Starting phenix.real_space_refine on Sat Jan 25 09:05:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v40_42962/01_2025/8v40_42962.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v40_42962/01_2025/8v40_42962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v40_42962/01_2025/8v40_42962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v40_42962/01_2025/8v40_42962.map" model { file = "/net/cci-nas-00/data/ceres_data/8v40_42962/01_2025/8v40_42962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v40_42962/01_2025/8v40_42962.cif" } resolution = 3.9 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= 0.001 sd= 0.007 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 300 5.16 5 C 48846 2.51 5 N 12378 2.21 5 O 14898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 76422 Number of models: 1 Model: "" Number of chains: 42 Chain: "h" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1081 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 3, 'TRANS': 132} Chain: "d" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "i" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "C" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Chain: "F" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Chain: "I" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1205 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain: "B" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Chain: "k" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1081 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 3, 'TRANS': 132} Chain: "f" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "n" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "P" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Chain: "U" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Chain: "Z" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1205 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain: "M" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Chain: "l" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1081 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 3, 'TRANS': 132} Chain: "g" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "o" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "Q" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Chain: "V" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Chain: "a" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1205 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain: "N" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Chain: "J" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1081 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 3, 'TRANS': 132} Chain: "H" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "K" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "D" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Chain: "E" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Chain: "G" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1205 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain: "A" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Chain: "m" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1081 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 3, 'TRANS': 132} Chain: "j" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "p" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "R" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Chain: "W" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Chain: "b" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1205 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain: "O" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Chain: "c" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1081 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 3, 'TRANS': 132} Chain: "Y" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "e" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "S" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Chain: "T" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Chain: "X" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1205 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain: "L" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Time building chain proxies: 33.41, per 1000 atoms: 0.44 Number of scatterers: 76422 At special positions: 0 Unit cell: (225.5, 225.5, 181.5, 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 300 16.00 O 14898 8.00 N 12378 7.00 C 48846 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: 13.95 Conformation dependent library (CDL) restraints added in 7.3 seconds 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18312 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 97 sheets defined 31.8% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.56 Creating SS restraints... Processing helix chain 'h' and resid 69 through 82 removed outlier: 3.705A pdb=" N LYS h 73 " --> pdb=" O SER h 69 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU h 74 " --> pdb=" O ARG h 70 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE h 75 " --> pdb=" O MET h 71 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N GLU h 77 " --> pdb=" O LYS h 73 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LYS h 78 " --> pdb=" O LEU h 74 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS h 80 " --> pdb=" O GLY h 76 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG h 81 " --> pdb=" O GLU h 77 " (cutoff:3.500A) Processing helix chain 'd' and resid 5 through 9 Processing helix chain 'd' and resid 11 through 13 No H-bonds generated for 'chain 'd' and resid 11 through 13' Processing helix chain 'd' and resid 69 through 82 removed outlier: 4.030A pdb=" N LYS d 73 " --> pdb=" O SER d 69 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU d 74 " --> pdb=" O ARG d 70 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE d 75 " --> pdb=" O MET d 71 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N GLU d 77 " --> pdb=" O LYS d 73 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LYS d 78 " --> pdb=" O LEU d 74 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS d 80 " --> pdb=" O GLY d 76 " (cutoff:3.500A) Processing helix chain 'i' and resid 5 through 9 Processing helix chain 'i' and resid 11 through 13 No H-bonds generated for 'chain 'i' and resid 11 through 13' Processing helix chain 'i' and resid 69 through 82 removed outlier: 3.586A pdb=" N ILE i 75 " --> pdb=" O MET i 71 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N GLU i 77 " --> pdb=" O LYS i 73 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LYS i 78 " --> pdb=" O LEU i 74 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS i 80 " --> pdb=" O GLY i 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 Processing helix chain 'C' and resid 86 through 96 Processing helix chain 'C' and resid 107 through 125 removed outlier: 3.730A pdb=" N ASP C 123 " --> pdb=" O ILE C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 174 removed outlier: 3.502A pdb=" N THR C 174 " --> pdb=" O LEU C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 205 Processing helix chain 'C' and resid 234 through 238 Processing helix chain 'C' and resid 239 through 261 removed outlier: 3.621A pdb=" N VAL C 243 " --> pdb=" O LYS C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 288 removed outlier: 3.640A pdb=" N LYS C 288 " --> pdb=" O GLU C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 313 Processing helix chain 'C' and resid 320 through 327 removed outlier: 3.720A pdb=" N LYS C 325 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU C 326 " --> pdb=" O GLN C 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 66 removed outlier: 4.007A pdb=" N MET F 66 " --> pdb=" O ASN F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 96 removed outlier: 4.646A pdb=" N ALA F 89 " --> pdb=" O ASP F 85 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU F 90 " --> pdb=" O ILE F 86 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR F 95 " --> pdb=" O ASP F 91 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS F 96 " --> pdb=" O PHE F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 124 removed outlier: 4.325A pdb=" N THR F 112 " --> pdb=" O GLU F 108 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA F 113 " --> pdb=" O ALA F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 174 removed outlier: 3.982A pdb=" N SER F 165 " --> pdb=" O ASP F 161 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG F 166 " --> pdb=" O GLU F 162 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR F 174 " --> pdb=" O LEU F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 206 removed outlier: 3.755A pdb=" N LYS F 205 " --> pdb=" O SER F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 238 Processing helix chain 'F' and resid 239 through 261 removed outlier: 3.633A pdb=" N ASP F 260 " --> pdb=" O VAL F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 289 removed outlier: 3.731A pdb=" N SER F 289 " --> pdb=" O GLU F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 312 Processing helix chain 'F' and resid 320 through 326 Processing helix chain 'I' and resid 3 through 19 removed outlier: 3.819A pdb=" N ILE I 7 " --> pdb=" O LYS I 3 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 33 removed outlier: 3.681A pdb=" N VAL I 30 " --> pdb=" O ASP I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 87 removed outlier: 3.627A pdb=" N MET I 76 " --> pdb=" O LYS I 72 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR I 77 " --> pdb=" O SER I 73 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS I 85 " --> pdb=" O ASP I 81 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU I 86 " --> pdb=" O GLU I 82 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE I 87 " --> pdb=" O LEU I 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 66 Processing helix chain 'B' and resid 86 through 96 removed outlier: 3.663A pdb=" N PHE B 92 " --> pdb=" O THR B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 125 removed outlier: 3.641A pdb=" N ASP B 123 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 174 removed outlier: 4.104A pdb=" N SER B 165 " --> pdb=" O ASP B 161 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ARG B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 205 Processing helix chain 'B' and resid 234 through 238 Processing helix chain 'B' and resid 239 through 261 Processing helix chain 'B' and resid 268 through 289 Processing helix chain 'B' and resid 301 through 312 removed outlier: 3.758A pdb=" N GLN B 305 " --> pdb=" O ASP B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 327 Processing helix chain 'k' and resid 69 through 82 removed outlier: 3.707A pdb=" N LYS k 73 " --> pdb=" O SER k 69 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU k 74 " --> pdb=" O ARG k 70 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE k 75 " --> pdb=" O MET k 71 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N GLU k 77 " --> pdb=" O LYS k 73 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LYS k 78 " --> pdb=" O LEU k 74 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS k 80 " --> pdb=" O GLY k 76 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG k 81 " --> pdb=" O GLU k 77 " (cutoff:3.500A) Processing helix chain 'f' and resid 5 through 9 Processing helix chain 'f' and resid 11 through 13 No H-bonds generated for 'chain 'f' and resid 11 through 13' Processing helix chain 'f' and resid 69 through 82 removed outlier: 4.012A pdb=" N LYS f 73 " --> pdb=" O SER f 69 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU f 74 " --> pdb=" O ARG f 70 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE f 75 " --> pdb=" O MET f 71 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N GLU f 77 " --> pdb=" O LYS f 73 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LYS f 78 " --> pdb=" O LEU f 74 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS f 80 " --> pdb=" O GLY f 76 " (cutoff:3.500A) Processing helix chain 'n' and resid 5 through 9 Processing helix chain 'n' and resid 11 through 13 No H-bonds generated for 'chain 'n' and resid 11 through 13' Processing helix chain 'n' and resid 69 through 82 removed outlier: 3.596A pdb=" N ILE n 75 " --> pdb=" O MET n 71 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLU n 77 " --> pdb=" O LYS n 73 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N LYS n 78 " --> pdb=" O LEU n 74 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS n 80 " --> pdb=" O GLY n 76 " (cutoff:3.500A) Processing helix chain 'P' and resid 54 through 66 Processing helix chain 'P' and resid 86 through 96 Processing helix chain 'P' and resid 107 through 125 removed outlier: 3.726A pdb=" N ASP P 123 " --> pdb=" O ILE P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 163 through 174 Processing helix chain 'P' and resid 195 through 205 Processing helix chain 'P' and resid 234 through 238 Processing helix chain 'P' and resid 239 through 261 removed outlier: 3.622A pdb=" N VAL P 243 " --> pdb=" O LYS P 239 " (cutoff:3.500A) Processing helix chain 'P' and resid 268 through 288 removed outlier: 3.637A pdb=" N LYS P 288 " --> pdb=" O GLU P 284 " (cutoff:3.500A) Processing helix chain 'P' and resid 301 through 313 Processing helix chain 'P' and resid 320 through 327 removed outlier: 3.705A pdb=" N LYS P 325 " --> pdb=" O LEU P 321 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU P 326 " --> pdb=" O GLN P 322 " (cutoff:3.500A) Processing helix chain 'U' and resid 54 through 66 removed outlier: 4.008A pdb=" N MET U 66 " --> pdb=" O ASN U 62 " (cutoff:3.500A) Processing helix chain 'U' and resid 85 through 96 removed outlier: 4.648A pdb=" N ALA U 89 " --> pdb=" O ASP U 85 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU U 90 " --> pdb=" O ILE U 86 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR U 95 " --> pdb=" O ASP U 91 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS U 96 " --> pdb=" O PHE U 92 " (cutoff:3.500A) Processing helix chain 'U' and resid 107 through 124 removed outlier: 4.319A pdb=" N THR U 112 " --> pdb=" O GLU U 108 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ALA U 113 " --> pdb=" O ALA U 109 " (cutoff:3.500A) Processing helix chain 'U' and resid 159 through 174 removed outlier: 3.952A pdb=" N SER U 165 " --> pdb=" O ASP U 161 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG U 166 " --> pdb=" O GLU U 162 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR U 174 " --> pdb=" O LEU U 170 " (cutoff:3.500A) Processing helix chain 'U' and resid 195 through 206 removed outlier: 3.757A pdb=" N LYS U 205 " --> pdb=" O SER U 201 " (cutoff:3.500A) Processing helix chain 'U' and resid 235 through 238 Processing helix chain 'U' and resid 239 through 261 removed outlier: 3.635A pdb=" N ASP U 260 " --> pdb=" O VAL U 256 " (cutoff:3.500A) Processing helix chain 'U' and resid 268 through 289 removed outlier: 3.733A pdb=" N SER U 289 " --> pdb=" O GLU U 285 " (cutoff:3.500A) Processing helix chain 'U' and resid 301 through 312 Processing helix chain 'U' and resid 320 through 326 Processing helix chain 'Z' and resid 3 through 19 removed outlier: 3.832A pdb=" N ILE Z 7 " --> pdb=" O LYS Z 3 " (cutoff:3.500A) Processing helix chain 'Z' and resid 26 through 33 removed outlier: 3.684A pdb=" N VAL Z 30 " --> pdb=" O ASP Z 26 " (cutoff:3.500A) Processing helix chain 'Z' and resid 72 through 87 removed outlier: 3.643A pdb=" N MET Z 76 " --> pdb=" O LYS Z 72 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR Z 77 " --> pdb=" O SER Z 73 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS Z 85 " --> pdb=" O ASP Z 81 