Starting phenix.real_space_refine on Tue Dec 31 08:17:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xb6_38212/12_2024/8xb6_38212.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xb6_38212/12_2024/8xb6_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_38212/12_2024/8xb6_38212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xb6_38212/12_2024/8xb6_38212.map" model { file = "/net/cci-nas-00/data/ceres_data/8xb6_38212/12_2024/8xb6_38212.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xb6_38212/12_2024/8xb6_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-5532/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: 28.39, per 1000 atoms: 0.42 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: 12.37 Conformation dependent library (CDL) restraints added in 6.5 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: 6.00 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: 32.01 Time building geometry restraints manager: 14.67 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.840 Check model and map are aligned: 0.370 Set scattering table: 0.450 Process input model: 118.300 Find NCS groups from input model: 2.740 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:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.840 ------------------------------------------------------------------------------- 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 : 5.608 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: 0.6784 time to fit residues: 2883.2150 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 : 6.371 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 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 : 5.731 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 16 LYS cc_start: 0.8474 (ptpp) cc_final: 0.8273 (ptpp) REVERT: A 410 LEU cc_start: 0.8208 (mt) cc_final: 0.7620 (mt) REVERT: A 419 MET cc_start: 0.8676 (ppp) cc_final: 0.8424 (ppp) REVERT: A 446 LYS cc_start: 0.8710 (mmtp) cc_final: 0.8478 (mmtt) REVERT: A 460 ASN cc_start: 0.8028 (m110) cc_final: 0.7753 (m110) REVERT: B 403 ASP cc_start: 0.7334 (t0) cc_final: 0.6928 (t0) REVERT: C 105 ASP cc_start: 0.7572 (p0) cc_final: 0.7264 (p0) REVERT: C 109 LEU cc_start: 0.8779 (tp) cc_final: 0.8251 (tt) REVERT: C 236 ASP cc_start: 0.7782 (p0) cc_final: 0.7510 (p0) REVERT: D 80 LEU cc_start: 0.8980 (tp) cc_final: 0.8607 (tp) REVERT: E 228 ASP cc_start: 0.6296 (OUTLIER) cc_final: 0.5995 (m-30) REVERT: E 370 GLU cc_start: 0.7136 (pm20) cc_final: 0.6830 (pm20) REVERT: E 419 MET cc_start: 0.7873 (ttm) cc_final: 0.7613 (ttm) REVERT: F 275 ASN cc_start: 0.8328 (OUTLIER) cc_final: 0.7185 (m110) REVERT: F 460 ASN cc_start: 0.7368 (m-40) cc_final: 0.6583 (m110) REVERT: G 236 ASP cc_start: 0.7972 (p0) cc_final: 0.7758 (p0) REVERT: G 245 PHE cc_start: 0.8152 (t80) cc_final: 0.7918 (t80) REVERT: G 460 ASN cc_start: 0.8154 (m-40) cc_final: 0.7744 (m110) REVERT: H 26 MET cc_start: 0.7078 (ptm) cc_final: 0.6806 (mtm) REVERT: H 165 LEU cc_start: 0.8474 (pt) cc_final: 0.7996 (pp) REVERT: H 380 ARG cc_start: 0.7915 (mtm-85) cc_final: 0.7586 (mtm-85) REVERT: I 69 TYR cc_start: 0.7894 (t80) cc_final: 0.7552 (t80) REVERT: I 259 MET cc_start: 0.7548 (ttp) cc_final: 0.7280 (ttp) REVERT: I 419 MET cc_start: 0.8087 (ppp) cc_final: 0.7293 (ppp) REVERT: J 46 ASP cc_start: 0.7091 (t0) cc_final: 0.6880 (t0) REVERT: J 346 GLN cc_start: 0.7384 (mt0) cc_final: 0.6429 (mt0) REVERT: K 184 ARG cc_start: 0.6880 (mtp180) cc_final: 0.6052 (mmm-85) REVERT: K 406 ILE cc_start: 0.9009 (pt) cc_final: 0.8600 (pt) REVERT: K 418 LYS cc_start: 0.7016 (mtmt) cc_final: 0.6770 (mtmt) REVERT: K 460 ASN cc_start: 0.8248 (m-40) cc_final: 0.7798 (m110) REVERT: L 94 GLU cc_start: 0.6689 (mp0) cc_final: 0.6481 (mp0) REVERT: L 342 GLN cc_start: 0.7451 (tt0) cc_final: 0.7175 (tt0) REVERT: L 343 LYS cc_start: 0.7939 (mtmm) cc_final: 0.7664 (mtpp) REVERT: L 354 LEU cc_start: 0.6347 (OUTLIER) cc_final: 0.6126 (pp) REVERT: L 412 SER cc_start: 0.8731 (p) cc_final: 0.8447 (p) REVERT: M 19 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: M 26 GLU cc_start: 0.6544 (mp0) cc_final: 0.5920 (mp0) REVERT: M 268 TYR cc_start: 0.7498 (t80) cc_final: 0.7276 (t80) REVERT: P 38 LEU cc_start: 0.8620 (tp) cc_final: 0.8416 (tt) REVERT: R 15 LYS cc_start: 0.6049 (OUTLIER) cc_final: 0.5036 (pttm) REVERT: R 155 MET cc_start: 0.6461 (tpp) cc_final: 0.6168 (tpp) REVERT: R 276 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8298 (mp) REVERT: S 155 MET cc_start: 0.7350 (tpp) cc_final: 0.7148 (tpp) REVERT: T 250 ASP cc_start: 0.6234 (p0) cc_final: 0.5928 (p0) REVERT: V 108 GLN cc_start: 0.7639 (tm-30) cc_final: 0.7353 (tm-30) outliers start: 188 outliers final: 103 residues processed: 1902 average time/residue: 0.6468 time to fit residues: 2057.8267 Evaluate side-chains 1681 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 1572 time to evaluate : 5.648 ------------------------------------------------------------------------------- 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 321 VAL Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain E residue 228 ASP 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 275 ASN 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 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 19 GLU 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 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 256 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 855 random chunks: chunk 431 optimal weight: 20.0000 chunk 240 optimal weight: 20.0000 chunk 646 optimal weight: 6.9990 chunk 528 optimal weight: 20.0000 chunk 214 optimal weight: 30.0000 chunk 777 optimal weight: 6.9990 chunk 840 optimal weight: 5.9990 chunk 692 optimal weight: 0.0170 chunk 771 optimal weight: 5.9990 chunk 265 optimal weight: 8.9990 chunk 624 optimal weight: 9.9990 overall best weight: 5.2026 ------------------------------------------------------------------------------- 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 6 ASN ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS B 303 ASN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** 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** I 460 ASN J 23 HIS J 346 GLN J 460 ASN ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN L 23 HIS L 220 ASN 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 N 10 ASN N 43 ASN O 43 ASN O 248 ASN ** P 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 247 GLN ** 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: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 68177 Z= 0.256 Angle : 0.660 9.224 92470 Z= 0.343 Chirality : 0.043 0.254 10048 Planarity : 0.004 0.075 12237 Dihedral : 4.816 65.775 9266 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.25 % Allowed : 16.63 % Favored : 80.12 % 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: -0.27 (0.09), residues: 8507 helix: 1.10 (0.09), residues: 3165 sheet: -0.48 (0.13), residues: 1565 loop : -1.11 (0.10), residues: 3777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP K 395 HIS 0.007 0.001 HIS H 299 PHE 0.030 0.002 PHE H 399 TYR 0.024 0.001 TYR S 268 ARG 0.011 0.001 ARG K 345 *********************** 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 1891 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 227 poor density : 1664 time to evaluate : 5.721 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: A 163 ASP cc_start: 0.6711 (t0) cc_final: 0.5442 (t0) REVERT: A 419 MET cc_start: 0.8610 (ppp) cc_final: 0.6831 (ppp) REVERT: A 458 MET cc_start: 0.7454 (tpt) cc_final: 0.6588 (tpp) REVERT: A 460 ASN cc_start: 0.7797 (m110) cc_final: 0.7462 (m110) REVERT: B 19 LYS cc_start: 0.8380 (pptt) cc_final: 0.7533 (pptt) REVERT: B 337 LYS cc_start: 0.7459 (tptp) cc_final: 0.7227 (tptp) REVERT: C 26 MET cc_start: 0.6681 (OUTLIER) cc_final: 0.6238 (ttm) REVERT: C 46 ASP cc_start: 0.7293 (t0) cc_final: 0.7034 (t0) REVERT: C 105 ASP cc_start: 0.7544 (p0) cc_final: 0.7284 (p0) REVERT: C 236 ASP cc_start: 0.7840 (p0) cc_final: 0.7527 (p0) REVERT: C 413 ASP cc_start: 0.7467 (t0) cc_final: 0.7249 (t0) REVERT: D 49 LYS cc_start: 0.7845 (ptmm) cc_final: 0.7141 (pttp) REVERT: D 458 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7438 (tpt) REVERT: E 415 ASP cc_start: 0.7553 (m-30) cc_final: 0.7276 (m-30) REVERT: E 419 MET cc_start: 0.7939 (ttm) cc_final: 0.7712 (ttm) REVERT: E 460 ASN cc_start: 0.8418 (m-40) cc_final: 0.8066 (m110) REVERT: G 236 ASP cc_start: 0.8028 (p0) cc_final: 0.7792 (p0) REVERT: G 460 ASN cc_start: 0.8012 (m-40) cc_final: 0.7726 (m110) REVERT: