Starting phenix.real_space_refine on Tue Jan 21 02:28:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xb6_38212/01_2025/8xb6_38212.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xb6_38212/01_2025/8xb6_38212.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xb6_38212/01_2025/8xb6_38212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xb6_38212/01_2025/8xb6_38212.map" model { file = "/net/cci-nas-00/data/ceres_data/8xb6_38212/01_2025/8xb6_38212.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xb6_38212/01_2025/8xb6_38212.cif" } resolution = 3.7 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= -0.000 sd= 0.003 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 254 5.16 5 C 41907 2.51 5 N 11599 2.21 5 O 13065 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 66825 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 3583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3583 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 17, 'TRANS': 432} Chain breaks: 1 Chain: "B" Number of atoms: 3583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3583 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 17, 'TRANS': 432} Chain breaks: 1 Chain: "C" Number of atoms: 3583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3583 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 17, 'TRANS': 432} Chain breaks: 1 Chain: "D" Number of atoms: 3583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3583 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 17, 'TRANS': 432} Chain breaks: 1 Chain: "E" Number of atoms: 3583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3583 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 17, 'TRANS': 432} Chain breaks: 1 Chain: "F" Number of atoms: 3583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3583 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 17, 'TRANS': 432} Chain breaks: 1 Chain: "G" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3545 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 17, 'TRANS': 427} Chain breaks: 1 Chain: "H" Number of atoms: 3583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3583 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 17, 'TRANS': 432} Chain breaks: 1 Chain: "I" Number of atoms: 3583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3583 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 17, 'TRANS': 432} Chain breaks: 1 Chain: "J" Number of atoms: 3583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3583 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 17, 'TRANS': 432} Chain breaks: 1 Chain: "K" Number of atoms: 3583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3583 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 17, 'TRANS': 432} Chain breaks: 1 Chain: "L" Number of atoms: 3583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3583 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 17, 'TRANS': 432} Chain breaks: 1 Chain: "M" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2357 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 301} Chain: "N" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2366 Classifications: {'peptide': 315} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 302} Chain: "O" Number of atoms: 2401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2401 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 307} Chain: "P" Number of atoms: 2350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2350 Classifications: {'peptide': 313} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 300} Chain: "Q" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2388 Classifications: {'peptide': 318} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 305} Chain: "R" Number of atoms: 2401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2401 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 307} Chain: "S" Number of atoms: 2401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2401 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 307} Chain: "T" Number of atoms: 2401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2401 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 307} Chain: "U" Number of atoms: 2401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2401 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 307} Chain: "V" Number of atoms: 2401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2401 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 307} Time building chain proxies: 29.34, per 1000 atoms: 0.44 Number of scatterers: 66825 At special positions: 0 Unit cell: (275.88, 282.48, 125.4, 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 254 16.00 O 13065 8.00 N 11599 7.00 C 41907 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 - 3.00 Amino acid : True - 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: 12.39 Conformation dependent library (CDL) restraints added in 6.3 seconds 17014 Ramachandran restraints generated. 8507 Oldfield, 0 Emsley, 8507 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15874 Finding SS restraints... Secondary structure from input PDB file: 281 helices and 99 sheets defined 41.1% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.13 Creating SS restraints... Processing helix chain 'A' and resid 11 through 30 removed outlier: 4.600A pdb=" N LYS A 19 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LEU A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 37 removed outlier: 3.638A pdb=" N ILE A 34 " --> pdb=" O GLY A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 42 removed outlier: 3.756A pdb=" N PHE A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 removed outlier: 3.991A pdb=" N THR A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 66 removed outlier: 3.680A pdb=" N ALA A 57 " --> pdb=" O PRO A 53 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 66 " --> pdb=" O TYR A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 84 removed outlier: 3.901A pdb=" N ASN A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 103 removed outlier: 3.700A pdb=" N ASP A 103 " --> pdb=" O MET A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 125 Processing helix chain 'A' and resid 262 through 287 Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 334 through 351 Processing helix chain 'A' and resid 365 through 375 removed outlier: 3.750A pdb=" N MET A 369 " --> pdb=" O GLY A 365 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ALA A 373 " --> pdb=" O MET A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 401 Processing helix chain 'A' and resid 420 through 433 Processing helix chain 'A' and resid 437 through 448 Processing helix chain 'A' and resid 454 through 463 Processing helix chain 'B' and resid 17 through 30 Processing helix chain 'B' and resid 30 through 37 removed outlier: 3.578A pdb=" N ILE B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 42 removed outlier: 4.451A pdb=" N PHE B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 52 removed outlier: 4.032A pdb=" N THR B 52 " --> pdb=" O THR B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 65 removed outlier: 3.759A pdb=" N ARG B 65 " --> pdb=" O ALA B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 84 removed outlier: 3.823A pdb=" N ASN B 74 " --> pdb=" O GLY B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 103 removed outlier: 3.756A pdb=" N ASP B 103 " --> pdb=" O MET B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 125 Processing helix chain 'B' and resid 262 through 287 removed outlier: 3.580A pdb=" N VAL B 266 " --> pdb=" O MET B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 304 Processing helix chain 'B' and resid 334 through 351 removed outlier: 4.140A pdb=" N GLY B 351 " --> pdb=" O MET B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 375 removed outlier: 4.473A pdb=" N ALA B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ALA B 373 " --> pdb=" O MET B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 401 Processing helix chain 'B' and resid 420 through 433 Processing helix chain 'B' and resid 437 through 448 Processing helix chain 'B' and resid 454 through 463 Processing helix chain 'C' and resid 11 through 30 removed outlier: 4.265A pdb=" N LYS C 19 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LEU C 20 " --> pdb=" O LYS C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 37 Processing helix chain 'C' and resid 38 through 41 Processing helix chain 'C' and resid 46 through 52 removed outlier: 3.744A pdb=" N THR C 52 " --> pdb=" O THR C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 65 Processing helix chain 'C' and resid 70 through 84 removed outlier: 3.880A pdb=" N ASN C 74 " --> pdb=" O GLY C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 96 No H-bonds generated for 'chain 'C' and resid 94 through 96' Processing helix chain 'C' and resid 97 through 103 Processing helix chain 'C' and resid 110 through 125 Processing helix chain 'C' and resid 262 through 287 Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 334 through 350 Processing helix chain 'C' and resid 366 through 375 removed outlier: 4.035A pdb=" N GLU C 370 " --> pdb=" O GLU C 366 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ALA C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ALA C 373 " --> pdb=" O MET C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 401 Processing helix chain 'C' and resid 420 through 433 Processing helix chain 'C' and resid 437 through 448 Processing helix chain 'C' and resid 454 through 463 Processing helix chain 'D' and resid 11 through 30 removed outlier: 4.784A pdb=" N LYS D 19 " --> pdb=" O LYS D 15 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LEU D 20 " --> pdb=" O LYS D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 37 removed outlier: 4.026A pdb=" N ILE D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 42 removed outlier: 4.086A pdb=" N PHE D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 52 Processing helix chain 'D' and resid 52 through 65 Processing helix chain 'D' and resid 70 through 84 removed outlier: 3.891A pdb=" N ASN D 74 " --> pdb=" O GLY D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 103 Processing helix chain 'D' and resid 110 through 125 Processing helix chain 'D' and resid 262 through 287 Processing helix chain 'D' and resid 297 through 304 Processing helix chain 'D' and resid 334 through 350 Processing helix chain 'D' and resid 366 through 375 removed outlier: 4.286A pdb=" N GLU D 370 " --> pdb=" O GLU D 366 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALA D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ALA D 373 " --> pdb=" O MET D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 401 Processing helix chain 'D' and resid 420 through 433 removed outlier: 3.513A pdb=" N SER D 433 " --> pdb=" O SER D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 448 Processing helix chain 'D' and resid 454 through 463 Processing helix chain 'E' and resid 11 through 30 removed outlier: 4.298A pdb=" N LYS E 19 " --> pdb=" O LYS E 15 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 37 removed outlier: 3.626A pdb=" N ILE E 34 " --> pdb=" O GLY E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 42 removed outlier: 4.049A pdb=" N PHE E 41 " --> pdb=" O ASN E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 52 removed outlier: 3.798A pdb=" N THR E 52 " --> pdb=" O THR E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 66 removed outlier: 3.635A pdb=" N ARG E 65 " --> pdb=" O ALA E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 84 removed outlier: 4.005A pdb=" N ASN E 74 " --> pdb=" O GLY E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 103 Processing helix chain 'E' and resid 110 through 126 Processing helix chain 'E' and resid 262 through 287 Processing helix chain 'E' and resid 297 through 304 Processing helix chain 'E' and resid 334 through 350 Processing helix chain 'E' and resid 366 through 375 removed outlier: 3.738A pdb=" N GLU E 370 " --> pdb=" O GLU E 366 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ALA E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ALA E 373 " --> pdb=" O MET E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 401 Processing helix chain 'E' and resid 420 through 433 Processing helix chain 'E' and resid 437 through 448 Processing helix chain 'E' and resid 454 through 464 removed outlier: 4.342A pdb=" N GLN E 464 " --> pdb=" O ASN E 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 30 removed outlier: 4.625A pdb=" N LYS F 19 " --> pdb=" O LYS F 15 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LEU F 20 " --> pdb=" O LYS F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 37 Processing helix chain 'F' and resid 38 through 41 Processing helix chain 'F' and resid 46 through 52 removed outlier: 3.851A pdb=" N THR F 52 " --> pdb=" O THR F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 66 removed outlier: 3.690A pdb=" N ALA F 66 " --> pdb=" O TYR F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 84 removed outlier: 3.607A pdb=" N ASN F 74 " --> pdb=" O GLY F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 103 Processing helix chain 'F' and resid 110 through 125 Processing helix chain 'F' and resid 219 through 223 Processing helix chain 'F' and resid 262 through 287 Processing helix chain 'F' and resid 297 through 305 Processing helix chain 'F' and resid 334 through 351 Processing helix chain 'F' and resid 365 through 375 removed outlier: 3.677A pdb=" N MET F 369 " --> pdb=" O GLY F 365 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU F 370 " --> pdb=" O GLU F 366 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ALA F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ALA F 373 " --> pdb=" O MET F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 401 Processing helix chain 'F' and resid 420 through 433 Processing helix chain 'F' and resid 437 through 448 Processing helix chain 'F' and resid 454 through 463 Processing helix chain 'G' and resid 17 through 30 removed outlier: 3.504A pdb=" N GLY G 30 " --> pdb=" O MET G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 36 removed outlier: 3.510A pdb=" N ILE G 34 " --> pdb=" O GLY G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 42 Processing helix chain 'G' and resid 46 through 52 removed outlier: 3.546A pdb=" N THR G 52 " --> pdb=" O THR G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 65 Processing helix chain 'G' and resid 70 through 84 removed outlier: 3.975A pdb=" N ASN G 74 " --> pdb=" O GLY G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 102 Processing helix chain 'G' and resid 110 through 126 Processing helix chain 'G' and resid 262 through 287 Processing helix chain 'G' and resid 297 through 304 Processing helix chain 'G' and resid 334 through 351 Processing helix chain 'G' and resid 365 through 375 removed outlier: 3.973A pdb=" N MET G 369 " --> pdb=" O GLY G 365 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU G 370 " --> pdb=" O GLU G 366 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ALA G 372 " --> pdb=" O SER G 368 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ALA G 373 " --> pdb=" O MET G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 375 through 401 Processing helix chain 'G' and resid 420 through 433 removed outlier: 3.531A pdb=" N SER G 433 " --> pdb=" O SER G 429 " (cutoff:3.500A) Processing helix chain 'G' and resid 437 through 448 Processing helix chain 'G' and resid 454 through 463 Processing helix chain 'H' and resid 11 through 30 removed outlier: 4.265A pdb=" N LYS H 19 " --> pdb=" O LYS H 15 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU H 20 " --> pdb=" O LYS H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 37 removed outlier: 3.544A pdb=" N ILE H 34 " --> pdb=" O GLY H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 42 removed outlier: 4.086A pdb=" N PHE H 41 " --> pdb=" O ASN H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 52 removed outlier: 3.826A pdb=" N THR H 52 " --> pdb=" O THR H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 65 removed outlier: 3.600A pdb=" N ARG H 65 " --> pdb=" O ALA H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 84 Processing helix chain 'H' and resid 97 through 103 Processing helix chain 'H' and resid 110 through 125 Processing helix chain 'H' and resid 219 through 223 Processing helix chain 'H' and resid 262 through 287 Processing helix chain 'H' and resid 297 through 304 Processing helix chain 'H' and resid 334 through 350 Processing helix chain 'H' and resid 366 through 375 removed outlier: 4.076A pdb=" N GLU H 370 " --> pdb=" O GLU H 366 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ALA H 372 " --> pdb=" O SER H 368 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ALA H 373 " --> pdb=" O MET H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 375 through 401 Processing helix chain 'H' and resid 420 through 433 Processing helix chain 'H' and resid 437 through 448 Processing helix chain 'H' and resid 454 through 463 Processing helix chain 'I' and resid 11 through 30 removed outlier: 4.302A pdb=" N LYS I 19 " --> pdb=" O LYS I 15 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU I 20 " --> pdb=" O LYS I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 37 removed outlier: 3.519A pdb=" N ILE I 34 " --> pdb=" O GLY I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 42 removed outlier: 4.116A pdb=" N PHE I 41 " --> pdb=" O ASN I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 52 removed outlier: 3.838A pdb=" N THR I 52 " --> pdb=" O THR I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 66 removed outlier: 3.569A pdb=" N ALA I 66 " --> pdb=" O TYR I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 84 Processing helix chain 'I' and resid 97 through 103 Processing helix chain 'I' and resid 110 through 125 Processing helix chain 'I' and resid 262 through 287 Processing helix chain 'I' and resid 297 through 304 Processing helix chain 'I' and resid 334 through 350 Processing helix chain 'I' and resid 366 through 375 removed outlier: 4.443A pdb=" N GLU I 370 " --> pdb=" O GLU I 366 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALA I 372 " --> pdb=" O SER I 368 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ALA I 373 " --> pdb=" O MET I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 375 through 401 Processing helix chain 'I' and resid 420 through 433 Processing helix chain 'I' and resid 437 through 448 Processing helix chain 'I' and resid 454 through 463 Processing helix chain 'J' and resid 11 through 30 removed outlier: 4.258A pdb=" N LYS J 19 " --> pdb=" O LYS J 15 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LEU J 20 " --> pdb=" O LYS J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 37 removed outlier: 3.565A pdb=" N ASP J 36 " --> pdb=" O ARG J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 42 removed outlier: 4.025A pdb=" N PHE J 41 " --> pdb=" O ASN J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 52 removed outlier: 4.222A pdb=" N THR J 52 " --> pdb=" O THR J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 65 Processing helix chain 'J' and resid 70 through 84 removed outlier: 3.881A pdb=" N ASN J 74 " --> pdb=" O GLY J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 96 No H-bonds generated for 'chain 'J' and resid 94 through 96' Processing helix chain 'J' and resid 97 through 103 removed outlier: 3.593A pdb=" N ASP J 103 " --> pdb=" O MET J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 126 Processing helix chain 'J' and resid 262 through 287 Processing helix chain 'J' and resid 297 through 304 Processing helix chain 'J' and resid 334 through 350 Processing helix chain 'J' and resid 366 through 375 removed outlier: 4.028A pdb=" N GLU J 370 " --> pdb=" O GLU J 366 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ALA J 372 " --> pdb=" O SER J 368 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ALA J 373 " --> pdb=" O MET J 369 " (cutoff:3.500A) Processing helix chain 'J' and resid 375 through 401 removed outlier: 3.792A pdb=" N LYS J 383 " --> pdb=" O SER J 379 " (cutoff:3.500A) Processing helix chain 'J' and resid 420 through 433 Processing helix chain 'J' and resid 437 through 448 Processing helix chain 'J' and resid 454 through 464 removed outlier: 4.300A pdb=" N GLN J 464 " --> pdb=" O ASN J 460 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 30 removed outlier: 3.929A pdb=" N LYS K 19 " --> pdb=" O LYS K 15 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU K 20 " --> pdb=" O LYS K 16 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY K 30 " --> pdb=" O MET K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 30 through 37 removed outlier: 3.769A pdb=" N ILE K 34 " --> pdb=" O GLY K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 42 Processing helix chain 'K' and resid 46 through 52 removed outlier: 3.772A pdb=" N THR K 52 " --> pdb=" O THR K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 66 removed outlier: 3.654A pdb=" N ALA K 66 " --> pdb=" O TYR K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 84 removed outlier: 4.005A pdb=" N ASN K 74 " --> pdb=" O GLY K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 102 Processing helix chain 'K' and resid 110 through 126 Processing helix chain 'K' and resid 262 through 287 Processing helix chain 'K' and resid 297 through 304 Processing helix chain 'K' and resid 334 through 350 Processing helix chain 'K' and resid 366 through 375 removed outlier: 3.920A pdb=" N GLU K 370 " --> pdb=" O GLU K 366 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ALA K 372 " --> pdb=" O SER K 368 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ALA K 373 " --> pdb=" O MET K 369 " (cutoff:3.500A) Processing helix chain 'K' and resid 375 through 401 Processing helix chain 'K' and resid 420 through 433 Processing helix chain 'K' and resid 437 through 448 Processing helix chain 'K' and resid 454 through 463 Processing helix chain 'L' and resid 11 through 30 removed outlier: 4.354A pdb=" N LYS L 19 " --> pdb=" O LYS L 15 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU L 20 " --> pdb=" O LYS L 16 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY L 30 " --> pdb=" O MET L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 31 through 37 Processing helix chain 'L' and resid 37 through 42 removed outlier: 4.099A pdb=" N PHE L 41 " --> pdb=" O ASN L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 52 removed outlier: 3.976A pdb=" N THR L 52 " --> pdb=" O THR L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 52 through 66 removed outlier: 3.582A pdb=" N ALA L 66 " --> pdb=" O TYR L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 84 removed outlier: 3.738A pdb=" N ASN L 74 " --> pdb=" O GLY L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 103 Processing helix chain 'L' and resid 110 through 125 Processing helix chain 'L' and resid 262 through 287 Processing helix chain 'L' and resid 297 through 305 Processing helix chain 'L' and resid 334 through 350 Processing helix chain 'L' and resid 365 through 375 removed outlier: 4.110A pdb=" N MET L 369 " --> pdb=" O GLY L 365 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU L 370 " --> pdb=" O GLU L 366 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ALA L 372 " --> pdb=" O SER L 368 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ALA L 373 " --> pdb=" O MET L 369 " (cutoff:3.500A) Processing helix chain 'L' and resid 375 through 401 Processing helix chain 'L' and resid 420 through 433 Processing helix chain 'L' and resid 437 through 448 Processing helix chain 'L' and resid 454 through 463 Processing helix chain 'M' and resid 28 through 33 Processing helix chain 'M' and resid 109 through 142 Processing helix chain 'M' and resid 157 through 168 removed outlier: 3.782A pdb=" N ASN M 161 " --> pdb=" O GLN M 157 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA M 162 " --> pdb=" O ARG M 158 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA M 163 " --> pdb=" O ALA M 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 169 through 174 removed outlier: 5.025A pdb=" N THR M 172 " --> pdb=" O ASP M 169 " (cutoff:3.500A) Processing helix chain 'M' and resid 180 through 193 removed outlier: 3.634A pdb=" N LEU M 184 " --> pdb=" O HIS M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 200 through 204 removed outlier: 3.778A pdb=" N VAL M 204 " --> pdb=" O PHE M 201 " (cutoff:3.500A) Processing helix chain 'M' and resid 220 through 222 No H-bonds generated for 'chain 'M' and resid 220 through 222' Processing helix chain 'M' and resid 227 through 231 removed outlier: 3.526A pdb=" N LEU M 231 " --> pdb=" O ALA M 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 298 Processing helix chain 'N' and resid 28 through 33 Processing helix chain 'N' and resid 109 through 141 Processing helix chain 'N' and resid 157 through 168 Processing helix chain 'N' and resid 170 through 174 Processing helix chain 'N' and resid 180 through 192 removed outlier: 3.771A pdb=" N LEU N 184 " --> pdb=" O HIS N 180 " (cutoff:3.500A) Processing helix chain 'N' and resid 200 through 204 removed outlier: 3.779A pdb=" N VAL N 204 " --> pdb=" O PHE N 201 " (cutoff:3.500A) Processing helix chain 'N' and resid 220 through 222 No H-bonds generated for 'chain 'N' and resid 220 through 222' Processing helix chain 'N' and resid 227 through 231 Processing helix chain 'N' and resid 293 through 299 Processing helix chain 'O' and resid 28 through 33 Processing helix chain 'O' and resid 108 through 141 removed outlier: 3.930A pdb=" N GLN O 116 " --> pdb=" O ALA O 112 " (cutoff:3.500A) Processing helix chain 'O' and resid 157 through 168 removed outlier: 3.715A pdb=" N ASN O 161 " --> pdb=" O GLN O 157 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA O 162 " --> pdb=" O ARG O 158 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA O 163 " --> pdb=" O ALA O 159 " (cutoff:3.500A) Processing helix chain 'O' and resid 169 through 174 removed outlier: 4.737A pdb=" N THR O 172 " --> pdb=" O ASP O 169 " (cutoff:3.500A) Processing helix chain 'O' and resid 180 through 193 removed outlier: 3.829A pdb=" N LEU O 184 " --> pdb=" O HIS O 180 " (cutoff:3.500A) Processing helix chain 'O' and resid 200 through 204 removed outlier: 3.763A pdb=" N VAL O 204 " --> pdb=" O PHE O 201 " (cutoff:3.500A) Processing helix chain 'O' and resid 220 through 222 No H-bonds generated for 'chain 'O' and resid 220 through 222' Processing helix chain 'O' and resid 227 through 231 Processing helix chain 'O' and resid 293 through 298 Processing helix chain 'P' and resid 28 through 33 Processing helix chain 'P' and resid 113 through 142 removed outlier: 4.302A pdb=" N GLY P 120 " --> pdb=" O GLN P 116 " (cutoff:3.500A) Processing helix chain 'P' and resid 157 through 168 Processing helix chain 'P' and resid 169 through 173 removed outlier: 4.491A pdb=" N THR P 172 " --> pdb=" O ASP P 169 " (cutoff:3.500A) Processing helix chain 'P' and resid 180 through 193 removed outlier: 3.738A pdb=" N LEU P 184 " --> pdb=" O HIS P 180 " (cutoff:3.500A) Processing helix chain 'P' and resid 220 through 222 No H-bonds generated for 'chain 'P' and resid 220 through 222' Processing helix chain 'P' and resid 227 through 231 removed outlier: 3.529A pdb=" N LEU P 231 " --> pdb=" O ALA P 228 " (cutoff:3.500A) Processing helix chain 'P' and resid 293 through 299 Processing helix chain 'Q' and resid 28 through 33 Processing helix chain 'Q' and resid 109 through 141 removed outlier: 3.935A pdb=" N VAL Q 113 " --> pdb=" O GLU Q 109 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE Q 114 " --> pdb=" O ALA Q 110 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY Q 120 " --> pdb=" O GLN Q 116 " (cutoff:3.500A) Processing helix chain 'Q' and resid 157 through 168 Processing helix chain 'Q' and resid 169 through 174 removed outlier: 4.375A pdb=" N THR Q 172 " --> pdb=" O ASP Q 169 " (cutoff:3.500A) Processing helix chain 'Q' and resid 180 through 193 Processing helix chain 'Q' and resid 200 through 204 removed outlier: 3.713A pdb=" N VAL Q 204 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) Processing helix chain 'Q' and resid 220 through 222 No H-bonds generated for 'chain 'Q' and resid 220 through 222' Processing helix chain 'Q' and resid 227 through 231 Processing helix chain 'Q' and resid 293 through 299 Processing helix chain 'R' and resid 28 through 33 Processing helix chain 'R' and resid 96 through 103 removed outlier: 4.064A pdb=" N LEU R 100 " --> pdb=" O PRO R 96 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE R 103 " --> pdb=" O MET R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 141 removed outlier: 4.138A pdb=" N ALA R 110 " --> pdb=" O ASN R 106 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY R 111 " --> pdb=" O PRO R 107 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 156 through 165 Processing helix chain 'R' and resid 166 through 172 removed outlier: 5.887A pdb=" N ASP R 169 " --> pdb=" O ILE R 166 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER R 171 " --> pdb=" O GLY R 168 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR R 172 " --> pdb=" O ASP R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 193 removed outlier: 3.697A pdb=" N LEU R 184 " --> pdb=" O HIS R 180 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA R 193 " --> pdb=" O ASP R 189 " (cutoff:3.500A) Processing helix chain 'R' and resid 227 through 231 removed outlier: 3.951A pdb=" N LEU R 231 " --> pdb=" O ALA R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 299 Processing helix chain 'S' and resid 97 through 102 Processing helix chain 'S' and resid 107 through 141 removed outlier: 4.032A pdb=" N GLY S 111 " --> pdb=" O PRO S 107 " (cutoff:3.500A) Processing helix chain 'S' and resid 156 through 166 removed outlier: 3.901A pdb=" N ILE S 166 " --> pdb=" O ALA S 162 " (cutoff:3.500A) Processing helix chain 'S' and resid 180 through 193 removed outlier: 3.762A pdb=" N LEU S 184 " --> pdb=" O HIS S 180 " (cutoff:3.500A) Processing helix chain 'S' and resid 200 through 204 removed outlier: 3.767A pdb=" N VAL S 204 " --> pdb=" O PHE S 201 " (cutoff:3.500A) Processing helix chain 'S' and resid 209 through 213 removed outlier: 3.916A pdb=" N GLY S 212 " --> pdb=" O ASP S 209 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 225 removed outlier: 3.735A pdb=" N VAL S 224 " --> pdb=" O SER S 220 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER S 225 " --> pdb=" O PRO S 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 220 through 225' Processing helix chain 'S' and resid 293 through 299 Processing helix chain 'S' and resid 309 through 313 Processing helix chain 'T' and resid 2 through 6 Processing helix chain 'T' and resid 96 through 102 removed outlier: 4.108A pdb=" N LEU T 100 " --> pdb=" O PRO T 96 " (cutoff:3.500A) Processing helix chain 'T' and resid 106 through 141 removed outlier: 4.279A pdb=" N ALA T 110 " --> pdb=" O ASN T 106 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY T 111 " --> pdb=" O PRO T 107 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY T 120 " --> pdb=" O GLN T 116 " (cutoff:3.500A) Processing helix chain 'T' and resid 156 through 165 Processing helix chain 'T' and resid 180 through 193 removed outlier: 3.644A pdb=" N LEU T 184 " --> pdb=" O HIS T 180 " (cutoff:3.500A) Processing helix chain 'T' and resid 200 through 204 Processing helix chain 'T' and resid 220 through 225 removed outlier: 3.530A pdb=" N VAL T 224 " --> pdb=" O SER T 220 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER T 225 " --> pdb=" O PRO T 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 220 through 225' Processing helix chain 'T' and resid 227 through 231 removed outlier: 3.964A pdb=" N LEU T 231 " --> pdb=" O ALA T 228 " (cutoff:3.500A) Processing helix chain 'T' and resid 293 through 299 Processing helix chain 'U' and resid 25 through 29 removed outlier: 4.564A pdb=" N ASN U 29 " --> pdb=" O GLU U 26 " (cutoff:3.500A) Processing helix chain 'U' and resid 96 through 103 removed outlier: 3.993A pdb=" N LEU U 100 " --> pdb=" O PRO U 96 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE U 103 " --> pdb=" O MET U 99 " (cutoff:3.500A) Processing helix chain 'U' and resid 107 through 142 removed outlier: 4.160A pdb=" N GLY U 111 " --> pdb=" O PRO U 107 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY U 120 " --> pdb=" O GLN U 116 " (cutoff:3.500A) Processing helix chain 'U' and resid 156 through 165 Processing helix chain 'U' and resid 180 through 193 removed outlier: 3.741A pdb=" N LEU U 184 " --> pdb=" O HIS U 180 " (cutoff:3.500A) Processing helix chain 'U' and resid 220 through 224 Processing helix chain 'U' and resid 293 through 298 Processing helix chain 'V' and resid 28 through 33 Processing helix chain 'V' and resid 96 through 103 removed outlier: 4.400A pdb=" N LEU V 100 " --> pdb=" O PRO V 96 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE V 103 " --> pdb=" O MET V 99 " (cutoff:3.500A) Processing helix chain 'V' and resid 107 through 141 removed outlier: 4.393A pdb=" N GLY V 111 " --> pdb=" O PRO V 107 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLY V 120 " --> pdb=" O GLN V 116 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N MET V 123 " --> pdb=" O ALA V 119 " (cutoff:3.500A) Processing helix chain 'V' and resid 156 through 166 removed outlier: 3.941A pdb=" N ILE V 166 " --> pdb=" O ALA V 162 " (cutoff:3.500A) Processing helix chain 'V' and resid 180 through 193 removed outlier: 3.692A pdb=" N LEU V 184 " --> pdb=" O HIS V 180 " (cutoff:3.500A) Processing helix chain 'V' and resid 201 through 205 removed outlier: 3.920A pdb=" N VAL V 204 " --> pdb=" O PHE V 201 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASN V 205 " --> pdb=" O GLY V 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 201 through 205' Processing helix chain 'V' and resid 220 through 225 removed outlier: 3.779A pdb=" N VAL V 224 " --> pdb=" O SER V 220 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER V 225 " --> pdb=" O PRO V 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 220 through 225' Processing helix chain 'V' and resid 293 through 299 removed outlier: 3.509A pdb=" N