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU Z 86 " --> pdb=" O GLU Z 82 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE Z 87 " --> pdb=" O LEU Z 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 66 Processing helix chain 'M' and resid 84 through 96 removed outlier: 4.519A pdb=" N THR M 88 " --> pdb=" O ALA M 84 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA M 89 " --> pdb=" O ASP M 85 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE M 92 " --> pdb=" O THR M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 125 removed outlier: 3.633A pdb=" N ASP M 123 " --> pdb=" O ILE M 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 159 through 174 removed outlier: 4.098A pdb=" N SER M 165 " --> pdb=" O ASP M 161 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ARG M 166 " --> pdb=" O GLU M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 205 Processing helix chain 'M' and resid 234 through 238 Processing helix chain 'M' and resid 239 through 261 Processing helix chain 'M' and resid 268 through 289 Processing helix chain 'M' and resid 301 through 312 removed outlier: 3.751A pdb=" N GLN M 305 " --> pdb=" O ASP M 301 " (cutoff:3.500A) Processing helix chain 'M' and resid 320 through 327 Processing helix chain 'l' and resid 69 through 82 removed outlier: 3.706A pdb=" N LYS l 73 " --> pdb=" O SER l 69 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU l 74 " --> pdb=" O ARG l 70 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE l 75 " --> pdb=" O MET l 71 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N GLU l 77 " --> pdb=" O LYS l 73 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LYS l 78 " --> pdb=" O LEU l 74 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS l 80 " --> pdb=" O GLY l 76 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG l 81 " --> pdb=" O GLU l 77 " (cutoff:3.500A) Processing helix chain 'g' and resid 5 through 9 Processing helix chain 'g' and resid 11 through 13 No H-bonds generated for 'chain 'g' and resid 11 through 13' Processing helix chain 'g' and resid 69 through 82 removed outlier: 4.012A pdb=" N LYS g 73 " --> pdb=" O SER g 69 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU g 74 " --> pdb=" O ARG g 70 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE g 75 " --> pdb=" O MET g 71 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N GLU g 77 " --> pdb=" O LYS g 73 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LYS g 78 " --> pdb=" O LEU g 74 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS g 80 " --> pdb=" O GLY g 76 " (cutoff:3.500A) Processing helix chain 'o' and resid 5 through 9 Processing helix chain 'o' and resid 11 through 13 No H-bonds generated for 'chain 'o' and resid 11 through 13' Processing helix chain 'o' and resid 69 through 82 removed outlier: 3.598A pdb=" N ILE o 75 " --> pdb=" O MET o 71 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLU o 77 " --> pdb=" O LYS o 73 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LYS o 78 " --> pdb=" O LEU o 74 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS o 80 " --> pdb=" O GLY o 76 " (cutoff:3.500A) Processing helix chain 'Q' and resid 54 through 66 Processing helix chain 'Q' and resid 86 through 96 Processing helix chain 'Q' and resid 107 through 125 removed outlier: 3.724A pdb=" N ASP Q 123 " --> pdb=" O ILE Q 119 " (cutoff:3.500A) Processing helix chain 'Q' and resid 163 through 174 removed outlier: 3.507A pdb=" N THR Q 174 " --> pdb=" O LEU Q 170 " (cutoff:3.500A) Processing helix chain 'Q' and resid 195 through 205 Processing helix chain 'Q' and resid 234 through 238 Processing helix chain 'Q' and resid 239 through 261 removed outlier: 3.628A pdb=" N VAL Q 243 " --> pdb=" O LYS Q 239 " (cutoff:3.500A) Processing helix chain 'Q' and resid 268 through 288 removed outlier: 3.640A pdb=" N LYS Q 288 " --> pdb=" O GLU Q 284 " (cutoff:3.500A) Processing helix chain 'Q' and resid 301 through 313 Processing helix chain 'Q' and resid 320 through 327 removed outlier: 3.710A pdb=" N LYS Q 325 " --> pdb=" O LEU Q 321 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU Q 326 " --> pdb=" O GLN Q 322 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 66 removed outlier: 3.995A pdb=" N MET V 66 " --> pdb=" O ASN V 62 " (cutoff:3.500A) Processing helix chain 'V' and resid 85 through 96 removed outlier: 4.639A pdb=" N ALA V 89 " --> pdb=" O ASP V 85 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU V 90 " --> pdb=" O ILE V 86 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR V 95 " --> pdb=" O ASP V 91 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS V 96 " --> pdb=" O PHE V 92 " (cutoff:3.500A) Processing helix chain 'V' and resid 107 through 124 removed outlier: 4.317A pdb=" N THR V 112 " --> pdb=" O GLU V 108 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA V 113 " --> pdb=" O ALA V 109 " (cutoff:3.500A) Processing helix chain 'V' and resid 159 through 174 removed outlier: 3.961A pdb=" N SER V 165 " --> pdb=" O ASP V 161 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG V 166 " --> pdb=" O GLU V 162 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR V 174 " --> pdb=" O LEU V 170 " (cutoff:3.500A) Processing helix chain 'V' and resid 195 through 206 removed outlier: 3.760A pdb=" N LYS V 205 " --> pdb=" O SER V 201 " (cutoff:3.500A) Processing helix chain 'V' and resid 235 through 238 Processing helix chain 'V' and resid 239 through 261 removed outlier: 3.633A pdb=" N ASP V 260 " --> pdb=" O VAL V 256 " (cutoff:3.500A) Processing helix chain 'V' and resid 268 through 289 removed outlier: 3.738A pdb=" N SER V 289 " --> pdb=" O GLU V 285 " (cutoff:3.500A) Processing helix chain 'V' and resid 301 through 312 Processing helix chain 'V' and resid 320 through 326 Processing helix chain 'a' and resid 3 through 19 removed outlier: 3.831A pdb=" N ILE a 7 " --> pdb=" O LYS a 3 " (cutoff:3.500A) Processing helix chain 'a' and resid 26 through 33 removed outlier: 3.684A pdb=" N VAL a 30 " --> pdb=" O ASP a 26 " (cutoff:3.500A) Processing helix chain 'a' and resid 72 through 87 removed outlier: 3.641A pdb=" N MET a 76 " --> pdb=" O LYS a 72 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR a 77 " --> pdb=" O SER a 73 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS a 85 " --> pdb=" O ASP a 81 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU a 86 " --> pdb=" O GLU a 82 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE a 87 " --> pdb=" O LEU a 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 54 through 66 Processing helix chain 'N' and resid 84 through 96 removed outlier: 4.522A pdb=" N THR N 88 " --> pdb=" O ALA N 84 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ALA N 89 " --> pdb=" O ASP N 85 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE N 92 " --> pdb=" O THR N 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 107 through 125 removed outlier: 3.629A pdb=" N ASP N 123 " --> pdb=" O ILE N 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 159 through 174 removed outlier: 4.107A pdb=" N SER N 165 " --> pdb=" O ASP N 161 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG N 166 " --> pdb=" O GLU N 162 " (cutoff:3.500A) Processing helix chain 'N' and resid 195 through 205 Processing helix chain 'N' and resid 234 through 238 Processing helix chain 'N' and resid 239 through 261 Processing helix chain 'N' and resid 268 through 289 Processing helix chain 'N' and resid 301 through 312 removed outlier: 3.756A pdb=" N GLN N 305 " --> pdb=" O ASP N 301 " (cutoff:3.500A) Processing helix chain 'N' and resid 320 through 327 Processing helix chain 'J' and resid 69 through 82 removed outlier: 3.707A pdb=" N LYS J 73 " --> pdb=" O SER J 69 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU J 74 " --> pdb=" O ARG J 70 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE J 75 " --> pdb=" O MET J 71 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N GLU J 77 " --> pdb=" O LYS J 73 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N LYS J 78 " --> pdb=" O LEU J 74 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS J 80 " --> pdb=" O GLY J 76 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG J 81 " --> pdb=" O GLU J 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 9 Processing helix chain 'H' and resid 11 through 13 No H-bonds generated for 'chain 'H' and resid 11 through 13' Processing helix chain 'H' and resid 69 through 82 removed outlier: 4.032A pdb=" N LYS H 73 " --> pdb=" O SER H 69 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU H 74 " --> pdb=" O ARG H 70 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE H 75 " --> pdb=" O MET H 71 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLU H 77 " --> pdb=" O LYS H 73 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N LYS H 78 " --> pdb=" O LEU H 74 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS H 80 " --> pdb=" O GLY H 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 9 Processing helix chain 'K' and resid 11 through 13 No H-bonds generated for 'chain 'K' and resid 11 through 13' Processing helix chain 'K' and resid 69 through 82 removed outlier: 3.587A pdb=" N ILE K 75 " --> pdb=" O MET K 71 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLU K 77 " --> pdb=" O LYS K 73 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LYS K 78 " --> pdb=" O LEU K 74 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS K 80 " --> pdb=" O GLY K 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 66 Processing helix chain 'D' and resid 86 through 96 Processing helix chain 'D' and resid 107 through 125 removed outlier: 3.729A pdb=" N ASP D 123 " --> pdb=" O ILE D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 174 Processing helix chain 'D' and resid 195 through 205 Processing helix chain 'D' and resid 234 through 238 Processing helix chain 'D' and resid 239 through 261 removed outlier: 3.621A pdb=" N VAL D 243 " --> pdb=" O LYS D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 288 removed outlier: 3.639A pdb=" N LYS D 288 " --> pdb=" O GLU D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 313 Processing helix chain 'D' and resid 320 through 327 removed outlier: 3.717A pdb=" N LYS D 325 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU D 326 " --> pdb=" O GLN D 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 66 removed outlier: 4.006A pdb=" N MET E 66 " --> pdb=" O ASN E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 96 removed outlier: 4.648A pdb=" N ALA E 89 " --> pdb=" O ASP E 85 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU E 90 " --> pdb=" O ILE E 86 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR E 95 " --> pdb=" O ASP E 91 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS E 96 " --> pdb=" O PHE E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 124 removed outlier: 4.325A pdb=" N THR E 112 " --> pdb=" O GLU E 108 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 174 removed outlier: 3.982A pdb=" N SER E 165 " --> pdb=" O ASP E 161 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG E 166 " --> pdb=" O GLU E 162 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR E 174 " --> pdb=" O LEU E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.755A pdb=" N LYS E 205 " --> pdb=" O SER E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 238 Processing helix chain 'E' and resid 239 through 261 removed outlier: 3.632A pdb=" N ASP E 260 " --> pdb=" O VAL E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 289 removed outlier: 3.732A pdb=" N SER E 289 " --> pdb=" O GLU E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 312 Processing helix chain 'E' and resid 320 through 326 Processing helix chain 'G' and resid 3 through 19 removed outlier: 3.820A pdb=" N ILE G 7 " --> pdb=" O LYS G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 33 removed outlier: 3.679A pdb=" N VAL G 30 " --> pdb=" O ASP G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 87 removed outlier: 3.635A pdb=" N MET G 76 " --> pdb=" O LYS G 72 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR G 77 " --> pdb=" O SER G 73 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS G 85 " --> pdb=" O ASP G 81 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU G 86 " --> pdb=" O GLU G 82 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 66 Processing helix chain 'A' and resid 86 through 96 removed outlier: 3.662A pdb=" N PHE A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 125 removed outlier: 3.640A pdb=" N ASP A 123 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 174 removed outlier: 4.103A pdb=" N SER A 165 " --> pdb=" O ASP A 161 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 239 through 261 Processing helix chain 'A' and resid 268 through 289 Processing helix chain 'A' and resid 301 through 312 removed outlier: 3.756A pdb=" N GLN A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 327 Processing helix chain 'm' and resid 69 through 82 removed outlier: 3.704A pdb=" N LYS m 73 " --> pdb=" O SER m 69 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU m 74 " --> pdb=" O ARG m 70 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE m 75 " --> pdb=" O MET m 71 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLU m 77 " --> pdb=" O LYS m 73 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LYS m 78 " --> pdb=" O LEU m 74 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS m 80 " --> pdb=" O GLY m 76 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG m 81 " --> pdb=" O GLU m 77 " (cutoff:3.500A) Processing helix chain 'j' and resid 5 through 9 Processing helix chain 'j' and resid 11 through 13 No H-bonds generated for 'chain 'j' and resid 11 through 13' Processing helix chain 'j' and resid 69 through 82 removed outlier: 4.010A pdb=" N LYS j 73 " --> pdb=" O SER j 69 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU j 74 " --> pdb=" O ARG j 70 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE j 75 " --> pdb=" O MET j 71 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLU j 77 " --> pdb=" O LYS j 73 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LYS j 78 " --> pdb=" O LEU j 74 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS j 80 " --> pdb=" O GLY j 76 " (cutoff:3.500A) Processing helix chain 'p' and resid 5 through 9 Processing helix chain 'p' and resid 11 through 13 No H-bonds generated for 'chain 'p' and resid 11 through 13' Processing helix chain 'p' and resid 69 through 82 removed outlier: 3.596A pdb=" N ILE p 75 " --> pdb=" O MET p 71 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N GLU p 77 " --> pdb=" O LYS p 73 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N LYS p 78 " --> pdb=" O LEU p 74 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS p 80 " --> pdb=" O GLY p 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 54 through 66 Processing helix chain 'R' and resid 86 through 96 Processing helix chain 'R' and resid 107 through 125 removed outlier: 3.727A pdb=" N ASP R 123 " --> pdb=" O ILE R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 163 through 174 Processing helix chain 'R' and resid 195 through 205 Processing helix chain 'R' and resid 234 through 238 Processing helix chain 'R' and resid 239 through 261 removed outlier: 3.622A pdb=" N VAL R 243 " --> pdb=" O LYS R 239 " (cutoff:3.500A) Processing helix chain 'R' and resid 268 through 288 removed outlier: 3.634A pdb=" N LYS R 288 " --> pdb=" O GLU R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 301 through 313 Processing helix chain 'R' and resid 320 through 327 removed outlier: 3.705A pdb=" N LYS R 325 " --> pdb=" O LEU R 321 