H 165 LEU cc_start: 0.8428 (pt) cc_final: 0.8054 (pp) REVERT: H 380 ARG cc_start: 0.7948 (mtm-85) cc_final: 0.7502 (mtm-85) REVERT: I 236 ASP cc_start: 0.8040 (p0) cc_final: 0.7773 (p0) REVERT: J 227 ASP cc_start: 0.7286 (p0) cc_final: 0.6922 (p0) REVERT: K 184 ARG cc_start: 0.7227 (mtp180) cc_final: 0.7014 (mmm-85) REVERT: K 342 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.6789 (pt0) REVERT: K 418 LYS cc_start: 0.6986 (mtmt) cc_final: 0.6715 (mtmt) REVERT: K 422 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7421 (tp30) REVERT: K 460 ASN cc_start: 0.8512 (m-40) cc_final: 0.8048 (m110) REVERT: L 109 LEU cc_start: 0.7946 (tp) cc_final: 0.7613 (tt) REVERT: L 221 ASP cc_start: 0.6417 (p0) cc_final: 0.6105 (p0) REVERT: L 343 LYS cc_start: 0.7939 (mtmm) cc_final: 0.7659 (mtpp) REVERT: L 412 SER cc_start: 0.8777 (p) cc_final: 0.8499 (p) REVERT: N 190 ASN cc_start: 0.7916 (OUTLIER) cc_final: 0.7692 (t0) REVERT: N 261 LYS cc_start: 0.5956 (pttm) cc_final: 0.5689 (pttm) REVERT: R 15 LYS cc_start: 0.5787 (OUTLIER) cc_final: 0.4579 (pttm) REVERT: R 155 MET cc_start: 0.6549 (tpp) cc_final: 0.6203 (tpp) REVERT: S 155 MET cc_start: 0.7290 (tpp) cc_final: 0.7055 (tpp) REVERT: T 250 ASP cc_start: 0.6482 (p0) cc_final: 0.6165 (p0) outliers start: 227 outliers final: 138 residues processed: 1781 average time/residue: 0.6630 time to fit residues: 1995.7940 Evaluate side-chains 1625 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 1481 time to evaluate : 5.654 ------------------------------------------------------------------------------- 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 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 346 GLN 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 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 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 D residue 51 THR 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 405 LYS Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 163 ASP 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 G residue 100 LEU Chi-restraints excluded: chain G residue 104 VAL 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 87 ASP Chi-restraints excluded: chain H residue 216 THR 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 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 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 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 230 ILE Chi-restraints excluded: chain K residue 285 ILE Chi-restraints excluded: chain K residue 290 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 377 VAL Chi-restraints excluded: chain L residue 439 THR Chi-restraints excluded: chain M residue 152 THR Chi-restraints excluded: chain N residue 27 LEU 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 178 VAL Chi-restraints excluded: chain N residue 190 ASN Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 244 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 Q residue 321 LYS 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 245 ILE Chi-restraints excluded: chain T residue 6 LEU Chi-restraints excluded: chain U residue 59 LEU Chi-restraints excluded: chain U residue 245 ILE Chi-restraints excluded: chain V residue 127 LEU Chi-restraints excluded: chain V residue 209 ASP Chi-restraints excluded: chain V residue 246 GLU 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 768 optimal weight: 0.0870 chunk 584 optimal weight: 5.9990 chunk 403 optimal weight: 0.6980 chunk 86 optimal weight: 10.0000 chunk 371 optimal weight: 20.0000 chunk 522 optimal weight: 6.9990 chunk 780 optimal weight: 0.0570 chunk 826 optimal weight: 0.2980 chunk 407 optimal weight: 9.9990 chunk 739 optimal weight: 10.0000 chunk 222 optimal weight: 20.0000 overall best weight: 1.4278 ------------------------------------------------------------------------------- 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 37 ASN ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 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 333 ASN D 346 GLN ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 ASN F 5 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 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 L 23 HIS ** L 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 124 GLN N 190 ASN ** N 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 267 GLN O 43 ASN O 247 GLN O 248 ASN P 145 HIS Q 108 GLN R 43 ASN S 248 ASN 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 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 68177 Z= 0.199 Angle : 0.667 10.741 92470 Z= 0.341 Chirality : 0.043 0.229 10048 Planarity : 0.004 0.071 12237 Dihedral : 4.717 63.042 9264 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.70 % Favored : 96.29 % Rotamer: Outliers : 2.91 % Allowed : 19.09 % Favored : 78.00 % 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: -0.29 (0.09), residues: 8507 helix: 1.00 (0.09), residues: 3172 sheet: -0.45 (0.13), residues: 1608 loop : -1.07 (0.10), residues: 3727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP P 102 HIS 0.014 0.001 HIS F 18 PHE 0.027 0.001 PHE P 251 TYR 0.024 0.001 TYR S 268 ARG 0.016 0.001 ARG T 266 *********************** 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: 203 poor density : 1683 time to evaluate : 5.647 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 458 MET cc_start: 0.7315 (tpt) cc_final: 0.6549 (tpp) REVERT: A 460 ASN cc_start: 0.7719 (m110) cc_final: 0.7203 (m110) REVERT: B 169 GLU cc_start: 0.6807 (tp30) cc_final: 0.6459 (tp30) REVERT: C 46 ASP cc_start: 0.7230 (t0) cc_final: 0.7008 (t0) REVERT: C 236 ASP cc_start: 0.7756 (p0) cc_final: 0.7490 (p0) REVERT: C 413 ASP cc_start: 0.7579 (t0) cc_final: 0.7339 (t0) REVERT: D 49 LYS cc_start: 0.7725 (ptmm) cc_final: 0.7037 (pttp) REVERT: D 278 ASP cc_start: 0.7810 (t0) cc_final: 0.7579 (t0) REVERT: D 369 MET cc_start: 0.7189 (mpp) cc_final: 0.6985 (mpp) REVERT: E 338 GLU cc_start: 0.7032 (tt0) cc_final: 0.6621 (tt0) REVERT: E 460 ASN cc_start: 0.8441 (m-40) cc_final: 0.8151 (m110) REVERT: F 42 VAL cc_start: 0.8920 (t) cc_final: 0.8663 (p) REVERT: F 83 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8446 (mp) REVERT: G 236 ASP cc_start: 0.7890 (p0) cc_final: 0.7682 (p0) REVERT: G 305 LEU cc_start: 0.7726 (mt) cc_final: 0.7213 (mt) REVERT: G 354 LEU cc_start: 0.5979 (OUTLIER) cc_final: 0.5225 (pt) REVERT: G 460 ASN cc_start: 0.7852 (m-40) cc_final: 0.7632 (m110) REVERT: H 165 LEU cc_start: 0.8571 (pt) cc_final: 0.8205 (pp) REVERT: H 205 LEU cc_start: 0.8612 (mt) cc_final: 0.8374 (mt) REVERT: H 380 ARG cc_start: 0.8009 (mtm-85) cc_final: 0.7725 (mtm-85) REVERT: I 236 ASP cc_start: 0.7982 (p0) cc_final: 0.7712 (p0) REVERT: J 227 ASP cc_start: 0.7253 (p0) cc_final: 0.6895 (p0) REVERT: J 413 ASP cc_start: 0.6559 (t70) cc_final: 0.5946 (t70) REVERT: K 347 MET cc_start: 0.6471 (mmm) cc_final: 0.6195 (mtt) REVERT: K 418 LYS cc_start: 0.7532 (mtmt) cc_final: 0.7181 (mtmt) REVERT: K 460 ASN cc_start: 0.8516 (m-40) cc_final: 0.8076 (m110) REVERT: L 221 ASP cc_start: 0.6393 (p0) cc_final: 0.6095 (p0) REVERT: L 228 ASP cc_start: 0.6864 (p0) cc_final: 0.6630 (p0) REVERT: L 280 GLU cc_start: 0.6614 (tp30) cc_final: 0.6338 (tp30) REVERT: L 458 MET cc_start: 0.8078 (tpt) cc_final: 0.7828 (tpt) REVERT: N 261 LYS cc_start: 0.5874 (pttm) cc_final: 0.5622 (pttm) REVERT: P 38 LEU cc_start: 0.8634 (tp) cc_final: 0.8415 (tt) REVERT: R 155 MET cc_start: 0.6520 (tpp) cc_final: 0.6240 (tpp) REVERT: S 126 MET cc_start: 0.6390 (mtm) cc_final: 0.5982 (mtm) REVERT: S 155 MET cc_start: 0.7352 (tpp) cc_final: 0.7105 (tpp) REVERT: T 250 ASP cc_start: 0.6395 (p0) cc_final: 0.6033 (p0) REVERT: U 276 LEU cc_start: 0.8188 (mm) cc_final: 0.7940 (mm) outliers start: 203 outliers final: 127 residues processed: 1787 average time/residue: 0.6502 time to fit residues: 1960.8717 Evaluate side-chains 1648 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 1519 time to evaluate : 5.