 THR Chi-restraints excluded: chain G residue 496 VAL Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 550 GLN Chi-restraints excluded: chain G residue 575 VAL Chi-restraints excluded: chain G residue 576 LEU Chi-restraints excluded: chain H residue 358 ILE Chi-restraints excluded: chain H residue 366 GLU Chi-restraints excluded: chain H residue 433 THR Chi-restraints excluded: chain H residue 468 ASN Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 482 THR Chi-restraints excluded: chain H residue 550 GLN Chi-restraints excluded: chain H residue 575 VAL Chi-restraints excluded: chain H residue 593 LEU Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 433 THR Chi-restraints excluded: chain I residue 448 SER Chi-restraints excluded: chain I residue 468 ASN Chi-restraints excluded: chain I residue 477 THR Chi-restraints excluded: chain I residue 482 THR Chi-restraints excluded: chain I residue 496 VAL Chi-restraints excluded: chain I residue 540 ILE Chi-restraints excluded: chain I residue 553 LEU Chi-restraints excluded: chain I residue 575 VAL Chi-restraints excluded: chain I residue 593 LEU Chi-restraints excluded: chain J residue 366 GLU Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain J residue 468 ASN Chi-restraints excluded: chain J residue 477 THR Chi-restraints excluded: chain J residue 480 ILE Chi-restraints excluded: chain J residue 482 THR Chi-restraints excluded: chain J residue 547 VAL Chi-restraints excluded: chain J residue 550 GLN Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 433 THR Chi-restraints excluded: chain K residue 468 ASN Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 482 THR Chi-restraints excluded: chain K residue 576 LEU Chi-restraints excluded: chain K residue 593 LEU Chi-restraints excluded: chain L residue 366 GLU Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain L residue 448 SER Chi-restraints excluded: chain L residue 468 ASN Chi-restraints excluded: chain L residue 477 THR Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 575 VAL Chi-restraints excluded: chain L residue 593 LEU Chi-restraints excluded: chain M residue 366 GLU Chi-restraints excluded: chain M residue 433 THR Chi-restraints excluded: chain M residue 448 SER Chi-restraints excluded: chain M residue 477 THR Chi-restraints excluded: chain M residue 482 THR Chi-restraints excluded: chain M residue 540 ILE Chi-restraints excluded: chain M residue 573 LEU Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 576 LEU Chi-restraints excluded: chain M residue 593 LEU Chi-restraints excluded: chain N residue 366 GLU Chi-restraints excluded: chain N residue 433 THR Chi-restraints excluded: chain N residue 468 ASN Chi-restraints excluded: chain N residue 477 THR Chi-restraints excluded: chain N residue 482 THR Chi-restraints excluded: chain N residue 496 VAL Chi-restraints excluded: chain N residue 575 VAL Chi-restraints excluded: chain O residue 297 LEU Chi-restraints excluded: chain O residue 353 ILE Chi-restraints excluded: chain O residue 366 GLU Chi-restraints excluded: chain O residue 433 THR Chi-restraints excluded: chain O residue 468 ASN Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 482 THR Chi-restraints excluded: chain O residue 499 LEU Chi-restraints excluded: chain O residue 540 ILE Chi-restraints excluded: chain O residue 575 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 422 optimal weight: 0.9990 chunk 288 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 377 optimal weight: 8.9990 chunk 209 optimal weight: 4.9990 chunk 433 optimal weight: 1.9990 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: 0.3980 overall best weight: 2.4788 ------------------------------------------------------------------------------- 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 534 ASN ** B 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 ASN ** C 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 ASN ** D 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 ASN ** 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 430 ASN ** H 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 333 HIS I 430 ASN ** 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 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 39840 Z= 0.252 Angle : 0.587 10.757 53895 Z= 0.302 Chirality : 0.046 0.154 6480 Planarity : 0.004 0.039 6990 Dihedral : 5.218 41.180 5430 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.47 % Favored : 92.34 % Rotamer: Outliers : 4.32 % Allowed : 17.10 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.12), residues: 5130 helix: 0.31 (0.16), residues: 1155 sheet: -2.28 (0.10), residues: 2595 loop : -2.74 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 384 HIS 0.003 0.001 HIS D 364 PHE 0.014 0.001 PHE G 489 TYR 0.022 0.001 TYR L 639 ARG 0.007 0.001 ARG I 626 *********************** 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 767 residues out of total 4350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 579 time to evaluate : 4.686 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: A 302 LYS cc_start: 0.8867 (mmmt) cc_final: 0.8292 (tptt) REVERT: A 332 LYS cc_start: 0.8977 (ttmm) cc_final: 0.8718 (tmtt) REVERT: A 333 HIS cc_start: 0.8566 (m90) cc_final: 0.8347 (m90) REVERT: A 346 MET cc_start: 0.8570 (tpp) cc_final: 0.7873 (mmt) REVERT: A 350 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8833 (tm-30) REVERT: A 392 MET cc_start: 0.7983 (mpt) cc_final: 0.7558 (mpp) REVERT: A 460 MET cc_start: 0.6708 (ttm) cc_final: 0.6363 (ttm) REVERT: A 462 LEU cc_start: 0.9005 (tp) cc_final: 0.8741 (tp) REVERT: A 649 ARG cc_start: 0.8584 (mmt180) cc_final: 0.8192 (mmt90) REVERT: B 346 MET cc_start: 0.8861 (tpp) cc_final: 0.8346 (tpp) REVERT: B 350 GLN cc_start: 0.9139 (tt0) cc_final: 0.8662 (pp30) REVERT: B 359 ARG cc_start: 0.7832 (tpt-90) cc_final: 0.7545 (tpt-90) REVERT: B 392 MET cc_start: 0.7692 (mpt) cc_final: 0.7177 (mpp) REVERT: B 462 LEU cc_start: 0.8872 (tp) cc_final: 0.8396 (mp) REVERT: B 541 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7311 (mp0) REVERT: B 649 ARG cc_start: 0.8745 (mmt180) cc_final: 0.8255 (mmm-85) REVERT: C 332 LYS cc_start: 0.8804 (tmtt) cc_final: 0.8430 (ttmt) REVERT: C 392 MET cc_start: 0.7913 (mpt) cc_final: 0.7485 (mpp) REVERT: C 462 LEU cc_start: 0.9034 (tp) cc_final: 0.8820 (tp) REVERT: C 468 ASN cc_start: 0.8057 (OUTLIER) cc_final: 0.7298 (p0) REVERT: C 523 MET cc_start: 0.6987 (ttm) cc_final: 0.6633 (ttm) REVERT: C 540 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8018 (pt) REVERT: C 649 ARG cc_start: 0.8667 (mmt180) cc_final: 0.8267 (mmm-85) REVERT: D 332 LYS cc_start: 0.8772 (tmtt) cc_final: 0.8450 (ttmt) REVERT: D 346 MET cc_start: 0.8680 (tpp) cc_final: 0.8418 (tpp) REVERT: D 350 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8819 (tm-30) REVERT: D 392 MET cc_start: 0.7766 (mpt) cc_final: 0.7230 (mpp) REVERT: D 460 MET cc_start: 0.7869 (ttp) cc_final: 0.7305 (ttm) REVERT: D 462 LEU cc_start: 0.8888 (tp) cc_final: 0.8416 (mp) REVERT: D 487 GLU cc_start: 0.7759 (pt0) cc_final: 0.7409 (pt0) REVERT: D 540 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.7944 (pt) REVERT: D 541 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7235 (mp0) REVERT: D 610 LYS cc_start: 0.8586 (ttmm) cc_final: 0.8311 (tttm) REVERT: D 614 ARG cc_start: 0.8149 (tmm-80) cc_final: 0.7916 (mtp-110) REVERT: D 649 ARG cc_start: 0.8601 (mmt180) cc_final: 0.8115 (mmm160) REVERT: E 346 MET cc_start: 0.8807 (tpp) cc_final: 0.8399 (tpp) REVERT: E 350 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8735 (tm-30) REVERT: E 366 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7453 (pt0) REVERT: E 392 MET cc_start: 0.7945 (mpt) cc_final: 0.7482 (mpp) REVERT: E 462 LEU cc_start: 0.8900 (tp) cc_final: 0.8382 (mp) REVERT: E 540 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8147 (pt) REVERT: E 612 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7485 (tm-30) REVERT: E 614 ARG cc_start: 0.8281 (tmm-80) cc_final: 0.7914 (mtp-110) REVERT: E 649 ARG cc_start: 0.8629 (mmt180) cc_final: 0.8231 (mmm-85) REVERT: F 299 ASP cc_start: 0.8158 (m-30) cc_final: 0.7810 (m-30) REVERT: F 332 LYS cc_start: 0.8813 (tmtt) cc_final: 0.8462 (ptmt) REVERT: F 346 MET cc_start: 0.8749 (tpp) cc_final: 0.8477 (tpp) REVERT: F 350 GLN cc_start: 0.9140 (tt0) cc_final: 0.8667 (pp30) REVERT: F 354 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8101 (mt-10) REVERT: F 359 ARG cc_start: 0.7756 (tpt-90) cc_final: 0.7523 (tpt-90) REVERT: F 392 MET cc_start: 0.7802 (mpt) cc_final: 0.7262 (mpp) REVERT: F 462 LEU cc_start: 0.8976 (tp) cc_final: 0.8725 (tp) REVERT: F 540 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8001 (pt) REVERT: G 332 LYS cc_start: 0.8837 (tmtt) cc_final: 0.8549 (tmtt) REVERT: G 359 ARG cc_start: 0.8067 (tpt-90) cc_final: 0.7530 (tpt-90) REVERT: G 392 MET cc_start: 0.7915 (mpt) cc_final: 0.7386 (mpp) REVERT: G 462 LEU cc_start: 0.8943 (tp) cc_final: 0.8464 (mp) REVERT: G 541 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7496 (tm-30) REVERT: G 610 LYS cc_start: 0.8679 (ttmm) cc_final: 0.8384 (tttm) REVERT: G 614 ARG cc_start: 0.8311 (tmm-80) cc_final: 0.7953 (mtp-110) REVERT: G 649 ARG cc_start: 0.8792 (mmt180) cc_final: 0.8317 (mmm-85) REVERT: H 346 MET cc_start: 0.8638 (tpp) cc_final: 0.8202 (tpp) REVERT: H 350 GLN cc_start: 0.9214 (tt0) cc_final: 0.8879 (tm-30) REVERT: H 392 MET cc_start: 0.7840 (mpt) cc_final: 0.7304 (mpp) REVERT: H 554 ASP cc_start: 0.7878 (t0) cc_final: 0.7597 (m-30) REVERT: I 308 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8236 (tt) REVERT: I 332 LYS cc_start: 0.8932 (tmtt) cc_final: 0.8481 (ttmt) REVERT: I 333 HIS cc_start: 0.8594 (m-70) cc_final: 0.8367 (m-70) REVERT: I 346 MET cc_start: 0.8838 (tpp) cc_final: 0.8353 (mmm) REVERT: I 350 GLN cc_start: 0.9138 (tt0) cc_final: 0.8622 (pp30) REVERT: I 366 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7329 (pm20) REVERT: I 371 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7702 (tm-30) REVERT: I 460 MET cc_start: 0.8050 (ttp) cc_final: 0.7551 (ttm) REVERT: I 462 LEU cc_start: 0.8979 (tp) cc_final: 0.8508 (mp) REVERT: J 332 LYS cc_start: 0.8856 (tmtt) cc_final: 0.8380 (ttmt) REVERT: J 350 GLN cc_start: 0.9098 (tt0) cc_final: 0.8475 (pp30) REVERT: J 366 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7379 (pt0) REVERT: J 392 MET cc_start: 0.7715 (mpt) cc_final: 0.7230 (mpp) REVERT: J 460 MET cc_start: 0.6721 (ttm) cc_final: 0.6255 (ttm) REVERT: J 462 LEU cc_start: 0.8923 (tp) cc_final: 0.8467 (mp) REVERT: J 487 GLU cc_start: 0.7773 (pt0) cc_final: 0.7501 (pt0) REVERT: J 541 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7425 (mp0) REVERT: J 610 LYS cc_start: 0.8539 (ttmm) cc_final: 0.8309 (tptt) REVERT: J 614 ARG cc_start: 0.8123 (tmm-80) cc_final: 0.7782 (mtp-110) REVERT: J 649 ARG cc_start: 0.8891 (mmt180) cc_final: 0.8422 (mmm-85) REVERT: K 346 MET cc_start: 0.8697 (tpp) cc_final: 0.8301 (tpp) REVERT: K 350 GLN cc_start: 0.9101 (tt0) cc_final: 0.8499 (pp30) REVERT: K 377 ASN cc_start: 0.8129 (OUTLIER) cc_final: 0.7821 (p0) REVERT: K 392 MET cc_start: 0.7667 (mpt) cc_final: 0.7206 (mpp) REVERT: K 462 LEU cc_start: 0.8943 (tp) cc_final: 0.8453 (mp) REVERT: K 610 LYS cc_start: 0.8585 (ttmm) cc_final: 0.8312 (ttmm) REVERT: K 614 ARG cc_start: 0.8347 (tmm-80) cc_final: 0.7985 (mtp-110) REVERT: L 346 MET cc_start: 0.8543 (tpp) cc_final: 0.8255 (mmm) REVERT: L 350 GLN cc_start: 0.9127 (tt0) cc_final: 0.8653 (tm-30) REVERT: L 359 ARG cc_start: 0.7841 (tpt-90) cc_final: 0.7550 (tpt-90) REVERT: L 392 MET cc_start: 0.7366 (mpp) cc_final: 0.7135 (mpp) REVERT: L 468 ASN cc_start: 0.7785 (OUTLIER) cc_final: 0.7220 (p0) REVERT: L 554 ASP cc_start: 0.8001 (t0) cc_final: 0.7671 (m-30) REVERT: M 332 LYS cc_start: 0.8810 (tmtt) cc_final: 0.8336 (ttmt) REVERT: M 346 MET cc_start: 0.8771 (tpp) cc_final: 0.8424 (tpp) REVERT: M 350 GLN cc_start: 0.9004 (tt0) cc_final: 0.8742 (pp30) REVERT: M 392 MET cc_start: 0.8025 (mpt) cc_final: 0.7546 (mpp) REVERT: M 460 MET cc_start: 0.7300 (ttm) cc_final: 0.6499 (ttm) REVERT: M 462 LEU cc_start: 0.8940 (tp) cc_final: 0.8404 (mp) REVERT: M 468 ASN cc_start: 0.7903 (OUTLIER) cc_final: 0.7365 (p0) REVERT: M 540 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8304 (pt) REVERT: M 614 ARG cc_start: 0.8231 (tmm-80) cc_final: 0.7945 (mtp-110) REVERT: M 629 MET cc_start: 0.5553 (tmm) cc_final: 0.5092 (tmm) REVERT: N 332 LYS cc_start: 0.8836 (tmtt) cc_final: 0.8470 (ttmt) REVERT: N 346 MET cc_start: 0.8709 (tpp) cc_final: 0.8306 (mmm) REVERT: N 350 GLN cc_start: 0.9091 (tt0) cc_final: 0.8731 (pp30) REVERT: N 392 MET cc_start: 0.7982 (mpt) cc_final: 0.7419 (mpp) REVERT: N 460 MET cc_start: 0.7036 (ttm) cc_final: 0.6644 (ttm) REVERT: O 346 MET cc_start: 0.8652 (tpp) cc_final: 0.8337 (mmm) REVERT: O 350 GLN cc_start: 0.9057 (tt0) cc_final: 0.8574 (pp30) REVERT: O 460 MET cc_start: 0.8055 (ttp) cc_final: 0.7644 (ttm) REVERT: O 462 LEU cc_start: 0.8981 (tp) cc_final: 0.8530 (mp) REVERT: O 610 LYS cc_start: 0.8562 (ttmm) cc_final: 0.8223 (tttm) REVERT: O 649 ARG cc_start: 0.8613 (mmt180) cc_final: 0.8256 (mmm-85) outliers start: 188 outliers final: 143 residues processed: 731 average time/residue: 0.5570 time to fit residues: 648.6545 Evaluate side-chains 686 residues out of total 4350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 527 time to evaluate : 4.