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU R 326 " --> pdb=" O GLN R 322 " (cutoff:3.500A) Processing helix chain 'W' and resid 54 through 66 removed outlier: 3.989A pdb=" N MET W 66 " --> pdb=" O ASN W 62 " (cutoff:3.500A) Processing helix chain 'W' and resid 85 through 96 removed outlier: 4.651A pdb=" N ALA W 89 " --> pdb=" O ASP W 85 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU W 90 " --> pdb=" O ILE W 86 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR W 95 " --> pdb=" O ASP W 91 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS W 96 " --> pdb=" O PHE W 92 " (cutoff:3.500A) Processing helix chain 'W' and resid 107 through 124 removed outlier: 4.324A pdb=" N THR W 112 " --> pdb=" O GLU W 108 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA W 113 " --> pdb=" O ALA W 109 " (cutoff:3.500A) Processing helix chain 'W' and resid 159 through 174 removed outlier: 3.952A pdb=" N SER W 165 " --> pdb=" O ASP W 161 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG W 166 " --> pdb=" O GLU W 162 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR W 174 " --> pdb=" O LEU W 170 " (cutoff:3.500A) Processing helix chain 'W' and resid 195 through 206 removed outlier: 3.756A pdb=" N LYS W 205 " --> pdb=" O SER W 201 " (cutoff:3.500A) Processing helix chain 'W' and resid 235 through 238 Processing helix chain 'W' and resid 239 through 261 removed outlier: 3.637A pdb=" N ASP W 260 " --> pdb=" O VAL W 256 " (cutoff:3.500A) Processing helix chain 'W' and resid 268 through 289 removed outlier: 3.733A pdb=" N SER W 289 " --> pdb=" O GLU W 285 " (cutoff:3.500A) Processing helix chain 'W' and resid 301 through 312 Processing helix chain 'W' and resid 320 through 326 Processing helix chain 'b' and resid 3 through 19 removed outlier: 3.831A pdb=" N ILE b 7 " --> pdb=" O LYS b 3 " (cutoff:3.500A) Processing helix chain 'b' and resid 26 through 33 removed outlier: 3.687A pdb=" N VAL b 30 " --> pdb=" O ASP b 26 " (cutoff:3.500A) Processing helix chain 'b' and resid 72 through 87 removed outlier: 3.637A pdb=" N MET b 76 " --> pdb=" O LYS b 72 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR b 77 " --> pdb=" O SER b 73 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS b 85 " --> pdb=" O ASP b 81 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU b 86 " --> pdb=" O GLU b 82 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE b 87 " --> pdb=" O LEU b 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 54 through 66 Processing helix chain 'O' and resid 84 through 96 removed outlier: 4.519A pdb=" N THR O 88 " --> pdb=" O ALA O 84 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ALA O 89 " --> pdb=" O ASP O 85 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE O 92 " --> pdb=" O THR O 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 107 through 125 removed outlier: 3.634A pdb=" N ASP O 123 " --> pdb=" O ILE O 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 159 through 174 removed outlier: 4.097A pdb=" N SER O 165 " --> pdb=" O ASP O 161 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ARG O 166 " --> pdb=" O GLU O 162 " (cutoff:3.500A) Processing helix chain 'O' and resid 195 through 205 Processing helix chain 'O' and resid 234 through 238 Processing helix chain 'O' and resid 239 through 261 Processing helix chain 'O' and resid 268 through 289 Processing helix chain 'O' and resid 301 through 312 removed outlier: 3.751A pdb=" N GLN O 305 " --> pdb=" O ASP O 301 " (cutoff:3.500A) Processing helix chain 'O' and resid 320 through 327 Processing helix chain 'c' and resid 69 through 82 removed outlier: 3.708A pdb=" N LYS c 73 " --> pdb=" O SER c 69 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU c 74 " --> pdb=" O ARG c 70 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE c 75 " --> pdb=" O MET c 71 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N GLU c 77 " --> pdb=" O LYS c 73 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LYS c 78 " --> pdb=" O LEU c 74 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS c 80 " --> pdb=" O GLY c 76 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG c 81 " --> pdb=" O GLU c 77 " (cutoff:3.500A) Processing helix chain 'Y' and resid 5 through 9 Processing helix chain 'Y' and resid 11 through 13 No H-bonds generated for 'chain 'Y' and resid 11 through 13' Processing helix chain 'Y' and resid 69 through 82 removed outlier: 4.011A pdb=" N LYS Y 73 " --> pdb=" O SER Y 69 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU Y 74 " --> pdb=" O ARG Y 70 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE Y 75 " --> pdb=" O MET Y 71 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N GLU Y 77 " --> pdb=" O LYS Y 73 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LYS Y 78 " --> pdb=" O LEU Y 74 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS Y 80 " --> pdb=" O GLY Y 76 " (cutoff:3.500A) Processing helix chain 'e' and resid 5 through 9 Processing helix chain 'e' and resid 11 through 13 No H-bonds generated for 'chain 'e' and resid 11 through 13' Processing helix chain 'e' and resid 69 through 82 removed outlier: 3.599A pdb=" N ILE e 75 " --> pdb=" O MET e 71 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLU e 77 " --> pdb=" O LYS e 73 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LYS e 78 " --> pdb=" O LEU e 74 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS e 80 " --> pdb=" O GLY e 76 " (cutoff:3.500A) Processing helix chain 'S' and resid 54 through 66 Processing helix chain 'S' and resid 86 through 96 Processing helix chain 'S' and resid 107 through 125 removed outlier: 3.721A pdb=" N ASP S 123 " --> pdb=" O ILE S 119 " (cutoff:3.500A) Processing helix chain 'S' and resid 163 through 174 removed outlier: 3.505A pdb=" N THR S 174 " --> pdb=" O LEU S 170 " (cutoff:3.500A) Processing helix chain 'S' and resid 195 through 205 Processing helix chain 'S' and resid 234 through 238 Processing helix chain 'S' and resid 239 through 261 removed outlier: 3.646A pdb=" N VAL S 243 " --> pdb=" O LYS S 239 " (cutoff:3.500A) Processing helix chain 'S' and resid 268 through 288 removed outlier: 3.641A pdb=" N LYS S 288 " --> pdb=" O GLU S 284 " (cutoff:3.500A) Processing helix chain 'S' and resid 301 through 313 Processing helix chain 'S' and resid 320 through 327 removed outlier: 3.712A pdb=" N LYS S 325 " --> pdb=" O LEU S 321 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU S 326 " --> pdb=" O GLN S 322 " (cutoff:3.500A) Processing helix chain 'T' and resid 54 through 66 removed outlier: 3.994A pdb=" N MET T 66 " --> pdb=" O ASN T 62 " (cutoff:3.500A) Processing helix chain 'T' and resid 85 through 96 removed outlier: 4.644A pdb=" N ALA T 89 " --> pdb=" O ASP T 85 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU T 90 " --> pdb=" O ILE T 86 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR T 95 " --> pdb=" O ASP T 91 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS T 96 " --> pdb=" O PHE T 92 " (cutoff:3.500A) Processing helix chain 'T' and resid 107 through 124 removed outlier: 4.324A pdb=" N THR T 112 " --> pdb=" O GLU T 108 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA T 113 " --> pdb=" O ALA T 109 " (cutoff:3.500A) Processing helix chain 'T' and resid 159 through 174 removed outlier: 3.960A pdb=" N SER T 165 " --> pdb=" O ASP T 161 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG T 166 " --> pdb=" O GLU T 162 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR T 174 " --> pdb=" O LEU T 170 " (cutoff:3.500A) Processing helix chain 'T' and resid 195 through 206 removed outlier: 3.761A pdb=" N LYS T 205 " --> pdb=" O SER T 201 " (cutoff:3.500A) Processing helix chain 'T' and resid 235 through 238 Processing helix chain 'T' and resid 239 through 261 removed outlier: 3.632A pdb=" N ASP T 260 " --> pdb=" O VAL T 256 " (cutoff:3.500A) Processing helix chain 'T' and resid 268 through 289 removed outlier: 3.738A pdb=" N SER T 289 " --> pdb=" O GLU T 285 " (cutoff:3.500A) Processing helix chain 'T' and resid 301 through 312 Processing helix chain 'T' and resid 320 through 326 Processing helix chain 'X' and resid 3 through 19 removed outlier: 3.832A pdb=" N ILE X 7 " --> pdb=" O LYS X 3 " (cutoff:3.500A) Processing helix chain 'X' and resid 26 through 33 removed outlier: 3.683A pdb=" N VAL X 30 " --> pdb=" O ASP X 26 " (cutoff:3.500A) Processing helix chain 'X' and resid 72 through 87 removed outlier: 3.648A pdb=" N MET X 76 " --> pdb=" O LYS X 72 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR X 77 " --> pdb=" O SER X 73 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS X 85 " --> pdb=" O ASP X 81 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU X 86 " --> pdb=" O GLU X 82 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE X 87 " --> pdb=" O LEU X 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 54 through 66 Processing helix chain 'L' and resid 84 through 96 removed outlier: 4.522A pdb=" N THR L 88 " --> pdb=" O ALA L 84 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA L 89 " --> pdb=" O ASP L 85 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE L 92 " --> pdb=" O THR L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 125 removed outlier: 3.628A pdb=" N ASP L 123 " --> pdb=" O ILE L 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 174 removed outlier: 4.105A pdb=" N SER L 165 " --> pdb=" O ASP L 161 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ARG L 166 " --> pdb=" O GLU L 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 205 Processing helix chain 'L' and resid 234 through 238 Processing helix chain 'L' and resid 239 through 261 Processing helix chain 'L' and resid 268 through 289 Processing helix chain 'L' and resid 301 through 312 removed outlier: 3.754A pdb=" N GLN L 305 " --> pdb=" O ASP L 301 " (cutoff:3.500A) Processing helix chain 'L' and resid 320 through 327 Processing sheet with id=AA1, first strand: chain 'h' and resid 22 through 23 removed outlier: 5.778A pdb=" N PHE h 87 " --> pdb=" O ASN h 108 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU h 135 " --> pdb=" O LYS h 107 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ILE h 109 " --> pdb=" O PHE h 133 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE h 133 " --> pdb=" O ILE h 109 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N PHE h 111 " --> pdb=" O PHE h 131 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE h 131 " --> pdb=" O PHE h 111 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE h 133 " --> pdb=" O GLY h 58 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY h 58 " --> pdb=" O PHE h 133 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N GLU h 135 " --> pdb=" O TYR h 56 " (cutoff:3.500A) removed outlier: 12.317A pdb=" N TYR h 56 " --> pdb=" O GLU h 135 " (cutoff:3.500A) removed outlier: 18.850A pdb=" N ASP h 137 " --> pdb=" O MET h 54 " (cutoff:3.500A) removed outlier: 21.938A pdb=" N MET h 54 " --> pdb=" O ASP h 137 " (cutoff:3.500A) removed outlier: 27.053A pdb=" N LEU h 139 " --> pdb=" O LYS h 52 " (cutoff:3.500A) removed outlier: 30.249A pdb=" N LYS h 52 " --> pdb=" O LEU h 139 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N THR h 51 " --> pdb=" O ILE h 41 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE h 41 " --> pdb=" O THR h 51 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N TYR h 53 " --> pdb=" O GLU h 39 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLU h 39 " --> pdb=" O TYR h 53 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY h 55 " --> pdb=" O THR h 37 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA k 117 " --> pdb=" O ALA h 32 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N MET h 34 " --> pdb=" O THR k 115 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N THR k 115 " --> pdb=" O MET h 34 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N PHE h 36 " --> pdb=" O ASP k 113 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ASP k 113 " --> pdb=" O PHE h 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'h' and resid 113 through 120 removed outlier: 6.330A pdb=" N ASP h 113 " --> pdb=" O PHE c 36 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE c 36 " --> pdb=" O ASP h 113 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N THR h 115 " --> pdb=" O MET c 34 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N MET c 34 " --> pdb=" O THR h 115 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA h 117 " --> pdb=" O ALA c 32 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE c 30 " --> pdb=" O TRP h 119 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY c 55 " --> pdb=" O THR c 37 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLU c 39 " --> pdb=" O TYR c 53 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N TYR c 53 " --> pdb=" O GLU c 39 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE c 41 " --> pdb=" O THR c 51 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N THR c 51 " --> pdb=" O ILE c 41 " (cutoff:3.500A) removed outlier: 30.244A pdb=" N LYS c 52 " --> pdb=" O LEU c 139 " (cutoff:3.500A) removed outlier: 27.044A pdb=" N LEU c 139 " --> pdb=" O LYS c 52 " (cutoff:3.500A) removed outlier: 21.911A pdb=" N MET c 54 " --> pdb=" O ASP c 137 " (cutoff:3.500A) removed outlier: 18.873A pdb=" N ASP c 137 " --> pdb=" O MET c 54 " (cutoff:3.500A) removed outlier: 12.321A pdb=" N TYR c 56 " --> pdb=" O GLU c 135 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N GLU c 135 " --> pdb=" O TYR c 56 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY c 58 " --> pdb=" O PHE c 133 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE c 133 " --> pdb=" O GLY c 58 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE c 131 " --> pdb=" O PHE c 111 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N PHE c 111 " --> pdb=" O PHE c 131 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N PHE c 133 " --> pdb=" O ILE c 109 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE c 109 " --> pdb=" O PHE c 133 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU c 135 " --> pdb=" O LYS c 107 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU c 102 " --> pdb=" O LEU c 93 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N PHE c 87 " --> pdb=" O ASN c 108 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'd' and resid 15 through 19 removed outlier: 4.617A pdb=" N LEU d 17 " --> pdb=" O VAL d 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 22 through 24 current: chain 'd' and resid 50 through 65 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 50 through 65 current: chain 'd' and resid 102 through 111 Processing sheet with id=AA4, first strand: chain 'd' and resid 113 through 120 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 113 through 120 current: chain 'Y' and resid 22 through 24 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 22 through 24 current: chain 'Y' and resid 50 through 65 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 50 through 65 current: chain 'Y' and resid 102 through 111 Processing sheet with id=AA5, first strand: chain 'i' and resid 15 through 19 removed outlier: 4.416A pdb=" N LEU i 17 " --> pdb=" O VAL i 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'i' and resid 22 through 24 current: chain 'i' and resid 50 through 65 WARNING: can't find start of bonding for strands! previous: chain 'i' and resid 50 through 65 current: chain 'i' and resid 102 through 111 Processing sheet with id=AA6, first strand: chain 'i' and resid 113 through 120 WARNING: can't find start of bonding for strands! previous: chain 'i' and resid 113 through 120 current: chain 'e' and resid 22 through 24 WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 22 through 24 current: chain 'e' and resid 50 through 65 WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 50 through 65 current: chain 'e' and resid 102 through 111 Processing sheet with id=AA7, first strand: chain 'C' and resid 8 through 13 removed outlier: 3.515A pdb=" N ASN C 9 " --> pdb=" O ILE S 348 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR L 297 " --> pdb=" O LYS L 338 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 39 through 40 removed outlier: 3.553A pdb=" N TYR C 100 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N CYS C 102 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL C 31 " --> pdb=" O CYS C 102 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 131 through 133 Processing sheet with id=AB1, first strand: chain 'C' and resid 157 through 158 removed outlier: 7.449A pdb=" N LEU C 152 " --> pdb=" O VAL C 189 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 210 through 213 removed outlier: 3.634A pdb=" N ILE C 211 " --> pdb=" O ARG C 218 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU C 213 " --> pdb=" O ALA C 216 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA C 216 " --> pdb=" O GLU C 213 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.278A pdb=" N VAL C 333 " --> pdb=" O ASP F 349 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N SER F 351 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU C 335 " --> pdb=" O SER F 351 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N GLU F 353 " --> pdb=" O LEU C 335 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ALA C 337 " --> pdb=" O GLU F 353 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN U 9 " --> pdb=" O ILE F 348 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 297 through 299 removed outlier: 3.570A pdb=" N THR B 297 " --> pdb=" O LYS B 338 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE C 348 " --> pdb=" O ASN P 9 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N SER P 11 " --> pdb=" O ILE C 348 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LEU C 350 " --> pdb=" O SER P 11 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N LYS P 13 " --> pdb=" O LEU C 350 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ILE C 352 " --> pdb=" O LYS P 13 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 8 through 13 removed outlier: 6.189A pdb=" N ASN F 9 " --> pdb=" O LEU T 350 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE T 352 " --> pdb=" O ASN F 9 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N SER F 11 " --> pdb=" O ILE T 352 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL S 333 " --> pdb=" O ASP T 349 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N SER T 351 " --> pdb=" O VAL S 333 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU S 335 " --> pdb=" O SER T 351 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N GLU T 353 " --> pdb=" O LEU S 335 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ALA S 337 " --> pdb=" O GLU T 353 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 39 through 40 removed outlier: 5.975A pdb=" N ILE F 28 " --> pdb=" O LEU F 76 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N TYR F 78 " --> pdb=" O ILE F 28 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N MET F 30 " --> pdb=" O TYR F 78 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE F 80 " --> pdb=" O MET F 30 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LEU F 32 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL F 31 " --> pdb=" O CYS F 102 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU F 101 " --> pdb=" O VAL F 132 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ALA F 131 " --> pdb=" O ILE F 144 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 209 through 213 removed outlier: 4.790A pdb=" N ILE F 209 " --> pdb=" O ALA F 220 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA F 220 " --> pdb=" O ILE F 209 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU F 213 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA F 216 " --> pdb=" O GLU F 213 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 297 through 300 removed outlier: 6.826A pdb=" N LEU F 335 " --> pdb=" O ASN I 144 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 23 through 24 removed outlier: 3.534A pdb=" N VAL I 40 " --> pdb=" O PHE I 24 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE I 38 " --> pdb=" O LEU I 66 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU I 66 " --> pdb=" O PHE I 38 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N VAL I 40 " --> pdb=" O LYS I 64 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LYS I 64 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ILE I 42 " --> pdb=" O SER I 62 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N SER I 62 " --> pdb=" O ILE I 42 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER I 44 " --> pdb=" O VAL I 60 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 54 through 66 current: chain 'I' and resid 96 through 110 removed outlier: 14.042A pdb=" N ARG I 96 " --> pdb=" O SER I 127 " (cutoff:3.500A) removed outlier: 12.744A pdb=" N SER I 127 " --> pdb=" O ARG I 96 " (cutoff:3.500A) removed outlier: 9.764A pdb=" N LEU I 98 " --> pdb=" O LEU I 125 " (cutoff:3.500A) removed outlier: 9.922A pdb=" N LEU I 125 " --> pdb=" O LEU I 98 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE I 100 " --> pdb=" O ASN I 123 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ASN I 123 " --> pdb=" O ILE I 100 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS I 102 " --> pdb=" O THR I 121 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS I 108 " --> pdb=" O VAL I 115 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 113 through 127 current: chain 'Z' and resid 37 through 49 removed outlier: 6.200A pdb=" N PHE Z 38 " --> pdb=" O LEU Z 66 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU Z 66 " --> pdb=" O PHE Z 38 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N VAL Z 40 " --> pdb=" O LYS Z 64 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LYS Z 64 " --> pdb=" O VAL Z 40 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ILE Z 42 " --> pdb=" O SER Z 62 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N SER Z 62 " --> pdb=" O ILE Z 42 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER Z 44 " --> pdb=" O VAL Z 60 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 54 through 66 current: chain 'Z' and resid 96 through 110 removed outlier: 14.041A pdb=" N ARG Z 96 " --> pdb=" O SER Z 127 " (cutoff:3.500A) removed outlier: 12.724A pdb=" N SER Z 127 " --> pdb=" O ARG Z 96 " (cutoff:3.500A) removed outlier: 9.754A pdb=" N LEU Z 98 " --> pdb=" O LEU Z 125 " (cutoff:3.500A) removed outlier: 9.901A pdb=" N LEU Z 125 " --> pdb=" O LEU Z 98 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ILE Z 100 " --> pdb=" O ASN Z 123 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ASN Z 123 " --> pdb=" O ILE Z 100 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYS Z 102 " --> pdb=" O THR Z 121 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS Z 108 " --> pdb=" O VAL Z 115 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 113 through 127 current: chain 'a' and resid 37 through 49 removed outlier: 6.194A pdb=" N PHE a 38 " --> pdb=" O LEU a 66 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU a 66 " --> pdb=" O PHE a 38 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL a 40 " --> pdb=" O LYS a 64 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LYS a 64 " --> pdb=" O VAL a 40 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ILE a 42 " --> pdb=" O SER a 62 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N SER a 62 " --> pdb=" O ILE a 42 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER a 44 " --> pdb=" O VAL a 60 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 54 through 66 current: chain 'a' and resid 96 through 110 removed outlier: 14.048A pdb=" N ARG a 96 " --> pdb=" O SER a 127 " (cutoff:3.500A) removed outlier: 12.738A pdb=" N SER a 127 " --> pdb=" O ARG a 96 " (cutoff:3.500A) removed outlier: 9.764A pdb=" N LEU a 98 " --> pdb=" O LEU a 125 " (cutoff:3.500A) removed outlier: 9.916A pdb=" N LEU a 125 " --> pdb=" O LEU a 98 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE a 100 " --> pdb=" O ASN a 123 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ASN a 123 " --> pdb=" O ILE a 100 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS a 102 " --> pdb=" O THR a 121 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS a 108 " --> pdb=" O VAL a 115 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 113 through 127 current: chain 'G' and resid 37 through 49 removed outlier: 6.197A pdb=" N PHE G 38 " --> pdb=" O LEU G 66 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU G 66 " --> pdb=" O PHE G 38 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL G 40 " --> pdb=" O LYS G 64 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LYS G 64 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ILE G 42 " --> pdb=" O SER G 62 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N SER G 62 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER G 44 " --> pdb=" O VAL G 60 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 54 through 66 current: chain 'G' and resid 96 through 110 removed outlier: 14.041A pdb=" N ARG G 96 " --> pdb=" O SER G 127 " (cutoff:3.500A) removed outlier: 12.741A pdb=" N SER G 127 " --> pdb=" O ARG G 96 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N LEU G 98 " --> pdb=" O LEU G 125 " (cutoff:3.500A) removed outlier: 9.918A pdb=" N LEU G 125 " --> pdb=" O LEU G 98 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ILE G 100 " --> pdb=" O ASN G 123 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ASN G 123 " --> pdb=" O ILE G 100 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS G 102 " --> pdb=" O THR G 121 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS G 108 " --> pdb=" O VAL G 115 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 113 through 127 current: chain 'b' and resid 37 through 49 removed outlier: 6.201A pdb=" N PHE b 38 " --> pdb=" O LEU b 66 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU b 66 " --> pdb=" O PHE b 38 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N VAL b 40 " --> pdb=" O LYS b 64 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LYS b 64 " --> pdb=" O VAL b 40 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ILE b 42 " --> pdb=" O SER b 62 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N SER b 62 " --> pdb=" O ILE b 42 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER b 44 " --> pdb=" O VAL b 60 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 54 through 66 current: chain 'b' and resid 96 through 110 removed outlier: 14.039A pdb=" N ARG b 96 " --> pdb=" O SER b 127 " (cutoff:3.500A) removed outlier: 12.722A pdb=" N SER b 127 " --> pdb=" O ARG b 96 " (cutoff:3.500A) removed outlier: 9.757A pdb=" N LEU b 98 " --> pdb=" O LEU b 125 " (cutoff:3.500A) removed outlier: 9.901A pdb=" N LEU b 125 " --> pdb=" O LEU b 98 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ILE b 100 " --> pdb=" O ASN b 123 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ASN b 123 " --> pdb=" O ILE b 100 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LYS b 102 " --> pdb=" O THR b 121 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS b 108 " --> pdb=" O VAL b 115 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 113 through 127 current: chain 'X' and resid 37 through 49 removed outlier: 6.192A pdb=" N PHE X 38 " --> pdb=" O LEU X 66 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU X 66 " --> pdb=" O PHE X 38 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL X 40 " --> pdb=" O LYS X 64 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LYS X 64 " --> pdb=" O VAL X 40 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ILE X 42 " --> pdb=" O SER X 62 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N SER X 62 " --> pdb=" O ILE X 42 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER X 44 " --> pdb=" O VAL X 60 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 54 through 66 current: chain 'X' and resid 96 through 110 removed outlier: 14.045A pdb=" N ARG X 96 " --> pdb=" O SER X 127 " (cutoff:3.500A) removed outlier: 12.733A pdb=" N SER X 127 " --> pdb=" O ARG X 96 " (cutoff:3.500A) removed outlier: 9.760A pdb=" N LEU X 98 " --> pdb=" O LEU X 125 " (cutoff:3.500A) removed outlier: 9.912A pdb=" N LEU X 125 " --> pdb=" O LEU X 98 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE X 100 " --> pdb=" O ASN X 123 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ASN X 123 " --> pdb=" O ILE X 100 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYS X 102 " --> pdb=" O THR X 121 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS X 108 " --> pdb=" O VAL X 115 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 8 through 13 removed outlier: 6.309A pdb=" N ASN B 9 " --> pdb=" O LEU L 350 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ILE L 352 " --> pdb=" O ASN B 9 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N SER B 11 " --> pdb=" O ILE L 352 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 39 through 40 removed outlier: 3.706A pdb=" N TYR B 100 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS B 102 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU B 101 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA B 131 " --> pdb=" O ILE B 144 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 157 through 158 removed outlier: 3.549A pdb=" N VAL B 151 " --> pdb=" O TYR B 158 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N LEU B 152 " --> pdb=" O VAL B 189 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 210 through 212 removed outlier: 3.565A pdb=" N ILE B 211 " --> pdb=" O ARG B 218 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 348 through 353 removed outlier: 3.689A pdb=" N ASN M 9 " --> pdb=" O ILE B 348 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 350 " --> pdb=" O ASN M 9 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'k' and resid 22 through 23 removed outlier: 5.786A pdb=" N PHE k 87 " --> pdb=" O ASN k 108 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU k 102 " --> pdb=" O LEU k 93 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU k 135 " --> pdb=" O LYS k 107 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ILE k 109 " --> pdb=" O PHE k 133 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE k 133 " --> pdb=" O ILE k 109 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N PHE k 111 " --> pdb=" O PHE k 131 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE k 131 " --> pdb=" O PHE k 111 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE k 133 " --> pdb=" O GLY k 58 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY k 58 " --> pdb=" O PHE k 133 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N GLU k 135 " --> pdb=" O TYR k 56 " (cutoff:3.500A) removed outlier: 12.304A pdb=" N TYR k 56 " --> pdb=" O GLU k 135 " (cutoff:3.500A) removed outlier: 18.832A pdb=" N ASP k 137 " --> pdb=" O MET k 54 " (cutoff:3.500A) removed outlier: 21.905A pdb=" N MET k 54 " --> pdb=" O ASP k 137 " (cutoff:3.500A) removed outlier: 27.044A pdb=" N LEU k 139 " --> pdb=" O LYS k 52 " (cutoff:3.500A) removed outlier: 30.243A pdb=" N LYS k 52 " --> pdb=" O LEU k 139 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N THR k 51 " --> pdb=" O ILE k 41 