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 374 GLN 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 156 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 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 291 LEU 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 D residue 51 THR 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 228 ASP 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 416 ILE 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 265 LEU Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 420 SER 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 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 192 ASP 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 74 ASN 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 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 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 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 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 47 ASN Chi-restraints excluded: chain K residue 209 ASP 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 132 VAL Chi-restraints excluded: chain L residue 164 ILE Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 374 GLN Chi-restraints excluded: chain L residue 377 VAL Chi-restraints excluded: chain N residue 27 LEU 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 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 156 THR Chi-restraints excluded: chain P residue 216 ILE Chi-restraints excluded: chain Q residue 187 LEU 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 S residue 20 VAL Chi-restraints excluded: chain S residue 46 ASP 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 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 688 optimal weight: 8.9990 chunk 469 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 615 optimal weight: 10.0000 chunk 340 optimal weight: 5.9990 chunk 705 optimal weight: 8.9990 chunk 571 optimal weight: 0.2980 chunk 0 optimal weight: 30.0000 chunk 422 optimal weight: 6.9990 chunk 741 optimal weight: 0.2980 chunk 208 optimal weight: 5.9990 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 GLN C 18 HIS C 37 ASN ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** 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 269 ASN ** H 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 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 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 23 HIS L 411 ASN ** M 106 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 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 43 ASN O 43 ASN O 117 GLN O 247 GLN O 248 ASN ** P 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 94 ASN ** Q 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 145 HIS Q 267 GLN R 262 GLN T 180 HIS ** U 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 68177 Z= 0.212 Angle : 0.665 10.237 92470 Z= 0.341 Chirality : 0.043 0.224 10048 Planarity : 0.004 0.070 12237 Dihedral : 4.683 62.845 9264 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.75 % Favored : 96.24 % Rotamer: Outliers : 3.29 % Allowed : 20.31 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.09), residues: 8507 helix: 0.98 (0.09), residues: 3144 sheet: -0.42 (0.13), residues: 1599 loop : -1.05 (0.10), residues: 3764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP P 102 HIS 0.009 0.001 HIS J 23 PHE 0.027 0.001 PHE O 251 TYR 0.031 0.001 TYR S 268 ARG 0.012 0.001 ARG K 345 *********************** 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 1844 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 230 poor density : 1614 time to evaluate : 5.664 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 32 ARG cc_start: 0.6520 (ttp80) cc_final: 0.5124 (ttp80) REVERT: A 76 VAL cc_start: 0.8754 (OUTLIER) cc_final: 0.8551 (p) REVERT: A 369 MET cc_start: 0.7566 (OUTLIER) cc_final: 0.7288 (ptp) REVERT: A 458 MET cc_start: 0.7408 (tpt) cc_final: 0.6733 (tpp) REVERT: A 460 ASN cc_start: 0.7714 (m110) cc_final: 0.7267 (m110) REVERT: B 169 GLU cc_start: 0.6849 (tp30) cc_final: 0.6527 (tp30) REVERT: B 278 ASP cc_start: 0.7378 (OUTLIER) cc_final: 0.7123 (t0) REVERT: C 46 ASP cc_start: 0.7273 (t0) cc_final: 0.7071 (t0) REVERT: C 236 ASP cc_start: 0.7763 (p0) cc_final: 0.7483 (p0) REVERT: C 310 VAL cc_start: 0.7746 (OUTLIER) cc_final: 0.7529 (m) REVERT: C 398 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7768 (mtm) REVERT: D 49 LYS cc_start: 0.7712 (ptmm) cc_final: 0.7087 (pttp) REVERT: D 198 LYS cc_start: 0.8309 (mmtt) cc_final: 0.8018 (mmtt) REVERT: D 418 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.8066 (mmtm) REVERT: E 415 ASP cc_start: 0.7375 (m-30) cc_final: 0.7129 (m-30) REVERT: E 458 MET cc_start: 0.7243 (OUTLIER) cc_final: 0.6846 (tpp) REVERT: E 460 ASN cc_start: 0.8539 (m-40) cc_final: 0.8268 (m110) REVERT: F 42 VAL cc_start: 0.8966 (t) cc_final: 0.8754 (p) REVERT: F 83 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8239 (mp) REVERT: F 347 MET cc_start: 0.7538 (mmm) cc_final: 0.7230 (mtm) REVERT: F 370 GLU cc_start: 0.7341 (mt-10) cc_final: 0.6963 (mp0) REVERT: G 95 ASP cc_start: 0.7336 (p0) cc_final: 0.6612 (p0) REVERT: G 96 LYS cc_start: 0.8366 (mmmt) cc_final: 0.7860 (mmmt) REVERT: G 236 ASP cc_start: 0.7953 (p0) cc_final: 0.7734 (p0) REVERT: G 283 CYS cc_start: 0.7715 (m) cc_final: 0.7459 (m) REVERT: G 460 ASN cc_start: 0.7889 (m-40) cc_final: 0.7586 (m110) REVERT: H 165 LEU cc_start: 0.8569 (pt) cc_final: 0.8246 (pp) REVERT: H 205 LEU cc_start: 0.8718 (mt) cc_final: 0.8482 (mt) REVERT: H 370 GLU cc_start: 0.7492 (tt0) cc_final: 0.7277 (tm-30) REVERT: H 380 ARG cc_start: 0.8006 (mtm-85) cc_final: 0.7737 (mtm-85) REVERT: H 419 MET cc_start: 0.6912 (OUTLIER) cc_final: 0.6643 (ttm) REVERT: I 236 ASP cc_start: 0.7997 (p0) cc_final: 0.7706 (p0) REVERT: J 227 ASP cc_start: 0.7295 (p0) cc_final: 0.6938 (p0) REVERT: J 342 GLN cc_start: 0.7901 (tm-30) cc_final: 0.7303 (tm-30) REVERT: J 345 ARG cc_start: 0.6837 (ttp80) cc_final: 0.6628 (ttp80) REVERT: K 162 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7535 (pm20) REVERT: K 422 GLU cc_start: 0.7663 (tp30) cc_final: 0.7447 (tp30) REVERT: K 460 ASN cc_start: 0.8589 (m-40) cc_final: 0.8352 (m-40) REVERT: L 26 MET cc_start: 0.6239 (ttt) cc_final: 0.6025 (ttt) REVERT: L 109 LEU cc_start: 0.7839 (tp) cc_final: 0.7547 (tt) REVERT: L 458 MET cc_start: 0.8212 (tpt) cc_final: 0.7915 (tpt) REVERT: O 39 ARG cc_start: 0.7224 (ttm-80) cc_final: 0.6825 (ttm-80) REVERT: R 109 GLU cc_start: 0.6263 (tt0) cc_final: 0.6015 (tt0) REVERT: T 250 ASP cc_start: 0.6376 (p0) cc_final: 0.5960 (p0) REVERT: U 276 LEU cc_start: 0.8198 (mm) cc_final: 0.7907 (mm) outliers start: 230 outliers final: 139 residues processed: 1747 average time/residue: 0.6253 time to fit residues: 1848.8440 Evaluate side-chains 1663 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 1514 time to evaluate : 5.642 ------------------------------------------------------------------------------- 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 162 GLU 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 346 GLN Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 338 GLU 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 156 ILE Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 257 ILE 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 326 GLU Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain D residue 51 THR 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 297 THR Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain D residue 418 LYS Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 405 LYS 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 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 100 LEU Chi-restraints excluded: chain G residue 104 VAL 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 350 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 64 GLU Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 164 ILE 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 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 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 291 LEU Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain I residue 419 MET Chi-restraints excluded: chain I residue 456 GLU Chi-restraints excluded: chain J residue 190 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 47 ASN Chi-restraints excluded: chain K residue 162 GLU 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 342 GLN Chi-restraints excluded: chain K residue 405 LYS Chi-restraints excluded: chain K residue 424 LEU 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 377 VAL Chi-restraints excluded: chain M residue 109 GLU Chi-restraints excluded: chain N residue 74 LYS 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 187 LEU Chi-restraints excluded: chain P residue 127 LEU Chi-restraints excluded: chain P residue 156 THR Chi-restraints excluded: chain P residue 178 VAL Chi-restraints excluded: chain Q residue 187 LEU 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 245 ILE Chi-restraints excluded: chain T residue 6 LEU 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 114 ILE Chi-restraints excluded: chain U residue 313 THR Chi-restraints excluded: chain U residue 316 VAL 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 278 optimal weight: 6.9990 chunk 744 optimal weight: 0.7980 chunk 163 optimal weight: 10.0000 chunk 485 optimal weight: 8.9990 chunk 204 optimal weight: 20.0000 chunk 827 optimal weight: 20.0000 chunk 686 optimal weight: 9.9990 chunk 383 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 273 optimal weight: 30.0000 chunk 434 optimal weight: 30.0000 overall best weight: 6.