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 468 ASN Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 468 ASN Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 350 GLN Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 468 ASN Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 482 THR Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 550 GLN Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 468 ASN Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 540 ILE Chi-restraints excluded: chain F residue 553 LEU Chi-restraints excluded: chain F residue 575 VAL Chi-restraints excluded: chain F residue 591 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 366 GLU Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 482 THR Chi-restraints excluded: chain G residue 496 VAL Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 550 GLN Chi-restraints excluded: chain G residue 575 VAL Chi-restraints excluded: chain G residue 576 LEU Chi-restraints excluded: chain H residue 366 GLU Chi-restraints excluded: chain H residue 468 ASN Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 482 THR Chi-restraints excluded: chain H residue 546 LYS Chi-restraints excluded: chain H residue 550 GLN Chi-restraints excluded: chain H residue 553 LEU Chi-restraints excluded: chain H residue 575 VAL Chi-restraints excluded: chain H residue 591 VAL Chi-restraints excluded: chain H residue 593 LEU Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 433 THR Chi-restraints excluded: chain I residue 448 SER Chi-restraints excluded: chain I residue 468 ASN Chi-restraints excluded: chain I residue 477 THR Chi-restraints excluded: chain I residue 482 THR Chi-restraints excluded: chain I residue 496 VAL Chi-restraints excluded: chain I residue 540 ILE Chi-restraints excluded: chain I residue 553 LEU Chi-restraints excluded: chain I residue 555 VAL Chi-restraints excluded: chain I residue 575 VAL Chi-restraints excluded: chain I residue 593 LEU Chi-restraints excluded: chain J residue 366 GLU Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain J residue 448 SER Chi-restraints excluded: chain J residue 468 ASN Chi-restraints excluded: chain J residue 477 THR Chi-restraints excluded: chain J residue 480 ILE Chi-restraints excluded: chain J residue 482 THR Chi-restraints excluded: chain J residue 495 ASP Chi-restraints excluded: chain J residue 547 VAL Chi-restraints excluded: chain J residue 550 GLN Chi-restraints excluded: chain J residue 553 LEU Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain J residue 591 VAL Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 377 ASN Chi-restraints excluded: chain K residue 468 ASN Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 482 THR Chi-restraints excluded: chain K residue 499 LEU Chi-restraints excluded: chain K residue 553 LEU Chi-restraints excluded: chain K residue 575 VAL Chi-restraints excluded: chain K residue 576 LEU Chi-restraints excluded: chain K residue 591 VAL Chi-restraints excluded: chain K residue 593 LEU Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain L residue 448 SER Chi-restraints excluded: chain L residue 468 ASN Chi-restraints excluded: chain L residue 477 THR Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 575 VAL Chi-restraints excluded: chain L residue 593 LEU Chi-restraints excluded: chain M residue 366 GLU Chi-restraints excluded: chain M residue 433 THR Chi-restraints excluded: chain M residue 468 ASN Chi-restraints excluded: chain M residue 477 THR Chi-restraints excluded: chain M residue 482 THR Chi-restraints excluded: chain M residue 540 ILE Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 576 LEU Chi-restraints excluded: chain M residue 593 LEU Chi-restraints excluded: chain N residue 366 GLU Chi-restraints excluded: chain N residue 433 THR Chi-restraints excluded: chain N residue 468 ASN Chi-restraints excluded: chain N residue 477 THR Chi-restraints excluded: chain N residue 482 THR Chi-restraints excluded: chain N residue 496 VAL Chi-restraints excluded: chain N residue 575 VAL Chi-restraints excluded: chain N residue 579 LEU Chi-restraints excluded: chain O residue 297 LEU Chi-restraints excluded: chain O residue 353 ILE Chi-restraints excluded: chain O residue 366 GLU Chi-restraints excluded: chain O residue 433 THR Chi-restraints excluded: chain O residue 468 ASN Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 482 THR Chi-restraints excluded: chain O residue 540 ILE Chi-restraints excluded: chain O residue 575 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 170 optimal weight: 1.9990 chunk 456 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 297 optimal weight: 0.9980 chunk 125 optimal weight: 6.9990 chunk 507 optimal weight: 5.9990 chunk 421 optimal weight: 6.9990 chunk 235 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 168 optimal weight: 6.9990 chunk 266 optimal weight: 0.1980 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 652 GLN ** B 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 ASN E 430 ASN ** E 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 333 HIS ** 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 430 ASN ** H 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 333 HIS ** J 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 602 ASN ** L 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 333 HIS ** N 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.4632 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= 0.216 Angle : 0.593 12.418 53895 Z= 0.297 Chirality : 0.046 0.171 6480 Planarity : 0.004 0.045 6990 Dihedral : 5.023 43.230 5430 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.35 % Favored : 93.43 % Rotamer: Outliers : 5.03 % Allowed : 17.06 % Favored : 77.91 % 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: -2.71 (0.12), residues: 5130 helix: 0.61 (0.16), residues: 1155 sheet: -2.14 (0.10), residues: 2595 loop : -2.74 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 384 HIS 0.003 0.001 HIS D 364 PHE 0.012 0.001 PHE G 489 TYR 0.023 0.001 TYR I 639 ARG 0.010 0.001 ARG D 626 *********************** 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 790 residues out of total 4350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 571 time to evaluate : 4.720 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: A 302 LYS cc_start: 0.8869 (mmmt) cc_final: 0.8303 (tptt) REVERT: A 332 LYS cc_start: 0.8947 (ttmm) cc_final: 0.8711 (tmtt) REVERT: A 392 MET cc_start: 0.8041 (mpt) cc_final: 0.7593 (mpp) REVERT: A 460 MET cc_start: 0.6679 (ttm) cc_final: 0.6068 (ttm) REVERT: A 462 LEU cc_start: 0.8992 (tp) cc_final: 0.8528 (mp) REVERT: A 614 ARG cc_start: 0.8237 (tmm-80) cc_final: 0.8021 (ttp80) REVERT: A 629 MET cc_start: 0.6553 (tmm) cc_final: 0.6271 (tmm) REVERT: A 649 ARG cc_start: 0.8560 (mmt180) cc_final: 0.8155 (mmm-85) REVERT: B 346 MET cc_start: 0.8835 (tpp) cc_final: 0.8377 (tpp) REVERT: B 350 GLN cc_start: 0.9141 (tt0) cc_final: 0.8650 (pp30) REVERT: B 392 MET cc_start: 0.7749 (mpt) cc_final: 0.7223 (mpp) REVERT: B 462 LEU cc_start: 0.8820 (tp) cc_final: 0.8358 (mp) REVERT: B 649 ARG cc_start: 0.8699 (mmt180) cc_final: 0.8217 (mmm-85) REVERT: C 332 LYS cc_start: 0.8682 (tmtt) cc_final: 0.8380 (ptmt) REVERT: C 346 MET cc_start: 0.8680 (tpp) cc_final: 0.8309 (mmm) REVERT: C 350 GLN cc_start: 0.8446 (tm-30) cc_final: 0.8007 (tm-30) REVERT: C 392 MET cc_start: 0.7976 (mpt) cc_final: 0.7529 (mpp) REVERT: C 462 LEU cc_start: 0.9023 (tp) cc_final: 0.8796 (tp) REVERT: C 523 MET cc_start: 0.7005 (ttm) cc_final: 0.6647 (ttm) REVERT: C 540 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8026 (pt) REVERT: C 612 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7700 (tm-30) REVERT: C 614 ARG cc_start: 0.7950 (mtp-110) cc_final: 0.7670 (mtm110) REVERT: C 649 ARG cc_start: 0.8619 (mmt180) cc_final: 0.8217 (mmm-85) REVERT: D 346 MET cc_start: 0.8720 (tpp) cc_final: 0.8438 (tpp) REVERT: D 377 ASN cc_start: 0.8286 (OUTLIER) cc_final: 0.8056 (p0) REVERT: D 392 MET cc_start: 0.7860 (mpt) cc_final: 0.7287 (mpp) REVERT: D 460 MET cc_start: 0.7844 (ttp) cc_final: 0.7269 (ttm) REVERT: D 462 LEU cc_start: 0.8838 (tp) cc_final: 0.8374 (mp) REVERT: D 487 GLU cc_start: 0.7753 (pt0) cc_final: 0.7431 (pt0) REVERT: D 540 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8059 (pt) REVERT: D 541 GLU cc_start: 0.7499 (tm-30) cc_final: 0.7222 (tm-30) REVERT: D 610 LYS cc_start: 0.8627 (ttmm) cc_final: 0.8353 (tttm) REVERT: D 614 ARG cc_start: 0.8090 (tmm-80) cc_final: 0.7879 (mtp-110) REVERT: D 649 ARG cc_start: 0.8577 (mmt180) cc_final: 0.8235 (mmm-85) REVERT: E 346 MET cc_start: 0.8790 (tpp) cc_final: 0.8394 (tpp) REVERT: E 350 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8780 (tm-30) REVERT: E 359 ARG cc_start: 0.7970 (tpt-90) cc_final: 0.7749 (tpt-90) REVERT: E 366 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7436 (pt0) REVERT: E 377 ASN cc_start: 0.8364 (OUTLIER) cc_final: 0.8097 (p0) REVERT: E 392 MET cc_start: 0.8000 (mpt) cc_final: 0.7532 (mpp) REVERT: E 462 LEU cc_start: 0.8891 (tp) cc_final: 0.8378 (mp) REVERT: E 540 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8162 (pt) REVERT: E 610 LYS cc_start: 0.8600 (ttmm) cc_final: 0.8343 (tptt) REVERT: E 614 ARG cc_start: 0.8208 (tmm-80) cc_final: 0.7827 (mtp-110) REVERT: E 649 ARG cc_start: 0.8593 (mmt180) cc_final: 0.8236 (mmm-85) REVERT: F 299 ASP cc_start: 0.8217 (m-30) cc_final: 0.7908 (m-30) REVERT: F 332 LYS cc_start: 0.8833 (tmtt) cc_final: 0.8393 (ptmt) REVERT: F 350 GLN cc_start: 0.9139 (tt0) cc_final: 0.8674 (pp30) REVERT: F 354 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8099 (mt-10) REVERT: F 377 ASN cc_start: 0.8264 (OUTLIER) cc_final: 0.8055 (p0) REVERT: F 462 LEU cc_start: 0.8820 (tp) cc_final: 0.8579 (tp) REVERT: F 540 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8034 (pt) REVERT: F 586 GLU cc_start: 0.7460 (tp30) cc_final: 0.7114 (tp30) REVERT: G 332 LYS cc_start: 0.8796 (tmtt) cc_final: 0.8497 (tmtt) REVERT: G 359 ARG cc_start: 0.8120 (tpt-90) cc_final: 0.7607 (tpt-90) REVERT: G 366 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7314 (mt-10) REVERT: G 392 MET cc_start: 0.7898 (mpt) cc_final: 0.7336 (mpp) REVERT: G 462 LEU cc_start: 0.8904 (tp) cc_final: 0.8415 (mp) REVERT: G 468 ASN cc_start: 0.7855 (OUTLIER) cc_final: 0.7268 (p0) REVERT: G 540 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8089 (pt) REVERT: G 541 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7324 (tm-30) REVERT: G 610 LYS cc_start: 0.8685 (ttmm) cc_final: 0.8396 (tttm) REVERT: G 614 ARG cc_start: 0.8256 (tmm-80) cc_final: 0.7937 (mtp-110) REVERT: G 649 ARG cc_start: 0.8729 (mmt180) cc_final: 0.8247 (mmm160) REVERT: H 332 LYS cc_start: 0.8846 (tmtt) cc_final: 0.8388 (ttmt) REVERT: H 346 MET cc_start: 0.8600 (tpp) cc_final: 0.8202 (tpp) REVERT: H 350 GLN cc_start: 0.9232 (tt0) cc_final: 0.8825 (tm-30) REVERT: H 377 ASN cc_start: 0.8444 (OUTLIER) cc_final: 0.8221 (p0) REVERT: H 392 MET cc_start: 0.7896 (mpt) cc_final: 0.7340 (mpp) REVERT: H 442 GLN cc_start: 0.9154 (pp30) cc_final: 0.8931 (pp30) REVERT: H 554 ASP cc_start: 0.7879 (t0) cc_final: 0.7547 (m-30) REVERT: I 308 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8271 (tt) REVERT: I 332 LYS cc_start: 0.8891 (tmtt) cc_final: 0.8378 (ttmt) REVERT: I 346 MET cc_start: 0.8916 (tpp) cc_final: 0.8423 (mmm) REVERT: I 350 GLN cc_start: 0.9140 (tt0) cc_final: 0.8637 (pp30) REVERT: I 366 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7414 (pm20) REVERT: I 371 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7666 (tm-30) REVERT: I 460 MET cc_start: 0.8075 (ttp) cc_final: 0.7591 (ttm) REVERT: I 462 LEU cc_start: 0.8914 (tp) cc_final: 0.8435 (mp) REVERT: J 332 LYS cc_start: 0.8835 (tmtt) cc_final: 0.8352 (ttmt) REVERT: J 346 MET cc_start: 0.8769 (tpp) cc_final: 0.8342 (mmm) REVERT: J 350 GLN cc_start: 0.9107 (tt0) cc_final: 0.8496 (pp30) REVERT: J 366 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7353 (pt0) REVERT: J 392 MET cc_start: 0.7815 (mpt) cc_final: 0.7382 (mpp) REVERT: J 460 MET cc_start: 0.6698 (ttm) cc_final: 0.6322 (ttm) REVERT: J 462 LEU cc_start: 0.8919 (tp) cc_final: 0.8443 (mp) REVERT: J 487 GLU cc_start: 0.7762 (pt0) cc_final: 0.7493 (pt0) REVERT: J 610 LYS cc_start: 0.8569 (ttmm) cc_final: 0.8344 (tptt) REVERT: J 649 ARG cc_start: 0.8834 (mmt180) cc_final: 0.8400 (mmm-85) REVERT: K 346 MET cc_start: 0.8675 (tpp) cc_final: 0.8383 (mmm) REVERT: K 350 GLN cc_start: 0.9097 (tt0) cc_final: 0.8496 (pp30) REVERT: K 392 MET cc_start: 0.7721 (mpt) cc_final: 0.7229 (mpp) REVERT: K 462 LEU cc_start: 0.8934 (tp) cc_final: 0.8439 (mp) REVERT: K 594 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8643 (pt) REVERT: K 610 LYS cc_start: 0.8569 (ttmm) cc_final: 0.8307 (tttm) REVERT: K 614 ARG cc_start: 0.8324 (tmm-80) cc_final: 0.7972 (mtp-110) REVERT: L 338 ILE cc_start: 0.9396 (mm) cc_final: 0.9192 (mm) REVERT: L 346 MET cc_start: 0.8539 (tpp) cc_final: 0.8263 (mmm) REVERT: L 350 GLN cc_start: 0.9126 (tt0) cc_final: 0.8659 (tm-30) REVERT: L 359 ARG cc_start: 0.7819 (tpt-90) cc_final: 0.7522 (tpt-90) REVERT: L 392 MET cc_start: 0.7431 (mpp) cc_final: 0.7217 (mpp) REVERT: L 554 ASP cc_start: 0.7964 (t0) cc_final: 0.7615 (m-30) REVERT: M 332 LYS cc_start: 0.8784 (tmtt) cc_final: 0.8426 (ptmt) REVERT: M 346 MET cc_start: 0.8785 (tpp) cc_final: 0.8463 (tpp) REVERT: M 354 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8237 (pt0) REVERT: M 392 MET cc_start: 0.8086 (mpt) cc_final: 0.7598 (mpp) REVERT: M 460 MET cc_start: 0.7303 (ttm) cc_final: 0.6578 (ttm) REVERT: M 462 LEU cc_start: 0.8897 (tp) cc_final: 0.8380 (mp) REVERT: M 468 ASN cc_start: 0.7892 (OUTLIER) cc_final: 0.7656 (p0) REVERT: M 487 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7518 (tt0) REVERT: M 540 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8303 (pt) REVERT: M 594 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8779 (pt) REVERT: M 614 ARG cc_start: 0.8139 (tmm-80) cc_final: 0.7908 (mtp-110) REVERT: M 629 MET cc_start: 0.6072 (tmm) cc_final: 0.5680 (tmm) REVERT: N 332 LYS cc_start: 0.8986 (tmtt) cc_final: 0.8533 (ptmt) REVERT: N 346 MET cc_start: 0.8703 (tpp) cc_final: 0.8327 (mmm) REVERT: N 350 GLN cc_start: 0.9145 (tt0) cc_final: 0.8783 (tm-30) REVERT: N 392 MET cc_start: 0.8045 (mpt) cc_final: 0.7555 (mpp) REVERT: N 460 MET cc_start: 0.7078 (ttm) cc_final: 0.6850 (ttm) REVERT: O 346 MET cc_start: 0.8573 (tpp) cc_final: 0.8264 (mmm) REVERT: O 350 GLN cc_start: 0.9072 (tt0) cc_final: 0.8519 (pp30) REVERT: O 359 ARG cc_start: 0.7788 (tpt-90) cc_final: 0.7572 (tpt-90) REVERT: O 377 ASN cc_start: 0.8469 (OUTLIER) cc_final: 0.8162 (p0) REVERT: O 460 MET cc_start: 0.8019 (ttp) cc_final: 0.7574 (ttm) REVERT: O 462 LEU cc_start: 0.8971 (tp) cc_final: 0.8462 (mp) REVERT: O 610 LYS cc_start: 0.8672 (ttmm) cc_final: 0.8300 (tttm) REVERT: O 649 ARG cc_start: 0.8667 (mmt180) cc_final: 0.8266 (mmm-85) outliers start: 219 outliers final: 157 residues processed: 756 average time/residue: 0.5362 time to fit residues: 651.2811 Evaluate side-chains 715 residues out of total 4350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 537 time to evaluate : 4.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 468 ASN Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 377 ASN Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 448 SER Chi-restraints excluded: chain E residue 468 ASN Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 482 THR Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 550 GLN Chi-restraints excluded: chain E residue 551 THR Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 468 ASN Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 540 ILE Chi-restraints excluded: chain F residue 575 VAL Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 591 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 594 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 366 GLU Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 468 ASN Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 482 THR Chi-restraints excluded: chain G residue 496 VAL Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 550 GLN Chi-restraints excluded: chain G residue 575 VAL Chi-restraints excluded: chain G residue 576 LEU Chi-restraints excluded: chain H residue 366 GLU Chi-restraints excluded: chain H residue 377 ASN Chi-restraints excluded: chain H residue 433 THR Chi-restraints excluded: chain H residue 468 ASN Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 482 THR Chi-restraints excluded: chain H residue 546 LYS Chi-restraints excluded: chain H residue 553 LEU Chi-restraints excluded: chain H residue 575 VAL Chi-restraints excluded: chain H residue 591 VAL Chi-restraints excluded: chain H residue 593 LEU Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 433 THR Chi-restraints excluded: chain I residue 448 SER Chi-restraints excluded: chain I residue 468 ASN Chi-restraints excluded: chain I residue 477 THR Chi-restraints excluded: chain I residue 482 THR Chi-restraints excluded: chain I residue 540 ILE Chi-restraints excluded: chain I residue 553 LEU Chi-restraints excluded: chain I residue 555 VAL Chi-restraints excluded: chain I residue 575 VAL Chi-restraints excluded: chain I residue 593 LEU Chi-restraints excluded: chain I residue 613 LYS Chi-restraints excluded: chain J residue 366 GLU Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain J residue 448 SER Chi-restraints excluded: chain J residue 468 ASN Chi-restraints excluded: chain J residue 477 THR Chi-restraints excluded: chain J residue 480 ILE Chi-restraints excluded: chain J residue 482 THR Chi-restraints excluded: chain J residue 495 ASP Chi-restraints excluded: chain J residue 547 VAL Chi-restraints excluded: chain J residue 550 GLN Chi-restraints excluded: chain J residue 551 THR Chi-restraints excluded: chain J residue 553 LEU Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain J residue 591 VAL Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 433 THR Chi-restraints excluded: chain K residue 468 ASN Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 482 THR Chi-restraints excluded: chain K residue 553 LEU Chi-restraints excluded: chain K residue 575 VAL Chi-restraints excluded: chain K residue 576 LEU Chi-restraints excluded: chain K residue 591 VAL Chi-restraints excluded: chain K residue 593 LEU Chi-restraints excluded: chain K residue 594 LEU Chi-restraints excluded: chain L residue 366 GLU Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain L residue 448 SER Chi-restraints excluded: chain L residue 477 THR Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 575 VAL Chi-restraints excluded: chain L residue 593 LEU Chi-restraints excluded: chain M residue 366 GLU Chi-restraints excluded: chain M residue 433 THR Chi-restraints excluded: chain M residue 448 SER Chi-restraints excluded: chain M residue 468 ASN Chi-restraints excluded: chain M residue 477 THR Chi-restraints excluded: chain M residue 482 THR Chi-restraints excluded: chain M residue 540 ILE Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 576 LEU Chi-restraints excluded: chain M residue 593 LEU Chi-restraints excluded: chain M residue 594 LEU Chi-restraints excluded: chain N residue 433 THR Chi-restraints excluded: chain N residue 468 ASN Chi-restraints excluded: chain N residue 477 THR Chi-restraints excluded: chain N residue 482 THR Chi-restraints excluded: chain N residue 496 VAL Chi-restraints excluded: chain N residue 551 THR Chi-restraints excluded: chain N residue 575 VAL Chi-restraints excluded: chain N residue 579 LEU Chi-restraints excluded: chain O residue 297 LEU Chi-restraints excluded: chain O residue 353 ILE Chi-restraints excluded: chain O residue 366 GLU Chi-restraints excluded: chain O residue 377 ASN Chi-restraints excluded: chain O residue 433 THR Chi-restraints excluded: chain O residue 468 ASN Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 482 THR Chi-restraints excluded: chain O residue 499 LEU Chi-restraints excluded: chain O residue 540 ILE Chi-restraints excluded: chain O residue 575 VAL Chi-restraints excluded: chain O residue 594 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 489 optimal weight: 20.0000 chunk 57 optimal weight: 2.9990 chunk 289 optimal weight: 10.0000 chunk 370 optimal weight: 3.9990 chunk 287 optimal weight: 6.9990 chunk 427 optimal weight: 1.9990 chunk 283 optimal weight: 20.0000 chunk 506 optimal weight: 3.9990 chunk 316 optimal weight: 6.9990 chunk 308 optimal weight: 10.0000 chunk 233 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 534 ASN ** 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 430 ASN ** E 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 615 ASN F 333 HIS ** 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 333 HIS ** H 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 333 HIS ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 333 HIS ** 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 333 HIS ** N 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.4768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 39840 Z= 0.334 Angle : 0.650 12.902 53895 Z= 0.327 Chirality : 0.047 0.177 6480 Planarity : 0.004 0.041 6990 Dihedral : 5.281 43.890 5430 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.03 % Favored : 91.68 % Rotamer: Outliers : 5.03 % Allowed : 17.56 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.12), residues: 5130 helix: 0.70 (0.16), residues: 1155 sheet: -2.15 (0.10), residues: 2580 loop : -2.80 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 384 HIS 0.005 0.001 HIS D 364 PHE 0.016 0.002 PHE E 489 TYR 0.023 0.001 TYR B 639 ARG 0.009 0.001 ARG D 626 *********************** 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 766 residues out of total 4350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 547 time to evaluate : 4.636 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: A 332 LYS cc_start: 0.8939 (ttmm) cc_final: 0.8706 (tmtt) REVERT: A 346 MET cc_start: 0.8545 (tpp) cc_final: 0.7901 (mmt) REVERT: A 392 MET cc_start: 0.8126 (mpt) cc_final: 0.7645 (mpp) REVERT: A 462 LEU cc_start: 0.9024 (tp) cc_final: 0.8554 (mp) REVERT: A 649 ARG cc_start: 0.8563 (mmt180) cc_final: 0.8036 (mmm160) REVERT: B 346 MET cc_start: 0.8817 (tpp) cc_final: 0.8361 (tpp) REVERT: B 350 GLN cc_start: 0.9144 (tt0) cc_final: 0.8656 (pp30) REVERT: B 392 MET cc_start: 0.7931 (mpt) cc_final: 0.7406 (mpp) REVERT: B 462 LEU cc_start: 0.8838 (tp) cc_final: 0.8359 (mp) REVERT: B 649 ARG cc_start: 0.8716 (mmt180) cc_final: 0.8197 (mmm-85) REVERT: C 332 LYS cc_start: 0.8736 (tmtt) cc_final: 0.8364 (ttmt) REVERT: C 346 MET cc_start: 0.8682 (tpp) cc_final: 0.8340 (mmm) REVERT: C 350 GLN cc_start: 0.8570 (tm-30) cc_final: 0.8157 (tm-30) REVERT: C 392 MET cc_start: 0.8053 (mpt) cc_final: 0.7586 (mpp) REVERT: C 523 MET cc_start: 0.6913 (ttm) cc_final: 0.6538 (ttm) REVERT: C 540 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8125 (pt) REVERT: C 612 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7674 (tm-30) REVERT: C 649 ARG cc_start: 0.8644 (mmt180) cc_final: 0.8110 (mmm-85) REVERT: D 332 LYS cc_start: 0.8800 (tmtt) cc_final: 0.8277 (ttmt) REVERT: D 346 MET cc_start: 0.8726 (tpp) cc_final: 0.8296 (mmm) REVERT: D 359 ARG cc_start: 0.7860 (tpt-90) cc_final: 