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE k 41 " --> pdb=" O THR k 51 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N TYR k 53 " --> pdb=" O GLU k 39 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLU k 39 " --> pdb=" O TYR k 53 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY k 55 " --> pdb=" O THR k 37 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA l 117 " --> pdb=" O ALA k 32 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N MET k 34 " --> pdb=" O THR l 115 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N THR l 115 " --> pdb=" O MET k 34 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N PHE k 36 " --> pdb=" O ASP l 113 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASP l 113 " --> pdb=" O PHE k 36 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'f' and resid 15 through 19 removed outlier: 4.617A pdb=" N LEU f 17 " --> pdb=" O VAL f 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 22 through 24 current: chain 'f' and resid 50 through 65 WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 50 through 65 current: chain 'f' and resid 102 through 111 Processing sheet with id=AC8, first strand: chain 'n' and resid 15 through 19 removed outlier: 4.434A pdb=" N LEU n 17 " --> pdb=" O VAL n 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'n' and resid 22 through 24 current: chain 'n' and resid 50 through 65 WARNING: can't find start of bonding for strands! previous: chain 'n' and resid 50 through 65 current: chain 'n' and resid 102 through 111 Processing sheet with id=AC9, first strand: chain 'P' and resid 39 through 40 removed outlier: 3.556A pdb=" N TYR P 100 " --> pdb=" O ILE P 27 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N CYS P 102 " --> pdb=" O ALA P 29 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL P 31 " --> pdb=" O CYS P 102 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'P' and resid 131 through 133 Processing sheet with id=AD2, first strand: chain 'P' and resid 157 through 158 removed outlier: 7.417A pdb=" N LEU P 152 " --> pdb=" O VAL P 189 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 210 through 213 removed outlier: 3.637A pdb=" N ILE P 211 " --> pdb=" O ARG P 218 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU P 213 " --> pdb=" O ALA P 216 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA P 216 " --> pdb=" O GLU P 213 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 297 through 300 removed outlier: 6.279A pdb=" N VAL P 333 " --> pdb=" O ASP U 349 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N SER U 351 " --> pdb=" O VAL P 333 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU P 335 " --> pdb=" O SER U 351 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N GLU U 353 " --> pdb=" O LEU P 335 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ALA P 337 " --> pdb=" O GLU U 353 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN V 9 " --> pdb=" O ILE U 348 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 297 through 300 removed outlier: 3.572A pdb=" N THR M 297 " --> pdb=" O LYS M 338 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE P 348 " --> pdb=" O ASN Q 9 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N SER Q 11 " --> pdb=" O ILE P 348 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LEU P 350 " --> pdb=" O SER Q 11 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N LYS Q 13 " --> pdb=" O LEU P 350 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ILE P 352 " --> pdb=" O LYS Q 13 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'U' and resid 39 through 40 removed outlier: 5.971A pdb=" N ILE U 28 " --> pdb=" O LEU U 76 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N TYR U 78 " --> pdb=" O ILE U 28 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N MET U 30 " --> pdb=" O TYR U 78 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ILE U 80 " --> pdb=" O MET U 30 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU U 32 " --> pdb=" O ILE U 80 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL U 31 " --> pdb=" O CYS U 102 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU U 101 " --> pdb=" O VAL U 132 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ALA U 131 " --> pdb=" O ILE U 144 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'U' and resid 209 through 213 removed outlier: 4.783A pdb=" N ILE U 209 " --> pdb=" O ALA U 220 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA U 220 " --> pdb=" O ILE U 209 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU U 213 " --> pdb=" O ALA U 216 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA U 216 " --> pdb=" O GLU U 213 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'U' and resid 297 through 300 removed outlier: 6.817A pdb=" N LEU U 335 " --> pdb=" O ASN Z 144 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 39 through 40 removed outlier: 3.708A pdb=" N TYR M 100 " --> pdb=" O ILE M 27 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS M 102 " --> pdb=" O ALA M 29 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU M 101 " --> pdb=" O VAL M 132 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA M 131 " --> pdb=" O ILE M 144 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 157 through 158 removed outlier: 3.582A pdb=" N VAL M 151 " --> pdb=" O TYR M 158 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LEU M 152 " --> pdb=" O VAL M 189 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 183 through 184 removed outlier: 3.796A pdb=" N THR M 183 " --> pdb=" O ILE M 219 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG M 218 " --> pdb=" O ILE M 211 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE M 211 " --> pdb=" O ARG M 218 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 348 through 353 removed outlier: 3.713A pdb=" N ASN N 9 " --> pdb=" O ILE M 348 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU M 350 " --> pdb=" O ASN N 9 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'l' and resid 22 through 23 removed outlier: 5.799A pdb=" N PHE l 87 " --> pdb=" O ASN l 108 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU l 102 " --> pdb=" O LEU l 93 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU l 135 " --> pdb=" O LYS l 107 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE l 109 " --> pdb=" O PHE l 133 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N PHE l 133 " --> pdb=" O ILE l 109 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N PHE l 111 " --> pdb=" O PHE l 131 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE l 131 " --> pdb=" O PHE l 111 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE l 133 " --> pdb=" O GLY l 58 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY l 58 " --> pdb=" O PHE l 133 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N GLU l 135 " --> pdb=" O TYR l 56 " (cutoff:3.500A) removed outlier: 12.320A pdb=" N TYR l 56 " --> pdb=" O GLU l 135 " (cutoff:3.500A) removed outlier: 18.881A pdb=" N ASP l 137 " --> pdb=" O MET l 54 " (cutoff:3.500A) removed outlier: 21.915A pdb=" N MET l 54 " --> pdb=" O ASP l 137 " (cutoff:3.500A) removed outlier: 27.037A pdb=" N LEU l 139 " --> pdb=" O LYS l 52 " (cutoff:3.500A) removed outlier: 30.235A pdb=" N LYS l 52 " --> pdb=" O LEU l 139 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N THR l 51 " --> pdb=" O ILE l 41 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE l 41 " --> pdb=" O THR l 51 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N TYR l 53 " --> pdb=" O GLU l 39 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLU l 39 " --> pdb=" O TYR l 53 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY l 55 " --> pdb=" O THR l 37 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE l 30 " --> pdb=" O TRP J 119 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA J 117 " --> pdb=" O ALA l 32 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N MET l 34 " --> pdb=" O THR J 115 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N THR J 115 " --> pdb=" O MET l 34 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N PHE l 36 " --> pdb=" O ASP J 113 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP J 113 " --> pdb=" O PHE l 36 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'g' and resid 15 through 19 removed outlier: 4.630A pdb=" N LEU g 17 " --> pdb=" O VAL g 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'g' and resid 22 through 24 current: chain 'g' and resid 50 through 65 WARNING: can't find start of bonding for strands! previous: chain 'g' and resid 50 through 65 current: chain 'g' and resid 102 through 111 Processing sheet with id=AE6, first strand: chain 'o' and resid 15 through 19 removed outlier: 4.411A pdb=" N LEU o 17 " --> pdb=" O VAL o 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'o' and resid 22 through 24 current: chain 'o' and resid 50 through 65 WARNING: can't find start of bonding for strands! previous: chain 'o' and resid 50 through 65 current: chain 'o' and resid 102 through 111 Processing sheet with id=AE7, first strand: chain 'Q' and resid 39 through 40 removed outlier: 3.558A pdb=" N TYR Q 100 " --> pdb=" O ILE Q 27 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N CYS Q 102 " --> pdb=" O ALA Q 29 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL Q 31 " --> pdb=" O CYS Q 102 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 131 through 133 Processing sheet with id=AE9, first strand: chain 'Q' and resid 157 through 158 removed outlier: 7.402A pdb=" N LEU Q 152 " --> pdb=" O VAL Q 189 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL Q 189 " --> pdb=" O LEU Q 152 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Q' and resid 210 through 213 removed outlier: 3.637A pdb=" N ILE Q 211 " --> pdb=" O ARG Q 218 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU Q 213 " --> pdb=" O ALA Q 216 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA Q 216 " --> pdb=" O GLU Q 213 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Q' and resid 297 through 300 removed outlier: 6.281A pdb=" N VAL Q 333 " --> pdb=" O ASP V 349 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N SER V 351 " --> pdb=" O VAL Q 333 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU Q 335 " --> pdb=" O SER V 351 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N GLU V 353 " --> pdb=" O LEU Q 335 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ALA Q 337 " --> pdb=" O GLU V 353 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN E 9 " --> pdb=" O ILE V 348 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 297 through 300 removed outlier: 3.584A pdb=" N THR N 297 " --> pdb=" O LYS N 338 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE Q 348 " --> pdb=" O ASN D 9 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N SER D 11 " --> pdb=" O ILE Q 348 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LEU Q 350 " --> pdb=" O SER D 11 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N LYS D 13 " --> pdb=" O LEU Q 350 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ILE Q 352 " --> pdb=" O LYS D 13 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'V' and resid 39 through 40 removed outlier: 5.981A pdb=" N ILE V 28 " --> pdb=" O LEU V 76 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N TYR V 78 " --> pdb=" O ILE V 28 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N MET V 30 " --> pdb=" O TYR V 78 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE V 80 " --> pdb=" O MET V 30 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N LEU V 32 " --> pdb=" O ILE V 80 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL V 31 " --> pdb=" O CYS V 102 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU V 101 " --> pdb=" O VAL V 132 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ALA V 131 " --> pdb=" O ILE V 144 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'V' and resid 209 through 213 removed outlier: 4.784A pdb=" N ILE V 209 " --> pdb=" O ALA V 220 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA V 220 " --> pdb=" O ILE V 209 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU V 213 " --> pdb=" O ALA V 216 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA V 216 " --> pdb=" O GLU V 213 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'V' and resid 297 through 300 removed outlier: 6.816A pdb=" N LEU V 335 " --> pdb=" O ASN a 144 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 39 through 40 removed outlier: 3.704A pdb=" N TYR N 100 " --> pdb=" O ILE N 27 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS N 102 " --> pdb=" O ALA N 29 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU N 101 " --> pdb=" O VAL N 132 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ALA N 131 " --> pdb=" O ILE N 144 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'N' and resid 157 through 158 removed outlier: 3.559A pdb=" N VAL N 151 " --> pdb=" O TYR N 158 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LEU N 152 " --> pdb=" O VAL N 189 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'N' and resid 183 through 184 removed outlier: 3.797A pdb=" N THR N 183 " --> pdb=" O ILE N 219 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG N 218 " --> pdb=" O ILE N 211 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE N 211 " --> pdb=" O ARG N 218 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'N' and resid 348 through 353 removed outlier: 3.686A pdb=" N ASN A 9 " --> pdb=" O ILE N 348 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU N 350 " --> pdb=" O ASN A 9 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 22 through 23 removed outlier: 5.786A pdb=" N PHE J 87 " --> pdb=" O ASN J 108 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU J 135 " --> pdb=" O LYS J 107 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE J 109 " --> pdb=" O PHE J 133 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N PHE J 133 " --> pdb=" O ILE J 109 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE J 111 " --> pdb=" O PHE J 131 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N PHE J 131 " --> pdb=" O PHE J 111 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE J 133 " --> pdb=" O GLY J 58 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY J 58 " --> pdb=" O PHE J 133 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N GLU J 135 " --> pdb=" O TYR J 56 " (cutoff:3.500A) removed outlier: 12.297A pdb=" N TYR J 56 " --> pdb=" O GLU J 135 " (cutoff:3.500A) removed outlier: 18.838A pdb=" N ASP J 137 " --> pdb=" O MET J 54 " (cutoff:3.500A) removed outlier: 21.933A pdb=" N MET J 54 " --> pdb=" O ASP J 137 " (cutoff:3.500A) removed outlier: 27.055A pdb=" N LEU J 139 " --> pdb=" O LYS J 52 " (cutoff:3.500A) removed outlier: 30.246A pdb=" N LYS J 52 " --> pdb=" O LEU J 139 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N THR J 51 " --> pdb=" O ILE J 41 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE J 41 " --> pdb=" O THR J 51 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N TYR J 53 " --> pdb=" O GLU J 39 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLU J 39 " --> pdb=" O TYR J 53 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY J 55 " --> pdb=" O THR J 37 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA m 117 " --> pdb=" O ALA J 32 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N MET J 34 " --> pdb=" O THR m 115 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N THR m 115 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N PHE J 36 " --> pdb=" O ASP m 113 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ASP