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 HIS ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 444 GLN D 74 ASN ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 275 ASN ** 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 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN ** J 346 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 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 23 HIS ** 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 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 43 ASN ** O 247 GLN ** 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 108 GLN ** 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 43 ASN ** U 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 247 GLN U 263 ASN ** 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 68177 Z= 0.290 Angle : 0.694 11.230 92470 Z= 0.356 Chirality : 0.043 0.191 10048 Planarity : 0.004 0.072 12237 Dihedral : 4.746 65.322 9264 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.33 % Favored : 95.66 % Rotamer: Outliers : 3.64 % Allowed : 20.78 % Favored : 75.58 % 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: -0.20 (0.09), residues: 8507 helix: 1.02 (0.09), residues: 3182 sheet: -0.31 (0.13), residues: 1601 loop : -1.02 (0.10), residues: 3724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP I 395 HIS 0.008 0.001 HIS H 299 PHE 0.027 0.002 PHE I 90 TYR 0.030 0.001 TYR S 268 ARG 0.013 0.001 ARG Q 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 1814 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 254 poor density : 1560 time to evaluate : 5.734 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: A 76 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8518 (p) REVERT: A 337 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.7246 (tptt) REVERT: A 347 MET cc_start: 0.7166 (mmm) cc_final: 0.6819 (mmt) REVERT: A 458 MET cc_start: 0.7550 (tpt) cc_final: 0.6902 (tpp) REVERT: A 460 ASN cc_start: 0.7789 (m110) cc_final: 0.7496 (m110) REVERT: B 169 GLU cc_start: 0.6849 (tp30) cc_final: 0.6563 (tp30) REVERT: B 278 ASP cc_start: 0.7554 (OUTLIER) cc_final: 0.7328 (t0) REVERT: C 46 ASP cc_start: 0.7365 (t0) cc_final: 0.7162 (t0) REVERT: C 398 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.7990 (mtm) REVERT: D 49 LYS cc_start: 0.7598 (ptmm) cc_final: 0.7100 (pttp) REVERT: D 105 ASP cc_start: 0.7616 (p0) cc_final: 0.7404 (p0) REVERT: D 278 ASP cc_start: 0.8006 (t0) cc_final: 0.7790 (t0) REVERT: D 350 LEU cc_start: 0.7902 (tp) cc_final: 0.7616 (tp) REVERT: E 121 ASP cc_start: 0.5836 (m-30) cc_final: 0.5597 (m-30) REVERT: E 458 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6866 (tpp) REVERT: E 460 ASN cc_start: 0.8539 (m-40) cc_final: 0.8229 (m110) REVERT: F 34 ILE cc_start: 0.8423 (mm) cc_final: 0.8081 (mm) REVERT: F 42 VAL cc_start: 0.8995 (t) cc_final: 0.8794 (p) REVERT: F 83 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8249 (mp) REVERT: G 95 ASP cc_start: 0.7480 (p0) cc_final: 0.6726 (p0) REVERT: G 96 LYS cc_start: 0.8411 (mmmt) cc_final: 0.8022 (mmmt) REVERT: G 236 ASP cc_start: 0.7947 (p0) cc_final: 0.7742 (p0) REVERT: G 283 CYS cc_start: 0.7760 (m) cc_final: 0.7453 (m) REVERT: G 460 ASN cc_start: 0.8052 (m-40) cc_final: 0.7776 (m110) REVERT: H 165 LEU cc_start: 0.8543 (pt) cc_final: 0.8231 (pp) REVERT: H 370 GLU cc_start: 0.7461 (tt0) cc_final: 0.7198 (tm-30) REVERT: H 380 ARG cc_start: 0.8098 (mtm-85) cc_final: 0.7807 (mtm-85) REVERT: H 405 LYS cc_start: 0.8625 (mmmt) cc_final: 0.8367 (mmmm) REVERT: I 236 ASP cc_start: 0.8126 (p0) cc_final: 0.7864 (p0) REVERT: I 262 MET cc_start: 0.7662 (mmm) cc_final: 0.7454 (tpp) REVERT: I 441 MET cc_start: 0.8078 (ppp) cc_final: 0.7740 (ppp) REVERT: I 458 MET cc_start: 0.7400 (tpp) cc_final: 0.6239 (mmm) REVERT: J 198 LYS cc_start: 0.8287 (mmmm) cc_final: 0.8005 (mmmt) REVERT: J 227 ASP cc_start: 0.7184 (OUTLIER) cc_final: 0.6958 (p0) REVERT: K 26 MET cc_start: 0.6918 (mmm) cc_final: 0.6713 (tpt) REVERT: K 162 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7538 (pm20) REVERT: K 418 LYS cc_start: 0.6611 (mttt) cc_final: 0.6324 (mttt) REVERT: K 460 ASN cc_start: 0.8636 (m-40) cc_final: 0.8194 (m-40) REVERT: L 280 GLU cc_start: 0.6864 (tp30) cc_final: 0.6305 (tp30) REVERT: Q 126 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.7233 (mmm) REVERT: R 15 LYS cc_start: 0.5596 (OUTLIER) cc_final: 0.4303 (pttm) REVERT: S 155 MET cc_start: 0.7176 (tpp) cc_final: 0.6916 (tpp) REVERT: T 250 ASP cc_start: 0.6564 (p0) cc_final: 0.6260 (p0) REVERT: U 276 LEU cc_start: 0.8214 (mm) cc_final: 0.7978 (mm) outliers start: 254 outliers final: 174 residues processed: 1703 average time/residue: 0.6353 time to fit residues: 1828.9285 Evaluate side-chains 1640 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 1456 time to evaluate : 5.687 ------------------------------------------------------------------------------- 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 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 268 LEU Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 104 VAL 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 291 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 102 ASN 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 297 THR Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain E residue 18 HIS Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 132 VAL 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 291 LEU Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 405 LYS 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 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 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 87 ASP 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 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 I residue 13 ASP 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 246 VAL Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 354 LEU 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 188 ASP Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 219 GLU 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 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 K residue 6 ASN Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 162 GLU 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 405 LYS Chi-restraints excluded: chain K residue 419 MET Chi-restraints excluded: chain K residue 424 LEU 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 342 GLN Chi-restraints excluded: chain L residue 377 VAL Chi-restraints excluded: chain L residue 439 THR Chi-restraints excluded: chain M residue 12 TRP Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 86 VAL 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 178 VAL 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 187 LEU Chi-restraints excluded: chain P residue 74 LYS Chi-restraints excluded: chain P residue 127 LEU Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain P residue 156 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 P residue 276 LEU Chi-restraints excluded: chain P residue 312 ASP Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 114 ILE Chi-restraints excluded: chain Q residue 126 MET 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 T residue 6 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 T residue 254 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 256 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 855 random chunks: chunk 797 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 471 optimal weight: 0.1980 chunk 604 optimal weight: 6.9990 chunk 468 optimal weight: 5.9990 chunk 696 optimal weight: 7.9990 chunk 461 optimal weight: 5.9990 chunk 824 optimal weight: 9.9990 chunk 515 optimal weight: 20.0000 chunk 502 optimal weight: 2.9990 chunk 380 optimal weight: 0.0040 overall best weight: 3.