THR V 299 " --> pdb=" O THR V 295 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 91 Processing sheet with id=AA2, first strand: chain 'A' and resid 155 through 159 removed outlier: 3.588A pdb=" N PHE A 131 " --> pdb=" O LYS A 157 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 171 removed outlier: 5.530A pdb=" N ILE A 164 " --> pdb=" O ARG A 184 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG A 184 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU A 180 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ARG A 170 " --> pdb=" O THR A 178 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N THR A 178 " --> pdb=" O ARG A 170 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N THR A 179 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.553A pdb=" N GLU B 409 " --> pdb=" O VAL B 89 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 154 through 159 removed outlier: 3.604A pdb=" N TYR B 155 " --> pdb=" O ASP B 133 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 164 through 172 removed outlier: 6.464A pdb=" N ILE B 164 " --> pdb=" O PHE B 183 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE B 183 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASN B 166 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU B 181 " --> pdb=" O ASN B 166 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ARG B 168 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N THR B 179 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N GLU B 200 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU B 219 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN B 223 " --> pdb=" O ASN B 220 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 89 through 91 Processing sheet with id=AA8, first strand: chain 'C' and resid 154 through 159 Processing sheet with id=AA9, first strand: chain 'C' and resid 164 through 171 removed outlier: 6.412A pdb=" N VAL C 182 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TRP C 167 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU C 180 " --> pdb=" O TRP C 167 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLU C 169 " --> pdb=" O THR C 178 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N THR C 178 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N TRP C 171 " --> pdb=" O LYS C 176 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LYS C 176 " --> pdb=" O TRP C 171 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N THR C 179 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLU C 200 " --> pdb=" O GLU C 219 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU C 219 " --> pdb=" O GLU C 200 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 89 through 91 Processing sheet with id=AB2, first strand: chain 'D' and resid 154 through 156 removed outlier: 3.686A pdb=" N VAL D 246 " --> pdb=" O LEU D 130 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 164 through 172 removed outlier: 6.501A pdb=" N ILE D 164 " --> pdb=" O PHE D 183 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N PHE D 183 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN D 166 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU D 181 " --> pdb=" O ASN D 166 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ARG D 168 " --> pdb=" O THR D 179 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR D 179 " --> pdb=" O ARG D 168 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N THR D 179 " --> pdb=" O LEU D 207 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 293 through 294 removed outlier: 3.613A pdb=" N SER D 294 " --> pdb=" O LYS D 324 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 89 through 91 Processing sheet with id=AB6, first strand: chain 'E' and resid 154 through 156 Processing sheet with id=AB7, first strand: chain 'E' and resid 164 through 171 removed outlier: 6.673A pdb=" N ILE E 164 " --> pdb=" O PHE E 183 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N PHE E 183 " --> pdb=" O ILE E 164 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASN E 166 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU E 181 " --> pdb=" O ASN E 166 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ARG E 168 " --> pdb=" O THR E 179 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N THR E 179 " --> pdb=" O LEU E 207 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 219 through 220 Processing sheet with id=AB9, first strand: chain 'F' and resid 89 through 91 removed outlier: 3.679A pdb=" N VAL F 89 " --> pdb=" O GLU F 409 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU F 409 " --> pdb=" O VAL F 89 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 154 through 156 Processing sheet with id=AC2, first strand: chain 'F' and resid 164 through 171 removed outlier: 6.469A pdb=" N VAL F 182 " --> pdb=" O LEU F 165 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TRP F 167 " --> pdb=" O LEU F 180 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU F 180 " --> pdb=" O TRP F 167 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLU F 169 " --> pdb=" O THR F 178 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N THR F 178 " --> pdb=" O GLU F 169 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N TRP F 171 " --> pdb=" O LYS F 176 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LYS F 176 " --> pdb=" O TRP F 171 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N THR F 179 " --> pdb=" O LEU F 207 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 89 through 91 Processing sheet with id=AC4, first strand: chain 'G' and resid 154 through 159 Processing sheet with id=AC5, first strand: chain 'G' and resid 164 through 167 removed outlier: 6.198A pdb=" N VAL G 182 " --> pdb=" O LEU G 165 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TRP G 167 " --> pdb=" O LEU G 180 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU G 180 " --> pdb=" O TRP G 167 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG G 203 " --> pdb=" O PHE G 183 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER G 187 " --> pdb=" O GLU G 199 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR G 197 " --> pdb=" O ALA G 189 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 89 through 91 Processing sheet with id=AC7, first strand: chain 'H' and resid 154 through 159 Processing sheet with id=AC8, first strand: chain 'H' and resid 164 through 167 removed outlier: 5.577A pdb=" N ILE H 164 " --> pdb=" O ARG H 184 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ARG H 184 " --> pdb=" O ILE H 164 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP H 202 " --> pdb=" O TRP H 217 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 170 through 172 Processing sheet with id=AD1, first strand: chain 'I' and resid 89 through 91 removed outlier: 3.603A pdb=" N VAL I 89 " --> pdb=" O GLU I 409 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU I 409 " --> pdb=" O VAL I 89 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU I 407 " --> pdb=" O THR I 91 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 154 through 160 removed outlier: 3.539A pdb=" N PHE I 131 " --> pdb=" O LYS I 157 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 164 through 172 removed outlier: 6.820A pdb=" N ILE I 164 " --> pdb=" O PHE I 183 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N PHE I 183 " --> pdb=" O ILE I 164 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN I 166 " --> pdb=" O LEU I 181 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU I 181 " --> pdb=" O ASN I 166 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ARG I 168 " --> pdb=" O THR I 179 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N THR I 179 " --> pdb=" O LEU I 207 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU I 200 " --> pdb=" O GLU I 219 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 293 through 294 removed outlier: 3.593A pdb=" N SER I 294 " --> pdb=" O LYS I 324 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 89 through 91 Processing sheet with id=AD6, first strand: chain 'J' and resid 154 through 156 Processing sheet with id=AD7, first strand: chain 'J' and resid 166 through 171 removed outlier: 6.824A pdb=" N ASN J 166 " --> pdb=" O LEU J 181 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU J 181 " --> pdb=" O ASN J 166 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ARG J 168 " --> pdb=" O THR J 179 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N THR J 179 " --> pdb=" O LEU J 207 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU J 200 " --> pdb=" O GLU J 219 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 89 through 91 Processing sheet with id=AD9, first strand: chain 'K' and resid 154 through 156 Processing sheet with id=AE1, first strand: chain 'K' and resid 166 through 167 Processing sheet with id=AE2, first strand: chain 'K' and resid 166 through 167 removed outlier: 4.224A pdb=" N GLU K 200 " --> pdb=" O GLU K 219 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 170 through 171 Processing sheet with id=AE4, first strand: chain 'K' and resid 293 through 294 removed outlier: 3.544A pdb=" N SER K 294 " --> pdb=" O LYS K 324 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 89 through 91 Processing sheet with id=AE6, first strand: chain 'L' and resid 154 through 156 Processing sheet with id=AE7, first strand: chain 'L' and resid 164 through 168 removed outlier: 6.383A pdb=" N VAL L 182 " --> pdb=" O LEU L 165 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TRP L 167 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU L 180 " --> pdb=" O TRP L 167 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLU L 200 " --> pdb=" O GLU L 219 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N GLU L 219 " --> pdb=" O GLU L 200 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG L 218 " --> pdb=" O TYR L 225 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 171 through 172 Processing sheet with id=AE9, first strand: chain 'L' and resid 293 through 294 Processing sheet with id=AF1, first strand: chain 'M' and resid 36 through 40 removed outlier: 6.005A pdb=" N ILE M 37 " --> pdb=" O ILE M 245 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N GLN M 247 " --> pdb=" O ILE M 37 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ARG M 39 " --> pdb=" O GLN M 247 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 93 through 94 removed outlier: 3.537A pdb=" N TRP M 272 " --> pdb=" O SER M 88 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 51 through 53 Processing sheet with id=AF4, first strand: chain 'M' and resid 144 through 147 Processing sheet with id=AF5, first strand: chain 'M' and resid 215 through 217 Processing sheet with id=AF6, first strand: chain 'M' and resid 281 through 283 Processing sheet with id=AF7, first strand: chain 'N' and resid 36 through 37 Processing sheet with id=AF8, first strand: chain 'N' and resid 36 through 37 removed outlier: 5.794A pdb=" N TYR N 268 " --> pdb=" O PRO N 92 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA N 270 " --> pdb=" O THR N 90 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'N' and resid 50 through 53 Processing sheet with id=AG1, first strand: chain 'N' and resid 144 through 147 removed outlier: 6.572A pdb=" N HIS N 145 " --> pdb=" O VAL N 319 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL N 176 " --> pdb=" O LEU N 238 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N TRP N 177 " --> pdb=" O ILE N 216 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'N' and resid 144 through 147 removed outlier: 6.572A pdb=" N HIS N 145 " --> pdb=" O VAL N 319 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 281 through 283 Processing sheet with id=AG4, first strand: chain 'O' and resid 36 through 40 removed outlier: 5.714A pdb=" N ILE O 37 " --> pdb=" O ILE O 245 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLN O 247 " --> pdb=" O ILE O 37 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ARG O 39 " --> pdb=" O GLN O 247 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 84 through 89 removed outlier: 4.197A pdb=" N ARG O 266 " --> pdb=" O ILE O 95 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'O' and resid 51 through 53 Processing sheet with id=AG7, first strand: chain 'O' and resid 144 through 146 removed outlier: 6.739A pdb=" N HIS O 145 " --> pdb=" O VAL O 319 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL O 176 " --> pdb=" O LEU O 238 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N TRP O 177 " --> pdb=" O ILE O 216 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'O' and resid 144 through 146 removed outlier: 6.739A pdb=" N HIS O 145 " --> pdb=" O VAL O 319 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'O' and resid 281 through 283 Processing sheet with id=AH1, first strand: chain 'P' and resid 36 through 37 Processing sheet with id=AH2, first strand: chain 'P' and resid 93 through 94 removed outlier: 3.779A pdb=" N TRP P 272 " --> pdb=" O SER P 88 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'P' and resid 50 through 53 Processing sheet with id=AH4, first strand: chain 'P' and resid 144 through 147 removed outlier: 6.362A pdb=" N HIS P 145 " --> pdb=" O VAL P 319 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL P 176 " --> pdb=" O LEU P 238 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TRP P 177 " --> pdb=" O ILE P 216 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'P' and resid 144 through 147 removed outlier: 6.362A pdb=" N HIS P 145 " --> pdb=" O VAL P 319 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'P' and resid 281 through 283 Processing sheet with id=AH7, first strand: chain 'Q' and resid 36 through 40 removed outlier: 6.093A pdb=" N ILE Q 37 " --> pdb=" O ILE Q 245 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLN Q 247 " --> pdb=" O ILE Q 37 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ARG Q 39 " --> pdb=" O GLN Q 247 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA Q 270 " --> pdb=" O THR Q 90 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'Q' and resid 36 through 40 removed outlier: 6.093A pdb=" N ILE Q 37 " --> pdb=" O ILE Q 245 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLN Q 247 " --> pdb=" O ILE Q 37 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ARG Q 39 " --> pdb=" O GLN Q 247 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'Q' and resid 51 through 53 Processing sheet with id=AI1, first strand: chain 'Q' and resid 93 through 94 Processing sheet with id=AI2, first strand: chain 'Q' and resid 144 through 147 removed outlier: 3.675A pdb=" N VAL Q 176 " --> pdb=" O LEU Q 238 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Q' and resid 144 through 147 Processing sheet with id=AI4, first strand: chain 'Q' and resid 281 through 283 Processing sheet with id=AI5, first strand: chain 'R' and resid 36 through 39 removed outlier: 5.931A pdb=" N ILE R 37 " --> pdb=" O ILE R 245 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N GLN R 247 " --> pdb=" O ILE R 37 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ARG R 39 " --> pdb=" O GLN R 247 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'R' and resid 84 through 88 removed outlier: 3.644A pdb=" N TRP R 272 " --> pdb=" O SER R 88 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'R' and resid 51 through 53 Processing sheet with id=AI8, first strand: chain 'R' and resid 144 through 146 removed outlier: 6.644A pdb=" N HIS R 145 " --> pdb=" O VAL R 319 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N ILE R 216 " --> pdb=" O GLN R 175 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TRP R 177 " --> pdb=" O ILE R 216 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'R' and resid 281 through 283 removed outlier: 3.520A pdb=" N ALA R 282 " --> pdb=" O ASP R 304 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'S' and resid 36 through 39 removed outlier: 5.898A pdb=" N ILE S 37 " --> pdb=" O ILE S 245 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N GLN S 247 " --> pdb=" O ILE S 37 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ARG S 39 " --> pdb=" O GLN S 247 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'S' and resid 84 through 89 removed outlier: 3.618A pdb=" N THR S 265 " --> pdb=" O GLY S 258 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'S' and resid 50 through 51 removed outlier: 3.843A pdb=" N ALA S 50 " --> pdb=" O ASP S 81 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'S' and resid 144 through 146 removed outlier: 6.822A pdb=" N HIS S 145 " --> pdb=" O VAL S 319 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N SER S 234 " --> pdb=" O SER S 179 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N SER S 179 " --> pdb=" O SER S 234 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU S 236 " --> pdb=" O TRP S 177 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N TRP S 177 " --> pdb=" O LEU S 236 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU S 238 " --> pdb=" O GLN S 175 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N ILE S 216 " --> pdb=" O GLN S 175 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TRP S 177 " --> pdb=" O ILE S 216 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'S' and resid 281 through 283 Processing sheet with id=AJ6, first strand: chain 'T' and resid 36 through 39 removed outlier: 5.719A pdb=" N ILE T 37 " --> pdb=" O ILE T 245 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLN T 247 " --> pdb=" O ILE T 37 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ARG T 39 " --> pdb=" O GLN T 247 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'T' and resid 36 through 39 removed outlier: 5.719A pdb=" N ILE T 37 " --> pdb=" O ILE T 245 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLN T 247 " --> pdb=" O ILE T 37 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ARG T 39 " --> pdb=" O GLN T 247 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'T' and resid 49 through 51 removed outlier: 3.657A pdb=" N ALA T 50 " --> pdb=" O ASP T 81 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'T' and resid 144 through 146 Processing sheet with id=AK1, first strand: chain 'T' and resid 281 through 283 Processing sheet with id=AK2, first strand: chain 'U' and resid 36 through 40 removed outlier: 5.949A pdb=" N ILE U 37 " --> pdb=" O ILE U 245 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N GLN U 247 " --> pdb=" O ILE U 37 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG U 39 " --> pdb=" O GLN U 247 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'U' and resid 84 through 89 Processing sheet with id=AK4, first strand: chain 'U' and resid 144 through 146 removed outlier: 7.004A pdb=" N HIS U 145 " --> pdb=" O VAL U 319 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'U' and resid 281 through 283 Processing sheet with id=AK6, first strand: chain 'V' and resid 36 through 39 removed outlier: 5.443A pdb=" N ILE V 37 " --> pdb=" O ILE V 245 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N GLN V 247 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ARG V 39 " --> pdb=" O GLN V 247 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'V' and resid 47 through 51 removed outlier: 6.453A pdb=" N ASN V 82 " --> pdb=" O VAL V 278 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL V 278 " --> pdb=" O ASN V 82 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR V 265 " --> pdb=" O GLY V 258 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'V' and resid 144 through 146 removed outlier: 7.098A pdb=" N HIS V 145 " --> pdb=" O VAL V 319 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'V' and resid 281 through 283 3004 hydrogen bonds defined for protein. 8427 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: 26.53 Time building geometry restraints manager: 14.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 22464 1.34 - 1.46: 10308 1.46 - 1.58: 34919 1.58 - 1.70: 2 1.70 - 1.82: 484 Bond restraints: 68177 Sorted by residual: bond pdb=" N VAL O 25 " pdb=" CA VAL O 25 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.04e-02 9.25e+03 1.38e+01 bond pdb=" N ILE K 355 " pdb=" CA ILE K 355 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.20e+01 bond pdb=" N VAL R 25 " pdb=" CA VAL R 25 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.09e-02 8.42e+03 1.18e+01 bond pdb=" N ILE I 355 " pdb=" CA ILE I 355 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.11e-02 8.12e+03 1.14e+01 bond pdb=" N ILE J 355 " pdb=" CA ILE J 355 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.11e-02 8.12e+03 1.13e+01 ... (remaining 68172 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 90225 2.00 - 3.99: 2029 3.99 - 5.99: 178 5.99 - 7.98: 28 7.98 - 9.98: 10 Bond angle restraints: 92470 Sorted by residual: angle pdb=" C ALA S 228 " pdb=" CA ALA S 228 " pdb=" CB ALA S 228 " ideal model delta sigma weight residual 116.54 109.93 6.61 1.15e+00 7.56e-01 3.31e+01 angle pdb=" C GLN K 239 " pdb=" CA GLN K 239 " pdb=" CB GLN K 239 " ideal model delta sigma weight residual 115.79 109.49 6.30 1.19e+00 7.06e-01 2.80e+01 angle pdb=" C ALA V 228 " pdb=" CA ALA V 228 " pdb=" CB ALA V 228 " ideal model delta sigma weight residual 116.63 110.53 6.10 1.16e+00 7.43e-01 2.77e+01 angle pdb=" C GLN E 239 " pdb=" CA GLN E 239 " pdb=" CB GLN E 239 " ideal model delta sigma weight residual 116.54 110.72 5.82 1.15e+00 7.56e-01 2.56e+01 angle pdb=" C ARG A 86 " pdb=" CA ARG A 86 " pdb=" CB ARG A 86 " ideal model delta sigma weight residual 117.23 110.43 6.80 1.36e+00 5.41e-01 2.50e+01 ... (remaining 92465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 36680 18.00 - 35.99: 3300 35.99 - 53.99: 574 53.99 - 71.99: 156 71.99 - 89.98: 60 Dihedral angle restraints: 40770 sinusoidal: 16107 harmonic: 24663 Sorted by residual: dihedral pdb=" CA LEU S 27 " pdb=" C LEU S 27 " pdb=" N PHE S 28 " pdb=" CA PHE S 28 " ideal model delta harmonic sigma weight residual -180.00 -152.66 -27.34 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA PHE H 84 " pdb=" C PHE H 84 " pdb=" N ALA H 85 " pdb=" CA ALA H 85 " ideal model delta harmonic sigma weight residual 180.00 154.91 25.09 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA THR S 320 " pdb=" C THR S 320 " pdb=" N LYS S 321 " pdb=" CA LYS S 321 " ideal model delta harmonic sigma weight residual -180.00 -155.29 -24.71 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 40767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 7384 0.042 - 0.084: 1758 0.084 - 0.126: 770 0.126 - 0.168: 108 0.168 - 0.210: 28 Chirality restraints: 10048 Sorted by residual: chirality pdb=" CA ILE A 355 " pdb=" N ILE A 355 " pdb=" C ILE A 355 " pdb=" CB ILE A 355 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ILE U 56 " pdb=" N ILE U 56 " pdb=" C ILE U 56 " pdb=" CB ILE U 56 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE R 36 " pdb=" N ILE R 36 " pdb=" C ILE R 36 " pdb=" CB ILE R 36 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 10045 not shown) Planarity restraints: 12237 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG Q 266 " 0.403 9.50e-02 1.11e+02 1.81e-01 2.00e+01 pdb=" NE ARG Q 266 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG Q 266 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG Q 266 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG Q 266 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 380 " -0.397 9.50e-02 1.11e+02 1.78e-01 1.94e+01 pdb=" NE ARG A 380 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG A 380 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 380 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 380 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Q 101 " -0.394 9.50e-02 1.11e+02 1.76e-01 1.91e+01 pdb=" NE ARG Q 101 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG Q 101 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG Q 101 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG Q 101 " -0.015 2.00e-02 2.50e+03 ... (remaining 12234 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 1015 2.64 - 3.21: 63358 3.21 - 3.77: 104159 3.77 - 4.34: 144344 4.34 - 4.90: 237344 Nonbonded interactions: 550220 Sorted by model distance: nonbonded pdb=" OH TYR K 197 " pdb=" NH2 ARG U 101 " model vdw 2.079 3.120 nonbonded pdb=" OH TYR L 62 " pdb=" OD1 ASP L 278 " model vdw 2.099 3.040 nonbonded pdb=" OH TYR F 62 " pdb=" OD1 ASP F 278 " model vdw 2.122 3.040 nonbonded pdb=" OD1 ASP O 81 " pdb=" N ASN O 82 " model vdw 2.125 3.120 nonbonded pdb=" OG1 THR E 216 " pdb=" OD2 ASP E 227 " model vdw 2.129 3.040 ... (remaining 550215 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 8 through 468) selection = (chain 'B' and resid 8 through 468) selection = (chain 'C' and resid 8 through 468) selection = (chain 'D' and resid 8 through 468) selection = (chain 'E' and resid 8 through 468) selection = (chain 'F' and resid 8 through 468) selection = chain 'G' selection = (chain 'H' and resid 8 through 468) selection = (chain 'I' and resid 8 through 468) selection = (chain 'J' and resid 8 through 468) selection = (chain 'K' and resid 8 through 468) selection = (chain 'L' and resid 8 through 468) } ncs_group { reference = (chain 'M' and resid 9 through 321) selection = (chain 'N' and resid 9 through 321) selection = (chain 'O' and resid 9 through 321) selection = chain 'P' selection = (chain 'Q' and resid 9 through 321) selection = (chain 'R' and resid 9 through 321) selection = (chain 'S' and resid 9 through 321) selection = (chain 'T' and resid 9 through 321) selection = (chain 'U' and resid 9 through 321) selection = (chain 'V' and resid 9 through 321) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 1.880 Check model and map are aligned: 0.380 Set scattering table: 0.460 Process input model: 114.220 Find NCS groups from input model: 2.910 Set up NCS constraints: 0.250 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: 0.020 Load rotamer database and sin/cos tables:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 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 : 0.004 0.057 68177 Z= 0.259 Angle : 0.660 9.977 92470 Z= 0.400 Chirality : 0.045 0.210 10048 Planarity : 0.006 0.181 12237 Dihedral : 14.570 89.984 24896 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.07 % Favored : 95.85 % Rotamer: Outliers : 0.27 % Allowed : 0.72 % Favored : 99.01 % 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: -0.36 (0.09), residues: 8507 helix: 1.14 (0.09), residues: 3086 sheet: -0.67 (0.14), residues: 1545 loop : -1.17 (0.10), residues: 3876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP J 171 HIS 0.014 0.001 HIS F 18 PHE 0.026 0.001 PHE F 84 TYR 0.027 0.001 TYR Q 268 ARG 0.010 0.001 ARG N 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17014 Ramachandran restraints generated. 8507 Oldfield, 0 Emsley, 8507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17014 Ramachandran restraints generated. 8507 Oldfield, 0 Emsley, 8507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2568 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 2549 time to evaluate : 5.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ILE cc_start: 0.9040 (mm) cc_final: 0.8322 (mm) REVERT: A 257 ILE cc_start: 0.8925 (mm) cc_final: 0.8694 (mm) REVERT: A 410 LEU cc_start: 0.8421 (mt) cc_final: 0.7822 (mt) REVERT: A 460 ASN cc_start: 0.8019 (m110) cc_final: 0.7734 (m110) REVERT: B 29 GLU cc_start: 0.6720 (tp30) cc_final: 0.6047 (tm-30) REVERT: B 60 LYS cc_start: 0.8324 (tttt) cc_final: 0.7958 (ttmt) REVERT: B 410 LEU cc_start: 0.8198 (mt) cc_final: 0.7980 (mt) REVERT: C 23 HIS cc_start: 0.7203 (m170) cc_final: 0.6892 (m-70) REVERT: C 105 ASP cc_start: 0.7611 (p0) cc_final: 0.7383 (p0) REVERT: D 24 ILE cc_start: 0.8549 (mt) cc_final: 0.7932 (mt) REVERT: D 95 ASP cc_start: 0.7156 (p0) cc_final: 0.6838 (p0) REVERT: D 120 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6132 (mt-10) REVERT: D 341 ASP cc_start: 0.7193 (m-30) cc_final: 0.6882 (m-30) REVERT: D 419 MET cc_start: 0.7596 (ptp) cc_final: 0.7119 (ptm) REVERT: E 159 ILE cc_start: 0.8843 (mm) cc_final: 0.8497 (mm) REVERT: E 346 GLN cc_start: 0.7520 (mt0) cc_final: 0.6733 (mt0) REVERT: F 418 LYS cc_start: 0.7963 (mttt) cc_final: 0.7737 (mttp) REVERT: F 460 ASN cc_start: 0.8107 (m-40) cc_final: 0.6056 (m-40) REVERT: G 236 ASP cc_start: 0.7919 (p0) cc_final: 0.7682 (p0) REVERT: G 458 MET cc_start: 0.8427 (ttp) cc_final: 0.8190 (ttt) REVERT: G 460 ASN cc_start: 0.7986 (m-40) cc_final: 0.7740 (m-40) REVERT: H 165 LEU cc_start: 0.8253 (pt) cc_final: 0.7570 (pp) REVERT: H 283 CYS cc_start: 0.7503 (t) cc_final: 0.7226 (t) REVERT: H 292 PHE cc_start: 0.6924 (m-80) cc_final: 0.6721 (m-80) REVERT: H 377 VAL cc_start: 0.8987 (p) cc_final: 0.8217 (m) REVERT: I 460 ASN cc_start: 0.8131 (m-40) cc_final: 0.7630 (m-40) REVERT: J 46 ASP cc_start: 0.7111 (t0) cc_final: 0.6900 (t0) REVERT: J 342 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7268 (tm-30) REVERT: J 346 GLN cc_start: 0.7238 (mt0) cc_final: 0.6895 (mt0) REVERT: K 46 ASP cc_start: 0.7766 (m-30) cc_final: 0.7461 (m-30) REVERT: K 98 ASP cc_start: 0.6963 (t0) cc_final: 0.6492 (t0) REVERT: K 257 ILE cc_start: 0.8984 (mp) cc_final: 0.8696 (mt) REVERT: K 285 ILE cc_start: 0.8834 (mm) cc_final: 0.8632 (mt) REVERT: K 418 LYS cc_start: 0.6994 (mtmt) cc_final: 0.5695 (mtmt) REVERT: K 460 ASN cc_start: 0.8029 (m-40) cc_final: 0.7645 (m110) REVERT: L 285 ILE cc_start: 0.8762 (mm) cc_final: 0.8508 (mt) REVERT: L 406 ILE cc_start: 0.8955 (pt) cc_final: 0.8356 (pt) REVERT: L 412 SER cc_start: 0.8403 (p) cc_final: 0.8061 (p) REVERT: L 461 GLU cc_start: 0.7802 (tt0) cc_final: 0.6890 (tm-30) REVERT: M 238 LEU cc_start: 0.7441 (mm) cc_final: 0.7154 (mm) REVERT: O 118 LEU cc_start: 0.8564 (tp) cc_final: 0.8357 (tp) REVERT: P 118 LEU cc_start: 0.8800 (tp) cc_final: 0.8436 (tp) REVERT: P 135 LYS cc_start: 0.7713 (tttt) cc_final: 0.7506 (tttt) REVERT: R 281 TYR cc_start: 0.7598 (m-80) cc_final: 0.7374 (m-10) REVERT: T 246 GLU cc_start: 0.5797 (mt-10) cc_final: 0.5499 (mt-10) REVERT: U 254 THR cc_start: 0.7195 (p) cc_final: 0.6510 (p) outliers start: 19 outliers final: 8 residues processed: 2562 average time/residue: 0.6854 time to fit residues: 2918.1366 Evaluate side-chains 1658 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 1649 time to evaluate : 5.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain G residue 350 LEU Chi-restraints excluded: chain H residue 354 LEU Chi-restraints excluded: chain H residue 355 ILE Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain J residue 342 GLN Chi-restraints excluded: chain J residue 354 LEU Chi-restraints excluded: chain R residue 27 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 855 random chunks: chunk 721 optimal weight: 8.9990 chunk 648 optimal weight: 10.0000 chunk 359 optimal weight: 20.0000 chunk 221 optimal weight: 3.9990 chunk 437 optimal weight: 6.9990 chunk 346 optimal weight: 9.9990 chunk 670 optimal weight: 0.9990 chunk 259 optimal weight: 50.0000 chunk 407 optimal weight: 9.9990 chunk 498 optimal weight: 20.0000 chunk 776 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 239 GLN ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS B 303 ASN C 18 HIS C 74 ASN C 333 ASN ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN D 214 GLN ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 444 GLN E 303 ASN E 333 ASN F 102 ASN ** F 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 322 ASN F 374 GLN ** F 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 299 HIS G 303 ASN H 269 ASN H 275 ASN ** H 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 374 GLN J 239 GLN J 303 ASN J 342 GLN J 460 ASN ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 44 HIS K 253 ASN K 346 GLN L 374 GLN ** L 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 129 ASN N 43 ASN ** N 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 129 ASN N 190 ASN O 24 GLN O 43 ASN O 248 ASN ** P 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 267 GLN ** R 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 108 GLN R 116 GLN S 94 ASN S 117 GLN ** S 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 43 ASN T 249 GLN ** U 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 10 ASN ** V 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 247 GLN V 248 ASN ** V 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.086071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.070710 restraints weight = 244103.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.072846 restraints weight = 142163.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.074335 restraints weight = 98048.433| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 68177 Z= 0.293 Angle : 0.701 9.798 92470 Z= 0.369 Chirality : 0.045 0.201 10048 Planarity : 0.005 0.088 12237 Dihedral : 4.942 67.886 9271 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.15 % Favored : 95.84 % Rotamer: Outliers : 2.69 % Allowed : 14.18 % Favored : 83.13 % 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: -0.26 (0.09), residues: 8507 helix: 1.13 (0.09), residues: 3128 sheet: -0.50 (0.13), residues: 1649 loop : -1.11 (0.10), residues: 3730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP I 395 HIS 0.008 0.001 HIS G 299 PHE 0.022 0.002 PHE D 97 TYR 0.023 0.002 TYR O 268 ARG 0.011 0.001 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17014 Ramachandran restraints generated. 8507 Oldfield, 0 Emsley, 8507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17014 Ramachandran restraints generated. 8507 Oldfield, 0 Emsley, 8507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1996 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 1808 time to evaluate : 5.