0.7607 (tpt-90) REVERT: D 377 ASN cc_start: 0.8295 (OUTLIER) cc_final: 0.8040 (p0) REVERT: D 392 MET cc_start: 0.7914 (mpt) cc_final: 0.7307 (mpp) REVERT: D 460 MET cc_start: 0.7895 (ttp) cc_final: 0.7289 (ttm) REVERT: D 462 LEU cc_start: 0.8877 (tp) cc_final: 0.8379 (mp) REVERT: D 487 GLU cc_start: 0.7772 (pt0) cc_final: 0.7449 (pt0) REVERT: D 540 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8078 (pt) REVERT: D 541 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7276 (tm-30) REVERT: D 610 LYS cc_start: 0.8600 (ttmm) cc_final: 0.8337 (tttm) REVERT: D 614 ARG cc_start: 0.8194 (tmm-80) cc_final: 0.7922 (mtp-110) REVERT: D 649 ARG cc_start: 0.8634 (mmt180) cc_final: 0.8077 (mmm-85) REVERT: E 346 MET cc_start: 0.8831 (tpp) cc_final: 0.8449 (tpp) REVERT: E 350 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.8811 (tm-30) REVERT: E 366 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7568 (pt0) REVERT: E 377 ASN cc_start: 0.8295 (OUTLIER) cc_final: 0.7926 (p0) REVERT: E 392 MET cc_start: 0.8079 (mpt) cc_final: 0.7582 (mpp) REVERT: E 462 LEU cc_start: 0.8913 (tp) cc_final: 0.8397 (mp) REVERT: E 540 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8229 (pt) REVERT: E 649 ARG cc_start: 0.8622 (mmt180) cc_final: 0.8228 (mmm-85) REVERT: F 299 ASP cc_start: 0.8276 (m-30) cc_final: 0.7972 (m-30) REVERT: F 332 LYS cc_start: 0.8867 (tmtt) cc_final: 0.8432 (ptmt) REVERT: F 350 GLN cc_start: 0.9160 (tt0) cc_final: 0.8882 (pp30) REVERT: F 462 LEU cc_start: 0.8881 (tp) cc_final: 0.8641 (tp) REVERT: F 540 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8060 (pt) REVERT: G 332 LYS cc_start: 0.8860 (tmtt) cc_final: 0.8562 (tmtt) REVERT: G 359 ARG cc_start: 0.8078 (tpt-90) cc_final: 0.7446 (tpt-90) REVERT: G 366 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7339 (mt-10) REVERT: G 392 MET cc_start: 0.7987 (mpt) cc_final: 0.7382 (mpp) REVERT: G 462 LEU cc_start: 0.8955 (tp) cc_final: 0.8462 (mp) REVERT: G 468 ASN cc_start: 0.7881 (OUTLIER) cc_final: 0.7291 (p0) REVERT: G 540 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8239 (pt) REVERT: G 610 LYS cc_start: 0.8691 (ttmm) cc_final: 0.8379 (tttm) REVERT: G 614 ARG cc_start: 0.8341 (tmm-80) cc_final: 0.8019 (mtp-110) REVERT: G 649 ARG cc_start: 0.8752 (mmt180) cc_final: 0.8268 (mmm-85) REVERT: H 332 LYS cc_start: 0.8882 (tmtt) cc_final: 0.8526 (ptmt) REVERT: H 346 MET cc_start: 0.8628 (tpp) cc_final: 0.8214 (tpp) REVERT: H 350 GLN cc_start: 0.9239 (tt0) cc_final: 0.8837 (tm-30) REVERT: H 392 MET cc_start: 0.8073 (mpt) cc_final: 0.7506 (mpp) REVERT: H 442 GLN cc_start: 0.9143 (pp30) cc_final: 0.8916 (pp30) REVERT: H 554 ASP cc_start: 0.7923 (t0) cc_final: 0.7567 (m-30) REVERT: H 642 MET cc_start: 0.9070 (mmt) cc_final: 0.8681 (mmt) REVERT: I 308 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8229 (tt) REVERT: I 332 LYS cc_start: 0.8984 (tmtt) cc_final: 0.8423 (ttmt) REVERT: I 346 MET cc_start: 0.8931 (tpp) cc_final: 0.8528 (tpp) REVERT: I 350 GLN cc_start: 0.9162 (tt0) cc_final: 0.8607 (pp30) REVERT: I 366 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7425 (pm20) REVERT: I 371 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7709 (tm-30) REVERT: I 462 LEU cc_start: 0.8969 (tp) cc_final: 0.8693 (tp) REVERT: I 540 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8324 (pt) REVERT: J 332 LYS cc_start: 0.8827 (tmtt) cc_final: 0.8344 (ttmt) REVERT: J 346 MET cc_start: 0.8764 (tpp) cc_final: 0.8410 (mmm) REVERT: J 350 GLN cc_start: 0.9131 (tt0) cc_final: 0.8505 (pp30) REVERT: J 366 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7424 (pt0) REVERT: J 392 MET cc_start: 0.7849 (mpt) cc_final: 0.7417 (mpp) REVERT: J 460 MET cc_start: 0.6750 (ttm) cc_final: 0.6368 (ttm) REVERT: J 462 LEU cc_start: 0.8934 (tp) cc_final: 0.8459 (mp) REVERT: J 487 GLU cc_start: 0.7702 (pt0) cc_final: 0.7439 (pt0) REVERT: J 554 ASP cc_start: 0.8015 (m-30) cc_final: 0.7632 (m-30) REVERT: J 610 LYS cc_start: 0.8571 (ttmm) cc_final: 0.8351 (ttmm) REVERT: J 649 ARG cc_start: 0.8859 (mmt180) cc_final: 0.8310 (mmm-85) REVERT: K 332 LYS cc_start: 0.8916 (tmtt) cc_final: 0.8327 (ttmm) REVERT: K 346 MET cc_start: 0.8636 (tpp) cc_final: 0.8290 (mmm) REVERT: K 350 GLN cc_start: 0.9121 (tt0) cc_final: 0.8531 (pp30) REVERT: K 392 MET cc_start: 0.7793 (mpt) cc_final: 0.7280 (mpp) REVERT: K 462 LEU cc_start: 0.8892 (tp) cc_final: 0.8395 (mp) REVERT: K 487 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7553 (tm-30) REVERT: K 594 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8716 (pt) REVERT: K 610 LYS cc_start: 0.8614 (ttmm) cc_final: 0.8332 (ttmm) REVERT: K 614 ARG cc_start: 0.8339 (tmm-80) cc_final: 0.8028 (mtp-110) REVERT: L 346 MET cc_start: 0.8556 (tpp) cc_final: 0.8207 (mmm) REVERT: L 350 GLN cc_start: 0.9155 (tt0) cc_final: 0.8670 (tm-30) REVERT: L 359 ARG cc_start: 0.7795 (tpt-90) cc_final: 0.7492 (tpt-90) REVERT: L 468 ASN cc_start: 0.7727 (OUTLIER) cc_final: 0.7197 (p0) REVERT: L 554 ASP cc_start: 0.7946 (t0) cc_final: 0.7575 (m-30) REVERT: M 332 LYS cc_start: 0.8848 (tmtt) cc_final: 0.8346 (ttmt) REVERT: M 346 MET cc_start: 0.8719 (tpp) cc_final: 0.8475 (tpp) REVERT: M 392 MET cc_start: 0.8096 (mpt) cc_final: 0.7655 (mpp) REVERT: M 460 MET cc_start: 0.7378 (ttm) cc_final: 0.6670 (ttm) REVERT: M 462 LEU cc_start: 0.8945 (tp) cc_final: 0.8396 (mp) REVERT: M 487 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7587 (tm-30) REVERT: M 540 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8255 (pt) REVERT: M 594 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8788 (pt) REVERT: M 614 ARG cc_start: 0.8222 (tmm-80) cc_final: 0.7977 (mtp-110) REVERT: N 332 LYS cc_start: 0.9005 (tmtt) cc_final: 0.8481 (ttmt) REVERT: N 346 MET cc_start: 0.8678 (tpp) cc_final: 0.8371 (mmm) REVERT: N 350 GLN cc_start: 0.9163 (tt0) cc_final: 0.8731 (tm-30) REVERT: N 392 MET cc_start: 0.8111 (mpt) cc_final: 0.7698 (mpp) REVERT: N 460 MET cc_start: 0.7132 (ttm) cc_final: 0.6803 (ttm) REVERT: O 346 MET cc_start: 0.8622 (tpp) cc_final: 0.8272 (mmm) REVERT: O 350 GLN cc_start: 0.9090 (tt0) cc_final: 0.8857 (pp30) REVERT: O 359 ARG cc_start: 0.7856 (tpt-90) cc_final: 0.7598 (tpt-90) REVERT: O 460 MET cc_start: 0.8167 (ttp) cc_final: 0.7714 (ttm) REVERT: O 462 LEU cc_start: 0.8974 (tp) cc_final: 0.8507 (mp) REVERT: O 610 LYS cc_start: 0.8635 (ttmm) cc_final: 0.8314 (tttm) REVERT: O 649 ARG cc_start: 0.8713 (mmt180) cc_final: 0.8305 (mmm-85) outliers start: 219 outliers final: 176 residues processed: 733 average time/residue: 0.5395 time to fit residues: 634.1820 Evaluate side-chains 708 residues out of total 4350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 513 time to evaluate : 4.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 468 ASN Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 377 ASN Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 448 SER Chi-restraints excluded: chain E residue 468 ASN Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 482 THR Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 550 GLN Chi-restraints excluded: chain E residue 551 THR Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 594 LEU Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 468 ASN Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 540 ILE Chi-restraints excluded: chain F residue 553 LEU Chi-restraints excluded: chain F residue 575 VAL Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 591 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 594 LEU Chi-restraints excluded: chain G residue 366 GLU Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 468 ASN Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 482 THR Chi-restraints excluded: chain G residue 496 VAL Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 550 GLN Chi-restraints excluded: chain G residue 575 VAL Chi-restraints excluded: chain G residue 576 LEU Chi-restraints excluded: chain H residue 366 GLU Chi-restraints excluded: chain H residue 433 THR Chi-restraints excluded: chain H residue 468 ASN Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 482 THR Chi-restraints excluded: chain H residue 546 LYS Chi-restraints excluded: chain H residue 550 GLN Chi-restraints excluded: chain H residue 553 LEU Chi-restraints excluded: chain H residue 575 VAL Chi-restraints excluded: chain H residue 576 LEU Chi-restraints excluded: chain H residue 591 VAL Chi-restraints excluded: chain H residue 593 LEU Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 433 THR Chi-restraints excluded: chain I residue 448 SER Chi-restraints excluded: chain I residue 468 ASN Chi-restraints excluded: chain I residue 477 THR Chi-restraints excluded: chain I residue 482 THR Chi-restraints excluded: chain I residue 538 MET Chi-restraints excluded: chain I residue 540 ILE Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 550 GLN Chi-restraints excluded: chain I residue 553 LEU Chi-restraints excluded: chain I residue 555 VAL Chi-restraints excluded: chain I residue 575 VAL Chi-restraints excluded: chain I residue 593 LEU Chi-restraints excluded: chain I residue 594 LEU Chi-restraints excluded: chain I residue 613 LYS Chi-restraints excluded: chain J residue 366 GLU Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain J residue 448 SER Chi-restraints excluded: chain J residue 468 ASN Chi-restraints excluded: chain J residue 477 THR Chi-restraints excluded: chain J residue 480 ILE Chi-restraints excluded: chain J residue 482 THR Chi-restraints excluded: chain J residue 495 ASP Chi-restraints excluded: chain J residue 547 VAL Chi-restraints excluded: chain J residue 550 GLN Chi-restraints excluded: chain J residue 551 THR Chi-restraints excluded: chain J residue 553 LEU Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain J residue 591 VAL Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 433 THR Chi-restraints excluded: chain K residue 468 ASN Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 482 THR Chi-restraints excluded: chain K residue 499 LEU Chi-restraints excluded: chain K residue 550 GLN Chi-restraints excluded: chain K residue 553 LEU Chi-restraints excluded: chain K residue 575 VAL Chi-restraints excluded: chain K residue 576 LEU Chi-restraints excluded: chain K residue 591 VAL Chi-restraints excluded: chain K residue 593 LEU Chi-restraints excluded: chain K residue 594 LEU Chi-restraints excluded: chain L residue 366 GLU Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain L residue 448 SER Chi-restraints excluded: chain L residue 468 ASN Chi-restraints excluded: chain L residue 477 THR Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 550 GLN Chi-restraints excluded: chain L residue 551 THR Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 575 VAL Chi-restraints excluded: chain L residue 576 LEU Chi-restraints excluded: chain L residue 593 LEU Chi-restraints excluded: chain M residue 366 GLU Chi-restraints excluded: chain M residue 433 THR Chi-restraints excluded: chain M residue 448 SER Chi-restraints excluded: chain M residue 477 THR Chi-restraints excluded: chain M residue 482 THR Chi-restraints excluded: chain M residue 538 MET Chi-restraints excluded: chain M residue 540 ILE Chi-restraints excluded: chain M residue 550 GLN Chi-restraints excluded: chain M residue 573 LEU Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 576 LEU Chi-restraints excluded: chain M residue 593 LEU Chi-restraints excluded: chain M residue 594 LEU Chi-restraints excluded: chain N residue 366 GLU Chi-restraints excluded: chain N residue 433 THR Chi-restraints excluded: chain N residue 468 ASN Chi-restraints excluded: chain N residue 477 THR Chi-restraints excluded: chain N residue 482 THR Chi-restraints excluded: chain N residue 496 VAL Chi-restraints excluded: chain N residue 550 GLN Chi-restraints excluded: chain N residue 551 THR Chi-restraints excluded: chain N residue 575 VAL Chi-restraints excluded: chain N residue 579 LEU Chi-restraints excluded: chain O residue 297 LEU Chi-restraints excluded: chain O residue 353 ILE Chi-restraints excluded: chain O residue 366 GLU Chi-restraints excluded: chain O residue 433 THR Chi-restraints excluded: chain O residue 468 ASN Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 482 THR Chi-restraints excluded: chain O residue 499 LEU Chi-restraints excluded: chain O residue 540 ILE Chi-restraints excluded: chain O residue 575 VAL Chi-restraints excluded: chain O residue 594 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 313 optimal weight: 20.0000 chunk 202 optimal weight: 8.9990 chunk 302 optimal weight: 3.9990 chunk 152 optimal weight: 20.0000 chunk 99 optimal weight: 4.9990 chunk 98 optimal weight: 20.0000 chunk 321 optimal weight: 4.9990 chunk 344 optimal weight: 3.9990 chunk 250 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 397 optimal weight: 20.