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS C 269 ASN ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN D 173 ASN ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 ASN F 74 ASN ** 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 239 GLN ** 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 220 ASN ** J 346 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 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 164 GLN N 43 ASN O 43 ASN ** O 247 GLN ** 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 108 GLN ** 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 117 GLN ** U 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 68177 Z= 0.226 Angle : 0.705 15.482 92470 Z= 0.358 Chirality : 0.043 0.475 10048 Planarity : 0.004 0.071 12237 Dihedral : 4.694 59.693 9264 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.87 % Favored : 96.12 % Rotamer: Outliers : 3.08 % Allowed : 22.23 % Favored : 74.70 % 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: -0.23 (0.09), residues: 8507 helix: 0.94 (0.09), residues: 3179 sheet: -0.26 (0.13), residues: 1580 loop : -1.01 (0.10), residues: 3748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP I 395 HIS 0.018 0.001 HIS A 18 PHE 0.030 0.001 PHE F 399 TYR 0.022 0.001 TYR L 197 ARG 0.013 0.001 ARG L 65 *********************** 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 1772 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 1557 time to evaluate : 5.845 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: A 32 ARG cc_start: 0.5928 (ttp80) cc_final: 0.4529 (ttp80) REVERT: A 347 MET cc_start: 0.7011 (mmm) cc_final: 0.6756 (mmt) REVERT: A 458 MET cc_start: 0.7768 (tpt) cc_final: 0.7172 (tpp) REVERT: B 169 GLU cc_start: 0.6902 (tp30) cc_final: 0.6580 (tp30) REVERT: B 278 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7301 (t0) REVERT: B 419 MET cc_start: 0.7873 (ppp) cc_final: 0.6897 (ptm) REVERT: C 46 ASP cc_start: 0.7313 (t0) cc_final: 0.7110 (t0) REVERT: C 310 VAL cc_start: 0.7598 (OUTLIER) cc_final: 0.7343 (m) REVERT: C 398 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7928 (mtm) REVERT: C 458 MET cc_start: 0.6875 (ttt) cc_final: 0.6060 (tpp) REVERT: D 49 LYS cc_start: 0.7543 (ptmm) cc_final: 0.7061 (pttp) REVERT: E 458 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.6873 (tpp) REVERT: E 460 ASN cc_start: 0.8564 (m-40) cc_final: 0.8272 (m110) REVERT: F 34 ILE cc_start: 0.8346 (mm) cc_final: 0.8020 (mm) REVERT: F 42 VAL cc_start: 0.8935 (t) cc_final: 0.8729 (p) REVERT: F 83 ILE cc_start: 0.8554 (mp) cc_final: 0.8217 (mp) REVERT: F 314 ARG cc_start: 0.4239 (tpm170) cc_final: 0.3450 (tpm170) REVERT: F 369 MET cc_start: 0.7387 (mmp) cc_final: 0.7155 (mmp) REVERT: G 95 ASP cc_start: 0.7344 (p0) cc_final: 0.6616 (p0) REVERT: G 96 LYS cc_start: 0.8308 (mmmt) cc_final: 0.7945 (mmmt) REVERT: G 236 ASP cc_start: 0.7873 (p0) cc_final: 0.7667 (p0) REVERT: G 283 CYS cc_start: 0.7678 (m) cc_final: 0.7435 (m) REVERT: G 460 ASN cc_start: 0.8085 (m-40) cc_final: 0.7819 (m110) REVERT: H 165 LEU cc_start: 0.8512 (pt) cc_final: 0.8211 (pp) REVERT: H 205 LEU cc_start: 0.8707 (mt) cc_final: 0.8410 (mt) REVERT: H 380 ARG cc_start: 0.8076 (mtm-85) cc_final: 0.7831 (mtm-85) REVERT: I 236 ASP cc_start: 0.8014 (p0) cc_final: 0.7738 (p0) REVERT: I 262 MET cc_start: 0.7497 (mmm) cc_final: 0.7089 (tpp) REVERT: I 441 MET cc_start: 0.8040 (ppp) cc_final: 0.7688 (ppp) REVERT: I 458 MET cc_start: 0.7470 (tpp) cc_final: 0.6476 (mmm) REVERT: J 227 ASP cc_start: 0.7297 (OUTLIER) cc_final: 0.6961 (p0) REVERT: J 458 MET cc_start: 0.6977 (ttt) cc_final: 0.6386 (ttt) REVERT: K 26 MET cc_start: 0.6884 (mmm) cc_final: 0.6680 (tpt) REVERT: K 184 ARG cc_start: 0.7366 (mmm-85) cc_final: 0.6871 (mmm-85) REVERT: K 347 MET cc_start: 0.6084 (mmm) cc_final: 0.5806 (mtt) REVERT: K 418 LYS cc_start: 0.6541 (mttt) cc_final: 0.6226 (mttt) REVERT: K 460 ASN cc_start: 0.8587 (m-40) cc_final: 0.8336 (m-40) REVERT: L 15 LYS cc_start: 0.8416 (mmmm) cc_final: 0.8067 (tppp) REVERT: L 419 MET cc_start: 0.7191 (mmm) cc_final: 0.6965 (tmm) REVERT: L 458 MET cc_start: 0.8029 (tpt) cc_final: 0.7793 (tpt) REVERT: M 15 LYS cc_start: 0.6558 (OUTLIER) cc_final: 0.5650 (ttmt) REVERT: O 74 LYS cc_start: 0.1647 (OUTLIER) cc_final: 0.0990 (pttm) REVERT: R 15 LYS cc_start: 0.5571 (OUTLIER) cc_final: 0.4274 (pttm) REVERT: R 105 LYS cc_start: 0.6575 (mmmm) cc_final: 0.6303 (mmmm) REVERT: S 155 MET cc_start: 0.7207 (tpp) cc_final: 0.6807 (tpp) REVERT: T 126 MET cc_start: 0.6909 (mmp) cc_final: 0.6527 (mmm) REVERT: T 250 ASP cc_start: 0.6539 (p0) cc_final: 0.6089 (p0) REVERT: U 276 LEU cc_start: 0.8128 (mm) cc_final: 0.7892 (mm) outliers start: 215 outliers final: 157 residues processed: 1672 average time/residue: 0.6425 time to fit residues: 1813.4393 Evaluate side-chains 1642 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 1477 time to evaluate : 5.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN 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 246 VAL 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 410 LEU Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 91 THR 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 338 GLU Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain D residue 51 THR 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 424 LEU Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 299 HIS Chi-restraints excluded: chain E residue 304 VAL 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 458 MET Chi-restraints excluded: chain F residue 52 THR 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 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 165 LEU Chi-restraints excluded: chain G residue 192 ASP Chi-restraints excluded: chain G residue 256 THR Chi-restraints excluded: chain G residue 265 LEU 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 87 ASP 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 247 ILE Chi-restraints excluded: chain H residue 286 CYS Chi-restraints excluded: chain H residue 354 LEU Chi-restraints excluded: chain I residue 13 ASP 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 317 VAL Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain I residue 399 PHE 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 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 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 102 ASN Chi-restraints excluded: chain K residue 209 ASP 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 K residue 419 MET Chi-restraints excluded: chain K residue 424 LEU 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 374 GLN Chi-restraints excluded: chain L residue 377 VAL Chi-restraints excluded: chain M residue 15 LYS Chi-restraints excluded: chain M residue 16 THR 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 43 ASN 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 178 VAL Chi-restraints excluded: chain N residue 313 THR Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 43 ASN Chi-restraints excluded: chain O residue 74 LYS Chi-restraints excluded: chain O residue 187 LEU Chi-restraints excluded: chain P residue 74 LYS Chi-restraints excluded: chain P residue 114 ILE Chi-restraints excluded: chain P residue 127 LEU Chi-restraints excluded: chain P residue 156 THR Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 216 ILE Chi-restraints excluded: chain P residue 321 LYS Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 74 LYS Chi-restraints excluded: chain Q residue 114 ILE 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 46 ASP Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain S residue 243 ILE Chi-restraints excluded: chain T residue 6 LEU Chi-restraints excluded: chain T residue 235 THR Chi-restraints excluded: chain T residue 236 LEU Chi-restraints excluded: chain U residue 114 ILE 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 126 MET Chi-restraints excluded: chain V residue 152 THR Chi-restraints excluded: chain V residue 244 LEU 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 509 optimal weight: 7.9990 chunk 329 optimal weight: 10.0000 chunk 492 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 161 optimal weight: 20.0000 chunk 159 optimal weight: 0.2980 chunk 523 optimal weight: 30.0000 chunk 561 optimal weight: 9.9990 chunk 407 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 647 optimal weight: 20.0000 overall best weight: 4.6588 ------------------------------------------------------------------------------- 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 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 ASN ** D 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 