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 8 LYS cc_start: 0.9049 (ttpp) cc_final: 0.8708 (ttpp) REVERT: A 16 LYS cc_start: 0.9317 (ptpp) cc_final: 0.8855 (ptpp) REVERT: A 18 HIS cc_start: 0.9049 (m90) cc_final: 0.8302 (m90) REVERT: A 29 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8538 (tm-30) REVERT: A 60 LYS cc_start: 0.9609 (mmtt) cc_final: 0.9351 (mtmm) REVERT: A 80 LEU cc_start: 0.9640 (tp) cc_final: 0.9438 (tt) REVERT: A 163 ASP cc_start: 0.9082 (m-30) cc_final: 0.8477 (t0) REVERT: A 198 LYS cc_start: 0.9242 (mmtt) cc_final: 0.8840 (mmtt) REVERT: A 241 ASP cc_start: 0.8137 (p0) cc_final: 0.7929 (p0) REVERT: A 346 GLN cc_start: 0.9226 (mt0) cc_final: 0.8768 (mp10) REVERT: A 380 ARG cc_start: 0.9135 (mtm-85) cc_final: 0.8753 (mtm-85) REVERT: A 410 LEU cc_start: 0.9017 (mt) cc_final: 0.8524 (mt) REVERT: A 419 MET cc_start: 0.8391 (ppp) cc_final: 0.7972 (ppp) REVERT: A 446 LYS cc_start: 0.9396 (mmtp) cc_final: 0.9140 (mmtt) REVERT: A 458 MET cc_start: 0.8079 (ttm) cc_final: 0.6825 (tpt) REVERT: A 460 ASN cc_start: 0.8882 (m110) cc_final: 0.8536 (m110) REVERT: B 9 TYR cc_start: 0.8244 (p90) cc_final: 0.7763 (p90) REVERT: B 18 HIS cc_start: 0.8152 (p-80) cc_final: 0.7881 (p-80) REVERT: B 32 ARG cc_start: 0.8036 (ttp80) cc_final: 0.7722 (ttp80) REVERT: B 64 GLU cc_start: 0.8583 (pt0) cc_final: 0.8358 (pt0) REVERT: B 188 ASP cc_start: 0.8620 (t0) cc_final: 0.7952 (t0) REVERT: B 206 ARG cc_start: 0.8439 (tpp-160) cc_final: 0.8063 (tpt170) REVERT: B 219 GLU cc_start: 0.8204 (pt0) cc_final: 0.7831 (pt0) REVERT: B 383 LYS cc_start: 0.9495 (ttmm) cc_final: 0.9189 (ttpt) REVERT: B 403 ASP cc_start: 0.8235 (t0) cc_final: 0.7405 (t0) REVERT: B 418 LYS cc_start: 0.8790 (mttt) cc_final: 0.8552 (mttt) REVERT: B 441 MET cc_start: 0.9399 (tmm) cc_final: 0.9162 (tmm) REVERT: B 460 ASN cc_start: 0.9486 (m110) cc_final: 0.9278 (m-40) REVERT: C 19 LYS cc_start: 0.9123 (tppt) cc_final: 0.8896 (tptt) REVERT: C 102 ASN cc_start: 0.7910 (m110) cc_final: 0.7605 (m110) REVERT: C 105 ASP cc_start: 0.9061 (p0) cc_final: 0.8678 (p0) REVERT: C 109 LEU cc_start: 0.9117 (tp) cc_final: 0.8714 (tt) REVERT: C 176 LYS cc_start: 0.8778 (tppp) cc_final: 0.8371 (tppt) REVERT: C 181 LEU cc_start: 0.9475 (tp) cc_final: 0.9229 (tt) REVERT: C 220 ASN cc_start: 0.8527 (t0) cc_final: 0.8247 (t0) REVERT: C 225 TYR cc_start: 0.8088 (m-80) cc_final: 0.7620 (m-80) REVERT: C 292 PHE cc_start: 0.9307 (m-80) cc_final: 0.9082 (m-80) REVERT: C 369 MET cc_start: 0.8641 (mpp) cc_final: 0.8393 (mpp) REVERT: C 413 ASP cc_start: 0.8696 (t0) cc_final: 0.8423 (t0) REVERT: C 441 MET cc_start: 0.9071 (tmm) cc_final: 0.8693 (ppp) REVERT: D 15 LYS cc_start: 0.9306 (mttt) cc_final: 0.8955 (mtmm) REVERT: D 17 MET cc_start: 0.9185 (mmm) cc_final: 0.7740 (tpp) REVERT: D 89 VAL cc_start: 0.9373 (t) cc_final: 0.9140 (p) REVERT: D 120 GLU cc_start: 0.9448 (mt-10) cc_final: 0.9034 (mt-10) REVERT: D 173 ASN cc_start: 0.8704 (m-40) cc_final: 0.8242 (p0) REVERT: D 186 GLU cc_start: 0.8409 (tp30) cc_final: 0.8007 (tp30) REVERT: D 251 LYS cc_start: 0.8970 (mptt) cc_final: 0.8737 (mptt) REVERT: D 278 ASP cc_start: 0.9304 (OUTLIER) cc_final: 0.9052 (t0) REVERT: D 341 ASP cc_start: 0.9179 (m-30) cc_final: 0.8740 (m-30) REVERT: D 374 GLN cc_start: 0.9272 (mt0) cc_final: 0.8780 (mp10) REVERT: D 380 ARG cc_start: 0.8796 (ttp-110) cc_final: 0.8549 (ttp-110) REVERT: D 398 MET cc_start: 0.8906 (mtt) cc_final: 0.8678 (mtt) REVERT: D 409 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7995 (tm-30) REVERT: D 422 GLU cc_start: 0.9160 (tp30) cc_final: 0.8916 (tp30) REVERT: D 441 MET cc_start: 0.9544 (tmm) cc_final: 0.9174 (ppp) REVERT: E 74 ASN cc_start: 0.8730 (t0) cc_final: 0.8500 (t0) REVERT: E 121 ASP cc_start: 0.9383 (m-30) cc_final: 0.9172 (m-30) REVERT: E 163 ASP cc_start: 0.8633 (m-30) cc_final: 0.7849 (t0) REVERT: E 184 ARG cc_start: 0.9022 (ttp80) cc_final: 0.8443 (ttp80) REVERT: E 251 LYS cc_start: 0.8881 (ttpp) cc_final: 0.8653 (tmmt) REVERT: E 259 MET cc_start: 0.8861 (mmm) cc_final: 0.8556 (mmm) REVERT: E 370 GLU cc_start: 0.8147 (pm20) cc_final: 0.7713 (pm20) REVERT: E 419 MET cc_start: 0.8312 (ttm) cc_final: 0.7722 (ttm) REVERT: E 443 TRP cc_start: 0.8917 (t60) cc_final: 0.8347 (t60) REVERT: F 54 GLU cc_start: 0.9527 (tt0) cc_final: 0.9312 (tm-30) REVERT: F 86 ARG cc_start: 0.7539 (mmt-90) cc_final: 0.7331 (mmt-90) REVERT: F 163 ASP cc_start: 0.9179 (m-30) cc_final: 0.8507 (m-30) REVERT: F 184 ARG cc_start: 0.9167 (ttp-110) cc_final: 0.8539 (ttp80) REVERT: F 340 MET cc_start: 0.9118 (mtp) cc_final: 0.8899 (mmm) REVERT: F 357 SER cc_start: 0.8635 (m) cc_final: 0.8388 (p) REVERT: F 370 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8266 (mt-10) REVERT: F 398 MET cc_start: 0.9421 (mtm) cc_final: 0.9106 (mtm) REVERT: F 460 ASN cc_start: 0.8342 (m-40) cc_final: 0.7667 (m110) REVERT: G 99 MET cc_start: 0.9143 (ppp) cc_final: 0.8862 (tmm) REVERT: G 163 ASP cc_start: 0.9326 (m-30) cc_final: 0.9080 (t0) REVERT: G 245 PHE cc_start: 0.9326 (t80) cc_final: 0.9091 (t80) REVERT: G 247 ILE cc_start: 0.9349 (mt) cc_final: 0.9098 (mm) REVERT: G 283 CYS cc_start: 0.9189 (t) cc_final: 0.8922 (m) REVERT: G 326 GLU cc_start: 0.9057 (pt0) cc_final: 0.8819 (pt0) REVERT: G 335 MET cc_start: 0.8984 (ttt) cc_final: 0.8665 (tmm) REVERT: G 347 MET cc_start: 0.9012 (mmm) cc_final: 0.8545 (mpp) REVERT: G 419 MET cc_start: 0.7835 (ptm) cc_final: 0.7208 (ptm) REVERT: G 423 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8710 (mt-10) REVERT: G 460 ASN cc_start: 0.9150 (m-40) cc_final: 0.8463 (m110) REVERT: H 17 MET cc_start: 0.9532 (mmm) cc_final: 0.9196 (mmm) REVERT: H 77 ASP cc_start: 0.9254 (m-30) cc_final: 0.9035 (m-30) REVERT: H 79 MET cc_start: 0.9031 (mmt) cc_final: 0.8481 (mmp) REVERT: H 165 LEU cc_start: 0.9553 (pt) cc_final: 0.9325 (pp) REVERT: H 200 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8128 (mp0) REVERT: H 283 CYS cc_start: 0.9288 (t) cc_final: 0.8886 (t) REVERT: H 328 LEU cc_start: 0.9208 (mp) cc_final: 0.8834 (mp) REVERT: H 347 MET cc_start: 0.9325 (mtm) cc_final: 0.8814 (mtt) REVERT: H 380 ARG cc_start: 0.8730 (mtm-85) cc_final: 0.7833 (mtm-85) REVERT: H 387 ASP cc_start: 0.9213 (m-30) cc_final: 0.8965 (m-30) REVERT: H 409 GLU cc_start: 0.8163 (mp0) cc_final: 0.7757 (mp0) REVERT: I 69 TYR cc_start: 0.9013 (t80) cc_final: 0.8569 (t80) REVERT: I 79 MET cc_start: 0.9422 (mtm) cc_final: 0.8931 (mtm) REVERT: I 131 PHE cc_start: 0.9278 (t80) cc_final: 0.9004 (t80) REVERT: I 219 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8312 (tp30) REVERT: I 259 MET cc_start: 0.7843 (ttp) cc_final: 0.7631 (ttp) REVERT: I 262 MET cc_start: 0.8626 (mmm) cc_final: 0.8382 (mmm) REVERT: I 280 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8795 (mm-30) REVERT: I 344 GLU cc_start: 0.9011 (tt0) cc_final: 0.8617 (tp30) REVERT: I 347 MET cc_start: 0.9486 (mtp) cc_final: 0.9196 (mtp) REVERT: I 419 MET cc_start: 0.7884 (ppp) cc_final: 0.7361 (ppp) REVERT: I 423 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8792 (tt0) REVERT: I 441 MET cc_start: 0.9143 (ppp) cc_final: 0.8845 (ppp) REVERT: I 460 ASN cc_start: 0.8821 (m-40) cc_final: 0.8613 (m-40) REVERT: J 46 ASP cc_start: 0.8373 (t0) cc_final: 0.7899 (t0) REVERT: J 79 MET cc_start: 0.9346 (mmm) cc_final: 0.9046 (mpp) REVERT: J 251 LYS cc_start: 0.9276 (mttp) cc_final: 0.8866 (mttt) REVERT: J 267 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8593 (mm-30) REVERT: J 342 GLN cc_start: 0.9539 (tt0) cc_final: 0.8437 (tm-30) REVERT: J 345 ARG cc_start: 0.8409 (ttp80) cc_final: 0.7606 (ttp80) REVERT: J 346 GLN cc_start: 0.9268 (mt0) cc_final: 0.7786 (mt0) REVERT: K 26 MET cc_start: 0.9195 (mmm) cc_final: 0.8916 (mmm) REVERT: K 184 ARG cc_start: 0.7506 (mtp180) cc_final: 0.7205 (mmm-85) REVERT: K 225 TYR cc_start: 0.7091 (m-80) cc_final: 0.6838 (m-80) REVERT: K 228 ASP cc_start: 0.9105 (OUTLIER) cc_final: 0.8897 (t0) REVERT: K 262 MET cc_start: 0.9188 (mmm) cc_final: 0.8275 (mmm) REVERT: K 266 VAL cc_start: 0.9836 (t) cc_final: 0.9625 (m) REVERT: K 340 MET cc_start: 0.9384 (mtp) cc_final: 0.9099 (mmm) REVERT: K 343 LYS cc_start: 0.9572 (mppt) cc_final: 0.9153 (mttt) REVERT: K 345 ARG cc_start: 0.8133 (tmm-80) cc_final: 0.7865 (ttp80) REVERT: K 395 TRP cc_start: 0.9564 (m-10) cc_final: 0.9333 (m-10) REVERT: K 406 ILE cc_start: 0.9076 (pt) cc_final: 0.8875 (pt) REVERT: K 418 LYS cc_start: 0.7987 (mtmt) cc_final: 0.7387 (mtmt) REVERT: K 454 GLU cc_start: 0.8290 (tm-30) cc_final: 0.8033 (tm-30) REVERT: K 460 ASN cc_start: 0.9100 (m-40) cc_final: 0.8750 (m110) REVERT: L 15 LYS cc_start: 0.9738 (mmmm) cc_final: 0.9452 (mmmm) REVERT: L 16 LYS cc_start: 0.9340 (mmmt) cc_final: 0.9120 (mmmt) REVERT: L 77 ASP cc_start: 0.8711 (m-30) cc_final: 0.8414 (m-30) REVERT: L 214 GLN cc_start: 0.9074 (pp30) cc_final: 0.8859 (pp30) REVERT: L 239 GLN cc_start: 0.9148 (pm20) cc_final: 0.8925 (pm20) REVERT: L 329 GLN cc_start: 0.8606 (pt0) cc_final: 0.7992 (pm20) REVERT: L 341 ASP cc_start: 0.9137 (m-30) cc_final: 0.8929 (m-30) REVERT: L 342 GLN cc_start: 0.9486 (tt0) cc_final: 0.9075 (tt0) REVERT: L 350 LEU cc_start: 0.8825 (mt) cc_final: 0.8535 (tt) REVERT: L 354 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7450 (pp) REVERT: L 458 MET cc_start: 0.8003 (tpt) cc_final: 0.7734 (tpt) REVERT: M 17 MET cc_start: 0.8545 (mpp) cc_final: 0.8213 (mmm) REVERT: M 26 GLU cc_start: 0.8120 (mp0) cc_final: 0.7501 (mp0) REVERT: M 99 MET cc_start: 0.7893 (pmm) cc_final: 0.7390 (ppp) REVERT: M 207 ARG cc_start: 0.9005 (tpp80) cc_final: 0.8751 (tpp80) REVERT: N 24 GLN cc_start: 0.8123 (tm-30) cc_final: 0.7780 (tm-30) REVERT: N 33 ARG cc_start: 0.9458 (mmm-85) cc_final: 0.9170 (mtm-85) REVERT: O 99 MET cc_start: 0.5222 (ppp) cc_final: 0.4870 (ppp) REVERT: O 121 ASP cc_start: 0.8683 (t0) cc_final: 0.8371 (t0) REVERT: O 236 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9157 (pt) REVERT: P 22 ASP cc_start: 0.8751 (p0) cc_final: 0.8251 (p0) REVERT: P 251 PHE cc_start: 0.9229 (t80) cc_final: 0.8981 (t80) REVERT: P 290 LYS cc_start: 0.8846 (mmmm) cc_final: 0.8414 (mtmt) REVERT: Q 125 ASP cc_start: 0.8740 (t0) cc_final: 0.8468 (t0) REVERT: Q 321 LYS cc_start: 0.8987 (ptmt) cc_final: 0.8773 (ptmm) REVERT: R 15 LYS cc_start: 0.7261 (OUTLIER) cc_final: 0.6378 (pttm) REVERT: R 126 MET cc_start: 0.9428 (mtm) cc_final: 0.9219 (mtm) REVERT: R 246 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8446 (mm-30) REVERT: R 276 LEU cc_start: 0.9644 (OUTLIER) cc_final: 0.9418 (mp) REVERT: S 39 ARG cc_start: 0.8873 (mpp80) cc_final: 0.8636 (mpp80) REVERT: S 47 LEU cc_start: 0.9200 (tt) cc_final: 0.8955 (mt) REVERT: S 105 LYS cc_start: 0.9573 (mtpt) cc_final: 0.9320 (mmmm) REVERT: S 246 GLU cc_start: 0.7495 (mp0) cc_final: 0.7160 (mp0) REVERT: T 39 ARG cc_start: 0.7988 (ptm160) cc_final: 0.7634 (ptp90) REVERT: T 126 MET cc_start: 0.9192 (mtm) cc_final: 0.8825 (mtm) REVERT: T 170 ARG cc_start: 0.8978 (ttp-110) cc_final: 0.8318 (ttp80) REVERT: T 246 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7535 (mt-10) REVERT: T 266 ARG cc_start: 0.8926 (mtm-85) cc_final: 0.8673 (mtm-85) REVERT: U 64 ASP cc_start: 0.9062 (t0) cc_final: 0.8813 (t0) REVERT: U 207 ARG cc_start: 0.9131 (mmm-85) cc_final: 0.8884 (mmm-85) REVERT: U 252 ASP cc_start: 0.8632 (t0) cc_final: 0.8313 (p0) REVERT: V 108 GLN cc_start: 0.8411 (tm-30) cc_final: 0.7871 (tm-30) REVERT: V 164 GLN cc_start: 0.9035 (tt0) cc_final: 0.8565 (pt0) REVERT: V 188 TYR cc_start: 0.9134 (m-80) cc_final: 0.8880 (m-80) REVERT: V 246 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8316 (pt0) outliers start: 188 outliers final: 103 residues processed: 1902 average time/residue: 0.6622 time to fit residues: 2111.7176 Evaluate side-chains 1701 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 1591 time to evaluate : 5.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 278 ASP Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 412 SER Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain F residue 23 HIS Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 264 ASP Chi-restraints excluded: chain F residue 299 HIS Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 342 GLN Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 256 THR Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 374 GLN Chi-restraints excluded: chain G residue 436 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 290 THR Chi-restraints excluded: chain H residue 342 GLN Chi-restraints excluded: chain H residue 354 LEU Chi-restraints excluded: chain H residue 355 ILE Chi-restraints excluded: chain H residue 419 MET Chi-restraints excluded: chain H residue 458 MET Chi-restraints excluded: chain I residue 63 ILE Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 243 ILE Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 336 VAL Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain J residue 121 ASP Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 236 ASP Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 286 CYS Chi-restraints excluded: chain J residue 291 LEU Chi-restraints excluded: chain J residue 336 VAL Chi-restraints excluded: chain J residue 354 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 465 ASP Chi-restraints excluded: chain K residue 6 ASN Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain K residue 156 ILE Chi-restraints excluded: chain K residue 209 ASP Chi-restraints excluded: chain K residue 228 ASP Chi-restraints excluded: chain K residue 297 THR Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 342 GLN Chi-restraints excluded: chain K residue 405 LYS Chi-restraints excluded: chain K residue 424 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 439 THR Chi-restraints excluded: chain M residue 152 THR Chi-restraints excluded: chain M residue 155 MET Chi-restraints excluded: chain M residue 276 LEU Chi-restraints excluded: chain N residue 102 TRP Chi-restraints excluded: chain N residue 313 THR Chi-restraints excluded: chain O residue 236 LEU Chi-restraints excluded: chain P residue 127 LEU Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain P residue 166 ILE Chi-restraints excluded: chain P residue 178 VAL Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 252 ASP Chi-restraints excluded: chain R residue 11 ASP Chi-restraints excluded: chain R residue 15 LYS Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 244 LEU Chi-restraints excluded: chain S residue 245 ILE Chi-restraints excluded: chain T residue 6 LEU Chi-restraints excluded: chain T residue 236 LEU Chi-restraints excluded: chain V residue 127 LEU Chi-restraints excluded: chain V residue 246 GLU Chi-restraints excluded: chain V residue 256 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 855 random chunks: chunk 634 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 766 optimal weight: 10.0000 chunk 258 optimal weight: 30.0000 chunk 474 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 chunk 141 optimal weight: 10.0000 chunk 110 optimal weight: 0.6980 chunk 472 optimal weight: 7.9990 chunk 834 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 overall best weight: 6.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS B 303 ASN C 18 HIS C 23 HIS C 74 ASN C 269 ASN C 333 ASN ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN D 214 GLN ** D 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN ** E 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 GLN ** F 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN ** H 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 23 HIS J 460 ASN ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN L 23 HIS L 220 ASN ** L 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 124 GLN N 10 ASN N 43 ASN O 43 ASN O 248 ASN ** P 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 GLN S 247 GLN ** S 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 43 ASN ** U 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 247 GLN ** V 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.085133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.069886 restraints weight = 245288.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.072004 restraints weight = 142105.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.073501 restraints weight = 97450.709| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 68177 Z= 0.277 Angle : 0.649 8.984 92470 Z= 0.339 Chirality : 0.043 0.237 10048 Planarity : 0.004 0.076 12237 Dihedral : 4.808 66.276 9266 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.11 % Allowed : 16.54 % Favored : 80.35 % 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: -0.21 (0.09), residues: 8507 helix: 1.19 (0.09), residues: 3164 sheet: -0.51 (0.13), residues: 1604 loop : -1.09 (0.10), residues: 3739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP M 12 HIS 0.007 0.001 HIS H 299 PHE 0.029 0.002 PHE H 399 TYR 0.022 0.001 TYR S 268 ARG 0.010 0.001 ARG P 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17014 Ramachandran restraints generated. 8507 Oldfield, 0 Emsley, 8507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17014 Ramachandran restraints generated. 8507 Oldfield, 0 Emsley, 8507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1888 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 1671 time to evaluate : 5.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 HIS cc_start: 0.9156 (m90) cc_final: 0.8545 (m-70) REVERT: A 29 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8586 (tm-30) REVERT: A 32 ARG cc_start: 0.8376 (ttp80) cc_final: 0.8171 (ttp80) REVERT: A 60 LYS cc_start: 0.9610 (mmtt) cc_final: 0.9113 (mtmm) REVERT: A 74 ASN cc_start: 0.9442 (t0) cc_final: 0.8913 (t0) REVERT: A 162 GLU cc_start: 0.9249 (mt-10) cc_final: 0.9037 (mp0) REVERT: A 163 ASP cc_start: 0.9114 (m-30) cc_final: 0.8511 (t0) REVERT: A 241 ASP cc_start: 0.8298 (p0) cc_final: 0.7929 (p0) REVERT: A 251 LYS cc_start: 0.9153 (ttpp) cc_final: 0.8861 (ttpp) REVERT: A 346 GLN cc_start: 0.9172 (mt0) cc_final: 0.8762 (mp10) REVERT: A 380 ARG cc_start: 0.9146 (mtm-85) cc_final: 0.8683 (mtm-85) REVERT: A 419 MET cc_start: 0.8258 (ppp) cc_final: 0.6650 (ppp) REVERT: A 458 MET cc_start: 0.7978 (ttm) cc_final: 0.7676 (tpt) REVERT: A 460 ASN cc_start: 0.8844 (m110) cc_final: 0.8423 (m110) REVERT: B 9 TYR cc_start: 0.8350 (p90) cc_final: 0.7883 (p90) REVERT: B 17 MET cc_start: 0.9003 (mmm) cc_final: 0.8625 (mmm) REVERT: B 18 HIS cc_start: 0.8185 (p-80) cc_final: 0.7973 (p-80) REVERT: B 64 GLU cc_start: 0.8629 (pt0) cc_final: 0.8387 (pt0) REVERT: B 103 ASP cc_start: 0.8975 (p0) cc_final: 0.8567 (p0) REVERT: B 219 GLU cc_start: 0.8239 (pt0) cc_final: 0.7919 (pt0) REVERT: B 267 GLU cc_start: 0.9096 (tt0) cc_final: 0.8793 (pt0) REVERT: B 296 LEU cc_start: 0.8990 (tp) cc_final: 0.8767 (tp) REVERT: B 331 GLU cc_start: 0.8517 (pm20) cc_final: 0.8257 (pm20) REVERT: B 344 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8422 (mt-10) REVERT: B 383 LYS cc_start: 0.9400 (ttmm) cc_final: 0.9106 (ttpt) REVERT: B 398 MET cc_start: 0.9389 (mtm) cc_final: 0.8665 (mpp) REVERT: B 419 MET cc_start: 0.8942 (ptm) cc_final: 0.8018 (ptm) REVERT: B 441 MET cc_start: 0.9347 (tmm) cc_final: 0.9079 (tmm) REVERT: B 460 ASN cc_start: 0.9462 (m110) cc_final: 0.9245 (m-40) REVERT: C 19 LYS cc_start: 0.9182 (tppt) cc_final: 0.8700 (tppt) REVERT: C 26 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8442 (ttm) REVERT: C 37 ASN cc_start: 0.9327 (m-40) cc_final: 0.8928 (m110) REVERT: C 46 ASP cc_start: 0.8243 (t0) cc_final: 0.7587 (t0) REVERT: C 74 ASN cc_start: 0.9572 (OUTLIER) cc_final: 0.9284 (t0) REVERT: C 105 ASP cc_start: 0.9183 (p0) cc_final: 0.8780 (p0) REVERT: C 176 LYS cc_start: 0.8925 (tppp) cc_final: 0.8444 (tppt) REVERT: C 280 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7496 (mt-10) REVERT: C 285 ILE cc_start: 0.9368 (mm) cc_final: 0.9145 (mt) REVERT: C 296 LEU cc_start: 0.8954 (tp) cc_final: 0.8730 (tp) REVERT: C 369 MET cc_start: 0.8688 (mpp) cc_final: 0.8302 (mpp) REVERT: C 398 MET cc_start: 0.9091 (mtm) cc_final: 0.8375 (mpp) REVERT: C 413 ASP cc_start: 0.8615 (t0) cc_final: 0.8139 (t0) REVERT: C 458 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7570 (ttt) REVERT: D 8 LYS cc_start: 0.9740 (mtmm) cc_final: 0.9536 (mtmm) REVERT: D 15 LYS cc_start: 0.9312 (mttt) cc_final: 0.8938 (mtmm) REVERT: D 16 LYS cc_start: 0.8975 (mppt) cc_final: 0.8769 (mppt) REVERT: D 17 MET cc_start: 0.9338 (mmm) cc_final: 0.7741 (tpp) REVERT: D 36 ASP cc_start: 0.9466 (m-30) cc_final: 0.9121 (m-30) REVERT: D 46 ASP cc_start: 0.8209 (t0) cc_final: 0.7838 (t0) REVERT: D 49 LYS cc_start: 0.9122 (ptmm) cc_final: 0.8817 (pttp) REVERT: D 54 GLU cc_start: 0.8944 (tp30) cc_final: 0.8578 (tp30) REVERT: D 89 VAL cc_start: 0.9376 (t) cc_final: 0.8940 (p) REVERT: D 120 GLU cc_start: 0.9501 (tt0) cc_final: 0.9214 (mt-10) REVERT: D 121 ASP cc_start: 0.9363 (OUTLIER) cc_final: 0.9051 (t70) REVERT: D 173 ASN cc_start: 0.8752 (m-40) cc_final: 0.8417 (p0) REVERT: D 251 LYS cc_start: 0.8967 (mptt) cc_final: 0.8740 (mptt) REVERT: D 337 LYS cc_start: 0.9372 (tptm) cc_final: 0.8981 (tptm) REVERT: D 341 ASP cc_start: 0.9248 (m-30) cc_final: 0.8747 (m-30) REVERT: D 347 MET cc_start: 0.9154 (mtt) cc_final: 0.8933 (mmt) REVERT: D 374 GLN cc_start: 0.9273 (mt0) cc_final: 0.8780 (mp10) REVERT: D 380 ARG cc_start: 0.8923 (ttp-110) cc_final: 0.8663 (ttp-110) REVERT: D 398 MET cc_start: 0.8980 (mtt) cc_final: 0.8750 (mtt) REVERT: D 409 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8100 (tm-30) REVERT: D 422 GLU cc_start: 0.9205 (tp30) cc_final: 0.8917 (tp30) REVERT: D 441 MET cc_start: 0.9465 (tmm) cc_final: 0.9102 (ppp) REVERT: D 457 ASP cc_start: 0.9404 (m-30) cc_final: 0.9174 (p0) REVERT: D 458 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.7217 (tpt) REVERT: E 42 VAL cc_start: 0.9678 (t) cc_final: 0.9476 (p) REVERT: E 74 ASN cc_start: 0.8921 (t0) cc_final: 0.8585 (t0) REVERT: E 121 ASP cc_start: 0.9370 (m-30) cc_final: 0.9166 (m-30) REVERT: E 163 ASP cc_start: 0.8770 (m-30) cc_final: 0.7894 (t0) REVERT: E 184 ARG cc_start: 0.9057 (ttp80) cc_final: 0.8481 (ttp80) REVERT: E 219 GLU cc_start: 0.7696 (pp20) cc_final: 0.7459 (pp20) REVERT: E 259 MET cc_start: 0.8901 (mmm) cc_final: 0.8606 (mmm) REVERT: E 315 ASP cc_start: 0.8560 (m-30) cc_final: 0.8174 (m-30) REVERT: E 370 GLU cc_start: 0.8141 (pm20) cc_final: 0.7713 (pm20) REVERT: E 419 MET cc_start: 0.8252 (ttm) cc_final: 0.7628 (ttm) REVERT: E 443 TRP cc_start: 0.8983 (t60) cc_final: 0.8349 (t60) REVERT: E 460 ASN cc_start: 0.9044 (m-40) cc_final: 0.8737 (m110) REVERT: F 18 HIS cc_start: 0.8800 (m90) cc_final: 0.7955 (m90) REVERT: F 26 MET cc_start: 0.9399 (mtp) cc_final: 0.9122 (ttt) REVERT: F 54 GLU cc_start: 0.9516 (tt0) cc_final: 0.9302 (tm-30) REVERT: F 83 ILE cc_start: 0.9565 (OUTLIER) cc_final: 0.9357 (mp) REVERT: F 99 MET cc_start: 0.9288 (pmm) cc_final: 0.9026 (pmm) REVERT: F 163 ASP cc_start: 0.9200 (m-30) cc_final: 0.8502 (m-30) REVERT: F 177 ARG cc_start: 0.9260 (mmm-85) cc_final: 0.8941 (mmm-85) REVERT: F 184 ARG cc_start: 0.9246 (ttp-110) cc_final: 0.8792 (ttp80) REVERT: F 357 SER cc_start: 0.8612 (m) cc_final: 0.8293 (p) REVERT: F 370 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8540 (mt-10) REVERT: F 374 GLN cc_start: 0.9461 (mt0) cc_final: 0.9147 (mt0) REVERT: F 413 ASP cc_start: 0.8803 (m-30) cc_final: 0.8498 (t70) REVERT: F 423 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8872 (mt-10) REVERT: F 460 ASN cc_start: 0.8509 (m-40) cc_final: 0.8195 (m110) REVERT: G 32 ARG cc_start: 0.7701 (tpp-160) cc_final: 0.7333 (tpp-160) REVERT: G 99 MET cc_start: 0.9157 (ppp) cc_final: 0.8931 (tmm) REVERT: G 103 ASP cc_start: 0.8756 (OUTLIER) cc_final: 0.8553 (p0) REVERT: G 124 SER cc_start: 0.9579 (OUTLIER) cc_final: 0.9290 (p) REVERT: G 335 MET cc_start: 0.9053 (ttt) cc_final: 0.8791 (ttp) REVERT: G 347 MET cc_start: 0.9014 (mmm) cc_final: 0.8569 (mpp) REVERT: G 460 ASN cc_start: 0.8941 (m-40) cc_final: 0.8481 (m110) REVERT: H 17 MET cc_start: 0.9552 (mmm) cc_final: 0.9134 (mmm) REVERT: H 26 MET cc_start: 0.9211 (mtm) cc_final: 0.8992 (mtm) REVERT: H 77 ASP cc_start: 0.9291 (m-30) cc_final: 0.9061 (m-30) REVERT: H 79 MET cc_start: 0.9071 (mmt) cc_final: 0.8632 (mmp) REVERT: H 185 GLU cc_start: 0.8585 (tm-30) cc_final: 0.7978 (tm-30) REVERT: H 200 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8128 (mp0) REVERT: H 326 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7582 (pm20) REVERT: H 347 MET cc_start: 0.9358 (mtm) cc_final: 0.8894 (mtt) REVERT: H 380 ARG cc_start: 0.8743 (mtm-85) cc_final: 0.7875 (mtm-85) REVERT: H 409 GLU cc_start: 0.8255 (mp0) cc_final: 0.7900 (mp0) REVERT: H 461 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7771 (pp20) REVERT: I 16 LYS cc_start: 0.9263 (mmtm) cc_final: 0.8804 (mmtm) REVERT: I 79 MET cc_start: 0.9342 (mtm) cc_final: 0.8874 (mtm) REVERT: I 219 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8258 (tp30) REVERT: I 227 ASP cc_start: 0.9019 (m-30) cc_final: 0.8776 (m-30) REVERT: I 262 MET cc_start: 0.8629 (mmm) cc_final: 0.8296 (mmm) REVERT: I 280 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8779 (mm-30) REVERT: I 335 MET cc_start: 0.9369 (ttt) cc_final: 0.8868 (tmm) REVERT: I 344 GLU cc_start: 0.8963 (tt0) cc_final: 0.8630 (tp30) REVERT: I 347 MET cc_start: 0.9465 (mtp) cc_final: 0.9128 (mtp) REVERT: I 409 GLU cc_start: 0.8264 (pm20) cc_final: 0.7683 (pm20) REVERT: I 441 MET cc_start: 0.9130 (ppp) cc_final: 0.8929 (ppp) REVERT: J 46 ASP cc_start: 0.8343 (t0) cc_final: 0.7848 (t0) REVERT: J 79 MET cc_start: 0.9305 (OUTLIER) cc_final: 0.9099 (mpp) REVERT: J 120 GLU cc_start: 0.9433 (pp20) cc_final: 0.9094 (pp20) REVERT: J 227 ASP cc_start: 0.8760 (p0) cc_final: 0.8483 (p0) REVERT: J 251 LYS cc_start: 0.9287 (mttp) cc_final: 0.9064 (mttt) REVERT: J 267 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8580 (mm-30) REVERT: J 342 GLN cc_start: 0.9569 (tt0) cc_final: 0.8422 (tm-30) REVERT: J 345 ARG cc_start: 0.8458 (ttp80) cc_final: 0.7570 (ttp80) REVERT: J 346 GLN cc_start: 0.9212 (mt0) cc_final: 0.7770 (mt0) REVERT: J 419 MET cc_start: 0.7137 (ttm) cc_final: 0.6918 (ttm) REVERT: K 26 MET cc_start: 0.9138 (mmm) cc_final: 0.8786 (mmm) REVERT: K 28 MET cc_start: 0.8912 (tpp) cc_final: 0.8597 (tpp) REVERT: K 60 LYS cc_start: 0.9529 (mmmm) cc_final: 0.9261 (tppt) REVERT: K 64 GLU cc_start: 0.9137 (mm-30) cc_final: 0.8820 (mm-30) REVERT: K 225 TYR cc_start: 0.7370 (m-80) cc_final: 0.7037 (m-80) REVERT: K 275 ASN cc_start: 0.9473 (m110) cc_final: 0.8999 (m110) REVERT: K 343 LYS cc_start: 0.9592 (mppt) cc_final: 0.9008 (mttt) REVERT: K 345 ARG cc_start: 0.8301 (tmm-80) cc_final: 0.7900 (ttp80) REVERT: K 347 MET cc_start: 0.9018 (mtt) cc_final: 0.8746 (mmm) REVERT: K 398 MET cc_start: 0.8939 (mtt) cc_final: 0.8705 (mtt) REVERT: K 409 GLU cc_start: 0.8327 (tm-30) cc_final: 0.8109 (tm-30) REVERT: K 418 LYS cc_start: 0.7989 (mtmt) cc_final: 0.7349 (mtmt) REVERT: K 422 GLU cc_start: 0.9356 (OUTLIER) cc_final: 0.9081 (tp30) REVERT: K 460 ASN cc_start: 0.9198 (m-40) cc_final: 0.8847 (m110) REVERT: L 15 LYS cc_start: 0.9724 (mmmm) cc_final: 0.9473 (mmmm) REVERT: L 17 MET cc_start: 0.9437 (tpp) cc_final: 0.9234 (mmm) REVERT: L 77 ASP cc_start: 0.8760 (m-30) cc_final: 0.8458 (m-30) REVERT: L 109 LEU cc_start: 0.9466 (tp) cc_final: 0.9060 (tt) REVERT: L 219 GLU cc_start: 0.7453 (pt0) cc_final: 0.7031 (pt0) REVERT: L 221 ASP cc_start: 0.8265 (p0) cc_final: 0.7471 (p0) REVERT: L 239 GLN cc_start: 0.9280 (pm20) cc_final: 0.9015 (pm20) REVERT: L 259 MET cc_start: 0.9108 (mmm) cc_final: 0.8827 (mmm) REVERT: L 322 ASN cc_start: 0.9357 (m-40) cc_final: 0.9109 (m-40) REVERT: L 342 GLN cc_start: 0.9310 (OUTLIER) cc_final: 0.8676 (tt0) REVERT: L 345 ARG cc_start: 0.9395 (tmm-80) cc_final: 0.8838 (tmm-80) REVERT: L 354 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7627 (pp) REVERT: L 369 MET cc_start: 0.8810 (mtm) cc_final: 0.8427 (mpp) REVERT: L 452 TYR cc_start: 0.9327 (p90) cc_final: 0.8688 (p90) REVERT: M 173 ASP cc_start: 0.9023 (m-30) cc_final: 0.8548 (t0) REVERT: M 207 ARG cc_start: 0.8991 (tpp80) cc_final: 0.8734 (tpp80) REVERT: N 24 GLN cc_start: 0.8191 (tm-30) cc_final: 0.7893 (tm-30) REVERT: N 123 MET cc_start: 0.9156 (mmm) cc_final: 0.8943 (mmm) REVERT: N 190 ASN cc_start: 0.9560 (OUTLIER) cc_final: 0.9297 (t0) REVERT: N 261 LYS cc_start: 0.8503 (pttm) cc_final: 0.8165 (pttm) REVERT: O 28 PHE cc_start: 0.9221 (m-10) cc_final: 0.8894 (m-10) REVERT: O 99 MET cc_start: 0.5430 (ppp) cc_final: 0.5013 (ppp) REVERT: O 121 ASP cc_start: 0.8656 (t0) cc_final: 0.8246 (t0) REVERT: O 124 GLN cc_start: 0.9515 (tt0) cc_final: 0.9096 (tt0) REVERT: O 207 ARG cc_start: 0.8795 (mmm-85) cc_final: 0.8454 (mmm-85) REVERT: O 247 GLN cc_start: 0.9082 (mt0) cc_final: 0.8669 (pt0) REVERT: P 22 ASP cc_start: 0.8840 (p0) cc_final: 0.8426 (p0) REVERT: P 290 LYS cc_start: 0.8988 (mmmm) cc_final: 0.8571 (mmmm) REVERT: Q 39 ARG cc_start: 0.8293 (mtm110) cc_final: 0.8018 (mtm110) REVERT: Q 125 ASP cc_start: 0.8938 (t0) cc_final: 0.8565 (t0) REVERT: Q 271 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7431 (mt-10) REVERT: Q 290 LYS cc_start: 0.9173 (mmmm) cc_final: 0.8957 (mmmm) REVERT: Q 321 LYS cc_start: 0.9110 (ptmt) cc_final: 0.8899 (ptmm) REVERT: R 15 LYS cc_start: 0.6785 (OUTLIER) cc_final: 0.5737 (pttm) REVERT: S 105 LYS cc_start: 0.9389 (mtpt) cc_final: 0.9156 (mmmm) REVERT: T 39 ARG cc_start: 0.7935 (ptm160) cc_final: 0.7626 (ptm160) REVERT: T 126 MET cc_start: 0.9134 (mtm) cc_final: 0.8682 (mtm) REVERT: T 170 ARG cc_start: 0.8944 (ttp-110) cc_final: 0.8321 (ttp80) REVERT: T 187 LEU cc_start: 0.9456 (tp) cc_final: 0.9198 (tp) REVERT: T 246 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7531 (mt-10) REVERT: U 64 ASP cc_start: 0.9068 (t0) cc_final: 0.8821 (t0) REVERT: U 114 ILE cc_start: 0.9734 (mt) cc_final: 0.9441 (tt) REVERT: U 207 ARG cc_start: 0.9205 (mmm-85) cc_final: 0.8946 (mmm-85) REVERT: V 188 TYR cc_start: 0.9152 (m-80) cc_final: 0.8824 (m-80) REVERT: V 247 GLN cc_start: 0.9175 (mt0) cc_final: 0.8869 (mm-40) outliers start: 217 outliers final: 136 residues processed: 1781 average time/residue: 0.6580 time to fit residues: 1974.7743 Evaluate side-chains 1674 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 1523 time to evaluate : 5.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 26 MET Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 413 ASP Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 264 ASP Chi-restraints excluded: chain F residue 299 HIS Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 420 SER Chi-restraints excluded: chain F residue 454 GLU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 103 ASP Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 256 THR Chi-restraints excluded: chain G residue 286 CYS Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 374 GLN Chi-restraints excluded: chain G residue 436 ILE Chi-restraints excluded: chain H residue 8 LYS Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 216 THR Chi-restraints excluded: chain H residue 286 CYS Chi-restraints excluded: chain H residue 290 THR Chi-restraints excluded: chain H residue 326 GLU Chi-restraints excluded: chain H residue 342 GLN Chi-restraints excluded: chain H residue 354 LEU Chi-restraints excluded: chain H residue 419 MET Chi-restraints excluded: chain H residue 458 MET Chi-restraints excluded: chain I residue 63 ILE Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 286 CYS Chi-restraints excluded: chain I residue 290 THR Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 336 VAL Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain J residue 79 MET Chi-restraints excluded: chain J residue 121 ASP Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 236 ASP Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 299 HIS Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 336 VAL Chi-restraints excluded: chain J residue 350 LEU Chi-restraints excluded: chain J residue 354 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain K residue 6 ASN Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 209 ASP Chi-restraints excluded: chain K residue 285 ILE Chi-restraints excluded: chain K residue 290 THR Chi-restraints excluded: chain K residue 297 THR Chi-restraints excluded: chain K residue 304 VAL Chi-restraints excluded: chain K residue 342 GLN Chi-restraints excluded: chain K residue 405 LYS Chi-restraints excluded: chain K residue 422 GLU Chi-restraints excluded: chain K residue 424 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 164 ILE Chi-restraints excluded: chain L residue 342 GLN Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 377 VAL Chi-restraints excluded: chain L residue 439 THR Chi-restraints excluded: chain M residue 152 THR Chi-restraints excluded: chain M residue 312 ASP Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 102 TRP Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain N residue 156 THR Chi-restraints excluded: chain N residue 178 VAL Chi-restraints excluded: chain N residue 190 ASN Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 313 THR Chi-restraints excluded: chain O residue 187 LEU Chi-restraints excluded: chain P residue 127 LEU Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain P residue 166 ILE Chi-restraints excluded: chain P residue 216 ILE Chi-restraints excluded: chain P residue 276 LEU Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain R residue 11 ASP Chi-restraints excluded: chain R residue 15 LYS Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain R residue 311 LYS Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain S residue 244 LEU Chi-restraints excluded: chain S residue 245 ILE Chi-restraints excluded: chain T residue 6 LEU Chi-restraints excluded: chain U residue 59 LEU Chi-restraints excluded: chain V residue 127 LEU Chi-restraints excluded: chain V residue 256 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 855 random chunks: chunk 781 optimal weight: 0.0270 chunk 665 optimal weight: 10.0000 chunk 467 optimal weight: 5.9990 chunk 809 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 845 optimal weight: 20.0000 chunk 317 optimal weight: 9.9990 chunk 557 optimal weight: 2.9990 chunk 666 optimal weight: 20.0000 chunk 365 optimal weight: 30.0000 chunk 553 optimal weight: 20.0000 overall best weight: 4.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 GLN B 166 ASN ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN D 102 ASN ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 333 ASN ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN ** E 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 ASN F 74 ASN ** F 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 322 ASN ** F 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 299 HIS ** G 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN ** H 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 460 ASN J 460 ASN ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 23 HIS L 342 GLN ** L 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 43 ASN O 248 ASN ** P 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 108 GLN R 43 ASN ** R 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 262 GLN ** S 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 43 ASN ** U 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 248 ASN ** V 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.085279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.070029 restraints weight = 244943.