m 113 " --> pdb=" O PHE J 36 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 15 through 19 removed outlier: 4.612A pdb=" N LEU H 17 " --> pdb=" O VAL H 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 22 through 24 current: chain 'H' and resid 50 through 65 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 50 through 65 current: chain 'H' and resid 102 through 111 Processing sheet with id=AG4, first strand: chain 'K' and resid 15 through 19 removed outlier: 4.435A pdb=" N LEU K 17 " --> pdb=" O VAL K 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 22 through 24 current: chain 'K' and resid 50 through 65 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 50 through 65 current: chain 'K' and resid 102 through 111 Processing sheet with id=AG5, first strand: chain 'D' and resid 39 through 40 removed outlier: 3.552A pdb=" N TYR D 100 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N CYS D 102 " --> pdb=" O ALA D 29 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL D 31 " --> pdb=" O CYS D 102 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 131 through 133 Processing sheet with id=AG7, first strand: chain 'D' and resid 157 through 158 removed outlier: 7.451A pdb=" N LEU D 152 " --> pdb=" O VAL D 189 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'D' and resid 210 through 213 removed outlier: 3.633A pdb=" N ILE D 211 " --> pdb=" O ARG D 218 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU D 213 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA D 216 " --> pdb=" O GLU D 213 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.279A pdb=" N VAL D 333 " --> pdb=" O ASP E 349 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER E 351 " --> pdb=" O VAL D 333 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU D 335 " --> pdb=" O SER E 351 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N GLU E 353 " --> pdb=" O LEU D 335 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ALA D 337 " --> pdb=" O GLU E 353 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN W 9 " --> pdb=" O ILE E 348 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'A' and resid 297 through 299 removed outlier: 3.576A pdb=" N THR A 297 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE D 348 " --> pdb=" O ASN R 9 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N SER R 11 " --> pdb=" O ILE D 348 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU D 350 " --> pdb=" O SER R 11 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N LYS R 13 " --> pdb=" O LEU D 350 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ILE D 352 " --> pdb=" O LYS R 13 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'E' and resid 39 through 40 removed outlier: 5.974A pdb=" N ILE E 28 " --> pdb=" O LEU E 76 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N TYR E 78 " --> pdb=" O ILE E 28 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N MET E 30 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE E 80 " --> pdb=" O MET E 30 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N LEU E 32 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL E 31 " --> pdb=" O CYS E 102 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU E 101 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ALA E 131 " --> pdb=" O ILE E 144 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 209 through 213 removed outlier: 4.788A pdb=" N ILE E 209 " --> pdb=" O ALA E 220 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA E 220 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU E 213 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA E 216 " --> pdb=" O GLU E 213 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.831A pdb=" N LEU E 335 " --> pdb=" O ASN G 144 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'A' and resid 39 through 40 removed outlier: 3.703A pdb=" N TYR A 100 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N CYS A 102 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU A 101 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA A 131 " --> pdb=" O ILE A 144 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'A' and resid 157 through 158 removed outlier: 3.551A pdb=" N VAL A 151 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N LEU A 152 " --> pdb=" O VAL A 189 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'A' and resid 210 through 212 removed outlier: 3.566A pdb=" N ILE A 211 " --> pdb=" O ARG A 218 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 218 " --> pdb=" O ILE A 211 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'A' and resid 348 through 353 removed outlier: 3.712A pdb=" N ASN O 9 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 350 " --> pdb=" O ASN O 9 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'm' and resid 22 through 23 removed outlier: 5.784A pdb=" N PHE m 87 " --> pdb=" O ASN m 108 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU m 102 " --> pdb=" O LEU m 93 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU m 135 " --> pdb=" O LYS m 107 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE m 109 " --> pdb=" O PHE m 133 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N PHE m 133 " --> pdb=" O ILE m 109 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N PHE m 111 " --> pdb=" O PHE m 131 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE m 131 " --> pdb=" O PHE m 111 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE m 133 " --> pdb=" O GLY m 58 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY m 58 " --> pdb=" O PHE m 133 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N GLU m 135 " --> pdb=" O TYR m 56 " (cutoff:3.500A) removed outlier: 12.302A pdb=" N TYR m 56 " --> pdb=" O GLU m 135 " (cutoff:3.500A) removed outlier: 18.831A pdb=" N ASP m 137 " --> pdb=" O MET m 54 " (cutoff:3.500A) removed outlier: 21.906A pdb=" N MET m 54 " --> pdb=" O ASP m 137 " (cutoff:3.500A) removed outlier: 27.039A pdb=" N LEU m 139 " --> pdb=" O LYS m 52 " (cutoff:3.500A) removed outlier: 30.242A pdb=" N LYS m 52 " --> pdb=" O LEU m 139 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N THR m 51 " --> pdb=" O ILE m 41 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE m 41 " --> pdb=" O THR m 51 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N TYR m 53 " --> pdb=" O GLU m 39 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLU m 39 " --> pdb=" O TYR m 53 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY m 55 " --> pdb=" O THR m 37 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA c 117 " --> pdb=" O ALA m 32 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N MET m 34 " --> pdb=" O THR c 115 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N THR c 115 " --> pdb=" O MET m 34 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE m 36 " --> pdb=" O ASP c 113 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASP c 113 " --> pdb=" O PHE m 36 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'j' and resid 15 through 19 removed outlier: 4.615A pdb=" N LEU j 17 " --> pdb=" O VAL j 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'j' and resid 22 through 24 current: chain 'j' and resid 50 through 65 WARNING: can't find start of bonding for strands! previous: chain 'j' and resid 50 through 65 current: chain 'j' and resid 102 through 111 Processing sheet with id=AI2, first strand: chain 'p' and resid 15 through 19 removed outlier: 4.432A pdb=" N LEU p 17 " --> pdb=" O VAL p 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'p' and resid 22 through 24 current: chain 'p' and resid 50 through 65 WARNING: can't find start of bonding for strands! previous: chain 'p' and resid 50 through 65 current: chain 'p' and resid 102 through 111 Processing sheet with id=AI3, first strand: chain 'R' and resid 39 through 40 removed outlier: 3.559A pdb=" N TYR R 100 " --> pdb=" O ILE R 27 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N CYS R 102 " --> pdb=" O ALA R 29 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL R 31 " --> pdb=" O CYS R 102 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'R' and resid 131 through 133 Processing sheet with id=AI5, first strand: chain 'R' and resid 157 through 158 removed outlier: 7.418A pdb=" N LEU R 152 " --> pdb=" O VAL R 189 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'R' and resid 210 through 213 removed outlier: 3.642A pdb=" N ILE R 211 " --> pdb=" O ARG R 218 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU R 213 " --> pdb=" O ALA R 216 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA R 216 " --> pdb=" O GLU R 213 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'R' and resid 297 through 300 removed outlier: 6.280A pdb=" N VAL R 333 " --> pdb=" O ASP W 349 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N SER W 351 " --> pdb=" O VAL R 333 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU R 335 " --> pdb=" O SER W 351 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N GLU W 353 " --> pdb=" O LEU R 335 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ALA R 337 " --> pdb=" O GLU W 353 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN T 9 " --> pdb=" O ILE W 348 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'O' and resid 297 through 299 removed outlier: 3.573A pdb=" N THR O 297 " --> pdb=" O LYS O 338 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE R 348 " --> pdb=" O ASN S 9 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N SER S 11 " --> pdb=" O ILE R 348 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU R 350 " --> pdb=" O SER S 11 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N LYS S 13 " --> pdb=" O LEU R 350 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE R 352 " --> pdb=" O LYS S 13 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'W' and resid 39 through 40 removed outlier: 5.969A pdb=" N ILE W 28 " --> pdb=" O LEU W 76 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N TYR W 78 " --> pdb=" O ILE W 28 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N MET W 30 " --> pdb=" O TYR W 78 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE W 80 " --> pdb=" O MET W 30 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU W 32 " --> pdb=" O ILE W 80 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL W 31 " --> pdb=" O CYS W 102 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU W 101 " --> pdb=" O VAL W 132 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ALA W 131 " --> pdb=" O ILE W 144 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'W' and resid 209 through 213 removed outlier: 4.788A pdb=" N ILE W 209 " --> pdb=" O ALA W 220 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA W 220 " --> pdb=" O ILE W 209 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU W 213 " --> pdb=" O ALA W 216 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA W 216 " --> pdb=" O GLU W 213 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'W' and resid 297 through 300 removed outlier: 6.819A pdb=" N LEU W 335 " --> pdb=" O ASN b 144 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'O' and resid 39 through 40 removed outlier: 3.707A pdb=" N TYR O 100 " --> pdb=" O ILE O 27 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS O 102 " --> pdb=" O ALA O 29 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU O 101 " --> pdb=" O VAL O 132 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA O 131 " --> pdb=" O ILE O 144 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'O' and resid 157 through 158 removed outlier: 3.575A pdb=" N VAL O 151 " --> pdb=" O TYR O 158 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LEU O 152 " --> pdb=" O VAL O 189 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'O' and resid 183 through 184 removed outlier: 3.792A pdb=" N THR O 183 " --> pdb=" O ILE O 219 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG O 218 " --> pdb=" O ILE O 211 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE O 211 " --> pdb=" O ARG O 218 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'O' and resid 348 through 353 removed outlier: 3.685A pdb=" N ASN L 9 " --> pdb=" O ILE O 348 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU O 350 " --> pdb=" O ASN L 9 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'S' and resid 39 through 40 removed outlier: 3.555A pdb=" N TYR S 100 " --> pdb=" O ILE S 27 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N CYS S 102 " --> pdb=" O ALA S 29 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL S 31 " --> pdb=" O CYS S 102 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'S' and resid 131 through 133 Processing sheet with id=AJ9, first strand: chain 'S' and resid 157 through 158 removed outlier: 7.402A pdb=" N LEU S 152 " --> pdb=" O VAL S 189 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL S 189 " --> pdb=" O LEU S 152 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'S' and resid 210 through 213 removed outlier: 3.657A pdb=" N ILE S 211 " --> pdb=" O ARG S 218 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU S 213 " --> pdb=" O ALA S 216 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA S 216 " --> pdb=" O GLU S 213 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'T' and resid 39 through 40 removed outlier: 5.974A pdb=" N ILE T 28 " --> pdb=" O LEU T 76 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N TYR T 78 " --> pdb=" O ILE T 28 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N MET T 30 " --> pdb=" O TYR T 78 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE T 80 " --> pdb=" O MET T 30 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LEU T 32 " --> pdb=" O ILE T 80 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL T 31 " --> pdb=" O CYS T 102 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU T 101 " --> pdb=" O VAL T 132 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ALA T 131 " --> pdb=" O ILE T 144 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'T' and resid 209 through 213 removed outlier: 4.785A pdb=" N ILE T 209 " --> pdb=" O ALA T 220 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA T 220 " --> pdb=" O ILE T 209 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU T 213 " --> pdb=" O ALA T 216 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA T 216 " --> pdb=" O GLU T 213 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'T' and resid 297 through 300 removed outlier: 6.815A pdb=" N LEU T 335 " --> pdb=" O ASN X 144 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'L' and resid 39 through 40 removed outlier: 3.697A pdb=" N TYR L 100 " --> pdb=" O ILE L 27 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS L 102 " --> pdb=" O ALA L 29 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU L 101 " --> pdb=" O VAL L 132 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ALA L 131 " --> pdb=" O ILE L 144 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'L' and resid 157 through 158 removed outlier: 3.560A pdb=" N VAL L 151 " --> pdb=" O TYR L 158 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LEU L 152 " --> pdb=" O VAL L 189 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'L' and resid 183 through 184 removed outlier: 3.803A pdb=" N THR L 183 " --> pdb=" O ILE L 219 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG L 218 " --> pdb=" O ILE L 211 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE L 211 " --> pdb=" O ARG L 218 " (cutoff:3.500A) 2566 hydrogen bonds defined for protein. 7344 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: 34.04 Time building geometry restraints manager: 16.