ASN ** F 18 HIS ** 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** ** H 239 GLN ** 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 346 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 444 GLN ** 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 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 43 ASN O 43 ASN ** O 247 GLN ** 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 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** V 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 68177 Z= 0.251 Angle : 0.730 14.921 92470 Z= 0.372 Chirality : 0.044 0.256 10048 Planarity : 0.004 0.109 12237 Dihedral : 4.712 59.995 9264 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.28 % Favored : 95.71 % Rotamer: Outliers : 3.02 % Allowed : 22.88 % Favored : 74.09 % 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: -0.24 (0.09), residues: 8507 helix: 0.89 (0.09), residues: 3195 sheet: -0.23 (0.13), residues: 1568 loop : -1.00 (0.10), residues: 3744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.001 TRP I 395 HIS 0.025 0.001 HIS F 18 PHE 0.027 0.001 PHE Q 28 TYR 0.046 0.001 TYR T 274 ARG 0.014 0.001 ARG P 39 *********************** 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 1731 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 211 poor density : 1520 time to evaluate : 5.796 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 337 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7297 (tptt) REVERT: A 347 MET cc_start: 0.7120 (mmm) cc_final: 0.6876 (mmt) REVERT: B 169 GLU cc_start: 0.6734 (tp30) cc_final: 0.6418 (tp30) REVERT: B 278 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7253 (t0) REVERT: C 236 ASP cc_start: 0.7652 (p0) cc_final: 0.7440 (p0) REVERT: D 49 LYS cc_start: 0.7554 (ptmm) cc_final: 0.7079 (pttp) REVERT: E 165 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8335 (pp) REVERT: E 441 MET cc_start: 0.7441 (tmm) cc_final: 0.7172 (tmm) REVERT: E 458 MET cc_start: 0.7234 (OUTLIER) cc_final: 0.6861 (tpp) REVERT: F 34 ILE cc_start: 0.8373 (mm) cc_final: 0.8065 (mm) REVERT: F 83 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8289 (mp) REVERT: F 314 ARG cc_start: 0.4127 (tpm170) cc_final: 0.3212 (tpm170) REVERT: F 370 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7035 (pm20) REVERT: G 26 MET cc_start: 0.6882 (mmp) cc_final: 0.6607 (mmt) REVERT: G 95 ASP cc_start: 0.7366 (p0) cc_final: 0.6743 (p0) REVERT: G 96 LYS cc_start: 0.8295 (mmmt) cc_final: 0.8092 (mmmt) REVERT: G 236 ASP cc_start: 0.7906 (p0) cc_final: 0.7697 (p0) REVERT: G 283 CYS cc_start: 0.7591 (m) cc_final: 0.7358 (m) REVERT: G 460 ASN cc_start: 0.8181 (m-40) cc_final: 0.7557 (m110) REVERT: H 165 LEU cc_start: 0.8531 (pt) cc_final: 0.8210 (pp) REVERT: H 370 GLU cc_start: 0.7355 (tt0) cc_final: 0.7132 (tm-30) REVERT: I 132 VAL cc_start: 0.8983 (OUTLIER) cc_final: 0.8743 (p) REVERT: I 236 ASP cc_start: 0.8020 (p0) cc_final: 0.7733 (p0) REVERT: I 441 MET cc_start: 0.8044 (ppp) cc_final: 0.7708 (ppp) REVERT: I 458 MET cc_start: 0.7387 (tpp) cc_final: 0.5968 (tpt) REVERT: J 227 ASP cc_start: 0.7275 (OUTLIER) cc_final: 0.7009 (p0) REVERT: K 26 MET cc_start: 0.6941 (mmm) cc_final: 0.6705 (tpt) REVERT: K 69 TYR cc_start: 0.7357 (t80) cc_final: 0.7153 (t80) REVERT: K 347 MET cc_start: 0.6041 (mmm) cc_final: 0.5608 (mtt) REVERT: K 369 MET cc_start: 0.7108 (mmp) cc_final: 0.6906 (mmt) REVERT: K 418 LYS cc_start: 0.6559 (mttt) cc_final: 0.6234 (mttt) REVERT: K 458 MET cc_start: 0.8378 (tpt) cc_final: 0.7775 (tpp) REVERT: K 460 ASN cc_start: 0.8546 (m-40) cc_final: 0.8284 (m-40) REVERT: L 15 LYS cc_start: 0.8416 (mmmm) cc_final: 0.8073 (tppp) REVERT: L 345 ARG cc_start: 0.7488 (tmm-80) cc_final: 0.7240 (tmm-80) REVERT: L 458 MET cc_start: 0.8080 (tpt) cc_final: 0.7849 (tpt) REVERT: O 74 LYS cc_start: 0.1502 (OUTLIER) cc_final: 0.0878 (pttm) REVERT: R 15 LYS cc_start: 0.5140 (OUTLIER) cc_final: 0.3921 (pttm) REVERT: S 155 MET cc_start: 0.7274 (tpp) cc_final: 0.6989 (tpp) REVERT: T 187 LEU cc_start: 0.7665 (tp) cc_final: 0.7222 (tp) REVERT: T 250 ASP cc_start: 0.6376 (p0) cc_final: 0.6038 (p0) REVERT: U 276 LEU cc_start: 0.8165 (mm) cc_final: 0.7948 (mm) outliers start: 211 outliers final: 164 residues processed: 1644 average time/residue: 0.6375 time to fit residues: 1774.3523 Evaluate side-chains 1625 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 1452 time to evaluate : 5.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 230 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 410 LEU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 354 LEU 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 104 VAL Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 304 VAL 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 D residue 51 THR 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 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 E residue 42 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 299 HIS Chi-restraints excluded: chain E residue 304 VAL 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 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 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 100 LEU Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 165 LEU 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 18 HIS Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 87 ASP 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 247 ILE Chi-restraints excluded: chain H residue 286 CYS Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 354 LEU Chi-restraints excluded: chain I residue 13 ASP 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 132 VAL Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 219 GLU Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain I residue 399 PHE 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 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 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 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 K residue 419 MET Chi-restraints excluded: chain K residue 424 LEU 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 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 187 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 152 THR Chi-restraints excluded: chain N residue 178 VAL Chi-restraints excluded: chain N residue 244 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 187 LEU Chi-restraints excluded: chain P residue 114 ILE Chi-restraints excluded: chain P residue 127 LEU Chi-restraints excluded: chain P residue 156 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 P residue 321 LYS Chi-restraints excluded: chain Q residue 59 LEU 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 225 SER Chi-restraints excluded: chain T residue 6 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 125 ASP Chi-restraints excluded: chain U residue 243 ILE Chi-restraints excluded: chain U residue 245 ILE Chi-restraints excluded: chain U residue 313 THR Chi-restraints excluded: chain U residue 316 VAL Chi-restraints excluded: chain V residue 126 MET Chi-restraints excluded: chain V residue 152 THR Chi-restraints excluded: chain V residue 244 LEU 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 749 optimal weight: 3.9990 chunk 789 optimal weight: 4.9990 chunk 720 optimal weight: 8.9990 chunk 767 optimal weight: 50.0000 chunk 462 optimal weight: 6.9990 chunk 334 optimal weight: 0.0000 chunk 603 optimal weight: 4.9990 chunk 235 optimal weight: 10.0000 chunk 693 optimal weight: 20.0000 chunk 726 optimal weight: 20.0000 chunk 765 optimal weight: 0.0870 overall best weight: 2.8168 ------------------------------------------------------------------------------- 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 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 ASN ** D 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 GLN ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 322 ASN ** 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 239 GLN ** 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 346 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 374 GLN ** K 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 322 ASN ** L 411 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** ** M 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 43 ASN N 248 ASN N 263 ASN ** O 247 GLN ** 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 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 108 GLN ** 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 