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.072158 restraints weight = 141794.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.073632 restraints weight = 97451.302| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 68177 Z= 0.235 Angle : 0.635 9.185 92470 Z= 0.328 Chirality : 0.042 0.199 10048 Planarity : 0.004 0.075 12237 Dihedral : 4.750 65.390 9264 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.15 % Favored : 95.84 % Rotamer: Outliers : 3.42 % Allowed : 18.14 % Favored : 78.43 % 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: -0.15 (0.09), residues: 8507 helix: 1.21 (0.09), residues: 3172 sheet: -0.44 (0.13), residues: 1593 loop : -1.06 (0.10), residues: 3742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP P 102 HIS 0.009 0.001 HIS G 299 PHE 0.019 0.001 PHE K 183 TYR 0.025 0.001 TYR S 268 ARG 0.008 0.001 ARG P 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17014 Ramachandran restraints generated. 8507 Oldfield, 0 Emsley, 8507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17014 Ramachandran restraints generated. 8507 Oldfield, 0 Emsley, 8507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1886 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 239 poor density : 1647 time to evaluate : 5.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 18 HIS cc_start: 0.9220 (m90) cc_final: 0.8546 (m-70) REVERT: A 29 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8576 (tm-30) REVERT: A 32 ARG cc_start: 0.8401 (ttp80) cc_final: 0.8122 (ttp80) REVERT: A 60 LYS cc_start: 0.9531 (mmtt) cc_final: 0.9319 (mttt) REVERT: A 162 GLU cc_start: 0.9256 (OUTLIER) cc_final: 0.9028 (mp0) REVERT: A 163 ASP cc_start: 0.9193 (m-30) cc_final: 0.8680 (t0) REVERT: A 198 LYS cc_start: 0.9306 (mmmt) cc_final: 0.8922 (mmmt) REVERT: A 241 ASP cc_start: 0.8443 (p0) cc_final: 0.8021 (p0) REVERT: A 251 LYS cc_start: 0.9174 (ttpp) cc_final: 0.8954 (ttpp) REVERT: A 342 GLN cc_start: 0.9239 (mt0) cc_final: 0.8898 (tt0) REVERT: A 346 GLN cc_start: 0.9121 (mt0) cc_final: 0.8743 (mp10) REVERT: A 369 MET cc_start: 0.8814 (mtm) cc_final: 0.8401 (ptp) REVERT: A 419 MET cc_start: 0.8478 (ppp) cc_final: 0.7992 (ppp) REVERT: A 423 GLU cc_start: 0.9201 (tt0) cc_final: 0.8853 (pt0) REVERT: A 458 MET cc_start: 0.7885 (ttm) cc_final: 0.7674 (tpt) REVERT: A 460 ASN cc_start: 0.8817 (m110) cc_final: 0.8413 (m110) REVERT: B 9 TYR cc_start: 0.8358 (p90) cc_final: 0.7889 (p90) REVERT: B 17 MET cc_start: 0.9067 (mmm) cc_final: 0.8780 (mmm) REVERT: B 18 HIS cc_start: 0.8221 (p-80) cc_final: 0.7954 (p-80) REVERT: B 64 GLU cc_start: 0.8636 (pt0) cc_final: 0.8369 (pt0) REVERT: B 103 ASP cc_start: 0.8972 (p0) cc_final: 0.8414 (p0) REVERT: B 188 ASP cc_start: 0.8254 (t0) cc_final: 0.7969 (t0) REVERT: B 219 GLU cc_start: 0.8247 (pt0) cc_final: 0.7842 (pt0) REVERT: B 267 GLU cc_start: 0.9187 (tt0) cc_final: 0.8809 (pt0) REVERT: B 296 LEU cc_start: 0.9053 (tp) cc_final: 0.8781 (tp) REVERT: B 340 MET cc_start: 0.8968 (mmm) cc_final: 0.8399 (mmm) REVERT: B 344 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8428 (mt-10) REVERT: B 383 LYS cc_start: 0.9405 (ttmm) cc_final: 0.9109 (ttpt) REVERT: B 398 MET cc_start: 0.9402 (mtm) cc_final: 0.8772 (mpp) REVERT: B 418 LYS cc_start: 0.8848 (mttt) cc_final: 0.8611 (mttt) REVERT: B 423 GLU cc_start: 0.9344 (pt0) cc_final: 0.9132 (pt0) REVERT: B 441 MET cc_start: 0.9314 (tmm) cc_final: 0.9024 (tmm) REVERT: B 460 ASN cc_start: 0.9435 (m110) cc_final: 0.9217 (m-40) REVERT: C 19 LYS cc_start: 0.9189 (tppt) cc_final: 0.8978 (tppt) REVERT: C 26 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8473 (ttm) REVERT: C 37 ASN cc_start: 0.9309 (m-40) cc_final: 0.8898 (m110) REVERT: C 46 ASP cc_start: 0.8241 (t0) cc_final: 0.7583 (t0) REVERT: C 77 ASP cc_start: 0.9225 (m-30) cc_final: 0.8955 (t70) REVERT: C 105 ASP cc_start: 0.9176 (p0) cc_final: 0.8927 (p0) REVERT: C 176 LYS cc_start: 0.8885 (tppp) cc_final: 0.8510 (tppt) REVERT: C 259 MET cc_start: 0.7836 (mtp) cc_final: 0.7467 (ttp) REVERT: C 296 LEU cc_start: 0.8956 (tp) cc_final: 0.8737 (tp) REVERT: C 314 ARG cc_start: 0.8789 (mmt90) cc_final: 0.8193 (tpm170) REVERT: C 335 MET cc_start: 0.8514 (tmm) cc_final: 0.8287 (tmm) REVERT: C 369 MET cc_start: 0.8565 (mpp) cc_final: 0.8114 (mpp) REVERT: C 413 ASP cc_start: 0.8550 (t0) cc_final: 0.8107 (t0) REVERT: C 423 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8615 (mt-10) REVERT: C 441 MET cc_start: 0.9101 (tmm) cc_final: 0.8711 (ppp) REVERT: C 453 LEU cc_start: 0.9590 (mt) cc_final: 0.9119 (pp) REVERT: C 458 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7132 (ttt) REVERT: D 8 LYS cc_start: 0.9626 (mtmm) cc_final: 0.9425 (mttp) REVERT: D 15 LYS cc_start: 0.9284 (mttt) cc_final: 0.8877 (mtmm) REVERT: D 17 MET cc_start: 0.9399 (mmm) cc_final: 0.7878 (tpp) REVERT: D 18 HIS cc_start: 0.9539 (m90) cc_final: 0.8439 (m90) REVERT: D 46 ASP cc_start: 0.8296 (t0) cc_final: 0.7952 (t0) REVERT: D 49 LYS cc_start: 0.9038 (ptmm) cc_final: 0.8755 (pttp) REVERT: D 54 GLU cc_start: 0.8937 (tp30) cc_final: 0.8580 (tp30) REVERT: D 89 VAL cc_start: 0.9460 (t) cc_final: 0.8938 (p) REVERT: D 97 PHE cc_start: 0.9306 (m-10) cc_final: 0.8968 (m-10) REVERT: D 120 GLU cc_start: 0.9433 (tt0) cc_final: 0.9191 (mt-10) REVERT: D 121 ASP cc_start: 0.9358 (OUTLIER) cc_final: 0.9049 (t70) REVERT: D 173 ASN cc_start: 0.8750 (m-40) cc_final: 0.8403 (p0) REVERT: D 184 ARG cc_start: 0.9063 (ttp80) cc_final: 0.6796 (ttp80) REVERT: D 185 GLU cc_start: 0.7547 (tm-30) cc_final: 0.6972 (tm-30) REVERT: D 217 TRP cc_start: 0.8750 (m-10) cc_final: 0.8526 (m-10) REVERT: D 241 ASP cc_start: 0.8587 (t0) cc_final: 0.8260 (t0) REVERT: D 251 LYS cc_start: 0.9019 (mptt) cc_final: 0.8642 (mmtp) REVERT: D 278 ASP cc_start: 0.9108 (t0) cc_final: 0.8835 (t0) REVERT: D 288 GLN cc_start: 0.8277 (mm-40) cc_final: 0.8048 (mm-40) REVERT: D 337 LYS cc_start: 0.9383 (tptm) cc_final: 0.8889 (tptm) REVERT: D 341 ASP cc_start: 0.9242 (m-30) cc_final: 0.8796 (m-30) REVERT: D 369 MET cc_start: 0.8638 (mpp) cc_final: 0.8223 (mpp) REVERT: D 374 GLN cc_start: 0.9269 (mt0) cc_final: 0.8770 (mp10) REVERT: D 380 ARG cc_start: 0.9012 (ttp-110) cc_final: 0.8737 (ttp-110) REVERT: D 398 MET cc_start: 0.9094 (mtt) cc_final: 0.8708 (mtt) REVERT: D 409 GLU cc_start: 0.8745 (tm-30) cc_final: 0.7818 (tm-30) REVERT: D 411 ASN cc_start: 0.8569 (t0) cc_final: 0.8324 (t0) REVERT: D 413 ASP cc_start: 0.8647 (t0) cc_final: 0.8343 (t0) REVERT: D 422 GLU cc_start: 0.9239 (tp30) cc_final: 0.8903 (tp30) REVERT: D 457 ASP cc_start: 0.9424 (m-30) cc_final: 0.9210 (p0) REVERT: D 458 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7032 (tpt) REVERT: E 64 GLU cc_start: 0.8100 (pp20) cc_final: 0.7894 (pp20) REVERT: E 74 ASN cc_start: 0.8937 (t0) cc_final: 0.8650 (t0) REVERT: E 162 GLU cc_start: 0.8827 (mp0) cc_final: 0.8612 (mm-30) REVERT: E 163 ASP cc_start: 0.8799 (OUTLIER) cc_final: 0.7935 (t0) REVERT: E 184 ARG cc_start: 0.9052 (ttp80) cc_final: 0.8483 (ttp80) REVERT: E 259 MET cc_start: 0.8900 (mmm) cc_final: 0.8605 (mmm) REVERT: E 314 ARG cc_start: 0.4165 (tpm170) cc_final: 0.3730 (tpm170) REVERT: E 338 GLU cc_start: 0.9049 (tt0) cc_final: 0.8787 (tt0) REVERT: E 340 MET cc_start: 0.9447 (OUTLIER) cc_final: 0.9169 (tpp) REVERT: E 370 GLU cc_start: 0.8231 (pm20) cc_final: 0.7749 (pm20) REVERT: E 399 PHE cc_start: 0.9377 (m-80) cc_final: 0.8961 (t80) REVERT: E 419 MET cc_start: 0.8149 (ttm) cc_final: 0.7503 (ttm) REVERT: E 441 MET cc_start: 0.9194 (tmm) cc_final: 0.8940 (tmm) REVERT: E 443 TRP cc_start: 0.8993 (t60) cc_final: 0.8448 (t60) REVERT: E 458 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7568 (tpp) REVERT: E 460 ASN cc_start: 0.9153 (m-40) cc_final: 0.8857 (m110) REVERT: F 54 GLU cc_start: 0.9532 (tt0) cc_final: 0.9318 (tm-30) REVERT: F 79 MET cc_start: 0.9198 (mtm) cc_final: 0.8913 (mtm) REVERT: F 83 ILE cc_start: 0.9544 (OUTLIER) cc_final: 0.9310 (mp) REVERT: F 163 ASP cc_start: 0.9211 (m-30) cc_final: 0.8634 (m-30) REVERT: F 177 ARG cc_start: 0.9252 (mmm-85) cc_final: 0.8900 (mmm-85) REVERT: F 184 ARG cc_start: 0.9255 (ttp-110) cc_final: 0.8687 (ttp80) REVERT: F 315 ASP cc_start: 0.8458 (m-30) cc_final: 0.7676 (p0) REVERT: F 340 MET cc_start: 0.9153 (mmm) cc_final: 0.8833 (mmm) REVERT: F 342 GLN cc_start: 0.9458 (pt0) cc_final: 0.8852 (pp30) REVERT: F 343 LYS cc_start: 0.9405 (ttmm) cc_final: 0.9137 (ttmt) REVERT: F 347 MET cc_start: 0.9333 (mmm) cc_final: 0.8577 (mtm) REVERT: F 357 SER cc_start: 0.8567 (m) cc_final: 0.8250 (p) REVERT: F 370 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8387 (mt-10) REVERT: F 413 ASP cc_start: 0.8785 (m-30) cc_final: 0.8420 (t70) REVERT: F 460 ASN cc_start: 0.8833 (m-40) cc_final: 0.8420 (m110) REVERT: G 32 ARG cc_start: 0.7583 (tpp-160) cc_final: 0.7171 (tpp-160) REVERT: G 99 MET cc_start: 0.9168 (ppp) cc_final: 0.8941 (tmm) REVERT: G 124 SER cc_start: 0.9620 (OUTLIER) cc_final: 0.9298 (p) REVERT: G 163 ASP cc_start: 0.9426 (m-30) cc_final: 0.9100 (t0) REVERT: G 283 CYS cc_start: 0.8863 (m) cc_final: 0.8636 (m) REVERT: G 335 MET cc_start: 0.9000 (ttt) cc_final: 0.8649 (ttp) REVERT: G 347 MET cc_start: 0.8960 (mmm) cc_final: 0.8560 (mpp) REVERT: G 460 ASN cc_start: 0.8950 (m-40) cc_final: 0.8512 (m110) REVERT: H 17 MET cc_start: 0.9570 (mmm) cc_final: 0.9144 (mmm) REVERT: H 26 MET cc_start: 0.9190 (mtm) cc_final: 0.8558 (mtm) REVERT: H 77 ASP cc_start: 0.9310 (m-30) cc_final: 0.9074 (m-30) REVERT: H 79 MET cc_start: 0.9083 (mmt) cc_final: 0.8635 (mmp) REVERT: H 170 ARG cc_start: 0.8472 (ttt90) cc_final: 0.8220 (mtp180) REVERT: H 185 GLU cc_start: 0.8543 (tm-30) cc_final: 0.7980 (tm-30) REVERT: H 200 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8478 (mp0) REVERT: H 251 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8500 (tptt) REVERT: H 259 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.6802 (ttm) REVERT: H 326 GLU cc_start: 0.8115 (mp0) cc_final: 0.7649 (pm20) REVERT: H 380 ARG cc_start: 0.8795 (mtm-85) cc_final: 0.7887 (mtm-85) REVERT: H 409 GLU cc_start: 0.8201 (mp0) cc_final: 0.7904 (mp0) REVERT: H 423 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8937 (mt-10) REVERT: H 454 GLU cc_start: 0.8842 (mp0) cc_final: 0.8596 (mp0) REVERT: H 458 MET cc_start: 0.5722 (OUTLIER) cc_final: 0.5477 (ttm) REVERT: I 16 LYS cc_start: 0.9309 (mmtm) cc_final: 0.9033 (mmtm) REVERT: I 28 MET cc_start: 0.9156 (mtm) cc_final: 0.8613 (tmm) REVERT: I 79 MET cc_start: 0.9337 (mtm) cc_final: 0.8878 (mtm) REVERT: I 219 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8268 (tp30) REVERT: I 227 ASP cc_start: 0.9020 (m-30) cc_final: 0.8775 (m-30) REVERT: I 262 MET cc_start: 0.8548 (mmm) cc_final: 0.8187 (mmm) REVERT: I 280 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8784 (mm-30) REVERT: I 340 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8637 (mtm) REVERT: I 344 GLU cc_start: 0.8960 (tt0) cc_final: 0.8583 (tp30) REVERT: I 347 MET cc_start: 0.9470 (mtp) cc_final: 0.8919 (mtp) REVERT: I 398 MET cc_start: 0.8877 (mtm) cc_final: 0.8387 (mtm) REVERT: I 441 MET cc_start: 0.9137 (ppp) cc_final: 0.8810 (ppp) REVERT: J 120 GLU cc_start: 0.9459 (pp20) cc_final: 0.9115 (pp20) REVERT: J 170 ARG cc_start: 0.7685 (mtp85) cc_final: 0.7335 (mtp85) REVERT: J 198 LYS cc_start: 0.9337 (mmmm) cc_final: 0.8857 (mmmm) REVERT: J 221 ASP cc_start: 0.9175 (m-30) cc_final: 0.8027 (t0) REVERT: J 227 ASP cc_start: 0.8843 (p0) cc_final: 0.8387 (p0) REVERT: J 251 LYS cc_start: 0.9319 (mttp) cc_final: 0.9106 (mptt) REVERT: J 267 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8589 (mm-30) REVERT: J 281 GLU cc_start: 0.9293 (tp30) cc_final: 0.8757 (tp30) REVERT: J 342 GLN cc_start: 0.9582 (tt0) cc_final: 0.8331 (tm-30) REVERT: J 345 ARG cc_start: 0.8526 (ttp80) cc_final: 0.7820 (ttp80) REVERT: J 346 GLN cc_start: 0.9156 (mt0) cc_final: 0.7624 (mt0) REVERT: J 369 MET cc_start: 0.8141 (mpp) cc_final: 0.7867 (mpp) REVERT: J 413 ASP cc_start: 0.8874 (t70) cc_final: 0.8433 (t70) REVERT: K 26 MET cc_start: 0.9140 (mmm) cc_final: 0.8760 (mmm) REVERT: K 28 MET cc_start: 0.8947 (tpp) cc_final: 0.8661 (tpp) REVERT: K 60 LYS cc_start: 0.9505 (mmmm) cc_final: 0.9233 (tppt) REVERT: K 64 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8798 (mm-30) REVERT: K 86 ARG cc_start: 0.9045 (mmp80) cc_final: 0.8783 (mmt180) REVERT: K 225 TYR cc_start: 0.7414 (m-80) cc_final: 0.7046 (m-80) REVERT: K 340 MET cc_start: 0.9277 (mmm) cc_final: 0.8931 (mmm) REVERT: K 342 GLN cc_start: 0.9486 (OUTLIER) cc_final: 0.8913 (pt0) REVERT: K 343 LYS cc_start: 0.9586 (mppt) cc_final: 0.9144 (mttt) REVERT: K 345 ARG cc_start: 0.8372 (tmm-80) cc_final: 0.7967 (ttp80) REVERT: K 398 MET cc_start: 0.8865 (mtt) cc_final: 0.8578 (mtt) REVERT: K 409 GLU cc_start: 0.8323 (tm-30) cc_final: 0.8059 (tm-30) REVERT: K 418 LYS cc_start: 0.7949 (mtmt) cc_final: 0.7308 (mtmt) REVERT: K 423 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8538 (mt-10) REVERT: K 458 MET cc_start: 0.8858 (tmm) cc_final: 0.8650 (tmm) REVERT: K 460 ASN cc_start: 0.9228 (m-40) cc_final: 0.8863 (m110) REVERT: L 15 LYS cc_start: 0.9730 (mmmm) cc_final: 0.9492 (mmmm) REVERT: L 16 LYS cc_start: 0.9379 (mmtt) cc_final: 0.9046 (mmmt) REVERT: L 65 ARG cc_start: 0.8978 (tpp-160) cc_final: 0.8726 (tpp80) REVERT: L 77 ASP cc_start: 0.8798 (m-30) cc_final: 0.8440 (m-30) REVERT: L 221 ASP cc_start: 0.8230 (p0) cc_final: 0.6832 (p0) REVERT: L 239 GLN cc_start: 0.9292 (pm20) cc_final: 0.8988 (pm20) REVERT: L 280 GLU cc_start: 0.8842 (tp30) cc_final: 0.8054 (tp30) REVERT: L 322 ASN cc_start: 0.9372 (m-40) cc_final: 0.9125 (m-40) REVERT: L 342 GLN cc_start: 0.9259 (tt0) cc_final: 0.8644 (tt0) REVERT: L 345 ARG cc_start: 0.9360 (tmm-80) cc_final: 0.8823 (tmm-80) REVERT: L 347 MET cc_start: 0.8973 (mtt) cc_final: 0.8751 (mtp) REVERT: L 369 MET cc_start: 0.8788 (mtm) cc_final: 0.8423 (mpp) REVERT: L 383 LYS cc_start: 0.9558 (mmmm) cc_final: 0.9073 (tppt) REVERT: L 452 TYR cc_start: 0.9294 (p90) cc_final: 0.8647 (p90) REVERT: L 458 MET cc_start: 0.7837 (tpt) cc_final: 0.7626 (tpt) REVERT: M 15 LYS cc_start: 0.7755 (pttt) cc_final: 0.7208 (pttt) REVERT: M 173 ASP cc_start: 0.9022 (m-30) cc_final: 0.8535 (t0) REVERT: M 207 ARG cc_start: 0.8965 (tpp80) cc_final: 0.8737 (tpp80) REVERT: N 33 ARG cc_start: 0.9492 (mmm-85) cc_final: 0.9202 (mtp85) REVERT: N 261 LYS cc_start: 0.8219 (pttm) cc_final: 0.7978 (pttm) REVERT: O 77 ARG cc_start: 0.8769 (mtm110) cc_final: 0.8539 (mtm110) REVERT: O 99 MET cc_start: 0.5534 (ppp) cc_final: 0.5140 (ppp) REVERT: O 121 ASP cc_start: 0.8688 (t0) cc_final: 0.8343 (t0) REVERT: O 207 ARG cc_start: 0.8773 (mmm-85) cc_final: 0.8402 (mmm-85) REVERT: P 22 ASP cc_start: 0.8782 (p0) cc_final: 0.8283 (p0) REVERT: P 116 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8760 (mm110) REVERT: P 229 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8622 (tm-30) REVERT: P 290 LYS cc_start: 0.8968 (mmmm) cc_final: 0.8497 (mmmm) REVERT: Q 39 ARG cc_start: 0.8359 (mtm110) cc_final: 0.8080 (mtm110) REVERT: Q 125 ASP cc_start: 0.9099 (t0) cc_final: 0.8765 (t0) REVERT: Q 126 MET cc_start: 0.9517 (mmm) cc_final: 0.9230 (mmm) REVERT: Q 271 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7675 (mt-10) REVERT: Q 290 LYS cc_start: 0.9193 (mmmm) cc_final: 0.8909 (mmmm) REVERT: Q 321 LYS cc_start: 0.9121 (ptmt) cc_final: 0.8893 (ptmm) REVERT: R 15 LYS cc_start: 0.6873 (OUTLIER) cc_final: 0.5750 (pttm) REVERT: R 126 MET cc_start: 0.9390 (mtm) cc_final: 0.9186 (mtm) REVERT: S 109 GLU cc_start: 0.8825 (mp0) cc_final: 0.8609 (mp0) REVERT: S 246 GLU cc_start: 0.7990 (mp0) cc_final: 0.7692 (mp0) REVERT: T 39 ARG cc_start: 0.7772 (ptm160) cc_final: 0.7443 (ptm160) REVERT: T 126 MET cc_start: 0.9164 (mtm) cc_final: 0.8688 (mtm) REVERT: T 170 ARG cc_start: 0.8949 (ttp-110) cc_final: 0.8278 (ttp80) REVERT: T 246 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7436 (mt-10) REVERT: U 64 ASP cc_start: 0.9074 (t0) cc_final: 0.8822 (t0) REVERT: U 105 LYS cc_start: 0.9483 (mttt) cc_final: 0.9223 (mmmm) REVERT: U 114 ILE cc_start: 0.9737 (mt) cc_final: 0.9443 (tt) REVERT: U 207 ARG cc_start: 0.9157 (mmm-85) cc_final: 0.8925 (mmm-85) REVERT: U 246 GLU cc_start: 0.7850 (mp0) cc_final: 0.7612 (pm20) REVERT: V 39 ARG cc_start: 0.9300 (ttp-110) cc_final: 0.8737 (ttm110) REVERT: V 164 GLN cc_start: 0.9049 (tt0) cc_final: 0.8566 (pt0) REVERT: V 188 TYR cc_start: 0.9189 (m-80) cc_final: 0.8986 (m-80) REVERT: V 247 GLN cc_start: 0.9173 (mt0) cc_final: 0.8904 (mp10) outliers start: 239 outliers final: 145 residues processed: 1783 average time/residue: 0.6441 time to fit residues: 1935.6940 Evaluate side-chains 1698 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 1536 time to evaluate : 6.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 26 MET Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain E residue 18 HIS Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 322 ASN Chi-restraints excluded: chain E residue 340 MET Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 458 MET Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 221 ASP Chi-restraints excluded: chain F residue 264 ASP Chi-restraints excluded: chain F residue 299 HIS Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 377 VAL Chi-restraints excluded: chain F residue 420 SER Chi-restraints excluded: chain F residue 454 GLU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 192 ASP Chi-restraints excluded: chain G residue 256 THR Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 374 GLN Chi-restraints excluded: chain G residue 436 ILE Chi-restraints excluded: chain H residue 8 LYS Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 226 VAL Chi-restraints excluded: chain H residue 251 LYS Chi-restraints excluded: chain H residue 259 MET Chi-restraints excluded: chain H residue 283 CYS Chi-restraints excluded: chain H residue 286 CYS Chi-restraints excluded: chain H residue 290 THR Chi-restraints excluded: chain H residue 342 GLN Chi-restraints excluded: chain H residue 354 LEU Chi-restraints excluded: chain H residue 419 MET Chi-restraints excluded: chain H residue 458 MET Chi-restraints excluded: chain I residue 13 ASP Chi-restraints excluded: chain I residue 46 ASP Chi-restraints excluded: chain I residue 63 ILE Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 336 VAL Chi-restraints excluded: chain I residue 340 MET Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain J residue 79 MET Chi-restraints excluded: chain J residue 121 ASP Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 236 ASP Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 299 HIS Chi-restraints excluded: chain J residue 336 VAL Chi-restraints excluded: chain J residue 350 LEU Chi-restraints excluded: chain J residue 354 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 423 GLU Chi-restraints excluded: chain K residue 6 ASN Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 209 ASP Chi-restraints excluded: chain K residue 230 ILE Chi-restraints excluded: chain K residue 304 VAL Chi-restraints excluded: chain K residue 342 GLN Chi-restraints excluded: chain K residue 405 LYS Chi-restraints excluded: chain K residue 424 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 164 ILE Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 377 VAL Chi-restraints excluded: chain L residue 439 THR Chi-restraints excluded: chain M residue 152 THR Chi-restraints excluded: chain M residue 312 ASP Chi-restraints excluded: chain N residue 102 TRP Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain N residue 156 THR Chi-restraints excluded: chain N residue 178 VAL Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 313 THR Chi-restraints excluded: chain O residue 187 LEU Chi-restraints excluded: chain P residue 116 GLN Chi-restraints excluded: chain P residue 127 LEU Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain P residue 166 ILE Chi-restraints excluded: chain P residue 178 VAL Chi-restraints excluded: chain P residue 216 ILE Chi-restraints excluded: chain Q residue 108 GLN Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain R residue 11 ASP Chi-restraints excluded: chain R residue 15 LYS Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 224 VAL Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 37 ILE Chi-restraints excluded: chain S residue 123 MET Chi-restraints excluded: chain S residue 245 ILE Chi-restraints excluded: chain S residue 320 THR Chi-restraints excluded: chain T residue 6 LEU Chi-restraints excluded: chain T residue 236 LEU Chi-restraints excluded: chain U residue 59 LEU Chi-restraints excluded: chain U residue 243 ILE Chi-restraints excluded: chain U residue 313 THR Chi-restraints excluded: chain V residue 127 LEU Chi-restraints excluded: chain V residue 256 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 855 random chunks: chunk 354 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 380 optimal weight: 20.0000 chunk 204 optimal weight: 5.9990 chunk 145 optimal weight: 30.0000 chunk 198 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 447 optimal weight: 20.0000 chunk 260 optimal weight: 20.0000 chunk 531 optimal weight: 10.0000 chunk 596 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 ASN ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 ASN ** E 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 GLN ** F 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 322 ASN ** F 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN ** H 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 460 ASN ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 ASN ** K 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 23 HIS ** L 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 124 GLN ** M 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 43 ASN N 190 ASN O 43 ASN O 117 GLN O 248 ASN ** P 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 293 ASN Q 108 GLN ** Q 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 248 ASN ** U 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.084009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.068886 restraints weight = 248503.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.070997 restraints weight = 143174.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.072445 restraints weight = 97958.480| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 68177 Z= 0.259 Angle : 0.641 11.628 92470 Z= 0.330 Chirality : 0.042 0.269 10048 Planarity : 0.004 0.076 12237 Dihedral : 4.726 65.571 9264 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.30 % Favored : 95.69 % Rotamer: Outliers : 3.65 % Allowed : 19.52 % 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: -0.10 (0.09), residues: 8507 helix: 1.27 (0.09), residues: 3163 sheet: -0.42 (0.13), residues: 1600 loop : -1.04 (0.10), residues: 3744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP P 102 HIS 0.009 0.001 HIS J 23 PHE 0.026 0.002 PHE O 251 TYR 0.019 0.001 TYR V 268 ARG 0.012 0.001 ARG D 263 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17014 Ramachandran restraints generated. 8507 Oldfield, 0 Emsley, 8507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17014 Ramachandran restraints generated. 8507 Oldfield, 0 Emsley, 8507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1865 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 255 poor density : 1610 time to evaluate : 5.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 12 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8483 (mt-10) REVERT: A 15 LYS cc_start: 0.9734 (mmtt) cc_final: 0.9512 (mtmt) REVERT: A 18 HIS cc_start: 0.9215 (m90) cc_final: 0.8493 (m90) REVERT: A 29 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8575 (tm-30) REVERT: A 32 ARG cc_start: 0.8426 (ttp80) cc_final: 0.8135 (ttp80) REVERT: A 60 LYS cc_start: 0.9544 (mmtt) cc_final: 0.9321 (mttt) REVERT: A 162 GLU cc_start: 0.9268 (OUTLIER) cc_final: 0.9018 (mp0) REVERT: A 163 ASP cc_start: 0.9228 (m-30) cc_final: 0.8684 (t0) REVERT: A 170 ARG cc_start: 0.8525 (ttm-80) cc_final: 0.8134 (ttp-170) REVERT: A 198 LYS cc_start: 0.9274 (mmmt) cc_final: 0.8977 (mmmt) REVERT: A 200 GLU cc_start: 0.8266 (mp0) cc_final: 0.8016 (mp0) REVERT: A 214 GLN cc_start: 0.8989 (pp30) cc_final: 0.8351 (pp30) REVERT: A 241 ASP cc_start: 0.8552 (p0) cc_final: 0.8015 (p0) REVERT: A 251 LYS cc_start: 0.9120 (ttpp) cc_final: 0.8907 (ttpp) REVERT: A 346 GLN cc_start: 0.9057 (mt0) cc_final: 0.8589 (mp10) REVERT: A 369 MET cc_start: 0.8812 (mtm) cc_final: 0.8389 (ptp) REVERT: A 419 MET cc_start: 0.8433 (ppp) cc_final: 0.7770 (ppp) REVERT: A 423 GLU cc_start: 0.9242 (tt0) cc_final: 0.9009 (pt0) REVERT: A 460 ASN cc_start: 0.8840 (m110) cc_final: 0.8288 (m110) REVERT: B 9 TYR cc_start: 0.8426 (p90) cc_final: 0.7943 (p90) REVERT: B 17 MET cc_start: 0.9129 (mmm) cc_final: 0.8925 (mmm) REVERT: B 18 HIS cc_start: 0.8249 (p-80) cc_final: 0.7983 (p-80) REVERT: B 32 ARG cc_start: 0.7535 (ttp80) cc_final: 0.7281 (ttp80) REVERT: B 64 GLU cc_start: 0.8661 (pt0) cc_final: 0.8394 (pt0) REVERT: B 79 MET cc_start: 0.9225 (mtm) cc_final: 0.8926 (mtm) REVERT: B 82 GLN cc_start: 0.9311 (mt0) cc_final: 0.8759 (mm110) REVERT: B 103 ASP cc_start: 0.8961 (p0) cc_final: 0.8407 (p0) REVERT: B 188 ASP cc_start: 0.7943 (t0) cc_final: 0.7426 (t0) REVERT: B 219 GLU cc_start: 0.8228 (pt0) cc_final: 0.7840 (pt0) REVERT: B 267 GLU cc_start: 0.9220 (tt0) cc_final: 0.8881 (pt0) REVERT: B 296 LEU cc_start: 0.9105 (tp) cc_final: 0.8812 (tp) REVERT: B 337 LYS cc_start: 0.8756 (tptp) cc_final: 0.8508 (tptp) REVERT: B 340 MET cc_start: 0.8934 (mmm) cc_final: 0.8418 (mmm) REVERT: B 344 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8386 (mt-10) REVERT: B 383 LYS cc_start: 0.9439 (ttmm) cc_final: 0.9136 (ttpt) REVERT: B 398 MET cc_start: 0.9409 (mtm) cc_final: 0.8744 (mpp) REVERT: B 418 LYS cc_start: 0.8885 (mttt) cc_final: 0.8581 (mttt) REVERT: B 423 GLU cc_start: 0.9336 (pt0) cc_final: 0.9052 (pt0) REVERT: B 441 MET cc_start: 0.9367 (tmm) cc_final: 0.9042 (tmm) REVERT: C 19 LYS cc_start: 0.9220 (tppt) cc_final: 0.8961 (tppt) REVERT: C 26 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8543 (ttm) REVERT: C 29 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8780 (mm-30) REVERT: C 37 ASN cc_start: 0.9319 (m-40) cc_final: 0.8904 (m110) REVERT: C 46 ASP cc_start: 0.8262 (t0) cc_final: 0.7644 (t0) REVERT: C 60 LYS cc_start: 0.9531 (mmmm) cc_final: 0.9287 (mmmm) REVERT: C 77 ASP cc_start: 0.9258 (m-30) cc_final: 0.8969 (t70) REVERT: C 105 ASP cc_start: 0.9210 (p0) cc_final: 0.8962 (p0) REVERT: C 158 PHE cc_start: 0.8432 (t80) cc_final: 0.8117 (t80) REVERT: C 190 ASP cc_start: 0.7080 (OUTLIER) cc_final: 0.6455 (m-30) REVERT: C 259 MET cc_start: 0.7840 (mtp) cc_final: 0.7444 (ttp) REVERT: C 296 LEU cc_start: 0.8989 (tp) cc_final: 0.8772 (tp) REVERT: C 314 ARG cc_start: 0.8799 (mmt90) cc_final: 0.8056 (tpm170) REVERT: C 398 MET cc_start: 0.9038 (mtm) cc_final: 0.8744 (mtt) REVERT: C 413 ASP cc_start: 0.8504 (t0) cc_final: 0.7991 (t0) REVERT: C 441 MET cc_start: 0.9153 (tmm) cc_final: 0.8875 (ppp) REVERT: C 458 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7586 (ttt) REVERT: D 8 LYS cc_start: 0.9675 (mtmm) cc_final: 0.9393 (mttp) REVERT: D 15 LYS cc_start: 0.9336 (mttt) cc_final: 0.8997 (mtmm) REVERT: D 16 LYS cc_start: 0.9230 (mmmm) cc_final: 0.9015 (mmmm) REVERT: D 17 MET cc_start: 0.9368 (mmm) cc_final: 0.8463 (mmm) REVERT: D 18 HIS cc_start: 0.9554 (m90) cc_final: 0.8456 (m90) REVERT: D 36 ASP cc_start: 0.9499 (m-30) cc_final: 0.9174 (m-30) REVERT: D 46 ASP cc_start: 0.8149 (t0) cc_final: 0.7790 (t0) REVERT: D 49 LYS cc_start: 0.9048 (ptmm) cc_final: 0.8786 (pttp) REVERT: D 54 GLU cc_start: 0.9019 (tp30) cc_final: 0.8693 (tp30) REVERT: D 89 VAL cc_start: 0.9402 (t) cc_final: 0.9057 (p) REVERT: D 120 GLU cc_start: 0.9386 (tt0) cc_final: 0.9159 (mt-10) REVERT: D 121 ASP cc_start: 0.9363 (OUTLIER) cc_final: 0.9058 (t70) REVERT: D 173 ASN cc_start: 0.8837 (m-40) cc_final: 0.8452 (p0) REVERT: D 184 ARG cc_start: 0.8885 (ttp80) cc_final: 0.8062 (ttp80) REVERT: D 200 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.7890 (mm-30) REVERT: D 217 TRP cc_start: 0.8769 (m100) cc_final: 0.8556 (m-10) REVERT: D 241 ASP cc_start: 0.8667 (t0) cc_final: 0.8278 (t0) REVERT: D 242 GLU cc_start: 0.8905 (pm20) cc_final: 0.8688 (pm20) REVERT: D 251 LYS cc_start: 0.9030 (mptt) cc_final: 0.8652 (mmtp) REVERT: D 265 LEU cc_start: 0.9379 (mt) cc_final: 0.8935 (mt) REVERT: D 278 ASP cc_start: 0.9074 (t0) cc_final: 0.8810 (t0) REVERT: D 288 GLN cc_start: 0.8223 (mm-40) cc_final: 0.7996 (mm-40) REVERT: D 337 LYS cc_start: 0.9394 (tptm) cc_final: 0.9181 (tmmt) REVERT: D 341 ASP cc_start: 0.9264 (m-30) cc_final: 0.9025 (m-30) REVERT: D 347 MET cc_start: 0.9098 (mmt) cc_final: 0.8793 (mmt) REVERT: D 374 GLN cc_start: 0.9285 (mt0) cc_final: 0.8782 (mp10) REVERT: D 380 ARG cc_start: 0.9053 (ttp-110) cc_final: 0.8759 (ttp-110) REVERT: D 409 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7950 (tm-30) REVERT: D 411 ASN cc_start: 0.8610 (t0) cc_final: 0.8387 (t0) REVERT: D 413 ASP cc_start: 0.8767 (t0) cc_final: 0.8425 (t0) REVERT: D 419 MET cc_start: 0.8885 (ptm) cc_final: 0.8165 (tmm) REVERT: D 420 SER cc_start: 0.9592 (m) cc_final: 0.9147 (p) REVERT: D 422 GLU cc_start: 0.9283 (tp30) cc_final: 0.8949 (tp30) REVERT: D 423 GLU cc_start: 0.9100 (tt0) cc_final: 0.8580 (pt0) REVERT: D 458 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7707 (tpt) REVERT: E 16 LYS cc_start: 0.9207 (mtmm) cc_final: 0.8950 (mtmm) REVERT: E 64 GLU cc_start: 0.7987 (pp20) cc_final: 0.7759 (pp20) REVERT: E 74 ASN cc_start: 0.8937 (t0) cc_final: 0.8619 (t0) REVERT: E 157 LYS cc_start: 0.9303 (mmmt) cc_final: 0.9078 (mmmt) REVERT: E 162 GLU cc_start: 0.8966 (mp0) cc_final: 0.8747 (mp0) REVERT: E 163 ASP cc_start: 0.8798 (OUTLIER) cc_final: 0.7914 (t0) REVERT: E 184 ARG cc_start: 0.9060 (ttp80) cc_final: 0.8475 (ttp80) REVERT: E 259 MET cc_start: 0.8953 (mmm) cc_final: 0.8630 (mmm) REVERT: E 340 MET cc_start: 0.9491 (OUTLIER) cc_final: 0.9102 (tpp) REVERT: E 370 GLU cc_start: 0.8248 (pm20) cc_final: 0.7760 (pm20) REVERT: E 419 MET cc_start: 0.8200 (ttm) cc_final: 0.7581 (ttm) REVERT: E 420 SER cc_start: 0.9536 (m) cc_final: 0.9117 (p) REVERT: E 441 MET cc_start: 0.9195 (tmm) cc_final: 0.8895 (tmm) REVERT: E 443 TRP cc_start: 0.9005 (t60) cc_final: 0.8301 (t60) REVERT: E 458 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7637 (tpp) REVERT: E 460 ASN cc_start: 0.9189 (m-40) cc_final: 0.8884 (m110) REVERT: F 26 MET cc_start: 0.9348 (mtp) cc_final: 0.9145 (ttt) REVERT: F 54 GLU cc_start: 0.9507 (tt0) cc_final: 0.9299 (tm-30) REVERT: F 79 MET cc_start: 0.9212 (mtm) cc_final: 0.8980 (mtm) REVERT: F 83 ILE cc_start: 0.9538 (OUTLIER) cc_final: 0.9294 (mp) REVERT: F 163 ASP cc_start: 0.9258 (m-30) cc_final: 0.8537 (m-30) REVERT: F 184 ARG cc_start: 0.9311 (ttp-110) cc_final: 0.8790 (ttp80) REVERT: F 315 ASP cc_start: 0.8493 (m-30) cc_final: 0.7516 (p0) REVERT: F 342 GLN cc_start: 0.9470 (pt0) cc_final: 0.8973 (pp30) REVERT: F 357 SER cc_start: 0.8553 (m) cc_final: 0.8267 (p) REVERT: F 370 GLU cc_start: 0.8939 (mt-10) cc_final: 0.7950 (mt-10) REVERT: F 380 ARG cc_start: 0.9211 (ttp80) cc_final: 0.8611 (ttt90) REVERT: F 413 ASP cc_start: 0.8885 (m-30) cc_final: 0.8490 (t70) REVERT: F 419 MET cc_start: 0.8541 (ppp) cc_final: 0.7950 (ppp) REVERT: F 460 ASN cc_start: 0.8870 (m-40) cc_final: 0.8460 (m110) REVERT: G 32 ARG cc_start: 0.7690 (tpp-160) cc_final: 0.7217 (tpp-160) REVERT: G 74 ASN cc_start: 0.9586 (t0) cc_final: 0.9076 (t0) REVERT: G 96 LYS cc_start: 0.9348 (mmtm) cc_final: 0.9145 (mmmt) REVERT: G 99 MET cc_start: 0.9200 (ppp) cc_final: 0.8999 (tmm) REVERT: G 124 SER cc_start: 0.9631 (OUTLIER) cc_final: 0.9354 (p) REVERT: G 163 ASP cc_start: 0.9424 (m-30) cc_final: 0.9113 (t0) REVERT: G 262 MET cc_start: 0.8898 (mmp) cc_final: 0.8480 (mmp) REVERT: G 283 CYS cc_start: 0.8784 (m) cc_final: 0.8566 (m) REVERT: G 335 MET cc_start: 0.8993 (ttt) cc_final: 0.8610 (ttp) REVERT: G 347 MET cc_start: 0.9063 (mmm) cc_final: 0.8608 (mpp) REVERT: G 460 ASN cc_start: 0.9020 (m-40) cc_final: 0.8533 (m110) REVERT: H 17 MET cc_start: 0.9613 (mmm) cc_final: 0.9089 (mmm) REVERT: H 26 MET cc_start: 0.9229 (mtm) cc_final: 0.8569 (mtm) REVERT: H 77 ASP cc_start: 0.9315 (m-30) cc_final: 0.9064 (m-30) REVERT: H 79 MET cc_start: 0.9110 (mmt) cc_final: 0.8644 (mmp) REVERT: H 185 GLU cc_start: 0.8452 (tm-30) cc_final: 0.7880 (tm-30) REVERT: H 200 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8462 (mp0) REVERT: H 251 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8515 (tptt) REVERT: H 326 GLU cc_start: 0.8092 (mp0) cc_final: 0.7522 (pm20) REVERT: H 328 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8900 (mp) REVERT: H 346 GLN cc_start: 0.9584 (mt0) cc_final: 0.9278 (mt0) REVERT: H 380 ARG cc_start: 0.8814 (mtm-85) cc_final: 0.7862 (mtm-85) REVERT: H 387 ASP cc_start: 0.9175 (m-30) cc_final: 0.8742 (m-30) REVERT: H 409 GLU cc_start: 0.8195 (mp0) cc_final: 0.7956 (mp0) REVERT: H 423 GLU cc_start: 0.9192 (mt-10) cc_final: 0.8967 (mt-10) REVERT: H 454 GLU cc_start: 0.8933 (mp0) cc_final: 0.8689 (mp0) REVERT: H 458 MET cc_start: 0.5751 (OUTLIER) cc_final: 0.5226 (ttm) REVERT: I 16 LYS cc_start: 0.9270 (mmtm) cc_final: 0.9056 (mmtm) REVERT: I 79 MET cc_start: 0.9367 (mtm) cc_final: 0.8861 (mtm) REVERT: I 158 PHE cc_start: 0.8893 (t80) cc_final: 0.8658 (t80) REVERT: I 177 ARG cc_start: 0.9079 (mmm-85) cc_final: 0.8866 (mmm-85) REVERT: I 219 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8302 (tp30) REVERT: I 227 ASP cc_start: 0.9050 (m-30) cc_final: 0.8764 (m-30) REVERT: I 262 MET cc_start: 0.8544 (mmm) cc_final: 0.8145 (mmm) REVERT: I 280 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8798 (mm-30) REVERT: I 335 MET cc_start: 0.9392 (ttt) cc_final: 0.8910 (tmm) REVERT: I 340 MET cc_start: 0.9234 (OUTLIER) cc_final: 0.8771 (mtm) REVERT: I 344 GLU