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 24654 1.34 - 1.46: 15385 1.46 - 1.58: 36827 1.58 - 1.70: 0 1.70 - 1.81: 552 Bond restraints: 77418 Sorted by residual: bond pdb=" N ARG F 22 " pdb=" CA ARG F 22 " ideal model delta sigma weight residual 1.457 1.477 -0.019 1.29e-02 6.01e+03 2.28e+00 bond pdb=" N ARG U 22 " pdb=" CA ARG U 22 " ideal model delta sigma weight residual 1.457 1.477 -0.019 1.29e-02 6.01e+03 2.22e+00 bond pdb=" N ARG E 22 " pdb=" CA ARG E 22 " ideal model delta sigma weight residual 1.457 1.476 -0.019 1.29e-02 6.01e+03 2.13e+00 bond pdb=" N ARG W 22 " pdb=" CA ARG W 22 " ideal model delta sigma weight residual 1.457 1.476 -0.019 1.29e-02 6.01e+03 2.06e+00 bond pdb=" N ARG V 22 " pdb=" CA ARG V 22 " ideal model delta sigma weight residual 1.457 1.476 -0.018 1.29e-02 6.01e+03 2.03e+00 ... (remaining 77413 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 102922 1.80 - 3.59: 1145 3.59 - 5.39: 154 5.39 - 7.19: 39 7.19 - 8.99: 8 Bond angle restraints: 104268 Sorted by residual: angle pdb=" N VAL O 137 " pdb=" CA VAL O 137 " pdb=" C VAL O 137 " ideal model delta sigma weight residual 111.88 107.11 4.77 1.06e+00 8.90e-01 2.03e+01 angle pdb=" N VAL M 137 " pdb=" CA VAL M 137 " pdb=" C VAL M 137 " ideal model delta sigma weight residual 111.88 107.13 4.75 1.06e+00 8.90e-01 2.01e+01 angle pdb=" C LYS F 20 " pdb=" N GLU F 21 " pdb=" CA GLU F 21 " ideal model delta sigma weight residual 121.54 129.06 -7.52 1.91e+00 2.74e-01 1.55e+01 angle pdb=" C LYS W 20 " pdb=" N GLU W 21 " pdb=" CA GLU W 21 " ideal model delta sigma weight residual 121.54 129.06 -7.52 1.91e+00 2.74e-01 1.55e+01 angle pdb=" C LYS E 20 " pdb=" N GLU E 21 " pdb=" CA GLU E 21 " ideal model delta sigma weight residual 121.54 129.03 -7.49 1.91e+00 2.74e-01 1.54e+01 ... (remaining 104263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 43049 15.07 - 30.15: 3618 30.15 - 45.22: 836 45.22 - 60.30: 107 60.30 - 75.37: 54 Dihedral angle restraints: 47664 sinusoidal: 19350 harmonic: 28314 Sorted by residual: dihedral pdb=" CA ASP Q 260 " pdb=" C ASP Q 260 " pdb=" N TYR Q 261 " pdb=" CA TYR Q 261 " ideal model delta harmonic sigma weight residual -180.00 -159.45 -20.55 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA ASP S 260 " pdb=" C ASP S 260 " pdb=" N TYR S 261 " pdb=" CA TYR S 261 " ideal model delta harmonic sigma weight residual -180.00 -159.51 -20.49 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA ASP C 260 " pdb=" C ASP C 260 " pdb=" N TYR C 261 " pdb=" CA TYR C 261 " ideal model delta harmonic sigma weight residual -180.00 -159.58 -20.42 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 47661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 8724 0.036 - 0.071: 2243 0.071 - 0.107: 949 0.107 - 0.143: 399 0.143 - 0.178: 27 Chirality restraints: 12342 Sorted by residual: chirality pdb=" CA ARG W 22 " pdb=" N ARG W 22 " pdb=" C ARG W 22 " pdb=" CB ARG W 22 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CA ARG V 22 " pdb=" N ARG V 22 " pdb=" C ARG V 22 " pdb=" CB ARG V 22 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.90e-01 chirality pdb=" CA ARG E 22 " pdb=" N ARG E 22 " pdb=" C ARG E 22 " pdb=" CB ARG E 22 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.69e-01 ... (remaining 12339 not shown) Planarity restraints: 13056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP e 140 " 0.008 2.00e-02 2.50e+03 1.70e-02 2.89e+00 pdb=" C ASP e 140 " -0.029 2.00e-02 2.50e+03 pdb=" O ASP e 140 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE e 141 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP o 140 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.78e+00 pdb=" C ASP o 140 " 0.029 2.00e-02 2.50e+03 pdb=" O ASP o 140 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE o 141 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE N 191 " -0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO N 192 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO N 192 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO N 192 " -0.022 5.00e-02 4.00e+02 ... (remaining 13053 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 5780 2.74 - 3.28: 77331 3.28 - 3.82: 117801 3.82 - 4.36: 134692 4.36 - 4.90: 241384 Nonbonded interactions: 576988 Sorted by model distance: nonbonded pdb=" ND2 ASN M 267 " pdb=" O GLY M 330 " model vdw 2.202 3.120 nonbonded pdb=" O GLY C 4 " pdb=" NH1 ARG S 221 " model vdw 2.203 3.120 nonbonded pdb=" ND2 ASN L 267 " pdb=" O GLY L 330 " model vdw 2.205 3.120 nonbonded pdb=" ND2 ASN N 267 " pdb=" O GLY N 330 " model vdw 2.206 3.120 nonbonded pdb=" O ASP A 161 " pdb=" OG1 THR A 164 " model vdw 2.210 3.040 ... (remaining 576983 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } ncs_group { reference = (chain 'H' and resid 7 through 142) selection = chain 'J' selection = (chain 'K' and resid 7 through 142) selection = (chain 'Y' and resid 7 through 142) selection = chain 'c' selection = (chain 'd' and resid 7 through 142) selection = (chain 'e' and resid 7 through 142) selection = (chain 'f' and resid 7 through 142) selection = (chain 'g' and resid 7 through 142) selection = chain 'h' selection = (chain 'i' and resid 7 through 142) selection = (chain 'j' and resid 7 through 142) selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = (chain 'n' and resid 7 through 142) selection = (chain 'o' and resid 7 through 142) selection = (chain 'p' and resid 7 through 142) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 2.400 Check model and map are aligned: 0.450 Set scattering table: 0.570 Process input model: 134.720 Find NCS groups from input model: 2.900 Set up NCS constraints: 0.660 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:2.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 146.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 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 : 0.003 0.032 77418 Z= 0.169 Angle : 0.514 8.987 104268 Z= 0.278 Chirality : 0.042 0.178 12342 Planarity : 0.003 0.040 13056 Dihedral : 11.989 75.370 29352 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: 0.49 (0.08), residues: 9648 helix: 2.13 (0.10), residues: 2454 sheet: 0.73 (0.12), residues: 1914 loop : -0.72 (0.08), residues: 5280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP W 117 HIS 0.003 0.001 HIS H 66 PHE 0.014 0.001 PHE M 92 TYR 0.012 0.001 TYR E 78 ARG 0.006 0.000 ARG U 25 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1551 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1551 time to evaluate : 6.952 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: h 31 GLN cc_start: 0.7428 (tt0) cc_final: 0.7142 (tt0) REVERT: h 54 MET cc_start: 0.8792 (mmm) cc_final: 0.8266 (mmt) REVERT: i 47 MET cc_start: 0.8556 (mmp) cc_final: 0.8266 (mmm) REVERT: i 81 ARG cc_start: 0.7135 (mtm-85) cc_final: 0.6733 (mtm110) REVERT: i 140 ASP cc_start: 0.8027 (t70) cc_final: 0.7715 (t0) REVERT: C 5 LEU cc_start: 0.7825 (pp) cc_final: 0.7368 (tt) REVERT: C 27 ILE cc_start: 0.7890 (tt) cc_final: 0.7508 (mt) REVERT: C 56 GLU cc_start: 0.6969 (tt0) cc_final: 0.5216 (tp30) REVERT: C 66 MET cc_start: 0.7140 (ptt) cc_final: 0.6826 (ptp) REVERT: C 103 MET cc_start: 0.3032 (tpt) cc_final: 0.2428 (mmm) REVERT: C 126 LYS cc_start: 0.6723 (mmtm) cc_final: 0.5885 (ptpp) REVERT: C 135 LYS cc_start: 0.7445 (tptp) cc_final: 0.6844 (mmtp) REVERT: C 152 LEU cc_start: 0.7077 (tt) cc_final: 0.6361 (mt) REVERT: C 161 ASP cc_start: 0.6765 (m-30) cc_final: 0.5745 (t0) REVERT: C 247 ASP cc_start: 0.8689 (m-30) cc_final: 0.8323 (m-30) REVERT: C 318 TYR cc_start: 0.6229 (m-80) cc_final: 0.4997 (m-80) REVERT: F 22 ARG cc_start: 0.6310 (mtt90) cc_final: 0.5724 (mtm-85) REVERT: F 59 GLU cc_start: 0.6804 (mm-30) cc_final: 0.6254 (tt0) REVERT: F 103 MET cc_start: 0.4587 (tmm) cc_final: 0.4102 (tpp) REVERT: F 135 LYS cc_start: 0.7598 (mmmm) cc_final: 0.7147 (mptt) REVERT: F 145 ASN cc_start: 0.5551 (p0) cc_final: 0.4277 (p0) REVERT: F 156 LYS cc_start: 0.6134 (ptpp) cc_final: 0.5897 (tptm) REVERT: F 158 TYR cc_start: 0.6850 (m-80) cc_final: 0.5465 (m-80) REVERT: F 293 GLU cc_start: 0.6859 (tp30) cc_final: 0.5894 (tm-30) REVERT: F 319 MET cc_start: 0.6582 (mmm) cc_final: 0.6029 (ttt) REVERT: B 60 TYR cc_start: 0.6320 (m-80) cc_final: 0.5922 (m-80) REVERT: B 101 LEU cc_start: 0.8047 (tp) cc_final: 0.7800 (mt) REVERT: B 178 GLN cc_start: 0.3672 (tp40) cc_final: 0.3167 (mp10) REVERT: k 31 GLN cc_start: 0.7736 (tt0) cc_final: 0.7394 (tt0) REVERT: f 4 MET cc_start: 0.7214 (tpt) cc_final: 0.6909 (tpt) REVERT: n 81 ARG cc_start: 0.7245 (mtm-85) cc_final: 0.6689 (mtm110) REVERT: n 140 ASP cc_start: 0.8112 (t70) cc_final: 0.7787 (t0) REVERT: P 20 LYS cc_start: 0.7413 (tttp) cc_final: 0.7169 (tptp) REVERT: P 27 ILE cc_start: 0.7896 (tt) cc_final: 0.7472 (mt) REVERT: P 56 GLU cc_start: 0.6903 (tt0) cc_final: 0.5186 (tp30) REVERT: P 66 MET cc_start: 0.6856 (ptt) cc_final: 0.6388 (ptt) REVERT: P 126 LYS cc_start: 0.6627 (mmtm) cc_final: 0.5729 (ptpt) REVERT: P 135 LYS cc_start: 0.7721 (tptp) cc_final: 0.7077 (mmtp) REVERT: P 152 LEU cc_start: 0.6909 (tt) cc_final: 0.6232 (mm) REVERT: P 161 ASP cc_start: 0.6658 (m-30) cc_final: 0.5572 (t0) REVERT: U 22 ARG cc_start: 0.6226 (mtt90) cc_final: 0.5261 (mtm-85) REVERT: U 103 MET cc_start: 0.4582 (tmm) cc_final: 0.4373 (tmm) REVERT: U 158 TYR cc_start: 0.6201 (m-80) cc_final: 0.4587 (m-80) REVERT: U 205 LYS cc_start: 0.7562 (tppp) cc_final: 0.7357 (ptmt) REVERT: U 306 LYS cc_start: 0.8158 (tttt) cc_final: 0.7885 (ttmt) REVERT: M 5 LEU cc_start: 0.8439 (tt) cc_final: 0.8219 (tt) REVERT: M 98 PHE cc_start: 0.7355 (p90) cc_final: 0.7100 (p90) REVERT: M 135 LYS cc_start: 0.7984 (tptp) cc_final: 0.7452 (ttpt) REVERT: M 158 TYR cc_start: 0.7487 (m-80) cc_final: 0.7225 (m-80) REVERT: M 160 VAL cc_start: 0.4240 (p) cc_final: 0.3893 (p) REVERT: M 163 PHE cc_start: 0.5971 (t80) cc_final: 0.5477 (t80) REVERT: l 33 LYS cc_start: 0.7775 (tttt) cc_final: 0.7417 (tttt) REVERT: o 81 ARG cc_start: 0.7097 (mtm-85) cc_final: 0.6626 (mtm110) REVERT: Q 20 LYS cc_start: 0.7253 (tttp) cc_final: 0.6929 (tptt) REVERT: Q 27 ILE cc_start: 0.7888 (tt) cc_final: 0.7490 (mt) REVERT: Q 56 GLU cc_start: 0.6693 (tt0) cc_final: 0.5069 (tp30) REVERT: Q 126 LYS cc_start: 0.6701 (mmtm) cc_final: 0.5891 (ptpt) REVERT: Q 152 LEU cc_start: 0.7352 (tt) cc_final: 0.6709 (mm) REVERT: Q 161 ASP cc_start: 0.6806 (m-30) cc_final: 0.5851 (t0) REVERT: V 20 LYS cc_start: 0.5512 (mmtt) cc_final: 0.5209 (tppt) REVERT: V 22 ARG cc_start: 0.6541 (mtt90) cc_final: 0.6010 (mtm-85) REVERT: V 59 GLU cc_start: 0.6910 (mm-30) cc_final: 0.6587 (mm-30) REVERT: V 117 TRP cc_start: 0.6746 (t60) cc_final: 0.6458 (t60) REVERT: V 135 LYS cc_start: 0.7523 (mmmm) cc_final: 0.7030 (mptt) REVERT: V 146 PHE cc_start: 0.6747 (t80) cc_final: 0.6519 (t80) REVERT: V 156 LYS cc_start: 0.5919 (ptpp) cc_final: 0.5376 (tptm) REVERT: V 158 TYR cc_start: 0.6386 (m-80) cc_final: 0.4831 (m-80) REVERT: V 205 LYS cc_start: 0.7470 (tppp) cc_final: 0.7251 (ptpt) REVERT: V 306 LYS cc_start: 0.8231 (tttt) cc_final: 0.7881 (ttpt) REVERT: V 319 MET cc_start: 0.6019 (tpt) cc_final: 0.5514 (ttt) REVERT: a 51 MET cc_start: 0.7722 (mtt) cc_final: 0.7391 (mtt) REVERT: a 93 VAL cc_start: 0.8151 (p) cc_final: 0.7839 (m) REVERT: N 41 ASN cc_start: 0.7380 (m110) cc_final: 0.7171 (m-40) REVERT: N 98 PHE cc_start: 0.7416 (p90) cc_final: 0.7160 (p90) REVERT: N 101 LEU cc_start: 0.7758 (tp) cc_final: 0.7511 (mt) REVERT: N 103 MET cc_start: 0.6440 (ptm) cc_final: 0.6208 (ptp) REVERT: N 135 LYS cc_start: 0.7830 (tptp) cc_final: 0.7428 (tttp) REVERT: N 247 ASP cc_start: 0.7027 (m-30) cc_final: 0.6696 (m-30) REVERT: J 31 GLN cc_start: 0.7528 (tt0) cc_final: 0.7240 (tt0) REVERT: J 54 MET cc_start: 0.8785 (mmm) cc_final: 0.8251 (mmt) REVERT: K 81 ARG cc_start: 0.7222 (mtm-85) cc_final: 0.6836 (mtm110) REVERT: K 123 VAL cc_start: 0.8525 (t) cc_final: 0.8308 (m) REVERT: K 140 ASP cc_start: 0.8077 (t70) cc_final: 0.7744 (t0) REVERT: D 5 LEU cc_start: 0.7564 (pp) cc_final: 0.7356 (tt) REVERT: D 27 ILE cc_start: 0.7819 (tt) cc_final: 0.7452 (mt) REVERT: D 56 GLU cc_start: 0.6812 (tt0) cc_final: 0.4985 (tp30) REVERT: D 66 MET cc_start: 0.6823 (ptt) cc_final: 0.6593 (ptt) REVERT: D 103 MET cc_start: 0.3095 (tpt) cc_final: 0.2460 (mmm) REVERT: D 126 LYS cc_start: 0.6701 (mmtm) cc_final: 0.5853 (ptpp) REVERT: D 135 LYS cc_start: 0.7329 (tptp) cc_final: 0.6713 (mmtp) REVERT: D 152 LEU cc_start: 0.7062 (tt) cc_final: 0.6305 (mt) REVERT: D 161 ASP cc_start: 0.6947 (m-30) cc_final: 0.5858 (t0) REVERT: D 247 ASP cc_start: 0.8642 (m-30) cc_final: 0.8262 (m-30) REVERT: D 318 TYR cc_start: 0.6249 (m-80) cc_final: 0.5021 (m-80) REVERT: E 22 ARG cc_start: 0.6318 (mtt90) cc_final: 0.5730 (mtm-85) REVERT: E 59 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6468 (tt0) REVERT: E 103 MET cc_start: 0.4708 (tmm) cc_final: 0.4201 (tpp) REVERT: E 135 LYS cc_start: 0.7606 (mmmm) cc_final: 0.7216 (mptt) REVERT: E 158 TYR cc_start: 0.6814 (m-80) cc_final: 0.5393 (m-80) REVERT: E 293 GLU cc_start: 0.6847 (tp30) cc_final: 0.5993 (tm-30) REVERT: E 319 MET cc_start: 0.5820 (tpt) cc_final: 0.5259 (ttt) REVERT: G 95 ASP cc_start: 0.5399 (m-30) cc_final: 0.5089 (m-30) REVERT: A 60 TYR cc_start: 0.6397 (m-80) cc_final: 0.6003 (m-80) REVERT: A 101 LEU cc_start: 0.8102 (tp) cc_final: 0.7875 (mt) REVERT: A 135 LYS cc_start: 0.7724 (tptp) cc_final: 0.7472 (ttpt) REVERT: A 178 GLN cc_start: 0.3721 (tp40) cc_final: 0.3230 (mp10) REVERT: m 31 GLN cc_start: 0.7723 (tt0) cc_final: 0.7352 (tt0) REVERT: j 4 MET cc_start: 0.7230 (tpt) cc_final: 0.6906 (tpt) REVERT: p 81 ARG cc_start: 0.7249 (mtm-85) cc_final: 0.6736 (mtm110) REVERT: R 27 ILE cc_start: 0.7927 (tt) cc_final: 0.7504 (mt) REVERT: R 56 GLU cc_start: 0.6868 (tt0) cc_final: 0.5187 (tp30) REVERT: R 66 MET cc_start: 0.6886 (ptt) cc_final: 0.6479 (ptt) REVERT: R 126 LYS cc_start: 0.6625 (mmtm) cc_final: 0.5709 (ptpt) REVERT: R 135 LYS cc_start: 0.7711 (tptp) cc_final: 0.7115 (mmtp) REVERT: R 152 LEU cc_start: 0.6914 (tt) cc_final: 0.6230 (mm) REVERT: R 161 ASP cc_start: 0.6655 (m-30) cc_final: 0.5561 (t0) REVERT: W 20 LYS cc_start: 0.5922 (mmtt) cc_final: 0.5649 (tptt) REVERT: W 22 ARG cc_start: 0.6209 (mtt90) cc_final: 0.5220 (mtm-85) REVERT: W 103 MET cc_start: 0.4476 (tmm) cc_final: 0.4047 (tpp) REVERT: W 158 TYR cc_start: 0.6157 (m-80) cc_final: 0.4534 (m-80) REVERT: W 306 LYS cc_start: 0.8094 (tttt) cc_final: 0.7807 (ttmt) REVERT: O 5 LEU cc_start: 0.8423 (tt) cc_final: 0.8202 (tt) REVERT: O 41 ASN cc_start: 0.7449 (m110) cc_final: 0.7221 (m-40) REVERT: O 98 PHE cc_start: 0.7374 (p90) cc_final: 0.7109 (p90) REVERT: O 135 LYS cc_start: 0.7999 (tptp) cc_final: 0.7481 (ttpt) REVERT: O 163 PHE cc_start: 0.5955 (t80) cc_final: 0.5473 (t80) REVERT: O 353 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6777 (pm20) REVERT: c 31 GLN cc_start: 0.7517 (tt0) cc_final: 0.7268 (tt0) REVERT: Y 54 MET cc_start: 0.8142 (mmm) cc_final: 0.7681 (mmm) REVERT: e 81 ARG cc_start: 0.7031 (mtm-85) cc_final: 0.6577 (mtm110) REVERT: S 20 LYS cc_start: 0.7295 (tttp) cc_final: 0.6938 (tptt) REVERT: S 27 ILE cc_start: 0.7766 (tt) cc_final: 0.7404 (mt) REVERT: S 56 GLU cc_start: 0.6644 (tt0) cc_final: 0.5062 (tp30) REVERT: S 126 LYS cc_start: 0.6688 (mmtm) cc_final: 0.5926 (ptpt) REVERT: S 152 LEU cc_start: 0.7278 (tt) cc_final: 0.6667 (mm) REVERT: S 161 ASP cc_start: 0.6796 (m-30) cc_final: 0.5819 (t0) REVERT: T 20 LYS cc_start: 0.5510 (mmtt) cc_final: 0.5197 (tppt) REVERT: T 22 ARG cc_start: 0.6585 (mtt90) cc_final: 0.6047 (mtm-85) REVERT: T 59 GLU cc_start: 0.6944 (mm-30) cc_final: 0.6590 (mm-30) REVERT: T 103 MET cc_start: 0.4692 (tmm) cc_final: 0.3987 (tpp) REVERT: T 117 TRP cc_start: 0.6780 (t60) cc_final: 0.6482 (t60) REVERT: T 135 LYS cc_start: 0.7501 (mmmm) cc_final: 0.7000 (mptt) REVERT: T 146 PHE cc_start: 0.6752 (t80) cc_final: 0.6531 (t80) REVERT: T 156 LYS cc_start: 0.6041 (ptpp) cc_final: 0.5538 (tptm) REVERT: T 158 TYR cc_start: 0.6588 (m-80) cc_final: 0.5126 (m-80) REVERT: T 205 LYS cc_start: 0.7495 (tppp) cc_final: 0.7261 (ptpt) REVERT: T 306 LYS cc_start: 0.8224 (tttt) cc_final: 0.7887 (ttpt) REVERT: X 51 MET cc_start: 0.7822 (mtt) cc_final: 0.7499 (mtt) REVERT: X 93 VAL cc_start: 0.8136 (p) cc_final: 0.7842 (m) REVERT: L 98 PHE cc_start: 0.7418 (p90) cc_final: 0.7149 (p90) REVERT: L 101 LEU cc_start: 0.7738 (tp) cc_final: 0.7484 (mt) REVERT: L 135 LYS cc_start: 0.7836 (tptp) cc_final: 0.7473 (tttp) REVERT: L 184 LYS cc_start: 0.7293 (ptpt) cc_final: 0.7079 (ptmt) REVERT: L 247 ASP cc_start: 0.7008 (m-30) cc_final: 0.6713 (m-30) outliers start: 0 outliers final: 0 residues processed: 1551 average time/residue: 0.6870 time to fit residues: 1812.2170 Evaluate side-chains 825 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 825 time to evaluate : 7.