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 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 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 615 ASN F 333 HIS ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 485 ASN ** G 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 333 HIS ** H 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 333 HIS ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 333 HIS ** 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 333 HIS ** N 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 39840 Z= 0.289 Angle : 0.638 13.951 53895 Z= 0.320 Chirality : 0.047 0.153 6480 Planarity : 0.004 0.047 6990 Dihedral : 5.195 44.268 5430 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.37 % Favored : 92.34 % Rotamer: Outliers : 4.87 % Allowed : 18.30 % Favored : 76.83 % 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: -2.65 (0.12), residues: 5130 helix: 0.80 (0.16), residues: 1155 sheet: -2.12 (0.10), residues: 2580 loop : -2.80 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 384 HIS 0.004 0.001 HIS D 364 PHE 0.015 0.001 PHE E 489 TYR 0.024 0.001 TYR K 639 ARG 0.011 0.001 ARG K 626 *********************** 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 751 residues out of total 4350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 539 time to evaluate : 4.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 LYS cc_start: 0.8932 (ttmm) cc_final: 0.8704 (tmtt) REVERT: A 346 MET cc_start: 0.8460 (tpp) cc_final: 0.7836 (mmt) REVERT: A 392 MET cc_start: 0.8188 (mpt) cc_final: 0.7700 (mpp) REVERT: A 460 MET cc_start: 0.6777 (ttm) cc_final: 0.6509 (ttm) REVERT: A 462 LEU cc_start: 0.8995 (tp) cc_final: 0.8731 (tp) REVERT: A 468 ASN cc_start: 0.7735 (OUTLIER) cc_final: 0.7321 (p0) REVERT: A 629 MET cc_start: 0.6810 (tmm) cc_final: 0.6533 (tmm) REVERT: A 649 ARG cc_start: 0.8571 (mmt180) cc_final: 0.7997 (mmm160) REVERT: B 346 MET cc_start: 0.8809 (tpp) cc_final: 0.8350 (tpp) REVERT: B 350 GLN cc_start: 0.9139 (tt0) cc_final: 0.8650 (pp30) REVERT: B 392 MET cc_start: 0.7991 (mpt) cc_final: 0.7450 (mpp) REVERT: B 462 LEU cc_start: 0.8884 (tp) cc_final: 0.8421 (mp) REVERT: B 649 ARG cc_start: 0.8706 (mmt180) cc_final: 0.8187 (mmm-85) REVERT: C 332 LYS cc_start: 0.8720 (tmtt) cc_final: 0.8314 (ttmt) REVERT: C 346 MET cc_start: 0.8670 (tpp) cc_final: 0.8309 (mmm) REVERT: C 350 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8095 (tm-30) REVERT: C 392 MET cc_start: 0.8105 (mpt) cc_final: 0.7632 (mpp) REVERT: C 523 MET cc_start: 0.6901 (ttm) cc_final: 0.6537 (ttm) REVERT: C 540 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8086 (pt) REVERT: C 612 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7621 (tm-30) REVERT: C 649 ARG cc_start: 0.8567 (mmt180) cc_final: 0.8150 (mmm-85) REVERT: D 332 LYS cc_start: 0.8713 (tmtt) cc_final: 0.8190 (ttmt) REVERT: D 346 MET cc_start: 0.8684 (tpp) cc_final: 0.8243 (mmm) REVERT: D 359 ARG cc_start: 0.7824 (tpt-90) cc_final: 0.7520 (tpt-90) REVERT: D 377 ASN cc_start: 0.8279 (OUTLIER) cc_final: 0.8029 (p0) REVERT: D 392 MET cc_start: 0.7906 (mpt) cc_final: 0.7285 (mpp) REVERT: D 460 MET cc_start: 0.7956 (ttp) cc_final: 0.7349 (ttm) REVERT: D 462 LEU cc_start: 0.8872 (tp) cc_final: 0.8380 (mp) REVERT: D 487 GLU cc_start: 0.7770 (pt0) cc_final: 0.7446 (pt0) REVERT: D 540 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8066 (pt) REVERT: D 541 GLU cc_start: 0.7538 (tm-30) cc_final: 0.7255 (tm-30) REVERT: D 610 LYS cc_start: 0.8565 (ttmm) cc_final: 0.8323 (tttm) REVERT: D 614 ARG cc_start: 0.8189 (tmm-80) cc_final: 0.7902 (mtp-110) REVERT: D 649 ARG cc_start: 0.8624 (mmt180) cc_final: 0.8059 (mmm-85) REVERT: E 346 MET cc_start: 0.8807 (tpp) cc_final: 0.8413 (tpp) REVERT: E 350 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8857 (tm-30) REVERT: E 366 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7525 (pt0) REVERT: E 377 ASN cc_start: 0.8194 (OUTLIER) cc_final: 0.7932 (p0) REVERT: E 392 MET cc_start: 0.8031 (mpt) cc_final: 0.7567 (mpp) REVERT: E 462 LEU cc_start: 0.8901 (tp) cc_final: 0.8374 (mp) REVERT: E 540 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8168 (pt) REVERT: E 614 ARG cc_start: 0.8218 (tmm-80) cc_final: 0.7984 (tmm-80) REVERT: E 649 ARG cc_start: 0.8607 (mmt180) cc_final: 0.8214 (mmm-85) REVERT: F 299 ASP cc_start: 0.8230 (m-30) cc_final: 0.7924 (m-30) REVERT: F 332 LYS cc_start: 0.8842 (tmtt) cc_final: 0.8413 (ptmt) REVERT: F 350 GLN cc_start: 0.9258 (tt0) cc_final: 0.8850 (tm-30) REVERT: F 462 LEU cc_start: 0.8807 (tp) cc_final: 0.8547 (tp) REVERT: F 540 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8061 (pt) REVERT: G 332 LYS cc_start: 0.8852 (tmtt) cc_final: 0.8567 (tmtt) REVERT: G 359 ARG cc_start: 0.8027 (tpt-90) cc_final: 0.7755 (tpt-90) REVERT: G 366 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7411 (mt-10) REVERT: G 392 MET cc_start: 0.8026 (mpt) cc_final: 0.7437 (mpp) REVERT: G 462 LEU cc_start: 0.8925 (tp) cc_final: 0.8677 (tp) REVERT: G 468 ASN cc_start: 0.7880 (OUTLIER) cc_final: 0.7392 (p0) REVERT: G 540 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8273 (pt) REVERT: G 610 LYS cc_start: 0.8667 (ttmm) cc_final: 0.8358 (tttm) REVERT: G 614 ARG cc_start: 0.8316 (tmm-80) cc_final: 0.7990 (mtp-110) REVERT: G 649 ARG cc_start: 0.8742 (mmt180) cc_final: 0.8254 (mmm-85) REVERT: H 332 LYS cc_start: 0.8871 (tmtt) cc_final: 0.8326 (ttmt) REVERT: H 346 MET cc_start: 0.8607 (tpp) cc_final: 0.8212 (tpp) REVERT: H 350 GLN cc_start: 0.9224 (tt0) cc_final: 0.8820 (tm-30) REVERT: H 392 MET cc_start: 0.8076 (mpt) cc_final: 0.7492 (mpp) REVERT: H 442 GLN cc_start: 0.9133 (pp30) cc_final: 0.8905 (pp30) REVERT: H 554 ASP cc_start: 0.7930 (t0) cc_final: 0.7577 (m-30) REVERT: H 642 MET cc_start: 0.9074 (mmt) cc_final: 0.8772 (mmt) REVERT: I 308 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8264 (tt) REVERT: I 332 LYS cc_start: 0.8969 (tmtt) cc_final: 0.8412 (ttmt) REVERT: I 346 MET cc_start: 0.8903 (tpp) cc_final: 0.8585 (tpp) REVERT: I 350 GLN cc_start: 0.9149 (tt0) cc_final: 0.8619 (pp30) REVERT: I 366 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7374 (pm20) REVERT: I 371 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7701 (tm-30) REVERT: I 462 LEU cc_start: 0.8951 (tp) cc_final: 0.8483 (mp) REVERT: J 332 LYS cc_start: 0.8834 (tmtt) cc_final: 0.8366 (ttmt) REVERT: J 346 MET cc_start: 0.8765 (tpp) cc_final: 0.8388 (mmm) REVERT: J 350 GLN cc_start: 0.9124 (tt0) cc_final: 0.8499 (pp30) REVERT: J 366 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7392 (pt0) REVERT: J 392 MET cc_start: 0.7841 (mpt) cc_final: 0.7392 (mpp) REVERT: J 460 MET cc_start: 0.6843 (ttm) cc_final: 0.6442 (ttm) REVERT: J 462 LEU cc_start: 0.8922 (tp) cc_final: 0.8402 (mp) REVERT: J 487 GLU cc_start: 0.7747 (pt0) cc_final: 0.7469 (pt0) REVERT: J 610 LYS cc_start: 0.8553 (ttmm) cc_final: 0.8342 (ttmm) REVERT: J 649 ARG cc_start: 0.8847 (mmt180) cc_final: 0.8339 (mmm-85) REVERT: K 332 LYS cc_start: 0.8823 (tmtt) cc_final: 0.8251 (ttmt) REVERT: K 346 MET cc_start: 0.8611 (tpp) cc_final: 0.8257 (mmm) REVERT: K 350 GLN cc_start: 0.9093 (tt0) cc_final: 0.8488 (pp30) REVERT: K 392 MET cc_start: 0.7841 (mpt) cc_final: 0.7323 (mpp) REVERT: K 462 LEU cc_start: 0.8914 (tp) cc_final: 0.8458 (mp) REVERT: K 487 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7551 (tm-30) REVERT: K 610 LYS cc_start: 0.8604 (ttmm) cc_final: 0.8308 (tttm) REVERT: K 614 ARG cc_start: 0.8300 (tmm-80) cc_final: 0.8024 (mtp-110) REVERT: L 346 MET cc_start: 0.8533 (tpp) cc_final: 0.8184 (mmm) REVERT: L 350 GLN cc_start: 0.9150 (tt0) cc_final: 0.8663 (tm-30) REVERT: L 468 ASN cc_start: 0.7757 (OUTLIER) cc_final: 0.7211 (p0) REVERT: L 554 ASP cc_start: 0.7994 (t0) cc_final: 0.7674 (m-30) REVERT: M 332 LYS cc_start: 0.8832 (tmtt) cc_final: 0.8341 (ttmt) REVERT: M 346 MET cc_start: 0.8698 (tpp) cc_final: 0.8434 (tpp) REVERT: M 392 MET cc_start: 0.8101 (mpt) cc_final: 0.7642 (mpp) REVERT: M 460 MET cc_start: 0.7186 (ttm) cc_final: 0.6494 (ttm) REVERT: M 462 LEU cc_start: 0.8919 (tp) cc_final: 0.8400 (mp) REVERT: M 487 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7577 (tm-30) REVERT: M 540 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8269 (pt) REVERT: M 594 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8773 (pt) REVERT: M 614 ARG cc_start: 0.8163 (tmm-80) cc_final: 0.7936 (mtp-110) REVERT: M 629 MET cc_start: 0.6256 (tmm) cc_final: 0.5540 (tmm) REVERT: N 332 LYS cc_start: 0.8997 (tmtt) cc_final: 0.8363 (ttmm) REVERT: N 346 MET cc_start: 0.8673 (tpp) cc_final: 0.8353 (mmm) REVERT: N 350 GLN cc_start: 0.9151 (tt0) cc_final: 0.8702 (tm-30) REVERT: N 392 MET cc_start: 0.8215 (mpt) cc_final: 0.7784 (mpp) REVERT: N 460 MET cc_start: 0.7137 (ttm) cc_final: 0.6773 (ttm) REVERT: O 346 MET cc_start: 0.8613 (tpp) cc_final: 0.8256 (mmm) REVERT: O 350 GLN cc_start: 0.9214 (tt0) cc_final: 0.8790 (tm-30) REVERT: O 353 ILE cc_start: 0.9466 (OUTLIER) cc_final: 0.9264 (mp) REVERT: O 377 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.8078 (p0) REVERT: O 460 MET cc_start: 0.8080 (ttp) cc_final: 0.7623 (ttm) REVERT: O 462 LEU cc_start: 0.8967 (tp) cc_final: 0.8500 (mp) REVERT: O 610 LYS cc_start: 0.8623 (ttmm) cc_final: 0.8315 (tttm) REVERT: O 649 ARG cc_start: 0.8644 (mmt180) cc_final: 0.8279 (mmm-85) outliers start: 212 outliers final: 180 residues processed: 716 average time/residue: 0.5487 time to fit residues: 637.4363 Evaluate side-chains 718 residues out of total 4350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 518 time to evaluate : 4.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 550 GLN Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 550 GLN Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 377 ASN Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 448 SER Chi-restraints excluded: chain E residue 468 ASN Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 482 THR Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 550 GLN Chi-restraints excluded: chain E residue 551 THR Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 594 LEU Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 540 ILE Chi-restraints excluded: chain F residue 550 GLN Chi-restraints excluded: chain F residue 553 LEU Chi-restraints excluded: chain F residue 575 VAL Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 591 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 594 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 366 GLU Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 468 ASN Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 482 THR Chi-restraints excluded: chain G residue 496 VAL Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 550 GLN Chi-restraints excluded: chain G residue 575 VAL Chi-restraints excluded: chain G residue 576 LEU Chi-restraints excluded: chain H residue 366 GLU Chi-restraints excluded: chain H residue 433 THR Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 482 THR Chi-restraints excluded: chain H residue 546 LYS Chi-restraints excluded: chain H residue 550 GLN Chi-restraints excluded: chain H residue 553 LEU Chi-restraints excluded: chain H residue 575 VAL Chi-restraints excluded: chain H residue 591 VAL Chi-restraints excluded: chain H residue 593 LEU Chi-restraints excluded: chain I residue 296 ASP Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 433 THR Chi-restraints excluded: chain I residue 448 SER Chi-restraints excluded: chain I residue 468 ASN Chi-restraints excluded: chain I residue 477 THR Chi-restraints excluded: chain I residue 482 THR Chi-restraints excluded: chain I residue 538 MET Chi-restraints excluded: chain I residue 540 