161 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 68177 Z= 0.223 Angle : 0.749 14.018 92470 Z= 0.380 Chirality : 0.044 0.346 10048 Planarity : 0.004 0.080 12237 Dihedral : 4.682 59.132 9264 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.08 % Favored : 95.91 % Rotamer: Outliers : 2.76 % Allowed : 23.37 % Favored : 73.87 % 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: -0.29 (0.09), residues: 8507 helix: 0.80 (0.09), residues: 3183 sheet: -0.18 (0.13), residues: 1562 loop : -1.00 (0.10), residues: 3762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP I 395 HIS 0.030 0.001 HIS F 18 PHE 0.025 0.001 PHE D 399 TYR 0.043 0.001 TYR T 274 ARG 0.017 0.001 ARG Q 39 *********************** 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 1734 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 1541 time to evaluate : 6.194 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 337 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7250 (tptt) REVERT: A 458 MET cc_start: 0.7977 (tpp) cc_final: 0.6912 (tpp) REVERT: B 278 ASP cc_start: 0.7519 (OUTLIER) cc_final: 0.7290 (t0) REVERT: C 310 VAL cc_start: 0.7658 (OUTLIER) cc_final: 0.7410 (m) REVERT: C 458 MET cc_start: 0.6838 (ttt) cc_final: 0.3760 (tpp) REVERT: D 49 LYS cc_start: 0.7556 (ptmm) cc_final: 0.7083 (pttp) REVERT: D 198 LYS cc_start: 0.8298 (mmtt) cc_final: 0.7876 (mmtt) REVERT: D 326 GLU cc_start: 0.7132 (pm20) cc_final: 0.6757 (pm20) REVERT: E 165 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8314 (pp) REVERT: E 218 ARG cc_start: 0.6258 (mtm-85) cc_final: 0.5941 (mtm-85) REVERT: E 441 MET cc_start: 0.7320 (tmm) cc_final: 0.7054 (tmm) REVERT: F 34 ILE cc_start: 0.8322 (mm) cc_final: 0.8025 (mm) REVERT: F 83 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8332 (mp) REVERT: F 314 ARG cc_start: 0.4249 (tpm170) cc_final: 0.3405 (tpm170) REVERT: F 347 MET cc_start: 0.7230 (mmm) cc_final: 0.6651 (mtp) REVERT: F 370 GLU cc_start: 0.7397 (mt-10) cc_final: 0.6981 (pm20) REVERT: G 95 ASP cc_start: 0.7328 (p0) cc_final: 0.6751 (p0) REVERT: G 96 LYS cc_start: 0.8210 (mmmt) cc_final: 0.7994 (mmmt) REVERT: G 236 ASP cc_start: 0.7835 (p0) cc_final: 0.7634 (p0) REVERT: G 283 CYS cc_start: 0.7602 (m) cc_final: 0.7307 (m) REVERT: G 460 ASN cc_start: 0.8024 (m-40) cc_final: 0.7666 (m110) REVERT: H 83 ILE cc_start: 0.8641 (tp) cc_final: 0.8429 (tp) REVERT: H 165 LEU cc_start: 0.8477 (pt) cc_final: 0.8187 (pp) REVERT: H 205 LEU cc_start: 0.8697 (mt) cc_final: 0.8391 (mt) REVERT: H 380 ARG cc_start: 0.7836 (mtm-85) cc_final: 0.7484 (mtm-85) REVERT: H 405 LYS cc_start: 0.8643 (mmmt) cc_final: 0.8299 (mmmm) REVERT: I 236 ASP cc_start: 0.8003 (p0) cc_final: 0.7707 (p0) REVERT: I 441 MET cc_start: 0.8102 (ppp) cc_final: 0.7800 (ppp) REVERT: I 458 MET cc_start: 0.7470 (tpp) cc_final: 0.7049 (mmm) REVERT: J 227 ASP cc_start: 0.7199 (OUTLIER) cc_final: 0.6943 (p0) REVERT: J 458 MET cc_start: 0.6958 (ttt) cc_final: 0.6541 (ttt) REVERT: K 26 MET cc_start: 0.6906 (mmm) cc_final: 0.6648 (tpt) REVERT: K 347 MET cc_start: 0.5987 (mmm) cc_final: 0.5543 (mtt) REVERT: K 418 LYS cc_start: 0.6630 (mttt) cc_final: 0.6283 (mttt) REVERT: K 458 MET cc_start: 0.8333 (tpt) cc_final: 0.7798 (tpp) REVERT: K 460 ASN cc_start: 0.8536 (m-40) cc_final: 0.8297 (m-40) REVERT: L 15 LYS cc_start: 0.8370 (mmmm) cc_final: 0.7994 (tppp) REVERT: L 345 ARG cc_start: 0.7589 (tmm-80) cc_final: 0.7370 (tmm-80) REVERT: L 458 MET cc_start: 0.8063 (tpt) cc_final: 0.7842 (tpt) REVERT: O 74 LYS cc_start: 0.1688 (OUTLIER) cc_final: 0.1108 (pttm) REVERT: R 105 LYS cc_start: 0.6517 (mmmm) cc_final: 0.6292 (mmmm) REVERT: S 155 MET cc_start: 0.7269 (tpp) cc_final: 0.6948 (tpp) REVERT: T 250 ASP cc_start: 0.6339 (p0) cc_final: 0.5887 (p0) outliers start: 193 outliers final: 154 residues processed: 1652 average time/residue: 0.6674 time to fit residues: 1873.2019 Evaluate side-chains 1635 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 1474 time to evaluate : 5.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN 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 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 348 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 221 ASP 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 342 GLN Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain D residue 51 THR 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 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 E residue 42 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 299 HIS Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 412 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 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 165 LEU 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 414 PHE 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 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 247 ILE Chi-restraints excluded: chain H residue 286 CYS Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 354 LEU Chi-restraints excluded: chain I residue 13 ASP 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 219 GLU Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 354 LEU 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 299 HIS Chi-restraints excluded: chain J residue 317 VAL 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 419 MET 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 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 K residue 424 LEU 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 190 ASP Chi-restraints excluded: chain L residue 196 ILE 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 187 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 244 LEU Chi-restraints excluded: chain N residue 313 THR Chi-restraints excluded: chain O residue 74 LYS Chi-restraints excluded: chain O residue 187 LEU Chi-restraints excluded: chain O residue 246 GLU Chi-restraints excluded: chain P residue 74 LYS Chi-restraints excluded: chain P residue 114 ILE Chi-restraints excluded: chain P residue 156 THR Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 216 ILE Chi-restraints excluded: chain P residue 321 LYS Chi-restraints excluded: chain Q residue 74 LYS 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 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 T residue 6 LEU 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 126 MET 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 504 optimal weight: 9.9990 chunk 812 optimal weight: 10.0000 chunk 495 optimal weight: 9.9990 chunk 385 optimal weight: 5.9990 chunk 564 optimal weight: 0.0000 chunk 851 optimal weight: 20.0000 chunk 783 optimal weight: 6.9990 chunk 678 optimal weight: 40.0000 chunk 70 optimal weight: 9.9990 chunk 523 optimal weight: 0.0010 chunk 415 optimal weight: 20.0000 overall best weight: 4.5996 ------------------------------------------------------------------------------- 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 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS C 411 ASN D 74 ASN ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** 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** ** H 239 GLN ** 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 37 ASN ** J 346 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 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 23 GLN ** 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 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 43 ASN N 248 ASN ** O 247 GLN ** 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 108 GLN ** 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** ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 68177 Z= 0.259 Angle : 0.774 14.659 92470 Z= 0.394 Chirality : 0.044 0.287 10048 Planarity : 0.004 0.094 12237 Dihedral : 4.711 59.351 9264 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.23 % Favored : 95.76 % Rotamer: Outliers : 2.56 % Allowed : 24.17 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.09), residues: 8507 helix: 0.74 (0.09), residues: 3198 sheet: -0.23 (0.13), residues: 1587 loop : -0.97 (0.10), residues: 3722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP I 395 HIS 0.029 0.001 HIS F 18 PHE 0.035 0.001 PHE P 251 TYR 0.043 0.001 TYR T 274 ARG 0.015 0.001 ARG P 39 ********************** 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 1689 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 1510 time to evaluate : 5.679 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: A 337 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7228 (tptt) REVERT: A 458 MET cc_start: 0.7978 (tpp) cc_final: 0.6733 (tpp) REVERT: B 169 GLU cc_start: 0.6808 (tp30) cc_final: 0.6452 (tp30) REVERT: B 278 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7291 (t0) REVERT: C 95 ASP cc_start: 0.7495 (p0) cc_final: 0.7290 (p0) REVERT: C 310 VAL cc_start: 0.7656 (OUTLIER) cc_final: 0.7378 (m) REVERT: C 458 MET cc_start: 0.6353 (ttt) cc_final: 0.5492 (tpp) REVERT: D 49 LYS cc_start: 0.7603 (ptmm) cc_final: 0.7126 (pttp) REVERT: D 458 MET cc_start: 0.6783 (tpt) cc_final: 0.6496 (tpt) REVERT: E 165 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8021 (pp) REVERT: E 218 ARG cc_start: 0.6272 (mtm-85) cc_final: 0.5940 (mtm-85) REVERT: E 314 ARG cc_start: 0.3928 (tpm170) cc_final: 0.3110 (tpm170) REVERT: E 441 MET cc_start: 0.7290 (tmm) cc_final: 0.7076 (tmm) REVERT: F 34 ILE cc_start: 0.8269 (mm) cc_final: 0.7973 (mm) REVERT: F 83 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8322 (mp) REVERT: F 314 ARG cc_start: 0.4430 (tpm170) cc_final: 0.3366 (tpm170) REVERT: F 347 MET cc_start: 0.7347 (mmm) cc_final: 0.6805 (mtp) REVERT: G 36 ASP cc_start: 0.6811 (p0) cc_final: 0.6287 (p0) REVERT: G 95 ASP cc_start: 0.7380 (p0) cc_final: 0.6699 (p0) REVERT: G 96 LYS cc_start: 0.8167 (mmmt) cc_final: 0.7944 (mmmt) REVERT: G 236 ASP cc_start: 0.7887 (p0) cc_final: 0.7675 (p0) REVERT: G 460 ASN cc_start: 0.8101 (m-40) cc_final: 0.7750 (m110) REVERT: H 165 LEU cc_start: 0.8508 (pt) cc_final: 0.8202 (pp) REVERT: H 380 ARG cc_start: 0.7779 (mtm-85) cc_final: 0.7474 (mtm-85) REVERT: I 236 ASP cc_start: 0.7952 (p0) cc_final: 0.7636 (p0) REVERT: I 259 MET cc_start: 0.8607 (tmm) cc_final: 0.7809 (tmm) REVERT: I 441 MET cc_start: 0.8119 (ppp) cc_final: 0.7818 (ppp) REVERT: I 458 MET cc_start: 0.7457 (tpp) cc_final: 0.5927 (mmm) REVERT: J 227 ASP cc_start: 0.7251 (OUTLIER) cc_final: 0.7012 (p0) REVERT: J 335 MET cc_start: 0.8140 (tmm) cc_final: 0.7713 (tmm) REVERT: J 458 MET cc_start: 0.7005 (ttt) cc_final: 0.6582 (ttt) REVERT: K 26 MET cc_start: 0.6956 (mmm) cc_final: 0.6675 (tpt) REVERT: K 169 GLU cc_start: 0.6146 (mm-30) cc_final: 0.5793 (mm-30) REVERT: K 176 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.7134 (mmmt) REVERT: K 347 MET cc_start: 0.6105 (mmm) cc_final: 0.5685 (mtt) REVERT: K 418 LYS cc_start: 0.6521 (mttt) cc_final: 0.6183 (mttt) REVERT: K 458 MET cc_start: 0.8336 (tpt) cc_final: 0.7384 (tpp) REVERT: K 460 ASN cc_start: 0.8581 (m-40) cc_final: 0.8179 (m-40) REVERT: L 15 LYS cc_start: 0.8365 (mmmm) cc_final: 0.8019 (tppp) REVERT: L 458 MET cc_start: 0.8090 (tpt) cc_final: 0.7882 (tpt) REVERT: O 74 LYS cc_start: 0.1780 (OUTLIER) cc_final: 0.1178 (pttm) REVERT: O 207 ARG cc_start: 0.6884 (mmm-85) cc_final: 0.6624 (mmm-85) REVERT: R 105 LYS cc_start: 0.6501 (mmmm) cc_final: 0.6266 (mmmm) REVERT: S 155 MET cc_start: 0.7271 (tpp) cc_final: 0.6960 (tpp) REVERT: T 187 LEU cc_start: 0.7763 (tp) cc_final: 0.7431 (tp) REVERT: T 250 ASP cc_start: 0.6359 (p0) cc_final: 0.6006 (p0) outliers start: 179 outliers final: 157 residues processed: 1616 average time/residue: 0.6409 time to fit residues: 1750.6839 Evaluate side-chains 1627 residues out of total 6983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 1462 time to evaluate : 5.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN 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 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 410 LEU Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 354 LEU 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 120 GLU Chi-restraints excluded: chain C residue 219 GLU 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 338 GLU Chi-restraints excluded: chain C residue 342 GLN Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain D residue 51 THR 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 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 E residue 42 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 299 HIS Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 412 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 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 165 LEU 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 419 MET Chi-restraints excluded: chain G residue 436 ILE Chi-restraints excluded: chain H residue 18 HIS 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 247 ILE Chi-restraints excluded: chain H residue 286 CYS Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 354 LEU Chi-restraints excluded: chain I residue 13 ASP 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 219 GLU Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain I residue 399 PHE 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 299 HIS Chi-restraints excluded: chain J residue 317 VAL 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 419 MET Chi-restraints excluded: chain K residue 6 ASN Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 176 LYS Chi-restraints excluded: chain K residue 209 ASP 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 K residue 424 LEU 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 190 ASP Chi-restraints excluded: chain L residue 291 LEU 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 187 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 244 LEU Chi-restraints excluded: chain N residue 313 THR Chi-restraints excluded: chain O residue 74 LYS Chi-restraints excluded: chain O residue 187 LEU Chi-restraints excluded: chain P residue 74 LYS Chi-restraints excluded: chain P residue 114 ILE Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 216 ILE Chi-restraints excluded: chain P residue 321 LYS Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain R residue 10 ASN 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 49 GLU Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain T residue 6 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 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 126 MET Chi-restraints excluded: chain V residue 152 THR 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 538 optimal weight: 6.9990 chunk 722 optimal weight: 20.0000 chunk 207 optimal weight: 9.9990 chunk 625 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 188 optimal weight: 8.9990 chunk 679 optimal weight: 7.9990 chunk 284 optimal weight: 20.0000 chunk 697 optimal weight: 0.5980 chunk 86 optimal weight: 30.0000 chunk 125 optimal weight: 0.5980 overall best weight: 4.0386 ------------------------------------------------------------------------------- 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 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 ASN ** B 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS D 74 ASN ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** 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 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 239 GLN ** 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 346 GLN 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 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 23 GLN ** 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 128 ASN ** 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 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 247 GLN ** 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 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 124 GLN ** U 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 GLN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.085410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.070351 restraints weight = 250417.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.072477 restraints weight = 144660.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.073964 restraints weight = 99005.624| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 68177 Z= 0.250 Angle : 0.777 13.881 92470 Z= 0.395 Chirality : 0.044 0.243 10048 Planarity : 0.004 0.075 12237 Dihedral : 4.712 59.835 9264 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.08 % Favored : 95.91 % Rotamer: Outliers : 2.72 % Allowed : 24.26 % Favored : 73.02 % 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: -0.34 (0.09), residues: 8507 helix: 0.68 (0.09), residues: 3208 sheet: -0.21 (0.13), residues: 1578 loop : -0.96 (0.10), residues: 3721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP I 395 HIS 0.029 0.001 HIS F 18 PHE 0.027 0.001 PHE B 131 TYR 0.040 0.001 TYR T 274 ARG 0.014 0.001 ARG Q 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24339.66 seconds wall clock time: 422 minutes 4.58 seconds (25324.58 seconds total)