cc_start: 0.8977 (tt0) cc_final: 0.8617 (tp30) REVERT: I 347 MET cc_start: 0.9449 (mtp) cc_final: 0.8895 (mtp) REVERT: I 398 MET cc_start: 0.8903 (mtm) cc_final: 0.8443 (mtt) REVERT: I 441 MET cc_start: 0.9207 (ppp) cc_final: 0.8837 (ppp) REVERT: J 46 ASP cc_start: 0.8188 (t0) cc_final: 0.7707 (t0) REVERT: J 103 ASP cc_start: 0.9021 (p0) cc_final: 0.8818 (p0) REVERT: J 120 GLU cc_start: 0.9487 (pp20) cc_final: 0.9141 (pp20) REVERT: J 170 ARG cc_start: 0.7736 (mtp85) cc_final: 0.7334 (mtp85) REVERT: J 221 ASP cc_start: 0.9198 (m-30) cc_final: 0.8043 (t0) REVERT: J 227 ASP cc_start: 0.8798 (p0) cc_final: 0.8335 (p0) REVERT: J 251 LYS cc_start: 0.9346 (mttp) cc_final: 0.9044 (mptt) REVERT: J 267 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8552 (mm-30) REVERT: J 281 GLU cc_start: 0.9307 (tp30) cc_final: 0.8790 (tp30) REVERT: J 342 GLN cc_start: 0.9592 (tt0) cc_final: 0.8380 (tm-30) REVERT: J 345 ARG cc_start: 0.8539 (ttp80) cc_final: 0.7936 (ttp80) REVERT: J 346 GLN cc_start: 0.9136 (mt0) cc_final: 0.7725 (mt0) REVERT: J 347 MET cc_start: 0.9176 (mmt) cc_final: 0.8952 (mmp) REVERT: K 28 MET cc_start: 0.8995 (tpp) cc_final: 0.8664 (tpp) REVERT: K 86 ARG cc_start: 0.9041 (mmp80) cc_final: 0.8719 (mmt180) REVERT: K 97 PHE cc_start: 0.9446 (m-10) cc_final: 0.9113 (m-10) REVERT: K 125 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8548 (pp) REVERT: K 225 TYR cc_start: 0.7608 (m-80) cc_final: 0.7125 (m-80) REVERT: K 275 ASN cc_start: 0.9542 (m110) cc_final: 0.9086 (m110) REVERT: K 340 MET cc_start: 0.9264 (mmm) cc_final: 0.8997 (mmm) REVERT: K 342 GLN cc_start: 0.9494 (OUTLIER) cc_final: 0.8889 (pt0) REVERT: K 343 LYS cc_start: 0.9608 (mppt) cc_final: 0.9185 (mttt) REVERT: K 345 ARG cc_start: 0.8464 (tmm-80) cc_final: 0.8002 (ttp80) REVERT: K 398 MET cc_start: 0.8904 (mtt) cc_final: 0.8556 (mtt) REVERT: K 409 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7852 (tm-30) REVERT: K 418 LYS cc_start: 0.7999 (mtmt) cc_final: 0.7293 (mtmt) REVERT: K 423 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8550 (mt-10) REVERT: K 460 ASN cc_start: 0.9203 (m-40) cc_final: 0.8820 (m110) REVERT: L 15 LYS cc_start: 0.9733 (mmmm) cc_final: 0.9508 (mmmm) REVERT: L 16 LYS cc_start: 0.9381 (mmtt) cc_final: 0.9104 (mmmt) REVERT: L 17 MET cc_start: 0.9509 (mmm) cc_final: 0.9246 (mmm) REVERT: L 77 ASP cc_start: 0.8862 (m-30) cc_final: 0.8438 (m-30) REVERT: L 239 GLN cc_start: 0.9355 (pm20) cc_final: 0.9021 (pm20) REVERT: L 322 ASN cc_start: 0.9415 (m-40) cc_final: 0.9136 (m-40) REVERT: L 345 ARG cc_start: 0.9393 (tmm-80) cc_final: 0.8949 (tmm-80) REVERT: L 347 MET cc_start: 0.9033 (mtt) cc_final: 0.8639 (mtm) REVERT: L 369 MET cc_start: 0.8820 (mtm) cc_final: 0.8420 (mpp) REVERT: L 383 LYS cc_start: 0.9570 (mmmm) cc_final: 0.9100 (tppt) REVERT: L 419 MET cc_start: 0.8354 (mtt) cc_final: 0.7455 (mmm) REVERT: L 423 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8657 (pt0) REVERT: L 452 TYR cc_start: 0.9298 (p90) cc_final: 0.8575 (p90) REVERT: L 458 MET cc_start: 0.7944 (tpt) cc_final: 0.7722 (tpt) REVERT: M 17 MET cc_start: 0.8472 (mpp) cc_final: 0.8117 (mmm) REVERT: M 173 ASP cc_start: 0.9082 (m-30) cc_final: 0.8564 (t0) REVERT: M 207 ARG cc_start: 0.9027 (tpp80) cc_final: 0.8765 (tpp80) REVERT: N 235 THR cc_start: 0.9455 (OUTLIER) cc_final: 0.9251 (t) REVERT: N 271 GLU cc_start: 0.8485 (mp0) cc_final: 0.8183 (mp0) REVERT: N 290 LYS cc_start: 0.8894 (mttp) cc_final: 0.8547 (mtpp) REVERT: O 77 ARG cc_start: 0.8810 (mtm110) cc_final: 0.8413 (mtm110) REVERT: O 99 MET cc_start: 0.5696 (ppp) cc_final: 0.5268 (ppp) REVERT: O 100 LEU cc_start: 0.3757 (OUTLIER) cc_final: 0.3238 (pp) REVERT: O 121 ASP cc_start: 0.8766 (t0) cc_final: 0.8351 (t0) REVERT: O 123 MET cc_start: 0.9300 (mmt) cc_final: 0.9035 (mmm) REVERT: O 124 GLN cc_start: 0.9545 (tt0) cc_final: 0.9108 (tt0) REVERT: O 207 ARG cc_start: 0.8793 (mmm-85) cc_final: 0.8478 (mmm-85) REVERT: P 21 LEU cc_start: 0.8468 (tp) cc_final: 0.8228 (tp) REVERT: P 22 ASP cc_start: 0.8819 (p0) cc_final: 0.8359 (p0) REVERT: P 116 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.8853 (mm110) REVERT: P 229 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8593 (tm-30) REVERT: P 290 LYS cc_start: 0.9003 (mmmm) cc_final: 0.8500 (mmmm) REVERT: Q 26 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8482 (tm-30) REVERT: Q 39 ARG cc_start: 0.8494 (mtm110) cc_final: 0.8266 (mtm110) REVERT: Q 109 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8352 (mp0) REVERT: Q 126 MET cc_start: 0.9519 (mmm) cc_final: 0.9273 (mmm) REVERT: Q 271 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7497 (mt-10) REVERT: Q 290 LYS cc_start: 0.9220 (mmmm) cc_final: 0.8895 (mmmm) REVERT: Q 321 LYS cc_start: 0.9126 (ptmt) cc_final: 0.8879 (ptmm) REVERT: R 15 LYS cc_start: 0.6197 (OUTLIER) cc_final: 0.5053 (pttm) REVERT: R 105 LYS cc_start: 0.9028 (mmmm) cc_final: 0.8755 (mmmm) REVERT: R 109 GLU cc_start: 0.8797 (tt0) cc_final: 0.8525 (tt0) REVERT: R 126 MET cc_start: 0.9425 (mtm) cc_final: 0.9205 (mtm) REVERT: S 109 GLU cc_start: 0.8891 (mp0) cc_final: 0.8669 (mp0) REVERT: S 199 TYR cc_start: 0.8471 (m-80) cc_final: 0.7953 (m-80) REVERT: S 246 GLU cc_start: 0.8285 (mp0) cc_final: 0.7720 (mp0) REVERT: T 20 VAL cc_start: 0.8626 (OUTLIER) cc_final: 0.8315 (t) REVERT: T 39 ARG cc_start: 0.7696 (ptm160) cc_final: 0.7287 (ptm160) REVERT: T 81 ASP cc_start: 0.9042 (t70) cc_final: 0.8512 (p0) REVERT: T 109 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8231 (mt-10) REVERT: T 135 LYS cc_start: 0.9673 (tttm) cc_final: 0.9341 (ttmt) REVERT: T 155 MET cc_start: 0.8739 (mmm) cc_final: 0.8330 (tmm) REVERT: T 187 LEU cc_start: 0.9395 (tp) cc_final: 0.9178 (tp) REVERT: T 246 GLU cc_start: 0.8500 (mt-10) cc_final: 0.7838 (mt-10) REVERT: U 49 GLU cc_start: 0.8174 (mp0) cc_final: 0.7954 (mp0) REVERT: U 105 LYS cc_start: 0.9513 (mttt) cc_final: 0.9234 (mmmm) REVERT: U 114 ILE cc_start: 0.9747 (mt) cc_final: 0.9443 (tt) REVERT: U 207 ARG cc_start: 0.9191 (mmm-85) cc_final: 0.8942 (mmm-85) REVERT: V 39 ARG cc_start: 0.9339 (ttp-110) cc_final: 0.8850 (ttp-110) REVERT: V 77 ARG cc_start: 0.7751 (mmm160) cc_final: 0.7442 (mmm160) REVERT: V 164 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8569 (pt0) REVERT: V 247 GLN cc_start: 0.9222 (mt0) cc_final: 0.8945 (mp10) outliers start: 255 outliers final: 170 residues processed: 1761 average time/residue: 0.6586 time to fit residues: 1977.1962 Evaluate side-chains 1705 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 1510 time to evaluate : 6.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 26 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain E residue 18 HIS Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 340 MET Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 458 MET Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 188 ASP Chi-restraints excluded: chain F residue 221 ASP Chi-restraints excluded: chain F residue 264 ASP Chi-restraints excluded: chain F residue 299 HIS Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 377 VAL Chi-restraints excluded: chain F residue 420 SER Chi-restraints excluded: chain F residue 454 GLU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 192 ASP Chi-restraints excluded: chain G residue 256 THR Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 374 GLN Chi-restraints excluded: chain G residue 436 ILE Chi-restraints excluded: chain H residue 8 LYS Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 194 TYR Chi-restraints excluded: chain H residue 216 THR Chi-restraints excluded: chain H residue 226 VAL Chi-restraints excluded: chain H residue 251 LYS Chi-restraints excluded: chain H residue 283 CYS Chi-restraints excluded: chain H residue 286 CYS Chi-restraints excluded: chain H residue 290 THR Chi-restraints excluded: chain H residue 328 LEU Chi-restraints excluded: chain H residue 342 GLN Chi-restraints excluded: chain H residue 354 LEU Chi-restraints excluded: chain H residue 355 ILE Chi-restraints excluded: chain H residue 419 MET Chi-restraints excluded: chain H residue 447 LYS Chi-restraints excluded: chain H residue 458 MET Chi-restraints excluded: chain I residue 13 ASP Chi-restraints excluded: chain I residue 46 ASP Chi-restraints excluded: chain I residue 63 ILE Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 336 VAL Chi-restraints excluded: chain I residue 340 MET Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain I residue 419 MET Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 236 ASP Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 299 HIS Chi-restraints excluded: chain J residue 336 VAL Chi-restraints excluded: chain J residue 350 LEU Chi-restraints excluded: chain J residue 354 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain K residue 6 ASN Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 209 ASP Chi-restraints excluded: chain K residue 297 THR Chi-restraints excluded: chain K residue 304 VAL Chi-restraints excluded: chain K residue 342 GLN Chi-restraints excluded: chain K residue 405 LYS Chi-restraints excluded: chain K residue 424 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 164 ILE Chi-restraints excluded: chain L residue 196 ILE Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 374 GLN Chi-restraints excluded: chain L residue 377 VAL Chi-restraints excluded: chain L residue 423 GLU Chi-restraints excluded: chain L residue 439 THR Chi-restraints excluded: chain M residue 109 GLU Chi-restraints excluded: chain M residue 152 THR Chi-restraints excluded: chain M residue 312 ASP Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 102 TRP Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain N residue 156 THR Chi-restraints excluded: chain N residue 178 VAL Chi-restraints excluded: chain N residue 235 THR Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 313 THR Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 187 LEU Chi-restraints excluded: chain P residue 116 GLN Chi-restraints excluded: chain P residue 127 LEU Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain P residue 166 ILE Chi-restraints excluded: chain P residue 178 VAL Chi-restraints excluded: chain P residue 216 ILE Chi-restraints excluded: chain P residue 276 LEU Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain R residue 11 ASP Chi-restraints excluded: chain R residue 15 LYS Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 224 VAL Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 37 ILE Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain S residue 123 MET Chi-restraints excluded: chain S residue 225 SER Chi-restraints excluded: chain S residue 244 LEU Chi-restraints excluded: chain S residue 245 ILE Chi-restraints excluded: chain T residue 6 LEU Chi-restraints excluded: chain T residue 20 VAL Chi-restraints excluded: chain T residue 209 ASP Chi-restraints excluded: chain T residue 235 THR Chi-restraints excluded: chain T residue 236 LEU Chi-restraints excluded: chain U residue 59 LEU Chi-restraints excluded: chain U residue 243 ILE Chi-restraints excluded: chain U residue 313 THR Chi-restraints excluded: chain U residue 316 VAL Chi-restraints excluded: chain V residue 127 LEU Chi-restraints excluded: chain V residue 152 THR Chi-restraints excluded: chain V residue 164 GLN Chi-restraints excluded: chain V residue 244 LEU Chi-restraints excluded: chain V residue 256 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 855 random chunks: chunk 6 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 663 optimal weight: 6.9990 chunk 832 optimal weight: 8.9990 chunk 130 optimal weight: 8.9990 chunk 583 optimal weight: 20.0000 chunk 418 optimal weight: 8.9990 chunk 648 optimal weight: 7.9990 chunk 769 optimal weight: 7.9990 chunk 424 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS C 269 ASN ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 322 ASN F 374 GLN ** F 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN H 74 ASN ** H 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN ** J 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 460 ASN ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 ASN L 23 HIS ** L 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 164 GLN ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 43 ASN ** P 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 180 HIS ** U 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 43 ASN ** U 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.083794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.068634 restraints weight = 249571.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.070701 restraints weight = 144435.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.072162 restraints weight = 99207.559| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 68177 Z= 0.263 Angle : 0.648 10.680 92470 Z= 0.333 Chirality : 0.043 0.218 10048 Planarity : 0.004 0.072 12237 Dihedral : 4.667 59.308 9264 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.46 % Favored : 95.53 % Rotamer: Outliers : 3.87 % Allowed : 20.39 % Favored : 75.74 % 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: -0.08 (0.09), residues: 8507 helix: 1.27 (0.09), residues: 3178 sheet: -0.37 (0.13), residues: 1610 loop : -1.04 (0.10), residues: 3719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP Q 12 HIS 0.008 0.001 HIS H 299 PHE 0.022 0.001 PHE S 28 TYR 0.033 0.001 TYR Q 274 ARG 0.012 0.001 ARG P 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17014 Ramachandran restraints generated. 8507 Oldfield, 0 Emsley, 8507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17014 Ramachandran restraints generated. 8507 Oldfield, 0 Emsley, 8507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1843 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 270 poor density : 1573 time to evaluate : 5.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8448 (mt-10) REVERT: A 15 LYS cc_start: 0.9714 (mmtt) cc_final: 0.9487 (mtmt) REVERT: A 18 HIS cc_start: 0.9287 (m90) cc_final: 0.8580 (m90) REVERT: A 29 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8550 (tm-30) REVERT: A 32 ARG cc_start: 0.8416 (ttp80) cc_final: 0.8111 (ttp80) REVERT: A 60 LYS cc_start: 0.9569 (mmtt) cc_final: 0.9350 (mttt) REVERT: A 163 ASP cc_start: 0.9242 (m-30) cc_final: 0.8690 (t0) REVERT: A 170 ARG cc_start: 0.8499 (ttm-80) cc_final: 0.8193 (ttp-170) REVERT: A 198 LYS cc_start: 0.9272 (mmmt) cc_final: 0.8986 (mmmt) REVERT: A 200 GLU cc_start: 0.8290 (mp0) cc_final: 0.7983 (mp0) REVERT: A 214 GLN cc_start: 0.8982 (pp30) cc_final: 0.8323 (pp30) REVERT: A 241 ASP cc_start: 0.8595 (p0) cc_final: 0.8071 (p0) REVERT: A 251 LYS cc_start: 0.9126 (ttpp) cc_final: 0.8904 (ttpp) REVERT: A 337 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8941 (tttp) REVERT: A 346 GLN cc_start: 0.9063 (mt0) cc_final: 0.8612 (mp10) REVERT: A 369 MET cc_start: 0.8814 (mtm) cc_final: 0.8430 (ptp) REVERT: A 419 MET cc_start: 0.8537 (ppp) cc_final: 0.8027 (ppp) REVERT: A 422 GLU cc_start: 0.9339 (tp30) cc_final: 0.9118 (tp30) REVERT: A 458 MET cc_start: 0.8006 (tpt) cc_final: 0.6886 (tpt) REVERT: A 460 ASN cc_start: 0.8766 (m110) cc_final: 0.8349 (m110) REVERT: B 9 TYR cc_start: 0.8458 (p90) cc_final: 0.7941 (p90) REVERT: B 18 HIS cc_start: 0.8152 (p-80) cc_final: 0.7872 (p-80) REVERT: B 64 GLU cc_start: 0.8667 (pt0) cc_final: 0.8399 (pt0) REVERT: B 82 GLN cc_start: 0.9325 (mt0) cc_final: 0.8769 (mm110) REVERT: B 103 ASP cc_start: 0.8959 (p0) cc_final: 0.8434 (p0) REVERT: B 188 ASP cc_start: 0.8107 (t0) cc_final: 0.7565 (t0) REVERT: B 219 GLU cc_start: 0.8215 (pt0) cc_final: 0.7851 (pt0) REVERT: B 267 GLU cc_start: 0.9237 (tt0) cc_final: 0.8824 (pt0) REVERT: B 296 LEU cc_start: 0.9162 (tp) cc_final: 0.8880 (tp) REVERT: B 331 GLU cc_start: 0.8915 (pm20) cc_final: 0.8713 (pm20) REVERT: B 340 MET cc_start: 0.8947 (mmm) cc_final: 0.8465 (mmm) REVERT: B 344 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8438 (mt-10) REVERT: B 383 LYS cc_start: 0.9455 (ttmm) cc_final: 0.9127 (ttpt) REVERT: B 398 MET cc_start: 0.9401 (mtm) cc_final: 0.8716 (mpp) REVERT: B 418 LYS cc_start: 0.8887 (mttt) cc_final: 0.8503 (mttt) REVERT: B 441 MET cc_start: 0.9407 (tmm) cc_final: 0.9086 (tmm) REVERT: B 447 LYS cc_start: 0.9281 (ttpt) cc_final: 0.8853 (mtmm) REVERT: C 19 LYS cc_start: 0.9234 (tppt) cc_final: 0.8755 (tppt) REVERT: C 26 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8437 (ttm) REVERT: C 37 ASN cc_start: 0.9312 (m-40) cc_final: 0.8880 (m-40) REVERT: C 46 ASP cc_start: 0.8299 (t0) cc_final: 0.7664 (t0) REVERT: C 60 LYS cc_start: 0.9535 (mmmm) cc_final: 0.9286 (mmmm) REVERT: C 77 ASP cc_start: 0.9297 (m-30) cc_final: 0.9062 (t70) REVERT: C 105 ASP cc_start: 0.9242 (p0) cc_final: 0.8997 (p0) REVERT: C 190 ASP cc_start: 0.7314 (OUTLIER) cc_final: 0.6672 (m-30) REVERT: C 259 MET cc_start: 0.7934 (mtp) cc_final: 0.7336 (ttm) REVERT: C 296 LEU cc_start: 0.8948 (tp) cc_final: 0.8732 (tp) REVERT: C 314 ARG cc_start: 0.8730 (mmt90) cc_final: 0.7920 (tpm170) REVERT: C 369 MET cc_start: 0.8552 (mpp) cc_final: 0.7899 (mpp) REVERT: C 398 MET cc_start: 0.9145 (mtm) cc_final: 0.8884 (mtt) REVERT: C 413 ASP cc_start: 0.8519 (t0) cc_final: 0.8277 (t0) REVERT: C 419 MET cc_start: 0.8269 (ptm) cc_final: 0.7942 (ptp) REVERT: C 441 MET cc_start: 0.9284 (tmm) cc_final: 0.9068 (ppp) REVERT: C 458 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7648 (ttt) REVERT: D 8 LYS cc_start: 0.9678 (mtmm) cc_final: 0.9409 (mttp) REVERT: D 15 LYS cc_start: 0.9412 (mttt) cc_final: 0.9038 (mtmm) REVERT: D 16 LYS cc_start: 0.9239 (mmmm) cc_final: 0.9020 (mmmm) REVERT: D 17 MET cc_start: 0.9382 (mmm) cc_final: 0.8467 (mmm) REVERT: D 18 HIS cc_start: 0.9559 (OUTLIER) cc_final: 0.8375 (m90) REVERT: D 32 ARG cc_start: 0.9091 (mtp-110) cc_final: 0.8761 (mtp-110) REVERT: D 36 ASP cc_start: 0.9503 (m-30) cc_final: 0.9161 (m-30) REVERT: D 46 ASP cc_start: 0.8203 (t0) cc_final: 0.7867 (t0) REVERT: D 49 LYS cc_start: 0.9053 (ptmm) cc_final: 0.8775 (pttp) REVERT: D 54 GLU cc_start: 0.9012 (tp30) cc_final: 0.8696 (tp30) REVERT: D 89 VAL cc_start: 0.9474 (t) cc_final: 0.9038 (p) REVERT: D 97 PHE cc_start: 0.9206 (m-10) cc_final: 0.8959 (m-10) REVERT: D 120 GLU cc_start: 0.9356 (tt0) cc_final: 0.9085 (mt-10) REVERT: D 121 ASP cc_start: 0.9303 (OUTLIER) cc_final: 0.9000 (t70) REVERT: D 173 ASN cc_start: 0.8912 (m-40) cc_final: 0.8550 (p0) REVERT: D 184 ARG cc_start: 0.8897 (ttp80) cc_final: 0.6865 (ttp80) REVERT: D 200 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.7812 (mm-30) REVERT: D 217 TRP cc_start: 0.8787 (m100) cc_final: 0.8572 (m-10) REVERT: D 241 ASP cc_start: 0.8675 (t0) cc_final: 0.8307 (t0) REVERT: D 251 LYS cc_start: 0.9115 (mptt) cc_final: 0.8877 (mmtp) REVERT: D 278 ASP cc_start: 0.9038 (OUTLIER) cc_final: 0.8754 (t0) REVERT: D 337 LYS cc_start: 0.9407 (tptm) cc_final: 0.9166 (tmmt) REVERT: D 341 ASP cc_start: 0.9264 (m-30) cc_final: 0.9043 (m-30) REVERT: D 347 MET cc_start: 0.9113 (mmt) cc_final: 0.8781 (mmt) REVERT: D 369 MET cc_start: 0.8737 (mpp) cc_final: 0.8372 (mpp) REVERT: D 370 GLU cc_start: 0.8596 (mt-10) cc_final: 0.7948 (mt-10) REVERT: D 374 GLN cc_start: 0.9281 (mt0) cc_final: 0.8743 (mp10) REVERT: D 380 ARG cc_start: 0.9115 (ttp-110) cc_final: 0.8808 (ttp-110) REVERT: D 409 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8128 (tm-30) REVERT: D 413 ASP cc_start: 0.8896 (t0) cc_final: 0.8614 (t0) REVERT: D 419 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8646 (ptm) REVERT: D 420 SER cc_start: 0.9575 (m) cc_final: 0.9353 (p) REVERT: D 422 GLU cc_start: 0.9302 (tp30) cc_final: 0.8936 (tp30) REVERT: D 423 GLU cc_start: 0.9119 (tt0) cc_final: 0.8758 (pt0) REVERT: D 458 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.7884 (tpt) REVERT: E 32 ARG cc_start: 0.8740 (tpp80) cc_final: 0.8481 (tpp80) REVERT: E 74 ASN cc_start: 0.8988 (t0) cc_final: 0.8652 (t0) REVERT: E 157 LYS cc_start: 0.9352 (mmmt) cc_final: 0.9064 (mmmt) REVERT: E 162 GLU cc_start: 0.9064 (mp0) cc_final: 0.8809 (mp0) REVERT: E 163 ASP cc_start: 0.8826 (OUTLIER) cc_final: 0.7933 (t0) REVERT: E 184 ARG cc_start: 0.9066 (ttp80) cc_final: 0.8485 (ttp80) REVERT: E 259 MET cc_start: 0.8956 (mmm) cc_final: 0.8628 (mmm) REVERT: E 267 GLU cc_start: 0.9327 (mm-30) cc_final: 0.9066 (mm-30) REVERT: E 340 MET cc_start: 0.9468 (OUTLIER) cc_final: 0.9111 (tpp) REVERT: E 346 GLN cc_start: 0.9479 (mt0) cc_final: 0.9278 (mt0) REVERT: E 370 GLU cc_start: 0.8259 (pm20) cc_final: 0.7761 (pm20) REVERT: E 419 MET cc_start: 0.8265 (ttm) cc_final: 0.7663 (ttm) REVERT: E 420 SER cc_start: 0.9521 (OUTLIER) cc_final: 0.9119 (p) REVERT: E 441 MET cc_start: 0.9079 (tmm) cc_final: 0.8738 (tmm) REVERT: E 454 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8339 (tm-30) REVERT: E 458 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7618 (tpp) REVERT: E 460 ASN cc_start: 0.9237 (m-40) cc_final: 0.8918 (m110) REVERT: F 26 MET cc_start: 0.9341 (mtp) cc_final: 0.9065 (ttt) REVERT: F 40 GLU cc_start: 0.9309 (mp0) cc_final: 0.9069 (mp0) REVERT: F 79 MET cc_start: 0.9225 (mtm) cc_final: 0.8978 (mtm) REVERT: F 83 ILE cc_start: 0.9524 (OUTLIER) cc_final: 0.9272 (mp) REVERT: F 163 ASP cc_start: 0.9305 (m-30) cc_final: 0.8690 (m-30) REVERT: F 177 ARG cc_start: 0.9207 (mmm-85) cc_final: 0.8880 (mmm-85) REVERT: F 184 ARG cc_start: 0.9305 (ttp-110) cc_final: 0.8676 (ttp80) REVERT: F 219 GLU cc_start: 0.8569 (tt0) cc_final: 0.8207 (pp20) REVERT: F 314 ARG cc_start: 0.3511 (tpm170) cc_final: 0.2923 (tpm170) REVERT: F 315 ASP cc_start: 0.8305 (m-30) cc_final: 0.7819 (p0) REVERT: F 322 ASN cc_start: 0.9216 (m110) cc_final: 0.9016 (m110) REVERT: F 340 MET cc_start: 0.9163 (mmm) cc_final: 0.8928 (mmm) REVERT: F 342 GLN cc_start: 0.9490 (pt0) cc_final: 0.8924 (pp30) REVERT: F 357 SER cc_start: 0.8532 (m) cc_final: 0.8247 (p) REVERT: F 374 GLN cc_start: 0.9184 (mt0) cc_final: 0.8870 (mt0) REVERT: F 413 ASP cc_start: 0.8948 (m-30) cc_final: 0.8480 (t70) REVERT: F 419 MET cc_start: 0.8596 (ppp) cc_final: 0.8097 (ppp) REVERT: F 460 ASN cc_start: 0.8899 (m-40) cc_final: 0.8526 (m-40) REVERT: G 32 ARG cc_start: 0.7603 (tpp-160) cc_final: 0.7052 (tpp-160) REVERT: G 74 ASN cc_start: 0.9592 (t0) cc_final: 0.9082 (t0) REVERT: G 99 MET cc_start: 0.9173 (ppp) cc_final: 0.8972 (tmm) REVERT: G 124 SER cc_start: 0.9622 (OUTLIER) cc_final: 0.9343 (p) REVERT: G 163 ASP cc_start: 0.9434 (m-30) cc_final: 0.9112 (t0) REVERT: G 262 MET cc_start: 0.8883 (mmp) cc_final: 0.8532 (mmp) REVERT: G 283 CYS cc_start: 0.8811 (m) cc_final: 0.8598 (m) REVERT: G 335 MET cc_start: 0.9112 (ttt) cc_final: 0.8826 (ttp) REVERT: G 344 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8900 (mt-10) REVERT: G 347 MET cc_start: 0.9075 (mmm) cc_final: 0.8626 (mpp) REVERT: G 460 ASN cc_start: 0.9069 (m-40) cc_final: 0.8656 (m110) REVERT: H 17 MET cc_start: 0.9626 (mmm) cc_final: 0.9093 (mmm) REVERT: H 26 MET cc_start: 0.9219 (mtm) cc_final: 0.8124 (mtm) REVERT: H 77 ASP cc_start: 0.9316 (m-30) cc_final: 0.9068 (m-30) REVERT: H 79 MET cc_start: 0.9111 (mmt) cc_final: 0.8749 (mmp) REVERT: H 185 GLU cc_start: 0.8476 (tm-30) cc_final: 0.7973 (tm-30) REVERT: H 200 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8460 (mp0) REVERT: H 326 GLU cc_start: 0.8075 (mp0) cc_final: 0.7530 (pm20) REVERT: H 328 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8909 (mp) REVERT: H 346 GLN cc_start: 0.9588 (mt0) cc_final: 0.9235 (mt0) REVERT: H 370 GLU cc_start: 0.8770 (tt0) cc_final: 0.7918 (tm-30) REVERT: H 380 ARG cc_start: 0.8845 (mtm-85) cc_final: 0.7909 (mtm-85) REVERT: H 409 GLU cc_start: 0.8224 (mp0) cc_final: 0.7964 (mp0) REVERT: H 423 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8986 (mt-10) REVERT: H 454 GLU cc_start: 0.9006 (mp0) cc_final: 0.8769 (mp0) REVERT: I 18 HIS cc_start: 0.9240 (OUTLIER) cc_final: 0.8769 (m90) REVERT: I 28 MET cc_start: 0.9212 (mtm) cc_final: 0.8802 (tmm) REVERT: I 79 MET cc_start: 0.9369 (mtm) cc_final: 0.8859 (mtm) REVERT: I 158 PHE cc_start: 0.8874 (t80) cc_final: 0.8600 (t80) REVERT: I 219 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8326 (tp30) REVERT: I 227 ASP cc_start: 0.9070 (m-30) cc_final: 0.8769 (m-30) REVERT: I 262 MET cc_start: 0.8509 (mmm) cc_final: 0.8084 (mmm) REVERT: I 280 GLU cc_start: 0.9116 (mm-30) cc_final: 0.8813 (mm-30) REVERT: I 335 MET cc_start: 0.9366 (ttt) cc_final: 0.8868 (tmm) REVERT: I 336 VAL cc_start: 0.9529 (OUTLIER) cc_final: 0.9166 (p) REVERT: I 340 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.8737 (mtm) REVERT: I 344 GLU cc_start: 0.8982 (tt0) cc_final: 0.8636 (tp30) REVERT: I 347 MET cc_start: 0.9444 (mtp) cc_final: 0.8889 (mtp) REVERT: I 398 MET cc_start: 0.8897 (mtm) cc_final: 0.8432 (mtt) REVERT: I 422 GLU cc_start: 0.9113 (tp30) cc_final: 0.8741 (tm-30) REVERT: I 441 MET cc_start: 0.9214 (ppp) cc_final: 0.8833 (ppp) REVERT: I 460 ASN cc_start: 0.8860 (m110) cc_final: 0.8575 (p0) REVERT: J 120 GLU cc_start: 0.9476 (pp20) cc_final: 0.9120 (pp20) REVERT: J 221 ASP cc_start: 0.9201 (m-30) cc_final: 0.8037 (t0) REVERT: J 227 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8245 (p0) REVERT: J 251 LYS cc_start: 0.9210 (mttp) cc_final: 0.8909 (mttt) REVERT: J 267 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8555 (mm-30) REVERT: J 281 GLU cc_start: 0.9282 (tp30) cc_final: 0.8864 (tp30) REVERT: J 342 GLN cc_start: 0.9593 (tt0) cc_final: 0.8443 (tm-30) REVERT: J 345 ARG cc_start: 0.8534 (ttp80) cc_final: 0.7917 (ttp80) REVERT: J 346 GLN cc_start: 0.9197 (mt0) cc_final: 0.7748 (mt0) REVERT: J 419 MET cc_start: 0.8226 (ptm) cc_final: 0.7924 (tmm) REVERT: K 26 MET cc_start: 0.9125 (mmm) cc_final: 0.8800 (mmm) REVERT: K 28 MET cc_start: 0.9044 (tpp) cc_final: 0.8697 (tpp) REVERT: K 60 LYS cc_start: 0.9508 (tppt) cc_final: 0.9204 (mttm) REVERT: K 86 ARG cc_start: 0.9064 (mmp80) cc_final: 0.8731 (mmt180) REVERT: K 97 PHE cc_start: 0.9477 (m-10) cc_final: 0.9167 (m-10) REVERT: K 120 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8701 (mm-30) REVERT: K 125 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8556 (pp) REVERT: K 157 LYS cc_start: 0.9256 (mmtm) cc_final: 0.9015 (mmtt) REVERT: K 169 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8070 (mm-30) REVERT: K 225 TYR cc_start: 0.7608 (m-80) cc_final: 0.7136 (m-80) REVERT: K 262 MET cc_start: 0.9120 (mmm) cc_final: 0.8196 (mmm) REVERT: K 275 ASN cc_start: 0.9573 (m110) cc_final: 0.9329 (m-40) REVERT: K 324 LYS cc_start: 0.9172 (mmmt) cc_final: 0.8927 (mmtt) REVERT: K 340 MET cc_start: 0.9241 (mmm) cc_final: 0.9024 (mmm) REVERT: K 345 ARG cc_start: 0.8571 (tmm-80) cc_final: 0.7988 (ttp80) REVERT: K 391 LYS cc_start: 0.9145 (tptp) cc_final: 0.8935 (tptp) REVERT: K 398 MET cc_start: 0.8890 (mtt) cc_final: 0.8550 (mtt) REVERT: K 409 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7846 (tm-30) REVERT: K 418 LYS cc_start: 0.8014 (mtmt) cc_final: 0.7358 (mtmt) REVERT: K 423 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8560 (mt-10) REVERT: K 460 ASN cc_start: 0.9237 (m-40) cc_final: 0.8850 (m-40) REVERT: L 15 LYS cc_start: 0.9734 (mmmm) cc_final: 0.9524 (mmmm) REVERT: L 16 LYS cc_start: 0.9382 (mmtt) cc_final: 0.9080 (mmmt) REVERT: L 77 ASP cc_start: 0.8890 (m-30) cc_final: 0.8489 (m-30) REVERT: L 239 GLN cc_start: 0.9375 (pm20) cc_final: 0.9016 (pm20) REVERT: L 280 GLU cc_start: 0.8851 (tp30) cc_final: 0.8249 (tp30) REVERT: L 322 ASN cc_start: 0.9433 (m-40) cc_final: 0.9168 (m-40) REVERT: L 342 GLN cc_start: 0.9392 (tt0) cc_final: 0.8949 (tt0) REVERT: L 345 ARG cc_start: 0.9397 (tmm-80) cc_final: 0.8998 (tmm-80) REVERT: L 347 MET cc_start: 0.9046 (mtt) cc_final: 0.8580 (mtm) REVERT: L 369 MET cc_start: 0.8821 (mtm) cc_final: 0.8489 (mpp) REVERT: L 383 LYS cc_start: 0.9537 (mmmm) cc_final: 0.9085 (tppt) REVERT: L 411 ASN cc_start: 0.8901 (t0) cc_final: 0.8597 (t0) REVERT: L 419 MET cc_start: 0.8531 (mtt) cc_final: 0.7829 (mmm) REVERT: L 452 TYR cc_start: 0.9311 (p90) cc_final: 0.8578 (p90) REVERT: L 458 MET cc_start: 0.7936 (tpt) cc_final: 0.7726 (tpt) REVERT: M 17 MET cc_start: 0.8444 (mpp) cc_final: 0.8119 (mmm) REVERT: M 173 ASP cc_start: 0.9073 (m-30) cc_final: 0.8824 (m-30) REVERT: M 207 ARG cc_start: 0.9031 (tpp80) cc_final: 0.8779 (tpp80) REVERT: N 170 ARG cc_start: 0.9175 (tpp80) cc_final: 0.8852 (ttm170) REVERT: N 235 THR cc_start: 0.9451 (OUTLIER) cc_final: 0.9251 (t) REVERT: N 271 GLU cc_start: 0.8434 (mp0) cc_final: 0.8133 (mp0) REVERT: N 290 LYS cc_start: 0.8906 (mttp) cc_final: 0.8572 (mtpp) REVERT: O 77 ARG cc_start: 0.8750 (mtm110) cc_final: 0.8487 (mtm110) REVERT: O 99 MET cc_start: 0.5769 (OUTLIER) cc_final: 0.5209 (ppp) REVERT: O 100 LEU cc_start: 0.4156 (OUTLIER) cc_final: 0.3520 (pp) REVERT: O 121 ASP cc_start: 0.8770 (t0) cc_final: 0.8345 (t0) REVERT: O 123 MET cc_start: 0.9305 (mmt) cc_final: 0.9004 (mmm) REVERT: O 124 GLN cc_start: 0.9556 (tt0) cc_final: 0.9125 (tt0) REVERT: O 126 MET cc_start: 0.9434 (mtm) cc_final: 0.8949 (mtm) REVERT: O 207 ARG cc_start: 0.8768 (mmm-85) cc_final: 0.8458 (mmm-85) REVERT: O 266 ARG cc_start: 0.9415 (mmm-85) cc_final: 0.9152 (tpp80) REVERT: P 21 LEU cc_start: 0.8435 (tp) cc_final: 0.8171 (tp) REVERT: P 22 ASP cc_start: 0.8899 (p0) cc_final: 0.8443 (p0) REVERT: P 116 GLN cc_start: 0.9218 (OUTLIER) cc_final: 0.8831 (mm110) REVERT: P 229 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8614 (tm-30) REVERT: P 290 LYS cc_start: 0.9035 (mmmm) cc_final: 0.8514 (mmmm) REVERT: Q 271 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7483 (mt-10) REVERT: Q 290 LYS cc_start: 0.9225 (mmmm) cc_final: 0.8899 (mmmm) REVERT: Q 321 LYS cc_start: 0.9098 (ptmt) cc_final: 0.8871 (ptmm) REVERT: R 15 LYS cc_start: 0.6336 (OUTLIER) cc_final: 0.5132 (pttm) REVERT: R 46 ASP cc_start: 0.7663 (t0) cc_final: 0.7381 (t0) REVERT: R 84 ILE cc_start: 0.9837 (tp) cc_final: 0.9576 (tp) REVERT: R 105 LYS cc_start: 0.8993 (mmmm) cc_final: 0.8671 (mmmm) REVERT: R 109 GLU cc_start: 0.8809 (tt0) cc_final: 0.8518 (tt0) REVERT: R 126 MET cc_start: 0.9399 (mtm) cc_final: 0.9169 (mtm) REVERT: S 155 MET cc_start: 0.8677 (tpp) cc_final: 0.8473 (mmm) REVERT: S 199 TYR cc_start: 0.8516 (m-80) cc_final: 0.8021 (m-80) REVERT: T 20 VAL cc_start: 0.8727 (OUTLIER) cc_final: 0.8504 (t) REVERT: T 39 ARG cc_start: 0.7785 (ptm160) cc_final: 0.7473 (ptm160) REVERT: T 81 ASP cc_start: 0.9091 (t70) cc_final: 0.8596 (p0) REVERT: T 187 LEU cc_start: 0.9404 (tp) cc_final: 0.9164 (tp) REVERT: T 246 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7424 (mt-10) REVERT: U 105 LYS cc_start: 0.9515 (mttt) cc_final: 0.9255 (mmmm) REVERT: U 114 ILE cc_start: 0.9745 (mt) cc_final: 0.9437 (tt) REVERT: U 207 ARG cc_start: 0.9184 (mmm-85) cc_final: 0.8911 (mmm-85) REVERT: V 164 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8603 (pt0) outliers start: 270 outliers final: 183 residues processed: 1726 average time/residue: 0.6357 time to fit residues: 1851.7335 Evaluate side-chains 1718 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 1506 time to evaluate : 5.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 26 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain D residue 278 ASP Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain E residue 18 HIS Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 340 MET Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 412 SER Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 458 MET Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 221 ASP Chi-restraints excluded: chain F residue 264 ASP Chi-restraints excluded: chain F residue 299 HIS Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 377 VAL Chi-restraints excluded: chain F residue 420 SER Chi-restraints excluded: chain F residue 454 GLU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 165 LEU Chi-restraints excluded: chain G residue 256 THR Chi-restraints excluded: chain G residue 286 CYS Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 374 GLN Chi-restraints excluded: chain G residue 414 PHE Chi-restraints excluded: chain G residue 436 ILE Chi-restraints excluded: chain H residue 8 LYS Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 194 TYR Chi-restraints excluded: chain H residue 216 THR Chi-restraints excluded: chain H residue 226 VAL Chi-restraints excluded: chain H residue 283 CYS Chi-restraints excluded: chain H residue 286 CYS Chi-restraints excluded: chain H residue 290 THR Chi-restraints excluded: chain H residue 328 LEU Chi-restraints excluded: chain H residue 342 GLN Chi-restraints excluded: chain H residue 354 LEU Chi-restraints excluded: chain H residue 419 MET Chi-restraints excluded: chain H residue 447 LYS Chi-restraints excluded: chain I residue 13 ASP Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 46 ASP Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 291 LEU Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 336 VAL Chi-restraints excluded: chain I residue 340 MET Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain I residue 406 ILE Chi-restraints excluded: chain I residue 419 MET Chi-restraints excluded: chain I residue 456 GLU Chi-restraints excluded: chain J residue 79 MET Chi-restraints excluded: chain J residue 121 ASP Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 227 ASP Chi-restraints excluded: chain J residue 236 ASP Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 299 HIS Chi-restraints excluded: chain J residue 336 VAL Chi-restraints excluded: chain J residue 350 LEU Chi-restraints excluded: chain J residue 354 LEU Chi-restraints excluded: chain K residue 6 ASN Chi-restraints excluded: chain K residue 23 HIS Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 209 ASP Chi-restraints excluded: chain K residue 230 ILE Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 297 THR Chi-restraints excluded: chain K residue 304 VAL Chi-restraints excluded: chain K residue 405 LYS Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 164 ILE Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 348 VAL Chi-restraints excluded: chain L residue 374 GLN Chi-restraints excluded: chain L residue 377 VAL Chi-restraints excluded: chain M residue 12 TRP Chi-restraints excluded: chain M residue 86 VAL Chi-restraints excluded: chain M residue 152 THR Chi-restraints excluded: chain M residue 312 ASP Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 68 ASN Chi-restraints excluded: chain N residue 102 TRP Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain N residue 156 THR Chi-restraints excluded: chain N residue 178 VAL Chi-restraints excluded: chain N residue 235 THR Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 313 THR Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 74 LYS Chi-restraints excluded: chain O residue 99 MET Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 187 LEU Chi-restraints excluded: chain P residue 116 GLN Chi-restraints excluded: chain P residue 127 LEU Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain P residue 166 ILE Chi-restraints excluded: chain P residue 178 VAL Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 216 ILE Chi-restraints excluded: chain P residue 276 LEU Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 81 ASP Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain R residue 10 ASN Chi-restraints excluded: chain R residue 11 ASP Chi-restraints excluded: chain R residue 15 LYS Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 224 VAL Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 37 ILE Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain S residue 123 MET Chi-restraints excluded: chain S residue 225 SER Chi-restraints excluded: chain S residue 244 LEU Chi-restraints excluded: chain S residue 245 ILE Chi-restraints excluded: chain S residue 320 THR Chi-restraints excluded: chain T residue 6 LEU Chi-restraints excluded: chain T residue 20 VAL Chi-restraints excluded: chain T residue 209 ASP Chi-restraints excluded: chain T residue 235 THR Chi-restraints excluded: chain T residue 236 LEU Chi-restraints excluded: chain U residue 59 LEU Chi-restraints excluded: chain U residue 70 ASP Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 243 ILE Chi-restraints excluded: chain U residue 313 THR Chi-restraints excluded: chain U residue 316 VAL Chi-restraints excluded: chain V residue 127 LEU Chi-restraints excluded: chain V residue 164 GLN Chi-restraints excluded: chain V residue 244 LEU Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 256 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 855 random chunks: chunk 798 optimal weight: 30.0000 chunk 260 optimal weight: 9.9990 chunk 647 optimal weight: 9.9990 chunk 401 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 610 optimal weight: 6.9990 chunk 463 optimal weight: 20.0000 chunk 391 optimal weight: 7.9990 chunk 369 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 844 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN C 18 HIS ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN ** F 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 342 GLN H 74 ASN ** H 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 220 ASN ** J 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 460 ASN ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 ASN K 275 ASN L 411 ASN ** M 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 157 GLN S 117 GLN ** U 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 247 GLN ** V 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.083054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.068082 restraints weight = 250820.