ILE Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 550 GLN Chi-restraints excluded: chain I residue 553 LEU Chi-restraints excluded: chain I residue 555 VAL Chi-restraints excluded: chain I residue 575 VAL Chi-restraints excluded: chain I residue 593 LEU Chi-restraints excluded: chain I residue 613 LYS Chi-restraints excluded: chain J residue 366 GLU Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain J residue 448 SER Chi-restraints excluded: chain J residue 468 ASN Chi-restraints excluded: chain J residue 477 THR Chi-restraints excluded: chain J residue 480 ILE Chi-restraints excluded: chain J residue 482 THR Chi-restraints excluded: chain J residue 495 ASP Chi-restraints excluded: chain J residue 547 VAL Chi-restraints excluded: chain J residue 550 GLN Chi-restraints excluded: chain J residue 551 THR Chi-restraints excluded: chain J residue 553 LEU Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain J residue 591 VAL Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 433 THR Chi-restraints excluded: chain K residue 468 ASN Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 482 THR Chi-restraints excluded: chain K residue 499 LEU Chi-restraints excluded: chain K residue 550 GLN Chi-restraints excluded: chain K residue 553 LEU Chi-restraints excluded: chain K residue 576 LEU Chi-restraints excluded: chain K residue 591 VAL Chi-restraints excluded: chain K residue 593 LEU Chi-restraints excluded: chain K residue 594 LEU Chi-restraints excluded: chain L residue 366 GLU Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain L residue 448 SER Chi-restraints excluded: chain L residue 468 ASN Chi-restraints excluded: chain L residue 477 THR Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 550 GLN Chi-restraints excluded: chain L residue 551 THR Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 575 VAL Chi-restraints excluded: chain L residue 593 LEU Chi-restraints excluded: chain M residue 296 ASP Chi-restraints excluded: chain M residue 366 GLU Chi-restraints excluded: chain M residue 433 THR Chi-restraints excluded: chain M residue 448 SER Chi-restraints excluded: chain M residue 477 THR Chi-restraints excluded: chain M residue 482 THR Chi-restraints excluded: chain M residue 538 MET Chi-restraints excluded: chain M residue 540 ILE Chi-restraints excluded: chain M residue 550 GLN Chi-restraints excluded: chain M residue 573 LEU Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 576 LEU Chi-restraints excluded: chain M residue 593 LEU Chi-restraints excluded: chain M residue 594 LEU Chi-restraints excluded: chain N residue 296 ASP Chi-restraints excluded: chain N residue 366 GLU Chi-restraints excluded: chain N residue 433 THR Chi-restraints excluded: chain N residue 468 ASN Chi-restraints excluded: chain N residue 477 THR Chi-restraints excluded: chain N residue 482 THR Chi-restraints excluded: chain N residue 496 VAL Chi-restraints excluded: chain N residue 550 GLN Chi-restraints excluded: chain N residue 551 THR Chi-restraints excluded: chain N residue 575 VAL Chi-restraints excluded: chain N residue 579 LEU Chi-restraints excluded: chain O residue 297 LEU Chi-restraints excluded: chain O residue 353 ILE Chi-restraints excluded: chain O residue 366 GLU Chi-restraints excluded: chain O residue 377 ASN Chi-restraints excluded: chain O residue 402 ILE Chi-restraints excluded: chain O residue 433 THR Chi-restraints excluded: chain O residue 468 ASN Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 482 THR Chi-restraints excluded: chain O residue 499 LEU Chi-restraints excluded: chain O residue 538 MET Chi-restraints excluded: chain O residue 540 ILE Chi-restraints excluded: chain O residue 550 GLN Chi-restraints excluded: chain O residue 575 VAL Chi-restraints excluded: chain O residue 594 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 460 optimal weight: 4.9990 chunk 484 optimal weight: 8.9990 chunk 442 optimal weight: 3.9990 chunk 471 optimal weight: 7.9990 chunk 283 optimal weight: 9.9990 chunk 205 optimal weight: 2.9990 chunk 370 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 426 optimal weight: 3.9990 chunk 445 optimal weight: 8.9990 chunk 469 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN ** 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** C 615 ASN ** D 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 615 ASN F 333 HIS ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 333 HIS ** H 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 333 HIS ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 333 HIS ** 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** M 615 ASN ** N 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 39840 Z= 0.387 Angle : 0.694 14.035 53895 Z= 0.348 Chirality : 0.048 0.180 6480 Planarity : 0.004 0.042 6990 Dihedral : 5.451 43.831 5430 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.28 % Favored : 90.43 % Rotamer: Outliers : 5.15 % Allowed : 18.34 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.12), residues: 5130 helix: 0.71 (0.16), residues: 1155 sheet: -2.21 (0.10), residues: 2580 loop : -2.84 (0.14), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 384 HIS 0.005 0.001 HIS D 364 PHE 0.018 0.002 PHE E 489 TYR 0.024 0.001 TYR B 639 ARG 0.009 0.001 ARG C 614 *********************** REFINEMENT MACRO_CYCLE 9 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 744 residues out of total 4350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 520 time to evaluate : 4.966 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: A 332 LYS cc_start: 0.8958 (ttmm) cc_final: 0.8741 (tmtt) REVERT: A 346 MET cc_start: 0.8497 (tpp) cc_final: 0.7780 (mmt) REVERT: A 392 MET cc_start: 0.8233 (mpt) cc_final: 0.7751 (mpp) REVERT: A 462 LEU cc_start: 0.9026 (tp) cc_final: 0.8555 (mp) REVERT: A 649 ARG cc_start: 0.8612 (mmt180) cc_final: 0.8047 (mmm160) REVERT: B 346 MET cc_start: 0.8826 (tpp) cc_final: 0.8319 (tpp) REVERT: B 350 GLN cc_start: 0.9171 (tt0) cc_final: 0.8660 (pp30) REVERT: B 392 MET cc_start: 0.8023 (mpt) cc_final: 0.7475 (mpp) REVERT: B 462 LEU cc_start: 0.8900 (tp) cc_final: 0.8424 (mp) REVERT: B 649 ARG cc_start: 0.8734 (mmt180) cc_final: 0.8212 (mmt90) REVERT: C 332 LYS cc_start: 0.8740 (tmtt) cc_final: 0.8349 (ttmt) REVERT: C 350 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8082 (tm-30) REVERT: C 392 MET cc_start: 0.8211 (mpt) cc_final: 0.7747 (mpp) REVERT: C 523 MET cc_start: 0.6947 (ttm) cc_final: 0.6592 (ttm) REVERT: C 540 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8117 (pt) REVERT: C 612 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7791 (tm-30) REVERT: C 629 MET cc_start: 0.6585 (tmm) cc_final: 0.6130 (tmm) REVERT: C 649 ARG cc_start: 0.8678 (mmt180) cc_final: 0.8172 (mmm-85) REVERT: D 332 LYS cc_start: 0.8735 (tmtt) cc_final: 0.8215 (ttmt) REVERT: D 346 MET cc_start: 0.8683 (tpp) cc_final: 0.8420 (tpp) REVERT: D 377 ASN cc_start: 0.8288 (OUTLIER) cc_final: 0.7997 (p0) REVERT: D 392 MET cc_start: 0.8062 (mpt) cc_final: 0.7438 (mpp) REVERT: D 460 MET cc_start: 0.7985 (ttp) cc_final: 0.7364 (ttm) REVERT: D 462 LEU cc_start: 0.8903 (tp) cc_final: 0.8413 (mp) REVERT: D 487 GLU cc_start: 0.7779 (pt0) cc_final: 0.7406 (pt0) REVERT: D 614 ARG cc_start: 0.8234 (tmm-80) cc_final: 0.7913 (mtp-110) REVERT: D 649 ARG cc_start: 0.8680 (mmt180) cc_final: 0.8083 (mmm-85) REVERT: E 346 MET cc_start: 0.8854 (tpp) cc_final: 0.8350 (tpp) REVERT: E 350 GLN cc_start: 0.9182 (OUTLIER) cc_final: 0.8954 (tm-30) REVERT: E 366 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7603 (pt0) REVERT: E 377 ASN cc_start: 0.8288 (OUTLIER) cc_final: 0.8000 (p0) REVERT: E 392 MET cc_start: 0.8139 (mpt) cc_final: 0.7711 (mpp) REVERT: E 460 MET cc_start: 0.6980 (ttm) cc_final: 0.6186 (ttm) REVERT: E 462 LEU cc_start: 0.8924 (tp) cc_final: 0.8377 (mp) REVERT: E 540 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8361 (pt) REVERT: E 649 ARG cc_start: 0.8675 (mmt180) cc_final: 0.8167 (mmm-85) REVERT: F 299 ASP cc_start: 0.8295 (m-30) cc_final: 0.7997 (m-30) REVERT: F 332 LYS cc_start: 0.8893 (tmtt) cc_final: 0.8349 (ttmt) REVERT: F 350 GLN cc_start: 0.9272 (tt0) cc_final: 0.8887 (tm-30) REVERT: F 462 LEU cc_start: 0.8823 (tp) cc_final: 0.8571 (tp) REVERT: F 540 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8085 (pt) REVERT: G 332 LYS cc_start: 0.8856 (tmtt) cc_final: 0.8578 (tmtt) REVERT: G 359 ARG cc_start: 0.7986 (tpt-90) cc_final: 0.7719 (tpt-90) REVERT: G 366 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7447 (mt-10) REVERT: G 392 MET cc_start: 0.8102 (mpt) cc_final: 0.7493 (mpp) REVERT: G 462 LEU cc_start: 0.8942 (tp) cc_final: 0.8712 (tp) REVERT: G 468 ASN cc_start: 0.7943 (OUTLIER) cc_final: 0.7386 (p0) REVERT: G 540 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8288 (pt) REVERT: G 554 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7863 (m-30) REVERT: G 610 LYS cc_start: 0.8633 (ttmm) cc_final: 0.8400 (ttmm) REVERT: G 614 ARG cc_start: 0.8364 (tmm-80) cc_final: 0.8037 (mtp-110) REVERT: G 649 ARG cc_start: 0.8766 (mmt180) cc_final: 0.8216 (mmm-85) REVERT: H 332 LYS cc_start: 0.8909 (tmtt) cc_final: 0.8338 (ttmt) REVERT: H 333 HIS cc_start: 0.8596 (m90) cc_final: 0.8354 (m-70) REVERT: H 346 MET cc_start: 0.8601 (tpp) cc_final: 0.8243 (tpp) REVERT: H 350 GLN cc_start: 0.9237 (tt0) cc_final: 0.8835 (tm-30) REVERT: H 392 MET cc_start: 0.8148 (mpt) cc_final: 0.7574 (mpp) REVERT: H 554 ASP cc_start: 0.7941 (t0) cc_final: 0.7554 (m-30) REVERT: H 614 ARG cc_start: 0.7970 (mtp-110) cc_final: 0.7749 (mtm110) REVERT: I 308 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8221 (tt) REVERT: I 332 LYS cc_start: 0.9002 (tmtt) cc_final: 0.8431 (ttmt) REVERT: I 346 MET cc_start: 0.8919 (tpp) cc_final: 0.8553 (tpp) REVERT: I 350 GLN cc_start: 0.9166 (tt0) cc_final: 0.8622 (pp30) REVERT: I 359 ARG cc_start: 0.7785 (tpt-90) cc_final: 0.7453 (tpt-90) REVERT: I 366 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7371 (pm20) REVERT: I 371 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7755 (tm-30) REVERT: I 462 LEU cc_start: 0.8962 (tp) cc_final: 0.8486 (mp) REVERT: J 332 LYS cc_start: 0.8858 (tmtt) cc_final: 0.8402 (ttmt) REVERT: J 350 GLN cc_start: 0.9135 (tt0) cc_final: 0.8508 (pp30) REVERT: J 366 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7415 (pt0) REVERT: J 392 MET cc_start: 0.7936 (mpt) cc_final: 0.7500 (mpp) REVERT: J 460 MET cc_start: 0.6883 (ttm) cc_final: 0.6462 (ttm) REVERT: J 462 LEU cc_start: 0.8935 (tp) cc_final: 0.8457 (mp) REVERT: J 487 GLU cc_start: 0.7696 (pt0) cc_final: 0.7405 (pt0) REVERT: J 649 ARG cc_start: 0.8853 (mmt180) cc_final: 0.8241 (mmm-85) REVERT: K 332 LYS cc_start: 0.8845 (tmtt) cc_final: 0.8263 (ttmt) REVERT: K 333 HIS cc_start: 0.8598 (m90) cc_final: 0.8335 (m-70) REVERT: K 346 MET cc_start: 0.8624 (tpp) cc_final: 0.8195 (tpp) REVERT: K 350 GLN cc_start: 0.9116 (tt0) cc_final: 0.8547 (pp30) REVERT: K 392 MET cc_start: 0.7932 (mpt) cc_final: 0.7420 (mpp) REVERT: K 462 LEU cc_start: 0.8905 (tp) cc_final: 0.8442 (mp) REVERT: K 487 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7571 (tm-30) REVERT: K 610 LYS cc_start: 0.8634 (ttmm) cc_final: 0.8402 (ttmm) REVERT: K 614 ARG cc_start: 0.8327 (tmm-80) cc_final: 0.8061 (mtp-110) REVERT: L 346 MET cc_start: 0.8588 (tpp) cc_final: 0.8163 (mmm) REVERT: L 350 GLN cc_start: 0.9161 (tt0) cc_final: 0.8676 (tm-30) REVERT: L 468 ASN cc_start: 0.7733 (OUTLIER) cc_final: 0.7224 (p0) REVERT: L 554 ASP cc_start: 0.7926 (t0) cc_final: 0.7595 (m-30) REVERT: L 580 MET cc_start: 0.8550 (mpp) cc_final: 0.8141 (mpp) REVERT: M 332 LYS cc_start: 0.8873 (tmtt) cc_final: 0.8434 (ttmt) REVERT: M 346 MET cc_start: 0.8710 (tpp) cc_final: 0.8360 (tpp) REVERT: M 392 MET cc_start: 0.8241 (mpt) cc_final: 0.7867 (mpp) REVERT: M 460 MET cc_start: 0.7113 (ttm) cc_final: 0.6869 (ttm) REVERT: M 462 LEU cc_start: 0.8937 (tp) cc_final: 0.8670 (tp) REVERT: M 594 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8799 (pt) REVERT: M 614 ARG cc_start: 0.8247 (tmm-80) cc_final: 0.7913 (mtp-110) REVERT: M 629 MET cc_start: 0.6629 (tmm) cc_final: 0.5908 (tmm) REVERT: N 332 LYS cc_start: 0.8924 (tmtt) cc_final: 0.8354 (ttmm) REVERT: N 346 MET cc_start: 0.8701 (tpp) cc_final: 0.8381 (mmm) REVERT: N 350 GLN cc_start: 0.9165 (tt0) cc_final: 0.8725 (tm-30) REVERT: N 392 MET cc_start: 0.8187 (mpt) cc_final: 0.7746 (mpp) REVERT: N 460 MET cc_start: 0.7157 (ttm) cc_final: 0.6794 (ttm) REVERT: O 346 MET cc_start: 0.8650 (tpp) cc_final: 0.8306 (tpp) REVERT: O 350 GLN cc_start: 0.9218 (tt0) cc_final: 0.8804 (tm-30) REVERT: O 353 ILE cc_start: 0.9439 (OUTLIER) cc_final: 0.9233 (mp) REVERT: O 377 ASN cc_start: 0.8478 (OUTLIER) cc_final: 0.8066 (p0) REVERT: O 460 MET cc_start: 0.8084 (ttp) cc_final: 0.7600 (ttm) REVERT: O 462 LEU cc_start: 0.8963 (tp) cc_final: 0.8483 (mp) REVERT: O 610 LYS cc_start: 0.8647 (ttmm) cc_final: 0.8360 (tttm) REVERT: O 649 ARG cc_start: 0.8659 (mmt180) cc_final: 0.8272 (mmm-85) outliers start: 224 outliers final: 192 residues processed: 707 average time/residue: 0.5308 time to fit residues: 607.6736 Evaluate side-chains 712 residues out of total 4350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 502 time to evaluate : 4.