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.070132 restraints weight = 144847.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.071549 restraints weight = 99322.634| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 68177 Z= 0.301 Angle : 0.672 11.179 92470 Z= 0.346 Chirality : 0.043 0.215 10048 Planarity : 0.004 0.072 12237 Dihedral : 4.710 59.716 9264 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.64 % Favored : 95.35 % Rotamer: Outliers : 3.77 % Allowed : 21.19 % Favored : 75.04 % 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: -0.08 (0.09), residues: 8507 helix: 1.24 (0.09), residues: 3200 sheet: -0.34 (0.14), residues: 1540 loop : -1.03 (0.10), residues: 3767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP Q 12 HIS 0.008 0.001 HIS H 299 PHE 0.031 0.002 PHE I 90 TYR 0.027 0.001 TYR Q 274 ARG 0.016 0.001 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17014 Ramachandran restraints generated. 8507 Oldfield, 0 Emsley, 8507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17014 Ramachandran restraints generated. 8507 Oldfield, 0 Emsley, 8507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1817 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 263 poor density : 1554 time to evaluate : 7.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 12 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8566 (mt-10) REVERT: A 15 LYS cc_start: 0.9707 (mmtt) cc_final: 0.9482 (mtmt) REVERT: A 18 HIS cc_start: 0.9284 (m90) cc_final: 0.8584 (m90) REVERT: A 29 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8487 (tm-30) REVERT: A 32 ARG cc_start: 0.8411 (ttp80) cc_final: 0.8121 (ttp80) REVERT: A 60 LYS cc_start: 0.9577 (mmtt) cc_final: 0.9317 (mtmm) REVERT: A 163 ASP cc_start: 0.9233 (m-30) cc_final: 0.8675 (t0) REVERT: A 170 ARG cc_start: 0.8440 (ttm-80) cc_final: 0.8043 (ttp-170) REVERT: A 198 LYS cc_start: 0.9208 (mmmt) cc_final: 0.8890 (mmmt) REVERT: A 200 GLU cc_start: 0.8330 (mp0) cc_final: 0.7991 (mp0) REVERT: A 214 GLN cc_start: 0.9006 (pp30) cc_final: 0.8339 (pp30) REVERT: A 241 ASP cc_start: 0.8664 (p0) cc_final: 0.8140 (p0) REVERT: A 251 LYS cc_start: 0.9104 (ttpp) cc_final: 0.8881 (ttpp) REVERT: A 331 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7569 (tm-30) REVERT: A 337 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8904 (tttp) REVERT: A 345 ARG cc_start: 0.9337 (ttp-110) cc_final: 0.9074 (ttp-110) REVERT: A 346 GLN cc_start: 0.9057 (mt0) cc_final: 0.8665 (mp10) REVERT: A 369 MET cc_start: 0.8746 (mtm) cc_final: 0.8447 (ptp) REVERT: A 419 MET cc_start: 0.8566 (ppp) cc_final: 0.8052 (ppp) REVERT: A 422 GLU cc_start: 0.9378 (tp30) cc_final: 0.9136 (tp30) REVERT: A 458 MET cc_start: 0.8014 (tpt) cc_final: 0.7494 (tpp) REVERT: A 460 ASN cc_start: 0.8808 (m110) cc_final: 0.8395 (m110) REVERT: B 9 TYR cc_start: 0.8520 (p90) cc_final: 0.8004 (p90) REVERT: B 64 GLU cc_start: 0.8692 (pt0) cc_final: 0.8409 (pt0) REVERT: B 82 GLN cc_start: 0.9332 (mt0) cc_final: 0.8871 (mm-40) REVERT: B 188 ASP cc_start: 0.8283 (t0) cc_final: 0.8016 (t0) REVERT: B 219 GLU cc_start: 0.8219 (pt0) cc_final: 0.7870 (pt0) REVERT: B 296 LEU cc_start: 0.9178 (tp) cc_final: 0.8887 (tp) REVERT: B 340 MET cc_start: 0.8917 (mmm) cc_final: 0.8337 (mmm) REVERT: B 344 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8376 (mt-10) REVERT: B 383 LYS cc_start: 0.9473 (ttmm) cc_final: 0.9141 (ttpt) REVERT: B 398 MET cc_start: 0.9332 (mtm) cc_final: 0.8530 (mpp) REVERT: B 418 LYS cc_start: 0.8783 (mttt) cc_final: 0.8369 (mttt) REVERT: B 441 MET cc_start: 0.9408 (tmm) cc_final: 0.9063 (tmm) REVERT: B 458 MET cc_start: 0.8289 (tpt) cc_final: 0.7988 (tpt) REVERT: C 19 LYS cc_start: 0.9253 (tppt) cc_final: 0.8768 (tppt) REVERT: C 29 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8348 (tm-30) REVERT: C 37 ASN cc_start: 0.9295 (m-40) cc_final: 0.8946 (m110) REVERT: C 60 LYS cc_start: 0.9549 (mmmm) cc_final: 0.9285 (mmmm) REVERT: C 77 ASP cc_start: 0.9339 (m-30) cc_final: 0.9090 (t70) REVERT: C 105 ASP cc_start: 0.9270 (p0) cc_final: 0.9024 (p0) REVERT: C 190 ASP cc_start: 0.7398 (OUTLIER) cc_final: 0.6721 (m-30) REVERT: C 296 LEU cc_start: 0.8964 (tp) cc_final: 0.8753 (tp) REVERT: C 310 VAL cc_start: 0.7818 (OUTLIER) cc_final: 0.7585 (m) REVERT: C 314 ARG cc_start: 0.8740 (mmt90) cc_final: 0.7934 (tpm170) REVERT: C 369 MET cc_start: 0.8387 (mpp) cc_final: 0.7769 (mpp) REVERT: C 398 MET cc_start: 0.9197 (mtm) cc_final: 0.8633 (mpp) REVERT: C 413 ASP cc_start: 0.8654 (t0) cc_final: 0.8333 (t0) REVERT: C 458 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7436 (ttt) REVERT: D 15 LYS cc_start: 0.9419 (mttt) cc_final: 0.9013 (mtmm) REVERT: D 16 LYS cc_start: 0.9276 (mmmm) cc_final: 0.9016 (mmmm) REVERT: D 17 MET cc_start: 0.9399 (mmm) cc_final: 0.8474 (mmm) REVERT: D 18 HIS cc_start: 0.9564 (OUTLIER) cc_final: 0.8366 (m90) REVERT: D 29 GLU cc_start: 0.8356 (tm-30) cc_final: 0.8145 (tm-30) REVERT: D 32 ARG cc_start: 0.9127 (mtp-110) cc_final: 0.8774 (mtp-110) REVERT: D 36 ASP cc_start: 0.9507 (m-30) cc_final: 0.9156 (m-30) REVERT: D 54 GLU cc_start: 0.9032 (tp30) cc_final: 0.8721 (tp30) REVERT: D 97 PHE cc_start: 0.9294 (m-10) cc_final: 0.9059 (m-10) REVERT: D 120 GLU cc_start: 0.9321 (tt0) cc_final: 0.9061 (mt-10) REVERT: D 121 ASP cc_start: 0.9296 (OUTLIER) cc_final: 0.8991 (t70) REVERT: D 173 ASN cc_start: 0.9043 (m-40) cc_final: 0.8619 (p0) REVERT: D 184 ARG cc_start: 0.8904 (ttp80) cc_final: 0.8548 (ttp80) REVERT: D 217 TRP cc_start: 0.8891 (m100) cc_final: 0.8683 (m-10) REVERT: D 259 MET cc_start: 0.8853 (ptp) cc_final: 0.8636 (ptp) REVERT: D 278 ASP cc_start: 0.9009 (OUTLIER) cc_final: 0.8788 (t0) REVERT: D 337 LYS cc_start: 0.9370 (tptm) cc_final: 0.8901 (tptm) REVERT: D 341 ASP cc_start: 0.9289 (m-30) cc_final: 0.8856 (m-30) REVERT: D 347 MET cc_start: 0.9114 (mmt) cc_final: 0.8740 (mmt) REVERT: D 369 MET cc_start: 0.8856 (mpp) cc_final: 0.8343 (mpp) REVERT: D 374 GLN cc_start: 0.9288 (mt0) cc_final: 0.8717 (mp10) REVERT: D 380 ARG cc_start: 0.9174 (ttp-110) cc_final: 0.8844 (ttp-110) REVERT: D 409 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8287 (tm-30) REVERT: D 419 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8582 (ptm) REVERT: D 420 SER cc_start: 0.9585 (m) cc_final: 0.9345 (p) REVERT: D 422 GLU cc_start: 0.9357 (tp30) cc_final: 0.9062 (tp30) REVERT: D 423 GLU cc_start: 0.9144 (tt0) cc_final: 0.8762 (pt0) REVERT: D 458 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.7873 (tpt) REVERT: E 32 ARG cc_start: 0.8766 (tpp80) cc_final: 0.8488 (tpp80) REVERT: E 74 ASN cc_start: 0.8990 (t0) cc_final: 0.8221 (t0) REVERT: E 157 LYS cc_start: 0.9348 (mmmt) cc_final: 0.8998 (mmmt) REVERT: E 162 GLU cc_start: 0.9121 (mp0) cc_final: 0.8840 (mp0) REVERT: E 163 ASP cc_start: 0.8861 (OUTLIER) cc_final: 0.8037 (t0) REVERT: E 184 ARG cc_start: 0.9063 (ttp80) cc_final: 0.8600 (ttp80) REVERT: E 259 MET cc_start: 0.8999 (mmm) cc_final: 0.8723 (mmm) REVERT: E 267 GLU cc_start: 0.9320 (mm-30) cc_final: 0.9037 (mm-30) REVERT: E 340 MET cc_start: 0.9484 (OUTLIER) cc_final: 0.9119 (tpp) REVERT: E 346 GLN cc_start: 0.9497 (mt0) cc_final: 0.9054 (mt0) REVERT: E 370 GLU cc_start: 0.8236 (pm20) cc_final: 0.7747 (pm20) REVERT: E 419 MET cc_start: 0.8297 (ttm) cc_final: 0.7640 (ttm) REVERT: E 420 SER cc_start: 0.9526 (OUTLIER) cc_final: 0.9123 (p) REVERT: E 441 MET cc_start: 0.9141 (tmm) cc_final: 0.8797 (tmm) REVERT: E 454 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8359 (tm-30) REVERT: E 458 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7583 (tpt) REVERT: E 460 ASN cc_start: 0.9255 (m-40) cc_final: 0.8994 (m110) REVERT: F 26 MET cc_start: 0.9382 (mtp) cc_final: 0.9039 (ttt) REVERT: F 79 MET cc_start: 0.9268 (mtm) cc_final: 0.9010 (mtm) REVERT: F 83 ILE cc_start: 0.9516 (OUTLIER) cc_final: 0.9269 (mp) REVERT: F 86 ARG cc_start: 0.7853 (mmt-90) cc_final: 0.7537 (mmt-90) REVERT: F 163 ASP cc_start: 0.9317 (m-30) cc_final: 0.8684 (m-30) REVERT: F 184 ARG cc_start: 0.9307 (ttp-110) cc_final: 0.8691 (ttp80) REVERT: F 315 ASP cc_start: 0.8294 (m-30) cc_final: 0.7549 (p0) REVERT: F 342 GLN cc_start: 0.9485 (OUTLIER) cc_final: 0.8974 (pp30) REVERT: F 346 GLN cc_start: 0.9404 (mt0) cc_final: 0.8063 (mt0) REVERT: F 357 SER cc_start: 0.8532 (m) cc_final: 0.8252 (p) REVERT: F 370 GLU cc_start: 0.8595 (mt-10) cc_final: 0.7990 (mp0) REVERT: F 374 GLN cc_start: 0.9259 (mt0) cc_final: 0.8902 (mt0) REVERT: F 380 ARG cc_start: 0.9185 (ttp80) cc_final: 0.8575 (ttt90) REVERT: F 413 ASP cc_start: 0.8994 (m-30) cc_final: 0.8510 (t70) REVERT: F 419 MET cc_start: 0.8604 (ppp) cc_final: 0.8102 (ppp) REVERT: F 460 ASN cc_start: 0.8929 (m-40) cc_final: 0.8562 (m110) REVERT: G 32 ARG cc_start: 0.7678 (tpp-160) cc_final: 0.7083 (tpp-160) REVERT: G 74 ASN cc_start: 0.9592 (t0) cc_final: 0.9077 (t0) REVERT: G 99 MET cc_start: 0.9097 (ppp) cc_final: 0.8868 (tmm) REVERT: G 124 SER cc_start: 0.9558 (OUTLIER) cc_final: 0.9240 (p) REVERT: G 163 ASP cc_start: 0.9369 (m-30) cc_final: 0.9112 (t0) REVERT: G 262 MET cc_start: 0.8839 (mmp) cc_final: 0.8518 (mmp) REVERT: G 280 GLU cc_start: 0.9336 (mm-30) cc_final: 0.8775 (tp30) REVERT: G 283 CYS cc_start: 0.8809 (m) cc_final: 0.8388 (m) REVERT: G 335 MET cc_start: 0.9081 (ttt) cc_final: 0.8777 (ttt) REVERT: G 347 MET cc_start: 0.9076 (mmm) cc_final: 0.8625 (mpp) REVERT: G 354 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.6681 (pt) REVERT: G 405 LYS cc_start: 0.9320 (mtmm) cc_final: 0.9063 (mtmm) REVERT: G 460 ASN cc_start: 0.9113 (m-40) cc_final: 0.8686 (m110) REVERT: H 17 MET cc_start: 0.9622 (mmm) cc_final: 0.9048 (mmm) REVERT: H 26 MET cc_start: 0.9255 (mtm) cc_final: 0.8423 (mtm) REVERT: H 29 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8201 (tm-30) REVERT: H 77 ASP cc_start: 0.9352 (m-30) cc_final: 0.9110 (m-30) REVERT: H 79 MET cc_start: 0.9108 (mmt) cc_final: 0.8751 (mmp) REVERT: H 185 GLU cc_start: 0.8432 (tm-30) cc_final: 0.7960 (tm-30) REVERT: H 200 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8334 (mp0) REVERT: H 259 MET cc_start: 0.7859 (ttm) cc_final: 0.7006 (ttt) REVERT: H 326 GLU cc_start: 0.8102 (mp0) cc_final: 0.7572 (pm20) REVERT: H 346 GLN cc_start: 0.9599 (mt0) cc_final: 0.9274 (mt0) REVERT: H 370 GLU cc_start: 0.8747 (tt0) cc_final: 0.7886 (tm-30) REVERT: H 380 ARG cc_start: 0.8896 (mtm-85) cc_final: 0.8032 (mtm-85) REVERT: H 409 GLU cc_start: 0.8250 (mp0) cc_final: 0.8047 (mp0) REVERT: H 423 GLU cc_start: 0.9234 (mt-10) cc_final: 0.8992 (mt-10) REVERT: H 454 GLU cc_start: 0.9046 (mp0) cc_final: 0.8809 (mp0) REVERT: I 16 LYS cc_start: 0.9306 (mmtm) cc_final: 0.8960 (mmtm) REVERT: I 18 HIS cc_start: 0.9260 (OUTLIER) cc_final: 0.8779 (m90) REVERT: I 28 MET cc_start: 0.9273 (mtm) cc_final: 0.8729 (tmm) REVERT: I 79 MET cc_start: 0.9399 (mtm) cc_final: 0.8909 (mtm) REVERT: I 90 PHE cc_start: 0.8601 (t80) cc_final: 0.8287 (t80) REVERT: I 109 LEU cc_start: 0.9168 (tp) cc_final: 0.8898 (tt) REVERT: I 158 PHE cc_start: 0.8888 (t80) cc_final: 0.8622 (t80) REVERT: I 219 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8365 (tp30) REVERT: I 227 ASP cc_start: 0.9032 (m-30) cc_final: 0.8709 (m-30) REVERT: I 259 MET cc_start: 0.8551 (ttp) cc_final: 0.8264 (ttp) REVERT: I 262 MET cc_start: 0.8504 (mmm) cc_final: 0.8074 (mmm) REVERT: I 280 GLU cc_start: 0.9167 (mm-30) cc_final: 0.8797 (mm-30) REVERT: I 340 MET cc_start: 0.9246 (OUTLIER) cc_final: 0.8707 (mtm) REVERT: I 347 MET cc_start: 0.9437 (mtp) cc_final: 0.8981 (mtp) REVERT: I 398 MET cc_start: 0.8919 (mtm) cc_final: 0.8433 (mtt) REVERT: I 406 ILE cc_start: 0.9564 (OUTLIER) cc_final: 0.9331 (mp) REVERT: I 422 GLU cc_start: 0.9172 (tp30) cc_final: 0.8766 (tm-30) REVERT: I 453 LEU cc_start: 0.9628 (mt) cc_final: 0.9420 (mt) REVERT: I 458 MET cc_start: 0.7926 (tpp) cc_final: 0.7449 (mmm) REVERT: I 460 ASN cc_start: 0.8854 (m110) cc_final: 0.8538 (p0) REVERT: J 219 GLU cc_start: 0.8711 (pp20) cc_final: 0.8321 (pp20) REVERT: J 221 ASP cc_start: 0.9156 (m-30) cc_final: 0.7974 (t0) REVERT: J 227 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.8285 (p0) REVERT: J 267 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8607 (mm-30) REVERT: J 342 GLN cc_start: 0.9609 (tt0) cc_final: 0.8454 (tm-30) REVERT: J 345 ARG cc_start: 0.8581 (ttp80) cc_final: 0.8013 (ttp80) REVERT: J 346 GLN cc_start: 0.9235 (mt0) cc_final: 0.7788 (mt0) REVERT: J 419 MET cc_start: 0.8329 (ptm) cc_final: 0.7997 (tmm) REVERT: J 458 MET cc_start: 0.7169 (ttt) cc_final: 0.6532 (ttt) REVERT: K 26 MET cc_start: 0.9214 (mmm) cc_final: 0.8844 (mmm) REVERT: K 28 MET cc_start: 0.9054 (tpp) cc_final: 0.8723 (tpp) REVERT: K 60 LYS cc_start: 0.9470 (tppt) cc_final: 0.9231 (mttp) REVERT: K 86 ARG cc_start: 0.9090 (mmp80) cc_final: 0.8726 (mmt180) REVERT: K 97 PHE cc_start: 0.9505 (m-10) cc_final: 0.9157 (m-10) REVERT: K 120 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8704 (mm-30) REVERT: K 125 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8523 (pp) REVERT: K 169 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8153 (mt-10) REVERT: K 176 LYS cc_start: 0.9409 (OUTLIER) cc_final: 0.9026 (mmmt) REVERT: K 225 TYR cc_start: 0.7587 (m-80) cc_final: 0.7149 (m-80) REVERT: K 262 MET cc_start: 0.9121 (mmm) cc_final: 0.8296 (mmm) REVERT: K 275 ASN cc_start: 0.9547 (m-40) cc_final: 0.9257 (m-40) REVERT: K 324 LYS cc_start: 0.9225 (mmmt) cc_final: 0.8919 (mmtt) REVERT: K 345 ARG cc_start: 0.8646 (tmm-80) cc_final: 0.8090 (ttp80) REVERT: K 369 MET cc_start: 0.8942 (mmt) cc_final: 0.8681 (mmp) REVERT: K 374 GLN cc_start: 0.9358 (mt0) cc_final: 0.9137 (mt0) REVERT: K 391 LYS cc_start: 0.9155 (tptp) cc_final: 0.8930 (tptp) REVERT: K 398 MET cc_start: 0.8890 (mtt) cc_final: 0.8527 (mtt) REVERT: K 409 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7862 (tm-30) REVERT: K 418 LYS cc_start: 0.7962 (mtmt) cc_final: 0.7213 (mtmt) REVERT: K 422 GLU cc_start: 0.9432 (OUTLIER) cc_final: 0.9180 (tp30) REVERT: K 423 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8588 (mt-10) REVERT: K 458 MET cc_start: 0.8723 (tmm) cc_final: 0.8282 (tpt) REVERT: K 460 ASN cc_start: 0.9257 (m-40) cc_final: 0.8868 (m-40) REVERT: L 16 LYS cc_start: 0.9374 (mmtt) cc_final: 0.9065 (mmmt) REVERT: L 17 MET cc_start: 0.9553 (mmm) cc_final: 0.9141 (mmm) REVERT: L 19 LYS cc_start: 0.9346 (tppt) cc_final: 0.9083 (tppt) REVERT: L 32 ARG cc_start: 0.8483 (ttp80) cc_final: 0.8279 (ttp80) REVERT: L 77 ASP cc_start: 0.8923 (m-30) cc_final: 0.8516 (m-30) REVERT: L 109 LEU cc_start: 0.9285 (tt) cc_final: 0.8994 (tt) REVERT: L 239 GLN cc_start: 0.9443 (pm20) cc_final: 0.9071 (pm20) REVERT: L 322 ASN cc_start: 0.9341 (m-40) cc_final: 0.9082 (m-40) REVERT: L 342 GLN cc_start: 0.9344 (tt0) cc_final: 0.8844 (tt0) REVERT: L 345 ARG cc_start: 0.9399 (tmm-80) cc_final: 0.9022 (tmm-80) REVERT: L 347 MET cc_start: 0.9080 (mtt) cc_final: 0.8602 (mtm) REVERT: L 369 MET cc_start: 0.8895 (mtm) cc_final: 0.8561 (mpp) REVERT: L 383 LYS cc_start: 0.9564 (mmmm) cc_final: 0.9088 (tppt) REVERT: L 411 ASN cc_start: 0.8955 (t0) cc_final: 0.8553 (t0) REVERT: L 419 MET cc_start: 0.8517 (mtt) cc_final: 0.7883 (mmm) REVERT: L 423 GLU cc_start: 0.9205 (OUTLIER) cc_final: 0.8723 (pt0) REVERT: L 452 TYR cc_start: 0.9328 (p90) cc_final: 0.8596 (p90) REVERT: M 15 LYS cc_start: 0.7951 (pttt) cc_final: 0.7494 (pttt) REVERT: M 99 MET cc_start: 0.7667 (pmm) cc_final: 0.7373 (pmm) REVERT: M 173 ASP cc_start: 0.9007 (m-30) cc_final: 0.8774 (m-30) REVERT: M 207 ARG cc_start: 0.9077 (tpp80) cc_final: 0.8783 (tpp80) REVERT: M 276 LEU cc_start: 0.9614 (OUTLIER) cc_final: 0.9351 (mp) REVERT: N 170 ARG cc_start: 0.9187 (tpp80) cc_final: 0.8962 (ttm170) REVERT: N 235 THR cc_start: 0.9447 (OUTLIER) cc_final: 0.9246 (t) REVERT: N 271 GLU cc_start: 0.8493 (mp0) cc_final: 0.8183 (mp0) REVERT: N 290 LYS cc_start: 0.8913 (mttp) cc_final: 0.8591 (mtpp) REVERT: O 77 ARG cc_start: 0.8752 (mtm110) cc_final: 0.8475 (mtm110) REVERT: O 99 MET cc_start: 0.5801 (OUTLIER) cc_final: 0.5230 (ppp) REVERT: O 100 LEU cc_start: 0.4117 (OUTLIER) cc_final: 0.3621 (pt) REVERT: O 121 ASP cc_start: 0.8767 (t0) cc_final: 0.8380 (t0) REVERT: O 123 MET cc_start: 0.9325 (mmt) cc_final: 0.9077 (mmm) REVERT: P 22 ASP cc_start: 0.8924 (p0) cc_final: 0.8603 (p0) REVERT: P 116 GLN cc_start: 0.9225 (OUTLIER) cc_final: 0.8787 (mm110) REVERT: P 229 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8613 (tm-30) REVERT: P 290 LYS cc_start: 0.9015 (mmmm) cc_final: 0.8597 (mmmm) REVERT: Q 26 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8482 (tm-30) REVERT: Q 39 ARG cc_start: 0.8383 (mtm110) cc_final: 0.8042 (mtm110) REVERT: Q 246 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8114 (mt-10) REVERT: Q 271 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7671 (mt-10) REVERT: Q 290 LYS cc_start: 0.9235 (mmmm) cc_final: 0.8919 (mmmm) REVERT: Q 321 LYS cc_start: 0.9102 (ptmt) cc_final: 0.8876 (ptmm) REVERT: R 15 LYS cc_start: 0.4976 (OUTLIER) cc_final: 0.3992 (pttm) REVERT: R 46 ASP cc_start: 0.7684 (t0) cc_final: 0.7465 (t0) REVERT: R 84 ILE cc_start: 0.9837 (tp) cc_final: 0.9551 (tp) REVERT: R 105 LYS cc_start: 0.8981 (mmmm) cc_final: 0.8700 (mmmm) REVERT: R 109 GLU cc_start: 0.8824 (tt0) cc_final: 0.8592 (tt0) REVERT: R 126 MET cc_start: 0.9390 (mtm) cc_final: 0.9156 (mtm) REVERT: R 321 LYS cc_start: 0.8373 (ttpp) cc_final: 0.7482 (tppt) REVERT: S 155 MET cc_start: 0.8733 (tpp) cc_final: 0.8452 (mmm) REVERT: S 199 TYR cc_start: 0.8570 (m-80) cc_final: 0.8069 (m-80) REVERT: T 20 VAL cc_start: 0.8642 (OUTLIER) cc_final: 0.8393 (t) REVERT: T 39 ARG cc_start: 0.7829 (ptm160) cc_final: 0.7445 (ptm160) REVERT: T 81 ASP cc_start: 0.9095 (t70) cc_final: 0.8593 (p0) REVERT: T 246 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7326 (mt-10) REVERT: U 105 LYS cc_start: 0.9511 (mttt) cc_final: 0.9255 (mmmm) REVERT: U 114 ILE cc_start: 0.9752 (mt) cc_final: 0.9460 (tt) outliers start: 263 outliers final: 183 residues processed: 1708 average time/residue: 0.6439 time to fit residues: 1859.7816 Evaluate side-chains 1706 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 1491 time to evaluate : 5.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 26 MET Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain D residue 278 ASP Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 340 MET Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 412 SER Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 458 MET Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 221 ASP Chi-restraints excluded: chain F residue 264 ASP Chi-restraints excluded: chain F residue 299 HIS Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 342 GLN Chi-restraints excluded: chain F residue 377 VAL Chi-restraints excluded: chain F residue 420 SER Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 165 LEU Chi-restraints excluded: chain G residue 256 THR Chi-restraints excluded: chain G residue 286 CYS Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 354 LEU Chi-restraints excluded: chain G residue 374 GLN Chi-restraints excluded: chain G residue 436 ILE Chi-restraints excluded: chain H residue 8 LYS Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 194 TYR Chi-restraints excluded: chain H residue 216 THR Chi-restraints excluded: chain H residue 226 VAL Chi-restraints excluded: chain H residue 251 LYS Chi-restraints excluded: chain H residue 283 CYS Chi-restraints excluded: chain H residue 286 CYS Chi-restraints excluded: chain H residue 290 THR Chi-restraints excluded: chain H residue 354 LEU Chi-restraints excluded: chain H residue 355 ILE Chi-restraints excluded: chain H residue 419 MET Chi-restraints excluded: chain H residue 447 LYS Chi-restraints excluded: chain I residue 13 ASP Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 46 ASP Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 291 LEU Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 336 VAL Chi-restraints excluded: chain I residue 340 MET Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain I residue 406 ILE Chi-restraints excluded: chain I residue 419 MET Chi-restraints excluded: chain J residue 79 MET Chi-restraints excluded: chain J residue 121 ASP Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 227 ASP Chi-restraints excluded: chain J residue 236 ASP Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 299 HIS Chi-restraints excluded: chain J residue 336 VAL Chi-restraints excluded: chain J residue 350 LEU Chi-restraints excluded: chain J residue 354 LEU Chi-restraints excluded: chain J residue 413 ASP Chi-restraints excluded: chain K residue 6 ASN Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 176 LYS Chi-restraints excluded: chain K residue 209 ASP Chi-restraints excluded: chain K residue 230 ILE Chi-restraints excluded: chain K residue 246 VAL Chi-restraints excluded: chain K residue 297 THR Chi-restraints excluded: chain K residue 304 VAL Chi-restraints excluded: chain K residue 405 LYS Chi-restraints excluded: chain K residue 422 GLU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 164 ILE Chi-restraints excluded: chain L residue 196 ILE Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 348 VAL Chi-restraints excluded: chain L residue 377 VAL Chi-restraints excluded: chain L residue 423 GLU Chi-restraints excluded: chain M residue 12 TRP Chi-restraints excluded: chain M residue 86 VAL Chi-restraints excluded: chain M residue 152 THR Chi-restraints excluded: chain M residue 187 LEU Chi-restraints excluded: chain M residue 240 THR Chi-restraints excluded: chain M residue 276 LEU Chi-restraints excluded: chain M residue 312 ASP Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 68 ASN Chi-restraints excluded: chain N residue 102 TRP Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain N residue 178 VAL Chi-restraints excluded: chain N residue 235 THR Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 313 THR Chi-restraints excluded: chain O residue 99 MET Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 187 LEU Chi-restraints excluded: chain P residue 116 GLN Chi-restraints excluded: chain P residue 127 LEU Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain P residue 166 ILE Chi-restraints excluded: chain P residue 178 VAL Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 216 ILE Chi-restraints excluded: chain P residue 276 LEU Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 81 ASP Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 236 LEU Chi-restraints excluded: chain R residue 10 ASN Chi-restraints excluded: chain R residue 11 ASP Chi-restraints excluded: chain R residue 15 LYS Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 224 VAL Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 37 ILE Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain S residue 123 MET Chi-restraints excluded: chain S residue 152 THR Chi-restraints excluded: chain S residue 225 SER Chi-restraints excluded: chain S residue 244 LEU Chi-restraints excluded: chain S residue 245 ILE Chi-restraints excluded: chain S residue 320 THR Chi-restraints excluded: chain T residue 6 LEU Chi-restraints excluded: chain T residue 20 VAL Chi-restraints excluded: chain T residue 209 ASP Chi-restraints excluded: chain T residue 235 THR Chi-restraints excluded: chain T residue 236 LEU Chi-restraints excluded: chain U residue 59 LEU Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 243 ILE Chi-restraints excluded: chain U residue 313 THR Chi-restraints excluded: chain U residue 316 VAL Chi-restraints excluded: chain V residue 21 LEU Chi-restraints excluded: chain V residue 152 THR Chi-restraints excluded: chain V residue 164 GLN Chi-restraints excluded: chain V residue 235 THR Chi-restraints excluded: chain V residue 244 LEU Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 256 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 855 random chunks: chunk 572 optimal weight: 20.0000 chunk 236 optimal weight: 20.0000 chunk 170 optimal weight: 20.0000 chunk 773 optimal weight: 0.4980 chunk 507 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 447 optimal weight: 9.9990 chunk 517 optimal weight: 8.9990 chunk 281 optimal weight: 8.9990 chunk 59 optimal weight: 20.0000 chunk 749 optimal weight: 0.3980 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 ASN C 18 HIS ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN D 74 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 ASN ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN F 74 ASN ** F 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 322 ASN ** F 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN ** H 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 460 ASN ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 ASN ** K 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 43 ASN N 190 ASN N 263 ASN ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 94 ASN ** Q 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 267 GLN ** R 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 248 ASN ** U 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.084186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.069089 restraints weight = 248303.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.071172 restraints weight = 142893.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.072632 restraints weight = 97805.718| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 68177 Z= 0.221 Angle : 0.673 11.883 92470 Z= 0.342 Chirality : 0.043 0.198 10048 Planarity : 0.004 0.072 12237 Dihedral : 4.643 58.838 9264 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.11 % Favored : 95.87 % Rotamer: Outliers : 3.39 % Allowed : 22.37 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.09), residues: 8507 helix: 1.22 (0.09), residues: 3179 sheet: -0.26 (0.14), residues: 1489 loop : -0.97 (0.10), residues: 3839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 202 HIS 0.008 0.001 HIS H 299 PHE 0.023 0.001 PHE I 90 TYR 0.026 0.001 TYR N 274 ARG 0.013 0.001 ARG P 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17014 Ramachandran restraints generated. 8507 Oldfield, 0 Emsley, 8507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17014 Ramachandran restraints generated. 8507 Oldfield, 0 Emsley, 8507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1838 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 237 poor density : 1601 time to evaluate : 7.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 HIS cc_start: 0.9296 (m90) cc_final: 0.8563 (m90) REVERT: A 26 MET cc_start: 0.9339 (mtp) cc_final: 0.8924 (ptp) REVERT: A 29 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8534 (tm-30) REVERT: A 32 ARG cc_start: 0.8420 (ttp80) cc_final: 0.8180 (ttp80) REVERT: A 60 LYS cc_start: 0.9588 (mmtt) cc_final: 0.9361 (mttt) REVERT: A 163 ASP cc_start: 0.9249 (m-30) cc_final: 0.8693 (t0) REVERT: A 170 ARG cc_start: 0.8451 (ttm-80) cc_final: 0.8153 (ttp-170) REVERT: A 200 GLU cc_start: 0.8357 (mp0) cc_final: 0.8020 (mp0) REVERT: A 214 GLN cc_start: 0.8952 (pp30) cc_final: 0.8254 (pp30) REVERT: A 241 ASP cc_start: 0.8710 (p0) cc_final: 0.8094 (p0) REVERT: A 259 MET cc_start: 0.8164 (mmm) cc_final: 0.7955 (mmm) REVERT: A 337 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8744 (tptp) REVERT: A 345 ARG cc_start: 0.9331 (ttp-110) cc_final: 0.9058 (ttp-110) REVERT: A 346 GLN cc_start: 0.9009 (mt0) cc_final: 0.8602 (mp10) REVERT: A 347 MET cc_start: 0.9331 (mmt) cc_final: 0.8916 (mmt) REVERT: A 369 MET cc_start: 0.8739 (mtm) cc_final: 0.8454 (ptp) REVERT: A 419 MET cc_start: 0.8565 (ppp) cc_final: 0.8029 (ppp) REVERT: A 422 GLU cc_start: 0.9364 (tp30) cc_final: 0.9111 (tp30) REVERT: A 460 ASN cc_start: 0.8838 (m110) cc_final: 0.8418 (m110) REVERT: B 9 TYR cc_start: 0.8514 (p90) cc_final: 0.7982 (p90) REVERT: B 32 ARG cc_start: 0.7586 (ttp80) cc_final: 0.7290 (ttp80) REVERT: B 64 GLU cc_start: 0.8662 (pt0) cc_final: 0.8365 (pt0) REVERT: B 79 MET cc_start: 0.9179 (mtm) cc_final: 0.8916 (mtm) REVERT: B 82 GLN cc_start: 0.9347 (mt0) cc_final: 0.8866 (mm-40) REVERT: B 188 ASP cc_start: 0.8301 (t0) cc_final: 0.7610 (t0) REVERT: B 219 GLU cc_start: 0.8180 (pt0) cc_final: 0.7835 (pt0) REVERT: B 267 GLU cc_start: 0.9244 (tt0) cc_final: 0.8880 (pt0) REVERT: B 296 LEU cc_start: 0.9149 (tp) cc_final: 0.8854 (tp) REVERT: B 340 MET cc_start: 0.8868 (mmm) cc_final: 0.8277 (mmm) REVERT: B 344 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8386 (mt-10) REVERT: B 383 LYS cc_start: 0.9475 (ttmm) cc_final: 0.9141 (ttpt) REVERT: B 398 MET cc_start: 0.9286 (mtm) cc_final: 0.8442 (mpp) REVERT: B 418 LYS cc_start: 0.8874 (mttt) cc_final: 0.8473 (mttt) REVERT: B 441 MET cc_start: 0.9425 (tmm) cc_final: 0.9097 (tmm) REVERT: C 19 LYS cc_start: 0.9322 (tppt) cc_final: 0.8957 (tppt) REVERT: C 37 ASN cc_start: 0.9342 (m-40) cc_final: 0.8989 (m110) REVERT: C 46 ASP cc_start: 0.8279 (t0) cc_final: 0.7651 (t0) REVERT: C 60 LYS cc_start: 0.9563 (mmmm) cc_final: 0.9278 (mmmm) REVERT: C 77 ASP cc_start: 0.9290 (m-30) cc_final: 0.9056 (t70) REVERT: C 105 ASP cc_start: 0.9258 (p0) cc_final: 0.8986 (p0) REVERT: C 190 ASP cc_start: 0.7481 (OUTLIER) cc_final: 0.6895 (m-30) REVERT: C 194 TYR cc_start: 0.8716 (t80) cc_final: 0.8385 (t80) REVERT: C 241 ASP cc_start: 0.9146 (p0) cc_final: 0.8932 (p0) REVERT: C 296 LEU cc_start: 0.9028 (tp) cc_final: 0.8820 (tp) REVERT: C 310 VAL cc_start: 0.7809 (OUTLIER) cc_final: 0.7565 (m) REVERT: C 314 ARG cc_start: 0.8774 (mmt90) cc_final: 0.7953 (tpm170) REVERT: C 369 MET cc_start: 0.8549 (mpp) cc_final: 0.7843 (mpp) REVERT: C 398 MET cc_start: 0.9217 (mtm) cc_final: 0.8970 (mtt) REVERT: C 413 ASP cc_start: 0.8741 (t0) cc_final: 0.8445 (t0) REVERT: C 441 MET cc_start: 0.9258 (tmm) cc_final: 0.8881 (ppp) REVERT: C 458 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.5876 (tpt) REVERT: C 460 ASN cc_start: 0.9657 (m-40) cc_final: 0.9349 (m110) REVERT: C 461 GLU cc_start: 0.9149 (tt0) cc_final: 0.8122 (pt0) REVERT: D 15 LYS cc_start: 0.9378 (mttt) cc_final: 0.8983 (mtmm) REVERT: D 16 LYS cc_start: 0.9222 (mmmm) cc_final: 0.8947 (mmmm) REVERT: D 17 MET cc_start: 0.9390 (mmm) cc_final: 0.8447 (mmm) REVERT: D 18 HIS cc_start: 0.9563 (OUTLIER) cc_final: 0.8366 (m90) REVERT: D 29 GLU cc_start: 0.8339 (tm-30) cc_final: 0.8079 (tm-30) REVERT: D 32 ARG cc_start: 0.9155 (mtp-110) cc_final: 0.8899 (mtp-110) REVERT: D 36 ASP cc_start: 0.9491 (m-30) cc_final: 0.9218 (m-30) REVERT: D 54 GLU cc_start: 0.9015 (tp30) cc_final: 0.8699 (tp30) REVERT: D 97 PHE cc_start: 0.9223 (m-10) cc_final: 0.8931 (m-10) REVERT: D 120 GLU cc_start: 0.9295 (tt0) cc_final: 0.9015 (mt-10) REVERT: D 121 ASP cc_start: 0.9285 (OUTLIER) cc_final: 0.8988 (t70) REVERT: D 173 ASN cc_start: 0.8971 (m-40) cc_final: 0.8586 (p0) REVERT: D 200 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.7765 (mm-30) REVERT: D 241 ASP cc_start: 0.8819 (t0) cc_final: 0.8540 (t0) REVERT: D 269 ASN cc_start: 0.9367 (OUTLIER) cc_final: 0.9031 (t0) REVERT: D 278 ASP cc_start: 0.8975 (OUTLIER) cc_final: 0.8764 (t0) REVERT: D 337 LYS cc_start: 0.9372 (tptm) cc_final: 0.9160 (tmmt) REVERT: D 341 ASP cc_start: 0.9247 (m-30) cc_final: 0.8975 (m-30) REVERT: D 347 MET cc_start: 0.9113 (mmt) cc_final: 0.8742 (mmt) REVERT: D 374 GLN cc_start: 0.9273 (mt0) cc_final: 0.8700 (mp10) REVERT: D 380 ARG cc_start: 0.9177 (ttp-110) cc_final: 0.8871 (ttp-110) REVERT: D 409 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8280 (tm-30) REVERT: D 419 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8559 (ptm) REVERT: D 420 SER cc_start: 0.9581 (m) cc_final: 0.9338 (p) REVERT: D 422 GLU cc_start: 0.9325 (tp30) cc_final: 0.9026 (tp30) REVERT: D 423 GLU cc_start: 0.9131 (tt0) cc_final: 0.8772 (pt0) REVERT: D 441 MET cc_start: 0.9193 (tmm) cc_final: 0.8787 (ppp) REVERT: D 458 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.7902 (tpt) REVERT: E 32 ARG cc_start: 0.8783 (tpp80) cc_final: 0.8533 (tpp80) REVERT: E 157 LYS cc_start: 0.9328 (mmmt) cc_final: 0.8928 (mmmt) REVERT: E 162 GLU cc_start: 0.9116 (mp0) cc_final: 0.8817 (mp0) REVERT: E 163 ASP cc_start: 0.8850 (OUTLIER) cc_final: 0.7973 (t0) REVERT: E 165 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.8864 (pp) REVERT: E 184 ARG cc_start: 0.9062 (ttp80) cc_final: 0.8625 (ttp80) REVERT: E 267 GLU cc_start: 0.9268 (mm-30) cc_final: 0.8943 (mm-30) REVERT: E 340 MET cc_start: 0.9498 (OUTLIER) cc_final: 0.9121 (tpp) REVERT: E 344 GLU cc_start: 0.9148 (pp20) cc_final: 0.8922 (pp20) REVERT: E 346 GLN cc_start: 0.9511 (mt0) cc_final: 0.9061 (mt0) REVERT: E 370 GLU cc_start: 0.8249 (pm20) cc_final: 0.7752 (pm20) REVERT: E 399 PHE cc_start: 0.9375 (m-80) cc_final: 0.9031 (t80) REVERT: E 419 MET cc_start: 0.8262 (ttm) cc_final: 0.7667 (ttm) REVERT: E 420 SER cc_start: 0.9513 (OUTLIER) cc_final: 0.9110 (p) REVERT: E 441 MET cc_start: 0.9096 (tmm) cc_final: 0.8729 (tmm) REVERT: E 454 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8346 (tm-30) REVERT: E 460 ASN cc_start: 0.9212 (m-40) cc_final: 0.8867 (m110) REVERT: F 18 HIS cc_start: 0.8767 (m90) cc_final: 0.8425 (m90) REVERT: F 42 VAL cc_start: 0.9587 (t) cc_final: 0.9301 (p) REVERT: F 79 MET cc_start: 0.9250 (mtm) cc_final: 0.8993 (mtm) REVERT: F 83 ILE cc_start: 0.9496 (OUTLIER) cc_final: 0.9249 (mp) REVERT: F 86 ARG cc_start: 0.7767 (mmt-90) cc_final: 0.7423 (mmt-90) REVERT: F 94 GLU cc_start: 0.8307 (mp0) cc_final: 0.7993 (mp0) REVERT: F 163 ASP cc_start: 0.9320 (m-30) cc_final: 0.8698 (m-30) REVERT: F 177 ARG cc_start: 0.9166 (mmm-85) cc_final: 0.8815 (mmm-85) REVERT: F 184 ARG cc_start: 0.9333 (ttp-110) cc_final: 0.8570 (ttp80) REVERT: F 314 ARG cc_start: 0.3390 (tpm170) cc_final: 0.2862 (tpm170) REVERT: F 315 ASP cc_start: 0.8394 (m-30) cc_final: 0.7789 (p0) REVERT: F 342 GLN cc_start: 0.9487 (pt0) cc_final: 0.8961 (pp30) REVERT: F 346 GLN cc_start: 0.9417 (mt0) cc_final: 0.7993 (mt0) REVERT: F 357 SER cc_start: 0.8531 (m) cc_final: 0.8232 (p) REVERT: F 370 GLU cc_start: 0.8532 (mt-10) cc_final: 0.7461 (mp0) REVERT: F 374 GLN cc_start: 0.9249 (mt0) cc_final: 0.8882 (mt0) REVERT: F 380 ARG cc_start: 0.9236 (ttp80) cc_final: 0.8613 (ttt90) REVERT: F 413 ASP cc_start: 0.8951 (m-30) cc_final: 0.8494 (t70) REVERT: F 419 MET cc_start: 0.8637 (ppp) cc_final: 0.8144 (ppp) REVERT: F 460 ASN cc_start: 0.8965 (m-40) cc_final: 0.8618 (m110) REVERT: G 26 MET cc_start: 0.8611 (mmp) cc_final: 0.8403 (mmt) REVERT: G 32 ARG cc_start: 0.7710 (tpp-160) cc_final: 0.7054 (tpp-160) REVERT: G 74 ASN cc_start: 0.9581 (t0) cc_final: 0.9076 (t0) REVERT: G 124 SER cc_start: 0.9533 (OUTLIER) cc_final: 0.9207 (p) REVERT: G 163 ASP cc_start: 0.9345 (m-30) cc_final: 0.9095 (t0) REVERT: G 202 TRP cc_start: 0.8975 (m-10) cc_final: 0.8547 (m-10) REVERT: G 262 MET cc_start: 0.8769 (mmp) cc_final: 0.8514 (mmp) REVERT: G 335 MET cc_start: 0.9060 (ttt) cc_final: 0.8802 (ttt) REVERT: G 344 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8851 (mt-10) REVERT: G 347 MET cc_start: 0.9044 (mmm) cc_final: 0.8613 (mpp) REVERT: G 354 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.6706 (pt) REVERT: G 460 ASN cc_start: 0.9172 (m-40) cc_final: 0.8765 (m110) REVERT: H 17 MET cc_start: 0.9620 (mmm) cc_final: 0.9065 (mmm) REVERT: H 26 MET cc_start: 0.9235 (mtm) cc_final: 0.8362 (mtm) REVERT: H 77 ASP cc_start: 0.9342 (m-30) cc_final: 0.9105 (m-30) REVERT: H 79 MET cc_start: 0.9084 (mmt) cc_final: 0.8720 (mmp) REVERT: H 185 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8034 (tm-30) REVERT: H 200 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8329 (mp0) REVERT: H 251 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8527 (tptt) REVERT: H 259 MET cc_start: 0.7850 (ttm) cc_final: 0.6965 (ttt) REVERT: H 326 GLU cc_start: 0.8016 (mp0) cc_final: 0.7559 (pm20) REVERT: H 335 MET cc_start: 0.9003 (ttp) cc_final: 0.8470 (tmm) REVERT: H 346 GLN cc_start: 0.9575 (mt0) cc_final: 0.9207 (mt0) REVERT: H 370 GLU cc_start: 0.8725 (tt0) cc_final: 0.7949 (tm-30) REVERT: H 380 ARG cc_start: 0.8880 (mtm-85) cc_final: 0.7982 (mtm-85) REVERT: H 398 MET cc_start: 0.9019 (ptp) cc_final: 0.8696 (ptp) REVERT: H 409 GLU cc_start: 0.8212 (mp0) cc_final: 0.8001 (mp0) REVERT: H 423 GLU cc_start: 0.9231 (mt-10) cc_final: 0.8981 (mt-10) REVERT: H 454 GLU cc_start: 0.9082 (mp0) cc_final: 0.8831 (mp0) REVERT: I 18 HIS cc_start: 0.9266 (OUTLIER) cc_final: 0.8812 (m90) REVERT: I 28 MET cc_start: 0.9248 (mtm) cc_final: 0.8713 (tmm) REVERT: I 79 MET cc_start: 0.9384 (mtm) cc_final: 0.8882 (mtm) REVERT: I 90 PHE cc_start: 0.8616 (t80) cc_final: 0.8275 (t80) REVERT: I 109 LEU cc_start: 0.9163 (tp) cc_final: 0.8859 (tt) REVERT: I 158 PHE cc_start: 0.8852 (t80) cc_final: 0.8586 (t80) REVERT: I 219 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8348 (tp30) REVERT: I 227 ASP cc_start: 0.9028 (m-30) cc_final: 0.8727 (m-30) REVERT: I 262 MET cc_start: 0.8471 (mmm) cc_final: 0.8049 (mmm) REVERT: I 280 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8690 (mm-30) REVERT: I 335 MET cc_start: 0.9310 (ttt) cc_final: 0.8836 (tmm) REVERT: I 336 VAL cc_start: 0.9542 (OUTLIER) cc_final: 0.9232 (p) REVERT: I 340 MET cc_start: 0.9148 (OUTLIER) cc_final: 0.8737 (mtm) REVERT: I 344 GLU cc_start: 0.9007 (tt0) cc_final: 0.8767 (tp30) REVERT: I 347 MET cc_start: 0.9423 (mtp) cc_final: 0.8949 (mtp) REVERT: I 395 TRP cc_start: 0.8832 (m-10) cc_final: 0.8503 (m-10) REVERT: I 398 MET cc_start: 0.8897 (mtm) cc_final: 0.8401 (mtt) REVERT: I 406 ILE cc_start: 0.9540 (OUTLIER) cc_final: 0.9311 (mp) REVERT: I 422 GLU cc_start: 0.9206 (tp30) cc_final: 0.8804 (tm-30) REVERT: I 458 MET cc_start: 0.7905 (tpp) cc_final: 0.7405 (mmm) REVERT: I 460 ASN cc_start: 0.8827 (m110) cc_final: 0.8519 (p0) REVERT: J 19 LYS cc_start: 0.9343 (tppt) cc_final: 0.9034 (tppt) REVERT: J 170 ARG cc_start: 0.7886 (mtp85) cc_final: 0.7555 (mtp85) REVERT: J 221 ASP cc_start: 0.9087 (m-30) cc_final: 0.7964 (t0) REVERT: J 227 ASP cc_start: 0.8733 (OUTLIER) cc_final: 0.8316 (p0) REVERT: J 267 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8594 (mm-30) REVERT: J 342 GLN cc_start: 0.9596 (tt0) cc_final: 0.8452 (tm-30) REVERT: J 345 ARG cc_start: 0.8652 (ttp80) cc_final: 0.8288 (ttp80) REVERT: J 346 GLN cc_start: 0.9211 (mt0) cc_final: 0.7760 (mt0) REVERT: K 26 MET cc_start: 0.9214 (mmm) cc_final: 0.8780 (mmm) REVERT: K 28 MET cc_start: 0.9024 (tpp) cc_final: 0.8687 (tpp) REVERT: K 60 LYS cc_start: 0.9418 (tppt) cc_final: 0.9140 (mttp) REVERT: K 86 ARG cc_start: 0.9057 (mmp80) cc_final: 0.8687 (mmt180) REVERT: K 97 PHE cc_start: 0.9493 (m-10) cc_final: 0.9180 (m-10) REVERT: K 120 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8692 (mm-30) REVERT: K 125 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8441 (pp) REVERT: K 169 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8133 (mt-10) REVERT: K 176 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.9007 (mmmt) REVERT: K 200 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7510 (tp30) REVERT: K 225 TYR cc_start: 0.7582 (m-80) cc_final: 0.7098 (m-80) REVERT: K 275 ASN cc_start: 0.9499 (m-40) cc_final: 0.9077 (m-40) REVERT: K 324 LYS cc_start: 0.9212 (mmmt) cc_final: 0.8936 (mmtt) REVERT: K 345 ARG cc_start: 0.8679 (tmm-80) cc_final: 0.8126 (ttp80) REVERT: K 369 MET cc_start: 0.8879 (mmt) cc_final: 0.8647 (mmp) REVERT: K 374 GLN cc_start: 0.9345 (mt0) cc_final: 0.9113 (mt0) REVERT: K 398 MET cc_start: 0.8906 (mtt) cc_final: 0.8516 (mtt) REVERT: K 409 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7895 (tm-30) REVERT: K 418 LYS cc_start: 0.7809 (mtmt) cc_final: 0.7094 (mtmt) REVERT: K 423 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8531 (mt-10) REVERT: K 458 MET cc_start: 0.8727 (tmm) cc_final: 0.8208 (tpt) REVERT: K 460 ASN cc_start: 0.9264 (m-40) cc_final: 0.8873 (m-40) REVERT: L 17 MET cc_start: 0.9529 (mmm) cc_final: 0.9115 (mmm) REVERT: L 77 ASP cc_start: 0.8920 (m-30) cc_final: 0.8508 (m-30) REVERT: L 219 GLU cc_start: 0.8250 (pt0) cc_final: 0.7570 (pm20) REVERT: L 228 ASP cc_start: 0.8940 (p0) cc_final: 0.8740 (p0) REVERT: L 239 GLN cc_start: 0.9435 (pm20) cc_final: 0.9051 (pm20) REVERT: L 280 GLU cc_start: 0.8870 (tp30) cc_final: 0.8624 (tp30) REVERT: L 322 ASN cc_start: 0.9338 (m-40) cc_final: 0.9075 (m-40) REVERT: L 342 GLN cc_start: 0.9334 (tt0) cc_final: 0.8863 (tt0) REVERT: L 345 ARG cc_start: 0.9394 (tmm-80) cc_final: 0.8995 (tmm-80) REVERT: L 347 MET cc_start: 0.9082 (mtt) cc_final: 0.8628 (mtm) REVERT: L 369 MET cc_start: 0.8835 (mtm) cc_final: 0.8509 (mpp) REVERT: L 383 LYS cc_start: 0.9555 (mmmm) cc_final: 0.9077 (tppt) REVERT: L 411 ASN cc_start: 0.8957 (t0) cc_final: 0.8712 (t0) REVERT: L 419 MET cc_start: 0.8489 (mtt) cc_final: 0.7995 (mmm) REVERT: L 423 GLU cc_start: 0.9227 (OUTLIER) cc_final: 0.8945 (pt0) REVERT: L 452 TYR cc_start: 0.9315 (p90) cc_final: 0.8560 (p90) REVERT: L 458 MET cc_start: 0.7572 (tpt) cc_final: 0.7224 (tpt) REVERT: M 26 GLU cc_start: 0.8378 (mp0) cc_final: 0.7712 (mp0) REVERT: M 99 MET cc_start: 0.7588 (pmm) cc_final: 0.7150 (pmm) REVERT: M 173 ASP cc_start: 0.8970 (m-30) cc_final: 0.8711 (m-30) REVERT: M 207 ARG cc_start: 0.9041 (tpp80) cc_final: 0.8814 (tpp80) REVERT: M 276 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.9299 (mp) REVERT: N 170 ARG cc_start: 0.9097 (tpp80) cc_final: 0.8822 (ttm170) REVERT: N 271 GLU cc_start: 0.8471 (mp0) cc_final: 0.8154 (mp0) REVERT: O 77 ARG cc_start: 0.8753 (mtm110) cc_final: 0.8523 (mtm110) REVERT: O 99 MET cc_start: 0.5656 (OUTLIER) cc_final: 0.5131 (ppp) REVERT: O 100 LEU cc_start: 0.4255 (OUTLIER) cc_final: 0.3779 (pt) REVERT: O 121 ASP cc_start: 0.8771 (t0) cc_final: 0.8327 (t0) REVERT: O 123 MET cc_start: 0.9297 (mmt) cc_final: 0.9027 (mmm) REVERT: O 124 GLN cc_start: 0.9562 (tt0) cc_final: 0.9121 (tt0) REVERT: O 207 ARG cc_start: 0.8605 (mmm-85) cc_final: 0.8108 (mmm-85) REVERT: P 22 ASP cc_start: 0.8814 (p0) cc_final: 0.8375 (p0) REVERT: P 33 ARG cc_start: 0.9252 (mtt-85) cc_final: 0.8823 (mtt180) REVERT: P 39 ARG cc_start: 0.9070 (mtm110) cc_final: 0.8279 (mtm110) REVERT: P 116 GLN cc_start: 0.9231 (OUTLIER) cc_final: 0.8784 (mm110) REVERT: P 229 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8613 (tm-30) REVERT: P 290 LYS cc_start: 0.9105 (mmmm) cc_final: 0.8549 (mmmm) REVERT: Q 26 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8512 (tm-30) REVERT: Q 39 ARG cc_start: 0.8536 (mtm110) cc_final: 0.8221 (mtm110) REVERT: Q 246 GLU cc_start: 0.8431 (mt-10) cc_final: 0.7974 (mt-10) REVERT: Q 257 ASP cc_start: 0.8432 (p0) cc_final: 0.7851 (m-30) REVERT: Q 271 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7543 (mt-10) REVERT: Q 290 LYS cc_start: 0.9212 (mmmm) cc_final: 0.8911 (mmmm) REVERT: Q 321 LYS cc_start: 0.9079 (ptmt) cc_final: 0.8857 (ptmm) REVERT: R 15 LYS cc_start: 0.5098 (OUTLIER) cc_final: 0.4095 (pttm) REVERT: R 84 ILE cc_start: 0.9844 (tp) cc_final: 0.9565 (tp) REVERT: R 109 GLU cc_start: 0.8754 (tt0) cc_final: 0.8523 (tt0) REVERT: R 126 MET cc_start: 0.9381 (mtm) cc_final: 0.9162 (mtm) REVERT: R 321 LYS cc_start: 0.8212 (ttpp) cc_final: 0.7297 (tppt) REVERT: S 28 PHE cc_start: 0.8615 (t80) cc_final: 0.8388 (t80) REVERT: S 109 GLU cc_start: 0.8743 (mp0) cc_final: 0.8534 (pm20) REVERT: S 155 MET cc_start: 0.8674 (tpp) cc_final: 0.8382 (mmm) REVERT: S 156 THR cc_start: 0.9604 (OUTLIER) cc_final: 0.9295 (p) REVERT: S 199 TYR cc_start: 0.8461 (m-80) cc_final: 0.7957 (m-80) REVERT: S 207 ARG cc_start: 0.8535 (mmm-85) cc_final: 0.8324 (mmm-85) REVERT: T 20 VAL cc_start: 0.8641 (OUTLIER) cc_final: 0.8371 (t) REVERT: T 81 ASP cc_start: 0.9075 (t70) cc_final: 0.8581 (p0) REVERT: T 135 LYS cc_start: 0.9663 (tttm) cc_final: 0.9340 (ttmt) REVERT: T 274 TYR cc_start: 0.8731 (p90) cc_final: 0.8441 (p90) REVERT: U 105 LYS cc_start: 0.9500 (mttt) cc_final: 0.9239 (mmmm) REVERT: U 114 ILE cc_start: 0.9742 (mt) cc_final: 0.9435 (tt) outliers start: 237 outliers final: 164 residues processed: 1739 average time/residue: 0.6405 time to fit residues: 1878.8032 Evaluate side-chains 1727 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 1529 time to evaluate : 5.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 26 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 278 ASP Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 340 MET Chi-restraints excluded: chain E residue 412 SER Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 221 ASP Chi-restraints excluded: chain F residue 264 ASP Chi-restraints excluded: chain F residue 299 HIS Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 377 VAL Chi-restraints excluded: chain F residue 420 SER Chi-restraints excluded: chain F residue 454 GLU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 165 LEU Chi-restraints excluded: chain G residue 256 THR Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 354 LEU Chi-restraints excluded: chain G residue 374 GLN Chi-restraints excluded: chain G residue 414 PHE Chi-restraints excluded: chain G residue 436 ILE Chi-restraints excluded: chain H residue 8 LYS Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 121 ASP Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 194 TYR Chi-restraints excluded: chain H residue 216 THR Chi-restraints excluded: chain H residue 226 VAL Chi-restraints excluded: chain H residue 251 LYS Chi-restraints excluded: chain H residue 283 CYS Chi-restraints excluded: chain H residue 286 CYS Chi-restraints excluded: chain H residue 290 THR Chi-restraints excluded: chain H residue 342 GLN Chi-restraints excluded: chain H residue 354 LEU Chi-restraints excluded: chain H residue 419 MET Chi-restraints excluded: chain H residue 424 LEU Chi-restraints excluded: chain H residue 447 LYS Chi-restraints excluded: chain H residue 460 ASN Chi-restraints excluded: chain I residue 13 ASP Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 46 ASP Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 291 LEU Chi-restraints excluded: chain I residue 336 VAL Chi-restraints excluded: chain I residue 340 MET Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain I residue 406 ILE Chi-restraints excluded: chain I residue 419 MET Chi-restraints excluded: chain J residue 121 ASP Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 227 ASP Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 299 HIS Chi-restraints excluded: chain J residue 336 VAL Chi-restraints excluded: chain J residue 354 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain K residue 6 ASN Chi-restraints excluded: chain K residue 102 ASN Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 176 LYS Chi-restraints excluded: chain K residue 209 ASP Chi-restraints excluded: chain K residue 290 THR Chi-restraints excluded: chain K residue 297 THR Chi-restraints excluded: chain K residue 304 VAL Chi-restraints excluded: chain K residue 405 LYS Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 164 ILE Chi-restraints excluded: chain L residue 196 ILE Chi-restraints excluded: chain L residue 328 LEU Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 377 VAL Chi-restraints excluded: chain L residue 423 GLU Chi-restraints excluded: chain M residue 12 TRP Chi-restraints excluded: chain M residue 86 VAL Chi-restraints excluded: chain M residue 152 THR Chi-restraints excluded: chain M residue 187 LEU Chi-restraints excluded: chain M residue 240 THR Chi-restraints excluded: chain M residue 276 LEU Chi-restraints excluded: chain M residue 312 ASP Chi-restraints excluded: chain N residue 43 ASN Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 68 ASN Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain N residue 178 VAL Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 313 THR Chi-restraints excluded: chain O residue 99 MET Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 187 LEU Chi-restraints excluded: chain P residue 116 GLN Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain P residue 178 VAL Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 216 ILE Chi-restraints excluded: chain Q residue 81 ASP Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 236 LEU Chi-restraints excluded: chain R residue 15 LYS Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 224 VAL Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 37 ILE Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain S residue 123 MET Chi-restraints excluded: chain S residue 152 THR Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 225 SER Chi-restraints excluded: chain S residue 244 LEU Chi-restraints excluded: chain S residue 320 THR Chi-restraints excluded: chain T residue 6 LEU Chi-restraints excluded: chain T residue 20 VAL Chi-restraints excluded: chain T residue 209 ASP Chi-restraints excluded: chain T residue 235 THR Chi-restraints excluded: chain T residue 236 LEU Chi-restraints excluded: chain U residue 59 LEU Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 152 THR Chi-restraints excluded: chain U residue 243 ILE Chi-restraints excluded: chain U residue 313 THR Chi-restraints excluded: chain U residue 316 VAL Chi-restraints excluded: chain V residue 152 THR Chi-restraints excluded: chain V residue 244 LEU Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 256 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 855 random chunks: chunk 594 optimal weight: 9.9990 chunk 473 optimal weight: 9.9990 chunk 815 optimal weight: 6.9990 chunk 741 optimal weight: 20.0000 chunk 465 optimal weight: 7.9990 chunk 456 optimal weight: 6.9990 chunk 315 optimal weight: 6.9990 chunk 403 optimal weight: 20.0000 chunk 330 optimal weight: 20.0000 chunk 350 optimal weight: 6.9990 chunk 548 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 ASN ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN ** H 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 460 ASN ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 43 ASN ** O 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 43 ASN ** U 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.082924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.068029 restraints weight = 251393.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.070074 restraints weight = 145069.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.071496 restraints weight = 99444.904| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 68177 Z= 0.306 Angle : 0.711 12.089 92470 Z= 0.364 Chirality : 0.043 0.257 10048 Planarity : 0.004 0.070 12237 Dihedral : 4.726 59.532 9264 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.68 % Favored : 95.31 % Rotamer: Outliers : 3.44 % Allowed : 22.80 % Favored : 73.76 % 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: -0.11 (0.09), residues: 8507 helix: 1.16 (0.09), residues: 3205 sheet: -0.34 (0.13), residues: 1563 loop : -1.01 (0.10), residues: 3739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP J 202 HIS 0.009 0.001 HIS H 299 PHE 0.031 0.002 PHE E 90 TYR 0.029 0.001 TYR S 268 ARG 0.017 0.001 ARG F 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17014 Ramachandran restraints generated. 8507 Oldfield, 0 Emsley, 8507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17014 Ramachandran restraints generated. 8507 Oldfield, 0 Emsley, 8507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1776 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 240 poor density : 1536 time to evaluate : 5.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 12 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8371 (mm-30) REVERT: A 15 LYS cc_start: 0.9492 (mtmt) cc_final: 0.8789 (mttp) REVERT: A 18 HIS cc_start: 0.9378 (m90) cc_final: 0.8616 (m90) REVERT: A 26 MET cc_start: 0.9371 (mtp) cc_final: 0.8997 (ptp) REVERT: A 29 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8560 (tm-30) REVERT: A 32 ARG cc_start: 0.8418 (ttp80) cc_final: 0.8141 (ttp80) REVERT: A 60 LYS cc_start: 0.9589 (mmtt) cc_final: 0.9321 (mtmm) REVERT: A 163 ASP cc_start: 0.9237 (m-30) cc_final: 0.8734 (t0) REVERT: A 170 ARG cc_start: 0.8457 (ttm-80) cc_final: 0.8161 (ttp-170) REVERT: A 214 GLN cc_start: 0.8993 (pp30) cc_final: 0.8268 (pp30) REVERT: A 241 ASP cc_start: 0.8778 (p0) cc_final: 0.8182 (p0) REVERT: A 337 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8804 (tptp) REVERT: A 345 ARG cc_start: 0.9362 (ttp-110) cc_final: 0.9088 (ttp-110) REVERT: A 346 GLN cc_start: 0.9066 (mt0) cc_final: 0.8629 (mp10) REVERT: A 369 MET cc_start: 0.8784 (mtm) cc_final: 0.8490 (ptp) REVERT: A 419 MET cc_start: 0.8542 (ppp) cc_final: 0.7977 (ppp) REVERT: A 422 GLU cc_start: 0.9382 (tp30) cc_final: 0.9133 (tp30) REVERT: A 458 MET cc_start: 0.8072 (tpt) cc_final: 0.7255 (tpt) REVERT: A 460 ASN cc_start: 0.8852 (m110) cc_final: 0.8428 (m110) REVERT: B 9 TYR cc_start: 0.8530 (p90) cc_final: 0.8018 (p90) REVERT: B 32 ARG cc_start: 0.7643 (ttp80) cc_final: 0.7351 (ttp80) REVERT: B 64 GLU cc_start: 0.8686 (pt0) cc_final: 0.8391 (pt0) REVERT: B 79 MET cc_start: 0.9139 (mtm) cc_final: 0.8852 (mtm) REVERT: B 82 GLN cc_start: 0.9350 (mt0) cc_final: 0.8881 (mm-40) REVERT: B 188 ASP cc_start: 0.8330 (t0) cc_final: 0.7983 (t0) REVERT: B 198 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.6812 (mtmm) REVERT: B 219 GLU cc_start: 0.8203 (pt0) cc_final: 0.7898 (pt0) REVERT: B 296 LEU cc_start: 0.9154 (tp) cc_final: 0.8852 (tp) REVERT: B 331 GLU cc_start: 0.8903 (pm20) cc_final: 0.8573 (pm20) REVERT: B 340 MET cc_start: 0.8854 (mmm) cc_final: 0.8358 (mmm) REVERT: B 344 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8396 (mt-10) REVERT: B 383 LYS cc_start: 0.9487 (ttmm) cc_final: 0.9149 (ttpt) REVERT: B 398 MET cc_start: 0.9307 (mtm) cc_final: 0.8461 (mpp) REVERT: B 416 ILE cc_start: 0.8980 (mm) cc_final: 0.8697 (mm) REVERT: B 418 LYS cc_start: 0.8927 (mttt) cc_final: 0.8510 (mttt) REVERT: B 441 MET cc_start: 0.9419 (tmm) cc_final: 0.9091 (tmm) REVERT: C 19 LYS cc_start: 0.9317 (tppt) cc_final: 0.8989 (tppt) REVERT: C 37 ASN cc_start: 0.9277 (m-40) cc_final: 0.8896 (m110) REVERT: C 46 ASP cc_start: 0.8204 (t0) cc_final: 0.7547 (t0) REVERT: C 60 LYS cc_start: 0.9536 (mmmm) cc_final: 0.9267 (mmmm) REVERT: C 77 ASP cc_start: 0.9366 (m-30) cc_final: 0.9130 (t70) REVERT: C 105 ASP cc_start: 0.9280 (p0) cc_final: 0.9017 (p0) REVERT: C 190 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.7179 (m-30) REVERT: C 296 LEU cc_start: 0.8949 (tp) cc_final: 0.8732 (tp) REVERT: C 310 VAL cc_start: 0.7926 (OUTLIER) cc_final: 0.7677 (m) REVERT: C 314 ARG cc_start: 0.8743 (mmt90) cc_final: 0.7933 (tpm170) REVERT: C 369 MET cc_start: 0.8375 (mpp) cc_final: 0.7720 (mpp) REVERT: C 398 MET cc_start: 0.9221 (mtm) cc_final: 0.8676 (mpp) REVERT: C 413 ASP cc_start: 0.8755 (t0) cc_final: 0.8473 (t0) REVERT: C 441 MET cc_start: 0.9268 (tmm) cc_final: 0.8899 (ppp) REVERT: C 458 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.6390 (ttt) REVERT: C 460 ASN cc_start: 0.9637 (m-40) cc_final: 0.9274 (m110) REVERT: D 15 LYS cc_start: 0.9398 (mttt) cc_final: 0.8996 (mtmm) REVERT: D 16 LYS cc_start: 0.9249 (mmmm) cc_final: 0.8960 (mmmm) REVERT: D 17 MET cc_start: 0.9407 (mmm) cc_final: 0.8463 (mmm) REVERT: D 18 HIS cc_start: 0.9565 (OUTLIER) cc_final: 0.8376 (m90) REVERT: D 29 GLU cc_start: 0.8318 (tm-30) cc_final: 0.8076 (tm-30) REVERT: D 32 ARG cc_start: 0.9160 (mtp-110) cc_final: 0.8870 (mtp-110) REVERT: D 36 ASP cc_start: 0.9517 (m-30) cc_final: 0.9159 (m-30) REVERT: D 54 GLU cc_start: 0.9032 (tp30) cc_final: 0.8726 (tp30) REVERT: D 97 PHE cc_start: 0.9282 (m-10) cc_final: 0.8948 (m-10) REVERT: D 120 GLU cc_start: 0.9316 (tt0) cc_final: 0.9086 (mt-10) REVERT: D 121 ASP cc_start: 0.9346 (OUTLIER) cc_final: 0.9051 (t70) REVERT: D 173 ASN cc_start: 0.9095 (m-40) cc_final: 0.8658 (p0) REVERT: D 184 ARG cc_start: 0.8814 (ttp80) cc_final: 0.8400 (ttp80) REVERT: D 269 ASN cc_start: 0.9639 (OUTLIER) cc_final: 0.9102 (t0) REVERT: D 337 LYS cc_start: 0.9401 (tptm) cc_final: 0.8932 (tptm) REVERT: D 341 ASP cc_start: 0.9220 (m-30) cc_final: 0.8852 (m-30) REVERT: D 347 MET cc_start: 0.9170 (mmt) cc_final: 0.8765 (mmt) REVERT: D 374 GLN cc_start: 0.9298 (mt0) cc_final: 0.8726 (mp10) REVERT: D 380 ARG cc_start: 0.9185 (ttp-110) cc_final: 0.8858 (ttp-110) REVERT: D 409 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8299 (tm-30) REVERT: D 419 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8501 (tmm) REVERT: D 422 GLU cc_start: 0.9344 (tp30) cc_final: 0.9009 (tp30) REVERT: D 441 MET cc_start: 0.9165 (tmm) cc_final: 0.8787 (ppp) REVERT: D 458 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8013 (tpt) REVERT: E 32 ARG cc_start: 0.8822 (tpp80) cc_final: 0.8577 (tpp80) REVERT: E 157 LYS cc_start: 0.9346 (mmmt) cc_final: 0.8946 (mmmt) REVERT: E 162 GLU cc_start: 0.9173 (mp0) cc_final: 0.8874 (mp0) REVERT: E 163 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.7939 (t0) REVERT: E 165 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.8965 (pp) REVERT: E 184 ARG cc_start: 0.9069 (ttp80) cc_final: 0.8625 (ttp80) REVERT: E 251 LYS cc_start: 0.8971 (ttpp) cc_final: 0.8728 (ptmm) REVERT: E 267 GLU cc_start: 0.9250 (mm-30) cc_final: 0.8926 (mm-30) REVERT: E 340 MET cc_start: 0.9510 (OUTLIER) cc_final: 0.9149 (tpp) REVERT: E 346 GLN cc_start: 0.9539 (mt0) cc_final: 0.9120 (mt0) REVERT: E 347 MET cc_start: 0.9077 (mmm) cc_final: 0.8491 (mpp) REVERT: E 370 GLU cc_start: 0.8251 (pm20) cc_final: 0.7767 (pm20) REVERT: E 419 MET cc_start: 0.8332 (ttm) cc_final: 0.7684 (ttm) REVERT: E 420 SER cc_start: 0.9533 (OUTLIER) cc_final: 0.9133 (p) REVERT: E 441 MET cc_start: 0.9072 (tmm) cc_final: 0.8684 (tmm) REVERT: E 454 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8262 (tm-30) REVERT: E 460 ASN cc_start: 0.9274 (m-40) cc_final: 0.8951 (m110) REVERT: F 18 HIS cc_start: 0.8787 (m90) cc_final: 0.8412 (m90) REVERT: F 42 VAL cc_start: 0.9628 (t) cc_final: 0.9376 (p) REVERT: F 74 ASN cc_start: 0.9205 (t160) cc_final: 0.8444 (t0) REVERT: F 77 ASP cc_start: 0.8829 (m-30) cc_final: 0.8399 (p0) REVERT: F 79 MET cc_start: 0.9286 (mtm) cc_final: 0.9017 (mtm) REVERT: F 83 ILE cc_start: 0.9502 (OUTLIER) cc_final: 0.9249 (mp) REVERT: F 94 GLU cc_start: 0.8357 (mp0) cc_final: 0.8090 (mp0) REVERT: F 163 ASP cc_start: 0.9228 (m-30) cc_final: 0.8621 (m-30) REVERT: F 177 ARG cc_start: 0.9198 (mmm-85) cc_final: 0.8796 (mmm-85) REVERT: F 184 ARG cc_start: 0.9191 (ttp-110) cc_final: 0.8677 (ttp80) REVERT: F 315 ASP cc_start: 0.8383 (m-30) cc_final: 0.7528 (p0) REVERT: F 340 MET cc_start: 0.9122 (mmm) cc_final: 0.8696 (mmt) REVERT: F 342 GLN cc_start: 0.9492 (OUTLIER) cc_final: 0.9001 (pp30) REVERT: F 343 LYS cc_start: 0.9400 (ptmm) cc_final: 0.8902 (ptmm) REVERT: F 346 GLN cc_start: 0.9427 (mt0) cc_final: 0.8051 (mt0) REVERT: F 357 SER cc_start: 0.8479 (m) cc_final: 0.8180 (p) REVERT: F 370 GLU cc_start: 0.8415 (mt-10) cc_final: 0.7994 (mp0) REVERT: F 374 GLN cc_start: 0.9261 (mt0) cc_final: 0.8873 (mt0) REVERT: F 380 ARG cc_start: 0.9264 (ttp80) cc_final: 0.8602 (ttt90) REVERT: F 413 ASP cc_start: 0.9002 (m-30) cc_final: 0.8499 (t70) REVERT: F 419 MET cc_start: 0.8554 (ppp) cc_final: 0.8071 (ppp) REVERT: F 460 ASN cc_start: 0.8981 (m-40) cc_final: 0.8624 (m110) REVERT: G 32 ARG cc_start: 0.7742 (tpp-160) cc_final: 0.7081 (tpp-160) REVERT: G 74 ASN cc_start: 0.9606 (t0) cc_final: 0.9138 (t0) REVERT: G 79 MET cc_start: 0.9365 (mtm) cc_final: 0.9072 (mpp) REVERT: G 124 SER cc_start: 0.9539 (OUTLIER) cc_final: 0.9208 (p) REVERT: G 163 ASP cc_start: 0.9323 (m-30) cc_final: 0.9069 (t0) REVERT: G 262 MET cc_start: 0.8848 (mmp) cc_final: 0.8569 (mmp) REVERT: G 267 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8282 (mm-30) REVERT: G 280 GLU cc_start: 0.9327 (mm-30) cc_final: 0.8832 (tp30) REVERT: G 335 MET cc_start: 0.9052 (ttt) cc_final: 0.8755 (ttt) REVERT: G 344 GLU cc_start: 0.9245 (mt-10) cc_final: 0.8901 (mt-10) REVERT: G 347 MET cc_start: 0.9080 (mmm) cc_final: 0.8522 (mpp) REVERT: G 405 LYS cc_start: 0.9333 (mtmm) cc_final: 0.9063 (mtmm) REVERT: G 460 ASN cc_start: 0.9182 (m-40) cc_final: 0.8768 (m110) REVERT: H 17 MET cc_start: 0.9655 (mmm) cc_final: 0.9036 (mmm) REVERT: H 26 MET cc_start: 0.9310 (mtm) cc_final: 0.8517 (mtm) REVERT: H 77 ASP cc_start: 0.9373 (m-30) cc_final: 0.9124 (m-30) REVERT: H 79 MET cc_start: 0.9077 (mmt) cc_final: 0.8698 (mmp) REVERT: H 185 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7967 (tm-30) REVERT: H 326 GLU cc_start: 0.7985 (mp0) cc_final: 0.7505 (pm20) REVERT: H 346 GLN cc_start: 0.9595 (mt0) cc_final: 0.9253 (mt0) REVERT: H 370 GLU cc_start: 0.8653 (tt0) cc_final: 0.7836 (tm-30) REVERT: H 380 ARG cc_start: 0.8907 (mtm-85) cc_final: 0.8032 (mtm-85) REVERT: H 409 GLU cc_start: 0.8281 (mp0) cc_final: 0.7976 (mp0) REVERT: H 423 GLU cc_start: 0.9220 (mt-10) cc_final: 0.8967 (mt-10) REVERT: H 454 GLU cc_start: 0.9073 (mp0) cc_final: 0.8816 (mp0) REVERT: I 16 LYS cc_start: 0.9260 (mmtm) cc_final: 0.8969 (mmtm) REVERT: I 18 HIS cc_start: 0.9264 (OUTLIER) cc_final: 0.8778 (m90) REVERT: I 79 MET cc_start: 0.9433 (mtm) cc_final: 0.8905 (mtm) REVERT: I 132 VAL cc_start: 0.9617 (t) cc_final: 0.9379 (m) REVERT: I 158 PHE cc_start: 0.8905 (t80) cc_final: 0.8633 (t80) REVERT: I 219 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8417 (tp30) REVERT: I 227 ASP cc_start: 0.9022 (m-30) cc_final: 0.8710 (m-30) REVERT: I 262 MET cc_start: 0.8487 (mmm) cc_final: 0.8096 (mmm) REVERT: I 280 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8730 (mm-30) REVERT: I 335 MET cc_start: 0.9276 (ttt) cc_final: 0.8901 (tmm) REVERT: I 336 VAL cc_start: 0.9582 (OUTLIER) cc_final: 0.9319 (p) REVERT: I 340 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.8678 (mtm) REVERT: I 344 GLU cc_start: 0.9052 (tt0) cc_final: 0.8680 (tp30) REVERT: I 347 MET cc_start: 0.9464 (mtp) cc_final: 0.9136 (mtp) REVERT: I 398 MET cc_start: 0.8958 (mtm) cc_final: 0.8437 (mtt) REVERT: I 422 GLU cc_start: 0.9216 (tp30) cc_final: 0.8926 (tm-30) REVERT: I 458 MET cc_start: 0.8030 (tpp) cc_final: 0.7041 (mmm) REVERT: I 460 ASN cc_start: 0.8753 (m110) cc_final: 0.8514 (p0) REVERT: J 19 LYS cc_start: 0.9367 (tppt) cc_final: 0.9061 (tppt) REVERT: J 26 MET cc_start: 0.9305 (mtm) cc_final: 0.9042 (ptm) REVERT: J 221 ASP cc_start: 0.9105 (m-30) cc_final: 0.8015 (t0) REVERT: J 227 ASP cc_start: 0.8708 (OUTLIER) cc_final: 0.8296 (p0) REVERT: J 267 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8623 (mm-30) REVERT: J 335 MET cc_start: 0.7988 (tmm) cc_final: 0.7640 (tmm) REVERT: J 342 GLN cc_start: 0.9598 (tt0) cc_final: 0.8455 (tm-30) REVERT: J 345 ARG cc_start: 0.8701 (ttp80) cc_final: 0.8320 (ttp80) REVERT: J 346 GLN cc_start: 0.9246 (mt0) cc_final: 0.7848 (mt0) REVERT: J 419 MET cc_start: 0.8527 (ptm) cc_final: 0.7932 (tmm) REVERT: J 424 LEU cc_start: 0.9696 (tp) cc_final: 0.9239 (mp) REVERT: J 458 MET cc_start: 0.7371 (ttt) cc_final: 0.6817 (ttt) REVERT: K 26 MET cc_start: 0.9278 (mmm) cc_final: 0.8884 (mmm) REVERT: K 28 MET cc_start: 0.9064 (tpp) cc_final: 0.8729 (tpp) REVERT: K 60 LYS cc_start: 0.9473 (tppt) cc_final: 0.9113 (mttp) REVERT: K 86 ARG cc_start: 0.9116 (mmp80) cc_final: 0.8727 (mmt180) REVERT: K 97 PHE cc_start: 0.9432 (m-10) cc_final: 0.9191 (m-10) REVERT: K 120 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8732 (mm-30) REVERT: K 125 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8431 (pp) REVERT: K 176 LYS cc_start: 0.9373 (OUTLIER) cc_final: 0.8948 (mtpp) REVERT: K 200 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7432 (tp30) REVERT: K 225 TYR cc_start: 0.7472 (m-80) cc_final: 0.6982 (m-80) REVERT: K 275 ASN cc_start: 0.9599 (m-40) cc_final: 0.9348 (m-40) REVERT: K 324 LYS cc_start: 0.9199 (mmmt) cc_final: 0.8899 (mmtt) REVERT: K 342 GLN cc_start: 0.9513 (OUTLIER) cc_final: 0.8396 (pp30) REVERT: K 345 ARG cc_start: 0.8780 (tmm-80) cc_final: 0.7812 (tmm-80) REVERT: K 369 MET cc_start: 0.8889 (mmt) cc_final: 0.8648 (mmp) REVERT: K 374 GLN cc_start: 0.9374 (mt0) cc_final: 0.9136 (mt0) REVERT: K 391 LYS cc_start: 0.9191 (tptp) cc_final: 0.8897 (tptp) REVERT: K 398 MET cc_start: 0.8911 (mtt) cc_final: 0.8523 (mtt) REVERT: K 409 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7912 (tm-30) REVERT: K 418 LYS cc_start: 0.7925 (mtmt) cc_final: 0.7193 (mtmt) REVERT: K 422 GLU cc_start: 0.9427 (OUTLIER) cc_final: 0.9167 (tp30) REVERT: K 423 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8562 (mt-10) REVERT: K 458 MET cc_start: 0.8835 (tmm) cc_final: 0.8231 (tpt) REVERT: K 460 ASN cc_start: 0.9283 (m-40) cc_final: 0.8888 (m-40) REVERT: L 17 MET cc_start: 0.9506 (mmm) cc_final: 0.9128 (mmm) REVERT: L 77 ASP cc_start: 0.8964 (m-30) cc_final: 0.8553 (m-30) REVERT: L 219 GLU cc_start: 0.8268 (pt0) cc_final: 0.7607 (pm20) REVERT: L 239 GLN cc_start: 0.9457 (pm20) cc_final: 0.9060 (pm20) REVERT: L 322 ASN cc_start: 0.9356 (m-40) cc_final: 0.9106 (m-40) REVERT: L 342 GLN cc_start: 0.9371 (tt0) cc_final: 0.8960 (tt0) REVERT: L 345 ARG cc_start: 0.9432 (tmm-80) cc_final: 0.8995 (tmm-80) REVERT: L 369 MET cc_start: 0.8982 (mtm) cc_final: 0.8614 (mpp) REVERT: L 383 LYS cc_start: 0.9558 (mmmm) cc_final: 0.9150 (tppt) REVERT: L 411 ASN cc_start: 0.8923 (t0) cc_final: 0.8595 (t0) REVERT: L 419 MET cc_start: 0.8621 (mtt) cc_final: 0.8224 (mmm) REVERT: L 423 GLU cc_start: 0.9225 (OUTLIER) cc_final: 0.8944 (pt0) REVERT: L 452 TYR cc_start: 0.9335 (p90) cc_final: 0.8613 (p90) REVERT: L 458 MET cc_start: 0.7826 (tpt) cc_final: 0.7491 (tpt) REVERT: M 15 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7336 (ptpt) REVERT: M 99 MET cc_start: 0.7702 (pmm) cc_final: 0.7096 (pmm) REVERT: M 109 GLU cc_start: 0.7502 (pt0) cc_final: 0.7283 (pt0) REVERT: M 173 ASP cc_start: 0.8956 (m-30) cc_final: 0.8717 (m-30) REVERT: M 188 TYR cc_start: 0.9253 (m-80) cc_final: 0.9003 (m-10) REVERT: M 207 ARG cc_start: 0.9146 (tpp80) cc_final: 0.8762 (tpp80) REVERT: M 276 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9265 (mp) REVERT: N 24 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8083 (mp10) REVERT: N 99 MET cc_start: 0.8517 (ptm) cc_final: 0.8262 (ppp) REVERT: N 170 ARG cc_start: 0.9120 (tpp80) cc_final: 0.8790 (ttm170) REVERT: N 271 GLU cc_start: 0.8516 (mp0) cc_final: 0.8196 (mp0) REVERT: N 290 LYS cc_start: 0.8943 (mttp) cc_final: 0.8634 (mtpp) REVERT: O 77 ARG cc_start: 0.8791 (mtm110) cc_final: 0.8473 (mtm110) REVERT: O 99 MET cc_start: 0.5697 (OUTLIER) cc_final: 0.5171 (ppp) REVERT: O 100 LEU cc_start: 0.4398 (OUTLIER) cc_final: 0.3915 (pt) REVERT: O 121 ASP cc_start: 0.8739 (t0) cc_final: 0.8327 (t0) REVERT: O 124 GLN cc_start: 0.9556 (tt0) cc_final: 0.9140 (tt0) REVERT: O 207 ARG cc_start: 0.8654 (mmm-85) cc_final: 0.8183 (mmm-85) REVERT: P 22 ASP cc_start: 0.8839 (p0) cc_final: 0.8262 (p0) REVERT: P 39 ARG cc_start: 0.9019 (mtm110) cc_final: 0.8757 (mtm110) REVERT: P 116 GLN cc_start: 0.9211 (OUTLIER) cc_final: 0.8706 (mm-40) REVERT: P 229 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8575 (tm-30) REVERT: P 290 LYS cc_start: 0.9108 (mmmm) cc_final: 0.8723 (mmmm) REVERT: Q 26 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8471 (tm-30) REVERT: Q 39 ARG cc_start: 0.8513 (mtm110) cc_final: 0.8164 (mtm110) REVERT: Q 123 MET cc_start: 0.9386 (mmm) cc_final: 0.9109 (mmm) REVERT: Q 246 GLU cc_start: 0.8365 (mt-10) cc_final: 0.7879 (mt-10) REVERT: Q 257 ASP cc_start: 0.8458 (p0) cc_final: 0.7896 (m-30) REVERT: Q 271 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7644 (mt-10) REVERT: Q 290 LYS cc_start: 0.9207 (mmmm) cc_final: 0.8912 (mmmm) REVERT: R 15 LYS cc_start: 0.4951 (OUTLIER) cc_final: 0.3945 (pttm) REVERT: R 126 MET cc_start: 0.9367 (mtm) cc_final: 0.9127 (mtm) REVERT: R 321 LYS cc_start: 0.8285 (ttpp) cc_final: 0.7335 (tppt) REVERT: S 155 MET cc_start: 0.8708 (tpp) cc_final: 0.8401 (mmm) REVERT: S 156 THR cc_start: 0.9607 (OUTLIER) cc_final: 0.9278 (p) REVERT: S 199 TYR cc_start: 0.8535 (m-80) cc_final: 0.8046 (m-80) REVERT: T 20 VAL cc_start: 0.8758 (OUTLIER) cc_final: 0.8506 (t) REVERT: T 81 ASP cc_start: 0.9035 (t70) cc_final: 0.8521 (p0) REVERT: T 135 LYS cc_start: 0.9652 (tttm) cc_final: 0.9418 (tttt) REVERT: T 274 TYR cc_start: 0.8737 (p90) cc_final: 0.8408 (p90) REVERT: U 105 LYS cc_start: 0.9501 (mttt) cc_final: 0.9249 (mmmm) REVERT: U 114 ILE cc_start: 0.9747 (mt) cc_final: 0.9461 (tt) outliers start: 240 outliers final: 181 residues processed: 1676 average time/residue: 0.6458 time to fit residues: 1827.7305 Evaluate side-chains 1705 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 1489 time to evaluate : 5.