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 468 ASN Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 550 GLN Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 550 GLN Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 377 ASN Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 448 SER Chi-restraints excluded: chain E residue 468 ASN Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 482 THR Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 550 GLN Chi-restraints excluded: chain E residue 551 THR Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 594 LEU Chi-restraints excluded: chain F residue 296 ASP Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 540 ILE Chi-restraints excluded: chain F residue 550 GLN Chi-restraints excluded: chain F residue 553 LEU Chi-restraints excluded: chain F residue 575 VAL Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 591 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 594 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 366 GLU Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 468 ASN Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 482 THR Chi-restraints excluded: chain G residue 496 VAL Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 550 GLN Chi-restraints excluded: chain G residue 554 ASP Chi-restraints excluded: chain G residue 575 VAL Chi-restraints excluded: chain G residue 576 LEU Chi-restraints excluded: chain H residue 296 ASP Chi-restraints excluded: chain H residue 366 GLU Chi-restraints excluded: chain H residue 433 THR Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 482 THR Chi-restraints excluded: chain H residue 546 LYS Chi-restraints excluded: chain H residue 550 GLN Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain H residue 553 LEU Chi-restraints excluded: chain H residue 575 VAL Chi-restraints excluded: chain H residue 591 VAL Chi-restraints excluded: chain H residue 593 LEU Chi-restraints excluded: chain I residue 296 ASP Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 433 THR Chi-restraints excluded: chain I residue 448 SER Chi-restraints excluded: chain I residue 468 ASN Chi-restraints excluded: chain I residue 477 THR Chi-restraints excluded: chain I residue 482 THR Chi-restraints excluded: chain I residue 538 MET Chi-restraints excluded: chain I residue 540 ILE Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 550 GLN Chi-restraints excluded: chain I residue 553 LEU Chi-restraints excluded: chain I residue 555 VAL Chi-restraints excluded: chain I residue 575 VAL Chi-restraints excluded: chain I residue 593 LEU Chi-restraints excluded: chain J residue 366 GLU Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain J residue 448 SER Chi-restraints excluded: chain J residue 468 ASN Chi-restraints excluded: chain J residue 477 THR Chi-restraints excluded: chain J residue 480 ILE Chi-restraints excluded: chain J residue 482 THR Chi-restraints excluded: chain J residue 495 ASP Chi-restraints excluded: chain J residue 547 VAL Chi-restraints excluded: chain J residue 550 GLN Chi-restraints excluded: chain J residue 551 THR Chi-restraints excluded: chain J residue 553 LEU Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain J residue 591 VAL Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 402 ILE Chi-restraints excluded: chain K residue 433 THR Chi-restraints excluded: chain K residue 468 ASN Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 482 THR Chi-restraints excluded: chain K residue 499 LEU Chi-restraints excluded: chain K residue 550 GLN Chi-restraints excluded: chain K residue 553 LEU Chi-restraints excluded: chain K residue 576 LEU Chi-restraints excluded: chain K residue 591 VAL Chi-restraints excluded: chain K residue 593 LEU Chi-restraints excluded: chain K residue 594 LEU Chi-restraints excluded: chain L residue 296 ASP Chi-restraints excluded: chain L residue 366 GLU Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain L residue 448 SER Chi-restraints excluded: chain L residue 468 ASN Chi-restraints excluded: chain L residue 477 THR Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 550 GLN Chi-restraints excluded: chain L residue 551 THR Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 575 VAL Chi-restraints excluded: chain L residue 576 LEU Chi-restraints excluded: chain L residue 593 LEU Chi-restraints excluded: chain M residue 296 ASP Chi-restraints excluded: chain M residue 366 GLU Chi-restraints excluded: chain M residue 433 THR Chi-restraints excluded: chain M residue 448 SER Chi-restraints excluded: chain M residue 477 THR Chi-restraints excluded: chain M residue 482 THR Chi-restraints excluded: chain M residue 538 MET Chi-restraints excluded: chain M residue 540 ILE Chi-restraints excluded: chain M residue 550 GLN Chi-restraints excluded: chain M residue 573 LEU Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 576 LEU Chi-restraints excluded: chain M residue 593 LEU Chi-restraints excluded: chain M residue 594 LEU Chi-restraints excluded: chain N residue 296 ASP Chi-restraints excluded: chain N residue 366 GLU Chi-restraints excluded: chain N residue 433 THR Chi-restraints excluded: chain N residue 468 ASN Chi-restraints excluded: chain N residue 477 THR Chi-restraints excluded: chain N residue 482 THR Chi-restraints excluded: chain N residue 496 VAL Chi-restraints excluded: chain N residue 523 MET Chi-restraints excluded: chain N residue 550 GLN Chi-restraints excluded: chain N residue 551 THR Chi-restraints excluded: chain N residue 575 VAL Chi-restraints excluded: chain N residue 579 LEU Chi-restraints excluded: chain O residue 297 LEU Chi-restraints excluded: chain O residue 353 ILE Chi-restraints excluded: chain O residue 366 GLU Chi-restraints excluded: chain O residue 377 ASN Chi-restraints excluded: chain O residue 402 ILE Chi-restraints excluded: chain O residue 433 THR Chi-restraints excluded: chain O residue 468 ASN Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 482 THR Chi-restraints excluded: chain O residue 499 LEU Chi-restraints excluded: chain O residue 538 MET Chi-restraints excluded: chain O residue 540 ILE Chi-restraints excluded: chain O residue 550 GLN Chi-restraints excluded: chain O residue 575 VAL Chi-restraints excluded: chain O residue 594 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 309 optimal weight: 3.9990 chunk 498 optimal weight: 3.9990 chunk 304 optimal weight: 8.9990 chunk 236 optimal weight: 3.9990 chunk 346 optimal weight: 9.9990 chunk 523 optimal weight: 8.9990 chunk 481 optimal weight: 3.9990 chunk 416 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 321 optimal weight: 4.9990 chunk 255 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** ** 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** C 615 ASN ** D 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 333 HIS ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 333 HIS ** 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 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7728 moved from start: 0.5098 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= 0.291 Angle : 0.665 14.502 53895 Z= 0.329 Chirality : 0.047 0.175 6480 Planarity : 0.004 0.046 6990 Dihedral : 5.256 45.389 5430 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.66 % Favored : 92.05 % Rotamer: Outliers : 4.74 % Allowed : 19.06 % Favored : 76.21 % 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: -2.68 (0.12), residues: 5130 helix: 0.80 (0.16), residues: 1155 sheet: -2.15 (0.10), residues: 2580 loop : -2.82 (0.14), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP I 384 HIS 0.004 0.001 HIS D 364 PHE 0.015 0.001 PHE E 489 TYR 0.022 0.001 TYR B 639 ARG 0.009 0.001 ARG I 626 ********************** REFINEMENT MACRO_CYCLE 10 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 738 residues out of total 4350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 532 time to evaluate : 4.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 LYS cc_start: 0.8912 (ttmm) cc_final: 0.8702 (tmtt) REVERT: A 346 MET cc_start: 0.8465 (tpp) cc_final: 0.7804 (mmt) REVERT: A 392 MET cc_start: 0.8168 (mpt) cc_final: 0.7682 (mpp) REVERT: A 462 LEU cc_start: 0.8995 (tp) cc_final: 0.8727 (tp) REVERT: A 468 ASN cc_start: 0.7829 (OUTLIER) cc_final: 0.7382 (p0) REVERT: A 649 ARG cc_start: 0.8567 (mmt180) cc_final: 0.7936 (mmm160) REVERT: B 346 MET cc_start: 0.8808 (tpp) cc_final: 0.8316 (tpp) REVERT: B 350 GLN cc_start: 0.9157 (tt0) cc_final: 0.8641 (pp30) REVERT: B 392 MET cc_start: 0.8008 (mpt) cc_final: 0.7432 (mpp) REVERT: B 649 ARG cc_start: 0.8718 (mmt180) cc_final: 0.8042 (mmm160) REVERT: C 332 LYS cc_start: 0.8713 (tmtt) cc_final: 0.8285 (ttmt) REVERT: C 350 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8009 (tm-30) REVERT: C 392 MET cc_start: 0.8083 (mpt) cc_final: 0.7593 (mpp) REVERT: C 523 MET cc_start: 0.6880 (ttm) cc_final: 0.6535 (ttm) REVERT: C 540 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8083 (pt) REVERT: C 612 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7653 (tm-30) REVERT: C 629 MET cc_start: 0.6682 (tmm) cc_final: 0.6297 (tmm) REVERT: C 649 ARG cc_start: 0.8622 (mmt180) cc_final: 0.8184 (mmm-85) REVERT: D 332 LYS cc_start: 0.8733 (tmtt) cc_final: 0.8176 (ttmt) REVERT: D 346 MET cc_start: 0.8696 (tpp) cc_final: 0.8262 (mmm) REVERT: D 353 ILE cc_start: 0.9391 (mt) cc_final: 0.9179 (mp) REVERT: D 377 ASN cc_start: 0.8172 (OUTLIER) cc_final: 0.7926 (p0) REVERT: D 392 MET cc_start: 0.7993 (mpt) cc_final: 0.7357 (mpp) REVERT: D 460 MET cc_start: 0.7947 (ttp) cc_final: 0.7639 (ttm) REVERT: D 487 GLU cc_start: 0.7773 (pt0) cc_final: 0.7458 (pt0) REVERT: D 614 ARG cc_start: 0.8232 (tmm-80) cc_final: 0.7929 (mtp-110) REVERT: D 649 ARG cc_start: 0.8650 (mmt180) cc_final: 0.8078 (mmm-85) REVERT: E 346 MET cc_start: 0.8834 (tpp) cc_final: 0.8346 (tpp) REVERT: E 350 GLN cc_start: 0.9167 (OUTLIER) cc_final: 0.8940 (tm-30) REVERT: E 366 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7521 (pt0) REVERT: E 377 ASN cc_start: 0.8249 (OUTLIER) cc_final: 0.7994 (p0) REVERT: E 392 MET cc_start: 0.8059 (mpt) cc_final: 0.7621 (mpp) REVERT: E 460 MET cc_start: 0.6957 (ttm) cc_final: 0.6139 (ttm) REVERT: E 462 LEU cc_start: 0.8941 (tp) cc_final: 0.8414 (mp) REVERT: E 540 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8305 (pt) REVERT: E 649 ARG cc_start: 0.8701 (mmt180) cc_final: 0.8211 (mmm-85) REVERT: F 299 ASP cc_start: 0.8239 (m-30) cc_final: 0.7930 (m-30) REVERT: F 332 LYS cc_start: 0.8848 (tmtt) cc_final: 0.8394 (ptmt) REVERT: F 350 GLN cc_start: 0.9263 (tt0) cc_final: 0.8905 (tm-30) REVERT: F 462 LEU cc_start: 0.8830 (tp) cc_final: 0.8601 (tp) REVERT: F 540 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8071 (pt) REVERT: F 586 GLU cc_start: 0.7592 (tp30) cc_final: 0.7317 (tp30) REVERT: G 332 LYS cc_start: 0.8839 (tmtt) cc_final: 0.8561 (tmtt) REVERT: G 359 ARG cc_start: 0.7971 (tpt-90) cc_final: 0.7710 (tpt-90) REVERT: G 366 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7430 (mt-10) REVERT: G 392 MET cc_start: 0.8043 (mpt) cc_final: 0.7436 (mpp) REVERT: G 462 LEU cc_start: 0.8927 (tp) cc_final: 0.8675 (tp) REVERT: G 468 ASN cc_start: 0.7930 (OUTLIER) cc_final: 0.7437 (p0) REVERT: G 540 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8299 (pt) REVERT: G 554 ASP cc_start: 0.8164 (OUTLIER) cc_final: 0.7784 (m-30) REVERT: G 610 LYS cc_start: 0.8622 (ttmm) cc_final: 0.8304 (tttm) REVERT: G 614 ARG cc_start: 0.8322 (tmm-80) cc_final: 0.7989 (mtp-110) REVERT: G 649 ARG cc_start: 0.8737 (mmt180) cc_final: 0.8230 (mmm-85) REVERT: H 332 LYS cc_start: 0.8853 (tmtt) cc_final: 0.8353 (ttmt) REVERT: H 346 MET cc_start: 0.8593 (tpp) cc_final: 0.8209 (tpp) REVERT: H 350 GLN cc_start: 0.9232 (tt0) cc_final: 0.8827 (tm-30) REVERT: H 392 MET cc_start: 0.8124 (mpt) cc_final: 0.7515 (mpp) REVERT: H 487 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7833 (tm-30) REVERT: H 554 ASP cc_start: 0.7956 (t0) cc_final: 0.7587 (m-30) REVERT: H 614 ARG cc_start: 0.7921 (mtp-110) cc_final: 0.7711 (mtm110) REVERT: I 308 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8250 (tt) REVERT: I 332 LYS cc_start: 0.8973 (tmtt) cc_final: 0.8388 (ttmt) REVERT: I 346 MET cc_start: 0.8897 (tpp) cc_final: 0.8604 (tpp) REVERT: I 350 GLN cc_start: 0.9162 (tt0) cc_final: 0.8608 (pp30) REVERT: I 359 ARG cc_start: 0.7803 (tpt-90) cc_final: 0.7451 (tpt-90) REVERT: I 366 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7357 (pm20) REVERT: I 371 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7726 (tm-30) REVERT: I 462 LEU cc_start: 0.8913 (tp) cc_final: 0.8659 (tp) REVERT: I 540 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8323 (pt) REVERT: I 579 LEU cc_start: 0.9276 (tp) cc_final: 0.9048 (tt) REVERT: J 332 LYS cc_start: 0.8826 (tmtt) cc_final: 0.8364 (ttmt) REVERT: J 346 MET cc_start: 0.8757 (tpp) cc_final: 0.8388 (mmm) REVERT: J 350 GLN cc_start: 0.9125 (tt0) cc_final: 0.8502 (pp30) REVERT: J 366 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7407 (pt0) REVERT: J 392 MET cc_start: 0.7867 (mpt) cc_final: 0.7406 (mpp) REVERT: J 460 MET cc_start: 0.6737 (ttm) cc_final: 0.6343 (ttm) REVERT: J 462 LEU cc_start: 0.8922 (tp) cc_final: 0.8396 (mp) REVERT: J 487 GLU cc_start: 0.7732 (pt0) cc_final: 0.7436 (pt0) REVERT: J 614 ARG cc_start: 0.8113 (tmm-80) cc_final: 0.7854 (mtp-110) REVERT: J 649 ARG cc_start: 0.8835 (mmt180) cc_final: 0.8315 (mmm-85) REVERT: K 332 LYS cc_start: 0.8810 (tmtt) cc_final: 0.8179 (ttmm) REVERT: K 333 HIS cc_start: 0.8545 (m90) cc_final: 0.8279 (m-70) REVERT: K 346 MET cc_start: 0.8626 (tpp) cc_final: 0.8246 (mmm) REVERT: K 350 GLN cc_start: 0.9084 (tt0) cc_final: 0.8493 (pp30) REVERT: K 392 MET cc_start: 0.7907 (mpt) cc_final: 0.7364 (mpp) REVERT: K 462 LEU cc_start: 0.8886 (tp) cc_final: 0.8455 (mp) REVERT: K 487 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7562 (tm-30) REVERT: K 610 LYS cc_start: 0.8566 (ttmm) cc_final: 0.8328 (ttmm) REVERT: K 614 ARG cc_start: 0.8309 (tmm-80) cc_final: 0.8059 (mtp-110) REVERT: L 346 MET cc_start: 0.8564 (tpp) cc_final: 0.8197 (mmm) REVERT: L 350 GLN cc_start: 0.9156 (tt0) cc_final: 0.8664 (tm-30) REVERT: L 468 ASN cc_start: 0.7712 (OUTLIER) cc_final: 0.7203 (p0) REVERT: L 542 GLN cc_start: 0.8105 (tm-30) cc_final: 0.7426 (tm-30) REVERT: L 554 ASP cc_start: 0.7869 (t0) cc_final: 0.7518 (m-30) REVERT: L 580 MET cc_start: 0.8590 (mpp) cc_final: 0.8257 (mpp) REVERT: M 332 LYS cc_start: 0.8895 (tmtt) cc_final: 0.8351 (ttmt) REVERT: M 346 MET cc_start: 0.8698 (tpp) cc_final: 0.8405 (tpp) REVERT: M 359 ARG cc_start: 0.7775 (tpt-90) cc_final: 0.7549 (tpt-90) REVERT: M 392 MET cc_start: 0.8132 (mpt) cc_final: 0.7629 (mpp) REVERT: M 460 MET cc_start: 0.6964 (ttm) cc_final: 0.6713 (ttm) REVERT: M 462 LEU cc_start: 0.8937 (tp) cc_final: 0.8672 (tp) REVERT: M 594 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8780 (pt) REVERT: M 614 ARG cc_start: 0.8177 (tmm-80) cc_final: 0.7956 (mtp-110) REVERT: N 332 LYS cc_start: 0.8900 (tmtt) cc_final: 0.8316 (ttmm) REVERT: N 346 MET cc_start: 0.8666 (tpp) cc_final: 0.8364 (mmm) REVERT: N 350 GLN cc_start: 0.9153 (tt0) cc_final: 0.8704 (tm-30) REVERT: N 392 MET cc_start: 0.8163 (mpt) cc_final: 0.7762 (mpp) REVERT: N 460 MET cc_start: 0.7173 (ttm) cc_final: 0.6785 (ttm) REVERT: O 346 MET cc_start: 0.8615 (tpp) cc_final: 0.8227 (mmm) REVERT: O 350 GLN cc_start: 0.9203 (tt0) cc_final: 0.8793 (tm-30) REVERT: O 353 ILE cc_start: 0.9437 (mt) cc_final: 0.9227 (mp) REVERT: O 377 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.8044 (p0) REVERT: O 460 MET cc_start: 0.8061 (ttp) cc_final: 0.7854 (ttm) REVERT: O 462 LEU cc_start: 0.8970 (tp) cc_final: 0.8735 (tp) REVERT: O 610 LYS cc_start: 0.8612 (ttmm) cc_final: 0.8328 (tttm) REVERT: O 649 ARG cc_start: 0.8621 (mmt180) cc_final: 0.8229 (mmm160) outliers start: 206 outliers final: 180 residues processed: 707 average time/residue: 0.5360 time to fit residues: 613.1030 Evaluate side-chains 716 residues out of total 4350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 517 time to evaluate : 4.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 550 GLN Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 550 GLN Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 377 ASN Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 448 SER Chi-restraints excluded: chain E residue 468 ASN Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 482 THR Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 550 GLN Chi-restraints excluded: chain E residue 551 THR Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain E residue 594 LEU Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 540 ILE Chi-restraints excluded: chain F residue 550 GLN Chi-restraints excluded: chain F residue 553 LEU Chi-restraints excluded: chain F residue 575 VAL Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 591 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 594 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 366 GLU Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 468 ASN Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 482 THR Chi-restraints excluded: chain G residue 496 VAL Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 550 GLN Chi-restraints excluded: chain G residue 554 ASP Chi-restraints excluded: chain G residue 575 VAL Chi-restraints excluded: chain G residue 576 LEU Chi-restraints excluded: chain H residue 296 ASP Chi-restraints excluded: chain H residue 366 GLU Chi-restraints excluded: chain H residue 433 THR Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 482 THR Chi-restraints excluded: chain H residue 546 LYS Chi-restraints excluded: chain H residue 550 GLN Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain H residue 553 LEU Chi-restraints excluded: chain H residue 575 VAL Chi-restraints excluded: chain H residue 591 VAL Chi-restraints excluded: chain H residue 593 LEU Chi-restraints excluded: chain I residue 296 ASP Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 433 THR Chi-restraints excluded: chain I residue 448 SER Chi-restraints excluded: chain I residue 477 THR Chi-restraints excluded: chain I residue 482 THR Chi-restraints excluded: chain I residue 538 MET Chi-restraints excluded: chain I residue 540 ILE Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 555 VAL Chi-restraints excluded: chain I residue 575 VAL Chi-restraints excluded: chain I residue 593 LEU Chi-restraints excluded: chain J residue 366 GLU Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain J residue 448 SER Chi-restraints excluded: chain J residue 468 ASN Chi-restraints excluded: chain J residue 477 THR Chi-restraints excluded: chain J residue 480 ILE Chi-restraints excluded: chain J residue 482 THR Chi-restraints excluded: chain J residue 495 ASP Chi-restraints excluded: chain J residue 547 VAL Chi-restraints excluded: chain J residue 550 GLN Chi-restraints excluded: chain J residue 551 THR Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain J residue 591 VAL Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 402 ILE Chi-restraints excluded: chain K residue 433 THR Chi-restraints excluded: chain K residue 468 ASN Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 482 THR Chi-restraints excluded: chain K residue 499 LEU Chi-restraints excluded: chain K residue 550 GLN Chi-restraints excluded: chain K residue 553 LEU Chi-restraints excluded: chain K residue 576 LEU Chi-restraints excluded: chain K residue 591 VAL Chi-restraints excluded: chain K residue 593 LEU Chi-restraints excluded: chain K residue 594 LEU Chi-restraints excluded: chain L residue 296 ASP Chi-restraints excluded: chain L residue 366 GLU Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain L residue 448 SER Chi-restraints excluded: chain L residue 468 ASN Chi-restraints excluded: chain L residue 477 THR Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 551 THR Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 575 VAL Chi-restraints excluded: chain L residue 576 LEU Chi-restraints excluded: chain L residue 593 LEU Chi-restraints excluded: chain M residue 296 ASP Chi-restraints excluded: chain M residue 366 GLU Chi-restraints excluded: chain M residue 433 THR Chi-restraints excluded: chain M residue 448 SER Chi-restraints excluded: chain M residue 477 THR Chi-restraints excluded: chain M residue 482 THR Chi-restraints excluded: chain M residue 538 MET Chi-restraints excluded: chain M residue 540 ILE Chi-restraints excluded: chain M residue 550 GLN Chi-restraints excluded: chain M residue 573 LEU Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 576 LEU Chi-restraints excluded: chain M residue 593 LEU Chi-restraints excluded: chain M residue 594 LEU Chi-restraints excluded: chain N residue 296 ASP Chi-restraints excluded: chain N residue 433 THR Chi-restraints excluded: chain N residue 468 ASN Chi-restraints excluded: chain N residue 477 THR Chi-restraints excluded: chain N residue 482 THR Chi-restraints excluded: chain N residue 496 VAL Chi-restraints excluded: chain N residue 550 GLN Chi-restraints excluded: chain N residue 551 THR Chi-restraints excluded: chain N residue 575 VAL Chi-restraints excluded: chain N residue 579 LEU Chi-restraints excluded: chain O residue 297 LEU Chi-restraints excluded: chain O residue 366 GLU Chi-restraints excluded: chain O residue 377 ASN Chi-restraints excluded: chain O residue 402 ILE Chi-restraints excluded: chain O residue 433 THR Chi-restraints excluded: chain O residue 468 ASN Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 482 THR Chi-restraints excluded: chain O residue 499 LEU Chi-restraints excluded: chain O residue 538 MET Chi-restraints excluded: chain O residue 540 ILE Chi-restraints excluded: chain O residue 550 GLN Chi-restraints excluded: chain O residue 575 VAL Chi-restraints excluded: chain O residue 594 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 330 optimal weight: 8.9990 chunk 443 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 384 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 417 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 chunk 428 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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** ** 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 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 333 HIS ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 333 HIS ** 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 333 HIS ** N 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.143313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.100235 restraints weight = 56124.050| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 3.24 r_work: 0.3415 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 39840 Z= 0.249 Angle : 0.646 14.115 53895 Z= 0.320 Chirality : 0.047 0.172 6480 Planarity : 0.004 0.045 6990 Dihedral : 5.121 45.996 5430 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.54 % Favored : 92.16 % Rotamer: Outliers : 4.67 % Allowed : 19.22 % Favored : 76.11 % 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: -2.60 (0.12), residues: 5130 helix: 0.87 (0.16), residues: 1155 sheet: -2.09 (0.10), residues: 2580 loop : -2.81 (0.14), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP I 384 HIS 0.003 0.001 HIS D 364 PHE 0.013 0.001 PHE E 489 TYR 0.021 0.001 TYR B 639 ARG 0.009 0.001 ARG I 626 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11434.96 seconds wall clock time: 207 minutes 2.58 seconds (12422.58 seconds total)