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 278 ASP Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 340 MET Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 412 SER Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 456 GLU Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 299 HIS Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 342 GLN Chi-restraints excluded: chain F residue 377 VAL Chi-restraints excluded: chain F residue 420 SER Chi-restraints excluded: chain F residue 454 GLU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 165 LEU Chi-restraints excluded: chain G residue 256 THR Chi-restraints excluded: chain G residue 286 CYS Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 374 GLN Chi-restraints excluded: chain G residue 436 ILE Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 121 ASP Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 194 TYR Chi-restraints excluded: chain H residue 216 THR Chi-restraints excluded: chain H residue 226 VAL Chi-restraints excluded: chain H residue 251 LYS Chi-restraints excluded: chain H residue 283 CYS Chi-restraints excluded: chain H residue 286 CYS Chi-restraints excluded: chain H residue 290 THR Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 354 LEU Chi-restraints excluded: chain H residue 419 MET Chi-restraints excluded: chain H residue 424 LEU Chi-restraints excluded: chain H residue 447 LYS Chi-restraints excluded: chain H residue 460 ASN Chi-restraints excluded: chain I residue 13 ASP Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 46 ASP Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 291 LEU Chi-restraints excluded: chain I residue 336 VAL Chi-restraints excluded: chain I residue 340 MET Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain I residue 406 ILE Chi-restraints excluded: chain I residue 419 MET Chi-restraints excluded: chain J residue 121 ASP Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 227 ASP Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 299 HIS Chi-restraints excluded: chain J residue 336 VAL Chi-restraints excluded: chain J residue 350 LEU Chi-restraints excluded: chain J residue 354 LEU Chi-restraints excluded: chain K residue 6 ASN Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 176 LYS Chi-restraints excluded: chain K residue 209 ASP Chi-restraints excluded: chain K residue 246 VAL Chi-restraints excluded: chain K residue 290 THR Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 297 THR Chi-restraints excluded: chain K residue 304 VAL Chi-restraints excluded: chain K residue 342 GLN Chi-restraints excluded: chain K residue 405 LYS Chi-restraints excluded: chain K residue 422 GLU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 164 ILE Chi-restraints excluded: chain L residue 196 ILE Chi-restraints excluded: chain L residue 328 LEU Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 377 VAL Chi-restraints excluded: chain L residue 423 GLU Chi-restraints excluded: chain M residue 12 TRP Chi-restraints excluded: chain M residue 15 LYS Chi-restraints excluded: chain M residue 86 VAL Chi-restraints excluded: chain M residue 152 THR Chi-restraints excluded: chain M residue 187 LEU Chi-restraints excluded: chain M residue 240 THR Chi-restraints excluded: chain M residue 276 LEU Chi-restraints excluded: chain M residue 312 ASP Chi-restraints excluded: chain N residue 24 GLN Chi-restraints excluded: chain N residue 43 ASN Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 68 ASN Chi-restraints excluded: chain N residue 102 TRP Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain N residue 178 VAL Chi-restraints excluded: chain N residue 313 THR Chi-restraints excluded: chain O residue 99 MET Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 187 LEU Chi-restraints excluded: chain P residue 74 LYS Chi-restraints excluded: chain P residue 116 GLN Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain P residue 166 ILE Chi-restraints excluded: chain P residue 178 VAL Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 216 ILE Chi-restraints excluded: chain P residue 276 LEU Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 81 ASP Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 236 LEU Chi-restraints excluded: chain R residue 10 ASN Chi-restraints excluded: chain R residue 11 ASP Chi-restraints excluded: chain R residue 15 LYS Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 224 VAL Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 37 ILE Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain S residue 123 MET Chi-restraints excluded: chain S residue 152 THR Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 225 SER Chi-restraints excluded: chain S residue 244 LEU Chi-restraints excluded: chain S residue 245 ILE Chi-restraints excluded: chain S residue 320 THR Chi-restraints excluded: chain T residue 6 LEU Chi-restraints excluded: chain T residue 20 VAL Chi-restraints excluded: chain T residue 209 ASP Chi-restraints excluded: chain T residue 235 THR Chi-restraints excluded: chain T residue 236 LEU Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 152 THR Chi-restraints excluded: chain U residue 243 ILE Chi-restraints excluded: chain U residue 313 THR Chi-restraints excluded: chain U residue 316 VAL Chi-restraints excluded: chain V residue 152 THR Chi-restraints excluded: chain V residue 164 GLN Chi-restraints excluded: chain V residue 244 LEU Chi-restraints excluded: chain V residue 256 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 855 random chunks: chunk 130 optimal weight: 7.9990 chunk 704 optimal weight: 0.6980 chunk 557 optimal weight: 1.9990 chunk 279 optimal weight: 6.9990 chunk 343 optimal weight: 20.0000 chunk 572 optimal weight: 20.0000 chunk 248 optimal weight: 20.0000 chunk 257 optimal weight: 7.9990 chunk 534 optimal weight: 7.9990 chunk 372 optimal weight: 7.9990 chunk 599 optimal weight: 8.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 ASN ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 GLN ** F 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN ** H 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 460 ASN ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 43 ASN N 248 ASN ** O 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.083583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.068690 restraints weight = 250055.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.070770 restraints weight = 143536.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.072213 restraints weight = 97998.446| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 68177 Z= 0.254 Angle : 0.718 12.359 92470 Z= 0.365 Chirality : 0.044 0.264 10048 Planarity : 0.004 0.069 12237 Dihedral : 4.716 59.935 9264 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.37 % Favored : 95.62 % Rotamer: Outliers : 3.22 % Allowed : 23.26 % Favored : 73.52 % 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: -0.13 (0.09), residues: 8507 helix: 1.11 (0.09), residues: 3200 sheet: -0.35 (0.14), residues: 1515 loop : -0.96 (0.10), residues: 3792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP J 202 HIS 0.008 0.001 HIS H 299 PHE 0.022 0.001 PHE P 251 TYR 0.021 0.001 TYR H 62 ARG 0.015 0.001 ARG P 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17014 Ramachandran restraints generated. 8507 Oldfield, 0 Emsley, 8507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17014 Ramachandran restraints generated. 8507 Oldfield, 0 Emsley, 8507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1769 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 1544 time to evaluate : 5.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 15 LYS cc_start: 0.9474 (mtmt) cc_final: 0.8977 (mttp) REVERT: A 18 HIS cc_start: 0.9342 (m90) cc_final: 0.8664 (m-70) REVERT: A 26 MET cc_start: 0.9296 (mtp) cc_final: 0.8959 (ptp) REVERT: A 29 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8553 (tm-30) REVERT: A 32 ARG cc_start: 0.8419 (ttp80) cc_final: 0.8096 (ttp80) REVERT: A 163 ASP cc_start: 0.9235 (m-30) cc_final: 0.8696 (t0) REVERT: A 214 GLN cc_start: 0.8980 (pp30) cc_final: 0.8258 (pp30) REVERT: A 241 ASP cc_start: 0.8739 (p0) cc_final: 0.8112 (p0) REVERT: A 259 MET cc_start: 0.8128 (mmm) cc_final: 0.7629 (mmm) REVERT: A 337 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8766 (tptp) REVERT: A 345 ARG cc_start: 0.9323 (ttp-110) cc_final: 0.9069 (ttp-110) REVERT: A 346 GLN cc_start: 0.9014 (mt0) cc_final: 0.8626 (mp10) REVERT: A 369 MET cc_start: 0.8718 (mtm) cc_final: 0.8222 (ptp) REVERT: A 407 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8599 (tm-30) REVERT: A 419 MET cc_start: 0.8619 (ppp) cc_final: 0.8112 (ppp) REVERT: A 422 GLU cc_start: 0.9383 (tp30) cc_final: 0.9125 (tp30) REVERT: A 457 ASP cc_start: 0.9151 (t0) cc_final: 0.8861 (t0) REVERT: A 458 MET cc_start: 0.8135 (tpt) cc_final: 0.7210 (tpt) REVERT: A 460 ASN cc_start: 0.8842 (m110) cc_final: 0.8458 (m110) REVERT: B 9 TYR cc_start: 0.8537 (p90) cc_final: 0.8027 (p90) REVERT: B 64 GLU cc_start: 0.8664 (pt0) cc_final: 0.8351 (pt0) REVERT: B 79 MET cc_start: 0.9181 (mtm) cc_final: 0.8432 (mtm) REVERT: B 82 GLN cc_start: 0.9349 (mt0) cc_final: 0.8885 (mm110) REVERT: B 188 ASP cc_start: 0.8300 (t0) cc_final: 0.7721 (t0) REVERT: B 219 GLU cc_start: 0.8235 (pt0) cc_final: 0.7898 (pt0) REVERT: B 296 LEU cc_start: 0.9155 (tp) cc_final: 0.8844 (tp) REVERT: B 331 GLU cc_start: 0.8893 (pm20) cc_final: 0.8602 (pm20) REVERT: B 340 MET cc_start: 0.8860 (mmm) cc_final: 0.8354 (mmm) REVERT: B 344 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8340 (mt-10) REVERT: B 383 LYS cc_start: 0.9477 (ttmm) cc_final: 0.9139 (ttpt) REVERT: B 398 MET cc_start: 0.9295 (mtm) cc_final: 0.8448 (mpp) REVERT: B 416 ILE cc_start: 0.9014 (mm) cc_final: 0.8715 (mm) REVERT: B 418 LYS cc_start: 0.8936 (mttt) cc_final: 0.8479 (mttt) REVERT: B 441 MET cc_start: 0.9435 (tmm) cc_final: 0.9125 (tmm) REVERT: C 19 LYS cc_start: 0.9293 (tppt) cc_final: 0.8952 (tppt) REVERT: C 37 ASN cc_start: 0.9276 (m-40) cc_final: 0.8889 (m110) REVERT: C 46 ASP cc_start: 0.8347 (t0) cc_final: 0.7732 (t0) REVERT: C 60 LYS cc_start: 0.9526 (mmmm) cc_final: 0.9241 (mmmm) REVERT: C 77 ASP cc_start: 0.9326 (m-30) cc_final: 0.9115 (t70) REVERT: C 98 ASP cc_start: 0.9279 (p0) cc_final: 0.9021 (p0) REVERT: C 105 ASP cc_start: 0.9269 (p0) cc_final: 0.8980 (p0) REVERT: C 190 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7257 (m-30) REVERT: C 296 LEU cc_start: 0.9009 (tp) cc_final: 0.8798 (tp) REVERT: C 310 VAL cc_start: 0.7883 (OUTLIER) cc_final: 0.7630 (m) REVERT: C 314 ARG cc_start: 0.8790 (mmt90) cc_final: 0.7956 (tpm170) REVERT: C 369 MET cc_start: 0.8245 (mpp) cc_final: 0.7577 (mpp) REVERT: C 398 MET cc_start: 0.9265 (mtm) cc_final: 0.8731 (mpp) REVERT: C 413 ASP cc_start: 0.8783 (t0) cc_final: 0.8506 (t0) REVERT: C 441 MET cc_start: 0.9352 (tmm) cc_final: 0.9010 (ppp) REVERT: C 458 MET cc_start: 0.7437 (OUTLIER) cc_final: 0.6787 (tpt) REVERT: C 460 ASN cc_start: 0.9563 (m-40) cc_final: 0.9171 (m110) REVERT: D 15 LYS cc_start: 0.9375 (mttt) cc_final: 0.8940 (mtmm) REVERT: D 16 LYS cc_start: 0.9244 (mmmm) cc_final: 0.8990 (mmmm) REVERT: D 17 MET cc_start: 0.9417 (mmm) cc_final: 0.8464 (mmm) REVERT: D 18 HIS cc_start: 0.9555 (OUTLIER) cc_final: 0.8365 (m90) REVERT: D 29 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8150 (tm-30) REVERT: D 32 ARG cc_start: 0.9164 (mtp-110) cc_final: 0.8856 (mtp-110) REVERT: D 36 ASP cc_start: 0.9513 (m-30) cc_final: 0.9168 (m-30) REVERT: D 54 GLU cc_start: 0.9010 (tp30) cc_final: 0.8696 (tp30) REVERT: D 120 GLU cc_start: 0.9308 (tt0) cc_final: 0.9075 (mt-10) REVERT: D 121 ASP cc_start: 0.9319 (OUTLIER) cc_final: 0.9018 (t70) REVERT: D 173 ASN cc_start: 0.9075 (m-40) cc_final: 0.8626 (p0) REVERT: D 184 ARG cc_start: 0.8740 (ttp80) cc_final: 0.8327 (ttp80) REVERT: D 251 LYS cc_start: 0.8923 (ptpt) cc_final: 0.8603 (pttm) REVERT: D 269 ASN cc_start: 0.9660 (OUTLIER) cc_final: 0.9071 (t0) REVERT: D 337 LYS cc_start: 0.9437 (tptm) cc_final: 0.8987 (tptm) REVERT: D 341 ASP cc_start: 0.9257 (m-30) cc_final: 0.8869 (m-30) REVERT: D 347 MET cc_start: 0.9125 (mmt) cc_final: 0.8742 (mmt) REVERT: D 374 GLN cc_start: 0.9273 (mt0) cc_final: 0.8709 (mp10) REVERT: D 380 ARG cc_start: 0.9192 (ttp-110) cc_final: 0.8894 (ttp-110) REVERT: D 409 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8313 (tm-30) REVERT: D 419 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8537 (tmm) REVERT: D 422 GLU cc_start: 0.9383 (tp30) cc_final: 0.9026 (tp30) REVERT: D 441 MET cc_start: 0.9183 (tmm) cc_final: 0.8799 (ppp) REVERT: D 458 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.7939 (tpt) REVERT: E 32 ARG cc_start: 0.8802 (tpp80) cc_final: 0.8569 (tpp80) REVERT: E 157 LYS cc_start: 0.9306 (mmmt) cc_final: 0.8893 (mmmt) REVERT: E 162 GLU cc_start: 0.9192 (mp0) cc_final: 0.8887 (mp0) REVERT: E 163 ASP cc_start: 0.8898 (m-30) cc_final: 0.8052 (t0) REVERT: E 165 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8775 (pp) REVERT: E 184 ARG cc_start: 0.9075 (ttp80) cc_final: 0.8648 (ttp80) REVERT: E 259 MET cc_start: 0.8950 (mmm) cc_final: 0.8692 (mmm) REVERT: E 267 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8875 (mm-30) REVERT: E 340 MET cc_start: 0.9498 (OUTLIER) cc_final: 0.9150 (tpp) REVERT: E 346 GLN cc_start: 0.9500 (mt0) cc_final: 0.9066 (mt0) REVERT: E 347 MET cc_start: 0.8885 (mmm) cc_final: 0.8303 (mpp) REVERT: E 370 GLU cc_start: 0.8217 (pm20) cc_final: 0.7727 (pm20) REVERT: E 399 PHE cc_start: 0.9366 (m-80) cc_final: 0.9049 (t80) REVERT: E 419 MET cc_start: 0.8314 (ttm) cc_final: 0.7700 (ttm) REVERT: E 420 SER cc_start: 0.9509 (OUTLIER) cc_final: 0.9118 (p) REVERT: E 441 MET cc_start: 0.9089 (tmm) cc_final: 0.8717 (tmm) REVERT: E 454 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8267 (tm-30) REVERT: E 460 ASN cc_start: 0.9289 (m-40) cc_final: 0.8970 (m110) REVERT: F 18 HIS cc_start: 0.8786 (m90) cc_final: 0.8427 (m90) REVERT: F 42 VAL cc_start: 0.9637 (t) cc_final: 0.9393 (p) REVERT: F 79 MET cc_start: 0.9263 (mtm) cc_final: 0.9002 (mtm) REVERT: F 83 ILE cc_start: 0.9495 (OUTLIER) cc_final: 0.9238 (mp) REVERT: F 94 GLU cc_start: 0.8361 (mp0) cc_final: 0.8104 (mp0) REVERT: F 163 ASP cc_start: 0.9205 (m-30) cc_final: 0.8618 (m-30) REVERT: F 177 ARG cc_start: 0.9200 (mmm-85) cc_final: 0.8796 (mmm-85) REVERT: F 184 ARG cc_start: 0.9231 (ttp-110) cc_final: 0.8714 (ttp80) REVERT: F 251 LYS cc_start: 0.9347 (tppp) cc_final: 0.9017 (tppp) REVERT: F 315 ASP cc_start: 0.8406 (m-30) cc_final: 0.7555 (p0) REVERT: F 335 MET cc_start: 0.8170 (ppp) cc_final: 0.7695 (ppp) REVERT: F 340 MET cc_start: 0.9127 (mmm) cc_final: 0.8742 (mmm) REVERT: F 342 GLN cc_start: 0.9487 (OUTLIER) cc_final: 0.8986 (pp30) REVERT: F 343 LYS cc_start: 0.9404 (ptmm) cc_final: 0.8971 (ptmm) REVERT: F 346 GLN cc_start: 0.9432 (mt0) cc_final: 0.8009 (mt0) REVERT: F 347 MET cc_start: 0.9282 (mmm) cc_final: 0.8618 (mtm) REVERT: F 357 SER cc_start: 0.8542 (m) cc_final: 0.8250 (p) REVERT: F 370 GLU cc_start: 0.8616 (mt-10) cc_final: 0.7946 (mp0) REVERT: F 374 GLN cc_start: 0.9348 (mt0) cc_final: 0.9066 (mt0) REVERT: F 380 ARG cc_start: 0.9245 (ttp80) cc_final: 0.8683 (ttp80) REVERT: F 398 MET cc_start: 0.9151 (ptp) cc_final: 0.8795 (ptp) REVERT: F 413 ASP cc_start: 0.8985 (m-30) cc_final: 0.8502 (t70) REVERT: F 419 MET cc_start: 0.8636 (ppp) cc_final: 0.8160 (ppp) REVERT: F 460 ASN cc_start: 0.9020 (m-40) cc_final: 0.8658 (m110) REVERT: G 32 ARG cc_start: 0.7725 (tpp-160) cc_final: 0.7048 (tpp-160) REVERT: G 74 ASN cc_start: 0.9568 (t0) cc_final: 0.8803 (t0) REVERT: G 79 MET cc_start: 0.9329 (mtm) cc_final: 0.9043 (mpp) REVERT: G 124 SER cc_start: 0.9525 (OUTLIER) cc_final: 0.9194 (p) REVERT: G 163 ASP cc_start: 0.9345 (m-30) cc_final: 0.9072 (t0) REVERT: G 262 MET cc_start: 0.8761 (mmp) cc_final: 0.8519 (mmp) REVERT: G 335 MET cc_start: 0.9073 (ttt) cc_final: 0.8803 (ttt) REVERT: G 344 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8843 (mm-30) REVERT: G 347 MET cc_start: 0.9035 (mmm) cc_final: 0.8410 (mpp) REVERT: G 354 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.6833 (pt) REVERT: G 405 LYS cc_start: 0.9317 (mtmm) cc_final: 0.9043 (mtmm) REVERT: G 460 ASN cc_start: 0.9184 (m-40) cc_final: 0.8778 (m110) REVERT: H 17 MET cc_start: 0.9630 (mmm) cc_final: 0.8650 (tpp) REVERT: H 26 MET cc_start: 0.9279 (mtm) cc_final: 0.8445 (mtm) REVERT: H 29 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8249 (tm-30) REVERT: H 77 ASP cc_start: 0.9342 (m-30) cc_final: 0.9114 (m-30) REVERT: H 79 MET cc_start: 0.9003 (mmt) cc_final: 0.8635 (mmp) REVERT: H 185 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8011 (tm-30) REVERT: H 200 GLU cc_start: 0.8082 (mp0) cc_final: 0.7693 (mp0) REVERT: H 326 GLU cc_start: 0.7919 (mp0) cc_final: 0.7459 (pm20) REVERT: H 342 GLN cc_start: 0.9495 (OUTLIER) cc_final: 0.9270 (pp30) REVERT: H 370 GLU cc_start: 0.8656 (tt0) cc_final: 0.7840 (tm-30) REVERT: H 380 ARG cc_start: 0.8933 (mtm-85) cc_final: 0.8040 (mtm-85) REVERT: H 409 GLU cc_start: 0.8272 (mp0) cc_final: 0.7729 (mp0) REVERT: H 423 GLU cc_start: 0.9191 (mt-10) cc_final: 0.8932 (mt-10) REVERT: H 454 GLU cc_start: 0.9071 (mp0) cc_final: 0.8812 (mp0) REVERT: I 16 LYS cc_start: 0.9248 (mmtm) cc_final: 0.8857 (mmtm) REVERT: I 18 HIS cc_start: 0.9303 (OUTLIER) cc_final: 0.8817 (m90) REVERT: I 24 ILE cc_start: 0.9575 (mt) cc_final: 0.9271 (tp) REVERT: I 28 MET cc_start: 0.9203 (mtm) cc_final: 0.8871 (mpp) REVERT: I 79 MET cc_start: 0.9415 (mtm) cc_final: 0.8899 (mtm) REVERT: I 131 PHE cc_start: 0.9252 (t80) cc_final: 0.8997 (t80) REVERT: I 158 PHE cc_start: 0.8836 (t80) cc_final: 0.8593 (t80) REVERT: I 219 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8419 (tp30) REVERT: I 227 ASP cc_start: 0.8999 (m-30) cc_final: 0.8690 (m-30) REVERT: I 262 MET cc_start: 0.8399 (mmm) cc_final: 0.8064 (mmm) REVERT: I 280 GLU cc_start: 0.9221 (mm-30) cc_final: 0.8755 (mm-30) REVERT: I 335 MET cc_start: 0.9237 (ttt) cc_final: 0.8872 (tmm) REVERT: I 336 VAL cc_start: 0.9563 (OUTLIER) cc_final: 0.9239 (p) REVERT: I 340 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8750 (mtm) REVERT: I 344 GLU cc_start: 0.9033 (tt0) cc_final: 0.8693 (tp30) REVERT: I 347 MET cc_start: 0.9429 (mtp) cc_final: 0.8837 (mtp) REVERT: I 398 MET cc_start: 0.8937 (mtm) cc_final: 0.8432 (mtt) REVERT: I 422 GLU cc_start: 0.9224 (tp30) cc_final: 0.8986 (tm-30) REVERT: I 458 MET cc_start: 0.7972 (tpp) cc_final: 0.7029 (mmm) REVERT: I 460 ASN cc_start: 0.8766 (m110) cc_final: 0.8529 (p0) REVERT: J 19 LYS cc_start: 0.9322 (tppt) cc_final: 0.8969 (tppt) REVERT: J 26 MET cc_start: 0.9269 (mtm) cc_final: 0.9009 (ptm) REVERT: J 221 ASP cc_start: 0.9127 (m-30) cc_final: 0.8009 (t0) REVERT: J 227 ASP cc_start: 0.8642 (OUTLIER) cc_final: 0.8324 (p0) REVERT: J 267 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8562 (mm-30) REVERT: J 281 GLU cc_start: 0.9283 (tp30) cc_final: 0.8888 (tp30) REVERT: J 335 MET cc_start: 0.7994 (tmm) cc_final: 0.7689 (tmm) REVERT: J 342 GLN cc_start: 0.9604 (tt0) cc_final: 0.8444 (tm-30) REVERT: J 345 ARG cc_start: 0.8708 (ttp80) cc_final: 0.8359 (ttp80) REVERT: J 346 GLN cc_start: 0.9206 (mt0) cc_final: 0.7797 (mt0) REVERT: J 380 ARG cc_start: 0.8268 (tpt-90) cc_final: 0.7700 (tpt-90) REVERT: J 419 MET cc_start: 0.8246 (ptm) cc_final: 0.7931 (tmm) REVERT: J 458 MET cc_start: 0.7358 (ttt) cc_final: 0.6792 (ttt) REVERT: K 26 MET cc_start: 0.9236 (mmm) cc_final: 0.8827 (mmm) REVERT: K 28 MET cc_start: 0.9044 (tpp) cc_final: 0.8731 (tpp) REVERT: K 60 LYS cc_start: 0.9477 (tppt) cc_final: 0.9079 (mttp) REVERT: K 86 ARG cc_start: 0.9097 (mmp80) cc_final: 0.8692 (mmt180) REVERT: K 120 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8665 (mm-30) REVERT: K 125 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8405 (pp) REVERT: K 169 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8058 (mm-30) REVERT: K 176 LYS cc_start: 0.9264 (OUTLIER) cc_final: 0.9036 (mmmt) REVERT: K 225 TYR cc_start: 0.7616 (m-80) cc_final: 0.7107 (m-80) REVERT: K 324 LYS cc_start: 0.9230 (mmmt) cc_final: 0.8909 (mmtt) REVERT: K 345 ARG cc_start: 0.8810 (tmm-80) cc_final: 0.8439 (ttp80) REVERT: K 369 MET cc_start: 0.8885 (mmt) cc_final: 0.8647 (mmp) REVERT: K 391 LYS cc_start: 0.9168 (tptp) cc_final: 0.8867 (tptp) REVERT: K 398 MET cc_start: 0.8956 (mtt) cc_final: 0.8644 (mtt) REVERT: K 409 GLU cc_start: 0.8318 (tm-30) cc_final: 0.7900 (tm-30) REVERT: K 418 LYS cc_start: 0.7854 (mtmt) cc_final: 0.7108 (mtmt) REVERT: K 423 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8536 (mt-10) REVERT: K 458 MET cc_start: 0.8778 (tmm) cc_final: 0.8118 (tpt) REVERT: K 460 ASN cc_start: 0.9266 (m-40) cc_final: 0.8855 (m110) REVERT: L 16 LYS cc_start: 0.9333 (mmtt) cc_final: 0.9095 (mmmt) REVERT: L 17 MET cc_start: 0.9455 (mmm) cc_final: 0.9130 (mmm) REVERT: L 77 ASP cc_start: 0.8945 (m-30) cc_final: 0.8529 (m-30) REVERT: L 219 GLU cc_start: 0.8229 (pt0) cc_final: 0.7572 (pm20) REVERT: L 239 GLN cc_start: 0.9447 (pm20) cc_final: 0.9042 (pm20) REVERT: L 242 GLU cc_start: 0.8755 (pt0) cc_final: 0.8471 (pm20) REVERT: L 322 ASN cc_start: 0.9376 (m-40) cc_final: 0.9127 (m-40) REVERT: L 342 GLN cc_start: 0.9302 (tt0) cc_final: 0.8869 (tt0) REVERT: L 345 ARG cc_start: 0.9405 (tmm-80) cc_final: 0.9011 (tmm-80) REVERT: L 369 MET cc_start: 0.8820 (mtm) cc_final: 0.8481 (mpp) REVERT: L 383 LYS cc_start: 0.9550 (mmmm) cc_final: 0.9145 (tppt) REVERT: L 411 ASN cc_start: 0.9039 (t0) cc_final: 0.8696 (t0) REVERT: L 419 MET cc_start: 0.8772 (mtt) cc_final: 0.8307 (mmm) REVERT: L 423 GLU cc_start: 0.9208 (OUTLIER) cc_final: 0.8691 (pt0) REVERT: L 452 TYR cc_start: 0.9330 (p90) cc_final: 0.8586 (p90) REVERT: L 458 MET cc_start: 0.7889 (tpt) cc_final: 0.7604 (tpt) REVERT: M 15 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7206 (ptpt) REVERT: M 109 GLU cc_start: 0.7518 (pt0) cc_final: 0.7248 (pt0) REVERT: M 173 ASP cc_start: 0.8968 (m-30) cc_final: 0.8723 (m-30) REVERT: M 207 ARG cc_start: 0.9157 (tpp80) cc_final: 0.8878 (tpp80) REVERT: M 276 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9273 (mp) REVERT: N 24 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8130 (mp10) REVERT: N 170 ARG cc_start: 0.9128 (tpp80) cc_final: 0.8828 (ttm170) REVERT: N 246 GLU cc_start: 0.8739 (mp0) cc_final: 0.8537 (mp0) REVERT: N 271 GLU cc_start: 0.8532 (mp0) cc_final: 0.8213 (mp0) REVERT: N 290 LYS cc_start: 0.8907 (mttp) cc_final: 0.8615 (mtpp) REVERT: O 77 ARG cc_start: 0.8834 (mtm110) cc_final: 0.8570 (mtm110) REVERT: O 99 MET cc_start: 0.5616 (OUTLIER) cc_final: 0.5100 (ppp) REVERT: O 100 LEU cc_start: 0.4254 (OUTLIER) cc_final: 0.3797 (pt) REVERT: O 121 ASP cc_start: 0.8777 (t0) cc_final: 0.8375 (t0) REVERT: O 207 ARG cc_start: 0.8696 (mmm-85) cc_final: 0.8388 (mmm160) REVERT: O 266 ARG cc_start: 0.9331 (mmm-85) cc_final: 0.8872 (mmm-85) REVERT: P 22 ASP cc_start: 0.8876 (p0) cc_final: 0.8281 (p0) REVERT: P 116 GLN cc_start: 0.9231 (OUTLIER) cc_final: 0.8746 (mm-40) REVERT: P 207 ARG cc_start: 0.9263 (tpp80) cc_final: 0.8759 (tpp80) REVERT: P 229 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8601 (tm-30) REVERT: P 290 LYS cc_start: 0.9099 (mmmm) cc_final: 0.8502 (mmmm) REVERT: Q 26 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8502 (tm-30) REVERT: Q 39 ARG cc_start: 0.8636 (mtm110) cc_final: 0.8374 (mtm110) REVERT: Q 123 MET cc_start: 0.9421 (mmm) cc_final: 0.9123 (mmm) REVERT: Q 246 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8008 (mt-10) REVERT: Q 257 ASP cc_start: 0.8490 (p0) cc_final: 0.7906 (m-30) REVERT: Q 290 LYS cc_start: 0.9186 (mmmm) cc_final: 0.8899 (mmmm) REVERT: R 105 LYS cc_start: 0.8914 (mmmm) cc_final: 0.8705 (mmmm) REVERT: R 126 MET cc_start: 0.9396 (mtm) cc_final: 0.9163 (mtm) REVERT: R 321 LYS cc_start: 0.8205 (ttpp) cc_final: 0.7269 (tppt) REVERT: S 81 ASP cc_start: 0.9048 (t70) cc_final: 0.8621 (p0) REVERT: S 155 MET cc_start: 0.8789 (tpp) cc_final: 0.8472 (mmm) REVERT: S 156 THR cc_start: 0.9601 (OUTLIER) cc_final: 0.9261 (p) REVERT: S 199 TYR cc_start: 0.8526 (m-80) cc_final: 0.8021 (m-80) REVERT: T 20 VAL cc_start: 0.8743 (OUTLIER) cc_final: 0.8454 (t) REVERT: T 81 ASP cc_start: 0.9089 (t70) cc_final: 0.8515 (p0) REVERT: T 135 LYS cc_start: 0.9670 (tttm) cc_final: 0.9446 (tttt) REVERT: T 188 TYR cc_start: 0.8782 (m-10) cc_final: 0.8493 (m-80) REVERT: T 274 TYR cc_start: 0.8508 (p90) cc_final: 0.8131 (p90) REVERT: U 114 ILE cc_start: 0.9750 (mt) cc_final: 0.9458 (tt) REVERT: U 246 GLU cc_start: 0.8753 (pm20) cc_final: 0.8391 (pm20) outliers start: 225 outliers final: 171 residues processed: 1674 average time/residue: 0.6428 time to fit residues: 1816.7250 Evaluate side-chains 1712 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 1509 time to evaluate : 5.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 278 ASP Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 340 MET Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 456 GLU Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 299 HIS Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 342 GLN Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 377 VAL Chi-restraints excluded: chain F residue 420 SER Chi-restraints excluded: chain F residue 454 GLU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 165 LEU Chi-restraints excluded: chain G residue 256 THR Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 354 LEU Chi-restraints excluded: chain G residue 374 GLN Chi-restraints excluded: chain G residue 436 ILE Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 121 ASP Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 194 TYR Chi-restraints excluded: chain H residue 216 THR Chi-restraints excluded: chain H residue 226 VAL Chi-restraints excluded: chain H residue 283 CYS Chi-restraints excluded: chain H residue 286 CYS Chi-restraints excluded: chain H residue 290 THR Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 342 GLN Chi-restraints excluded: chain H residue 354 LEU Chi-restraints excluded: chain H residue 419 MET Chi-restraints excluded: chain H residue 447 LYS Chi-restraints excluded: chain H residue 460 ASN Chi-restraints excluded: chain I residue 13 ASP Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 46 ASP Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 336 VAL Chi-restraints excluded: chain I residue 340 MET Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain I residue 374 GLN Chi-restraints excluded: chain I residue 406 ILE Chi-restraints excluded: chain I residue 419 MET Chi-restraints excluded: chain J residue 121 ASP Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 227 ASP Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 299 HIS Chi-restraints excluded: chain J residue 354 LEU Chi-restraints excluded: chain K residue 6 ASN Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 176 LYS Chi-restraints excluded: chain K residue 209 ASP Chi-restraints excluded: chain K residue 290 THR Chi-restraints excluded: chain K residue 297 THR Chi-restraints excluded: chain K residue 304 VAL Chi-restraints excluded: chain K residue 405 LYS Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 164 ILE Chi-restraints excluded: chain L residue 196 ILE Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 328 LEU Chi-restraints excluded: chain L residue 377 VAL Chi-restraints excluded: chain L residue 423 GLU Chi-restraints excluded: chain M residue 12 TRP Chi-restraints excluded: chain M residue 15 LYS Chi-restraints excluded: chain M residue 86 VAL Chi-restraints excluded: chain M residue 152 THR Chi-restraints excluded: chain M residue 187 LEU Chi-restraints excluded: chain M residue 240 THR Chi-restraints excluded: chain M residue 276 LEU Chi-restraints excluded: chain M residue 312 ASP Chi-restraints excluded: chain N residue 24 GLN Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 68 ASN Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain N residue 178 VAL Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 313 THR Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 99 MET Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 187 LEU Chi-restraints excluded: chain P residue 74 LYS Chi-restraints excluded: chain P residue 116 GLN Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain P residue 166 ILE Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 216 ILE Chi-restraints excluded: chain P residue 276 LEU Chi-restraints excluded: chain Q residue 81 ASP Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 236 LEU Chi-restraints excluded: chain R residue 10 ASN Chi-restraints excluded: chain R residue 15 LYS Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 224 VAL Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 37 ILE Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain S residue 123 MET Chi-restraints excluded: chain S residue 152 THR Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 225 SER Chi-restraints excluded: chain S residue 245 ILE Chi-restraints excluded: chain S residue 320 THR Chi-restraints excluded: chain T residue 6 LEU Chi-restraints excluded: chain T residue 20 VAL Chi-restraints excluded: chain T residue 52 PHE Chi-restraints excluded: chain T residue 184 LEU Chi-restraints excluded: chain T residue 209 ASP Chi-restraints excluded: chain T residue 235 THR Chi-restraints excluded: chain T residue 236 LEU Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 152 THR Chi-restraints excluded: chain U residue 243 ILE Chi-restraints excluded: chain U residue 313 THR Chi-restraints excluded: chain U residue 316 VAL Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 152 THR Chi-restraints excluded: chain V residue 164 GLN Chi-restraints excluded: chain V residue 244 LEU Chi-restraints excluded: chain V residue 256 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 855 random chunks: chunk 482 optimal weight: 9.9990 chunk 263 optimal weight: 7.9990 chunk 825 optimal weight: 10.0000 chunk 641 optimal weight: 0.0270 chunk 171 optimal weight: 7.9990 chunk 727 optimal weight: 0.2980 chunk 543 optimal weight: 10.0000 chunk 837 optimal weight: 30.0000 chunk 173 optimal weight: 30.0000 chunk 753 optimal weight: 7.9990 chunk 644 optimal weight: 5.9990 overall best weight: 4.4644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 GLN ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 ASN ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN ** H 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 374 GLN ** J 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 460 ASN ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 7 GLN ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.083716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.068810 restraints weight = 249541.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.070874 restraints weight = 143789.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.072327 restraints weight = 98397.109| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 68177 Z= 0.246 Angle : 0.724 18.394 92470 Z= 0.367 Chirality : 0.044 0.259 10048 Planarity : 0.004 0.059 12237 Dihedral : 4.716 59.710 9264 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.49 % Favored : 95.50 % Rotamer: Outliers : 3.22 % Allowed : 23.50 % Favored : 73.28 % 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: -0.14 (0.09), residues: 8507 helix: 1.06 (0.09), residues: 3205 sheet: -0.33 (0.14), residues: 1524 loop : -0.95 (0.10), residues: 3778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP J 202 HIS 0.009 0.001 HIS H 299 PHE 0.020 0.001 PHE S 52 TYR 0.023 0.001 TYR H 62 ARG 0.019 0.001 ARG B 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29263.76 seconds wall clock time: 505 minutes 18.86 seconds (30318.86 seconds total)