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 810 optimal weight: 6.9990 chunk 727 optimal weight: 20.0000 chunk 403 optimal weight: 40.0000 chunk 248 optimal weight: 6.9990 chunk 490 optimal weight: 7.9990 chunk 388 optimal weight: 10.0000 chunk 752 optimal weight: 8.9990 chunk 291 optimal weight: 0.9990 chunk 457 optimal weight: 7.9990 chunk 560 optimal weight: 6.9990 chunk 871 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN f 66 HIS ** P 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 99 ASN g 66 HIS ** V 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 99 ASN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN j 66 HIS ** R 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 328 ASN ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 99 ASN O 140 HIS c 8 ASN ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.133396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.114528 restraints weight = 158147.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.113290 restraints weight = 364578.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.113773 restraints weight = 344217.785| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 77418 Z= 0.322 Angle : 0.633 9.466 104268 Z= 0.336 Chirality : 0.047 0.187 12342 Planarity : 0.004 0.047 13056 Dihedral : 4.733 22.846 10254 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.81 % Allowed : 10.48 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.08), residues: 9648 helix: 1.94 (0.10), residues: 2448 sheet: 0.20 (0.11), residues: 2106 loop : -0.94 (0.08), residues: 5094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 117 HIS 0.008 0.001 HIS V 140 PHE 0.027 0.002 PHE O 92 TYR 0.032 0.002 TYR M 60 ARG 0.007 0.001 ARG O 221 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 974 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 820 time to evaluate : 7.178 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: C 5 LEU cc_start: 0.7886 (pp) cc_final: 0.7678 (tt) REVERT: C 27 ILE cc_start: 0.7062 (tt) cc_final: 0.6801 (mt) REVERT: C 152 LEU cc_start: 0.6895 (tt) cc_final: 0.6592 (mm) REVERT: C 161 ASP cc_start: 0.6172 (m-30) cc_final: 0.5967 (t0) REVERT: C 247 ASP cc_start: 0.8355 (m-30) cc_final: 0.8015 (m-30) REVERT: C 318 TYR cc_start: 0.6003 (m-80) cc_final: 0.4712 (m-80) REVERT: F 103 MET cc_start: 0.4359 (tmm) cc_final: 0.4103 (tpp) REVERT: F 156 LYS cc_start: 0.7010 (ptpp) cc_final: 0.6213 (tptm) REVERT: F 158 TYR cc_start: 0.6656 (m-80) cc_final: 0.6129 (m-80) REVERT: k 31 GLN cc_start: 0.7536 (tt0) cc_final: 0.7199 (tt0) REVERT: k 34 MET cc_start: 0.8630 (ttm) cc_final: 0.8376 (mtp) REVERT: f 4 MET cc_start: 0.7198 (tpt) cc_final: 0.6852 (tpt) REVERT: n 127 ILE cc_start: 0.8803 (mt) cc_final: 0.8601 (tt) REVERT: P 27 ILE cc_start: 0.7033 (tt) cc_final: 0.6735 (mt) REVERT: P 126 LYS cc_start: 0.6659 (mmtm) cc_final: 0.6393 (ptpp) REVERT: P 152 LEU cc_start: 0.6683 (tt) cc_final: 0.6394 (mm) REVERT: P 345 MET cc_start: 0.7019 (ptp) cc_final: 0.6603 (ptp) REVERT: U 103 MET cc_start: 0.4568 (tmm) cc_final: 0.4088 (tpp) REVERT: U 194 MET cc_start: 0.5262 (ttm) cc_final: 0.5033 (ttp) REVERT: U 306 LYS cc_start: 0.8310 (tttt) cc_final: 0.8107 (ttpt) REVERT: U 319 MET cc_start: 0.5682 (OUTLIER) cc_final: 0.5432 (ttp) REVERT: Z 79 ILE cc_start: 0.8900 (mt) cc_final: 0.8560 (mm) REVERT: M 135 LYS cc_start: 0.7287 (tptp) cc_final: 0.6865 (ttpt) REVERT: M 160 VAL cc_start: 0.6491 (p) cc_final: 0.5998 (p) REVERT: M 345 MET cc_start: 0.5997 (mtm) cc_final: 0.5625 (mtm) REVERT: g 4 MET cc_start: 0.7144 (tpt) cc_final: 0.6739 (tpt) REVERT: g 54 MET cc_start: 0.8605 (mmm) cc_final: 0.8285 (mmt) REVERT: o 47 MET cc_start: 0.7987 (mmp) cc_final: 0.7773 (mmm) REVERT: Q 56 GLU cc_start: 0.6076 (tt0) cc_final: 0.4542 (tp30) REVERT: Q 161 ASP cc_start: 0.6217 (m-30) cc_final: 0.5907 (t0) REVERT: V 145 ASN cc_start: 0.5137 (OUTLIER) cc_final: 0.4615 (p0) REVERT: V 146 PHE cc_start: 0.6628 (t80) cc_final: 0.6370 (t80) REVERT: a 79 ILE cc_start: 0.9007 (mt) cc_final: 0.8765 (mm) REVERT: a 93 VAL cc_start: 0.8762 (p) cc_final: 0.8529 (m) REVERT: N 178 GLN cc_start: 0.5122 (tp40) cc_final: 0.4627 (tp40) REVERT: D 27 ILE cc_start: 0.6995 (tt) cc_final: 0.6741 (mt) REVERT: D 152 LEU cc_start: 0.6921 (tt) cc_final: 0.6631 (mm) REVERT: D 161 ASP cc_start: 0.6214 (m-30) cc_final: 0.5984 (t0) REVERT: D 247 ASP cc_start: 0.8370 (m-30) cc_final: 0.8038 (m-30) REVERT: D 318 TYR cc_start: 0.6083 (m-80) cc_final: 0.4805 (m-80) REVERT: E 156 LYS cc_start: 0.6988 (ptpp) cc_final: 0.6311 (tptm) REVERT: m 31 GLN cc_start: 0.7487 (tt0) cc_final: 0.7203 (tt0) REVERT: j 4 MET cc_start: 0.7197 (tpt) cc_final: 0.6867 (tpt) REVERT: p 127 ILE cc_start: 0.8825 (mt) cc_final: 0.8610 (tt) REVERT: R 10 ILE cc_start: 0.8463 (mm) cc_final: 0.8187 (mm) REVERT: R 27 ILE cc_start: 0.7075 (tt) cc_final: 0.6758 (mt) REVERT: R 126 LYS cc_start: 0.6650 (mmtm) cc_final: 0.6381 (ptpp) REVERT: R 152 LEU cc_start: 0.6705 (tt) cc_final: 0.6417 (mm) REVERT: W 103 MET cc_start: 0.4472 (tmm) cc_final: 0.3957 (tpp) REVERT: W 194 MET cc_start: 0.5260 (ttm) cc_final: 0.5026 (ttp) REVERT: W 306 LYS cc_start: 0.8311 (tttt) cc_final: 0.8107 (ttpt) REVERT: W 319 MET cc_start: 0.5876 (OUTLIER) cc_final: 0.5610 (ttp) REVERT: b 79 ILE cc_start: 0.8897 (mt) cc_final: 0.8576 (mm) REVERT: O 135 LYS cc_start: 0.7256 (tptp) cc_final: 0.6743 (tttp) REVERT: O 345 MET cc_start: 0.6023 (mtm) cc_final: 0.5640 (mtm) REVERT: Y 4 MET cc_start: 0.7188 (tpt) cc_final: 0.6804 (tpt) REVERT: Y 54 MET cc_start: 0.8623 (mmm) cc_final: 0.8313 (mmm) REVERT: e 47 MET cc_start: 0.8006 (mmp) cc_final: 0.7749 (mmm) REVERT: S 3 ILE cc_start: 0.6864 (mm) cc_final: 0.6650 (mm) REVERT: S 30 MET cc_start: 0.4498 (tpp) cc_final: 0.4187 (tpp) REVERT: S 56 GLU cc_start: 0.6103 (tt0) cc_final: 0.4532 (tp30) REVERT: S 161 ASP cc_start: 0.6224 (m-30) cc_final: 0.5897 (t0) REVERT: T 103 MET cc_start: 0.4710 (tmm) cc_final: 0.4491 (tpp) REVERT: T 146 PHE cc_start: 0.6579 (t80) cc_final: 0.6275 (t80) REVERT: X 79 ILE cc_start: 0.9020 (mt) cc_final: 0.8758 (mm) REVERT: X 93 VAL cc_start: 0.8757 (p) cc_final: 0.8536 (m) REVERT: L 98 PHE cc_start: 0.7243 (p90) cc_final: 0.6933 (p90) REVERT: L 135 LYS cc_start: 0.7142 (tptp) cc_final: 0.6941 (tttp) REVERT: L 178 GLN cc_start: 0.5141 (tp40) cc_final: 0.4640 (tp40) outliers start: 154 outliers final: 117 residues processed: 950 average time/residue: 0.6569 time to fit residues: 1090.3417 Evaluate side-chains 762 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 642 time to evaluate : 7.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 27 VAL Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain i residue 135 GLU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 127 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 202 ARG Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain k residue 139 LEU Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 40 ASP Chi-restraints excluded: chain n residue 69 SER Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 318 TYR Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 181 THR Chi-restraints excluded: chain U residue 223 VAL Chi-restraints excluded: chain U residue 297 THR Chi-restraints excluded: chain U residue 319 MET Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain Z residue 95 ASP Chi-restraints excluded: chain Z residue 127 SER Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 137 VAL Chi-restraints excluded: chain l residue 139 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 69 SER Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 338 LYS Chi-restraints excluded: chain V residue 86 ILE Chi-restraints excluded: chain V residue 145 ASN Chi-restraints excluded: chain V residue 151 VAL Chi-restraints excluded: chain V residue 223 VAL Chi-restraints excluded: chain V residue 285 GLU Chi-restraints excluded: chain V residue 297 THR Chi-restraints excluded: chain a residue 20 THR Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 83 LEU Chi-restraints excluded: chain a residue 127 SER Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 191 ILE Chi-restraints excluded: chain N residue 265 VAL Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain m residue 139 LEU Chi-restraints excluded: chain p residue 27 VAL Chi-restraints excluded: chain p residue 40 ASP Chi-restraints excluded: chain p residue 69 SER Chi-restraints excluded: chain p residue 77 GLU Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 318 TYR Chi-restraints excluded: chain W residue 86 ILE Chi-restraints excluded: chain W residue 151 VAL Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 223 VAL Chi-restraints excluded: chain W residue 297 THR Chi-restraints excluded: chain W residue 319 MET Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 95 ASP Chi-restraints excluded: chain b residue 127 SER Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain c residue 139 LEU Chi-restraints excluded: chain e residue 27 VAL Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 338 LYS Chi-restraints excluded: chain T residue 86 ILE Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain T residue 223 VAL Chi-restraints excluded: chain T residue 285 GLU Chi-restraints excluded: chain T residue 297 THR Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 83 LEU Chi-restraints excluded: chain X residue 127 SER Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 160 VAL Chi-restraints excluded: chain L residue 191 ILE Chi-restraints excluded: chain L residue 265 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 786 optimal weight: 4.9990 chunk 182 optimal weight: 8.9990 chunk 869 optimal weight: 0.0570 chunk 695 optimal weight: 9.9990 chunk 810 optimal weight: 4.9990 chunk 939 optimal weight: 8.9990 chunk 127 optimal weight: 40.0000 chunk 641 optimal weight: 2.9990 chunk 519 optimal weight: 0.8980 chunk 637 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 overall best weight: 2.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN M 140 HIS A 68 ASN ** R 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 84 ASN ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.131549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.113252 restraints weight = 105268.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.111534 restraints weight = 244571.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.110730 restraints weight = 214371.636| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 77418 Z= 0.177 Angle : 0.521 10.118 104268 Z= 0.278 Chirality : 0.044 0.163 12342 Planarity : 0.003 0.048 13056 Dihedral : 4.387 22.333 10254 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.23 % Favored : 96.76 % Rotamer: Outliers : 1.85 % Allowed : 13.94 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.08), residues: 9648 helix: 2.06 (0.10), residues: 2460 sheet: 0.08 (0.11), residues: 2124 loop : -1.00 (0.08), residues: 5064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP W 117 HIS 0.008 0.001 HIS F 140 PHE 0.028 0.001 PHE B 92 TYR 0.028 0.001 TYR M 60 ARG 0.005 0.000 ARG M 221 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 734 time to evaluate : 7.058 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: C 103 MET cc_start: 0.3789 (tpt) cc_final: 0.3251 (mmm) REVERT: C 247 ASP cc_start: 0.8351 (m-30) cc_final: 0.8047 (m-30) REVERT: C 318 TYR cc_start: 0.5931 (m-80) cc_final: 0.4618 (m-80) REVERT: F 103 MET cc_start: 0.4507 (tmm) cc_final: 0.3955 (tpp) REVERT: F 158 TYR cc_start: 0.6365 (m-80) cc_final: 0.5803 (m-80) REVERT: k 34 MET cc_start: 0.8586 (ttm) cc_final: 0.8368 (mtp) REVERT: f 4 MET cc_start: 0.7096 (tpt) cc_final: 0.6807 (tpt) REVERT: P 27 ILE cc_start: 0.7124 (tt) cc_final: 0.6804 (mt) REVERT: P 345 MET cc_start: 0.6915 (ptp) cc_final: 0.6519 (ptp) REVERT: U 103 MET cc_start: 0.4617 (tmm) cc_final: 0.4297 (tpp) REVERT: M 135 LYS cc_start: 0.6861 (tptp) cc_final: 0.6572 (tttp) REVERT: M 345 MET cc_start: 0.5778 (mtm) cc_final: 0.5400 (mtm) REVERT: g 4 MET cc_start: 0.7384 (tpt) cc_final: 0.6970 (tpt) REVERT: g 54 MET cc_start: 0.8582 (mmm) cc_final: 0.8312 (mmt) REVERT: Q 27 ILE cc_start: 0.6780 (tt) cc_final: 0.6523 (mt) REVERT: Q 56 GLU cc_start: 0.5745 (tt0) cc_final: 0.4424 (tp30) REVERT: Q 96 LYS cc_start: 0.6014 (ttpt) cc_final: 0.5515 (mtmm) REVERT: V 145 ASN cc_start: 0.5103 (OUTLIER) cc_final: 0.4649 (p0) REVERT: V 146 PHE cc_start: 0.6597 (t80) cc_final: 0.6381 (t80) REVERT: V 158 TYR cc_start: 0.6527 (m-80) cc_final: 0.6315 (m-80) REVERT: N 98 PHE cc_start: 0.7081 (p90) cc_final: 0.6742 (p90) REVERT: N 178 GLN cc_start: 0.5151 (tp40) cc_final: 0.4670 (tp40) REVERT: D 103 MET cc_start: 0.3726 (tpt) cc_final: 0.3391 (mmm) REVERT: D 247 ASP cc_start: 0.8410 (m-30) cc_final: 0.8081 (m-30) REVERT: E 145 ASN cc_start: 0.5004 (p0) cc_final: 0.4054 (p0) REVERT: j 4 MET cc_start: 0.7107 (tpt) cc_final: 0.6841 (tpt) REVERT: R 10 ILE cc_start: 0.8472 (mm) cc_final: 0.8205 (mm) REVERT: R 27 ILE cc_start: 0.6985 (tt) cc_final: 0.6706 (mt) REVERT: W 306 LYS cc_start: 0.8239 (tttt) cc_final: 0.7950 (ttpt) REVERT: O 135 LYS cc_start: 0.6957 (tptp) cc_final: 0.6606 (tttp) REVERT: O 345 MET cc_start: 0.5744 (mtm) cc_final: 0.5347 (mtm) REVERT: Y 4 MET cc_start: 0.7366 (tpt) cc_final: 0.6915 (tpt) REVERT: S 3 ILE cc_start: 0.6776 (mm) cc_final: 0.6513 (mm) REVERT: S 27 ILE cc_start: 0.7008 (tt) cc_final: 0.6682 (mt) REVERT: S 56 GLU cc_start: 0.5672 (tt0) cc_final: 0.4320 (tp30) REVERT: S 96 LYS cc_start: 0.6429 (ttpt) cc_final: 0.5813 (mtmm) REVERT: T 103 MET cc_start: 0.4518 (tmm) cc_final: 0.4006 (tpp) REVERT: T 158 TYR cc_start: 0.6506 (m-80) cc_final: 0.6284 (m-80) REVERT: L 178 GLN cc_start: 0.5045 (tp40) cc_final: 0.4586 (tp40) outliers start: 157 outliers final: 109 residues processed: 861 average time/residue: 0.6546 time to fit residues: 995.7391 Evaluate side-chains 715 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 605 time to evaluate : 7.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 79 ILE Chi-restraints excluded: chain h residue 112 ASP Chi-restraints excluded: chain h residue 139 LEU Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain i residue 135 GLU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 25 ARG Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 127 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain n residue 40 ASP Chi-restraints excluded: chain n residue 69 SER Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain P residue 318 TYR Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 88 THR Chi-restraints excluded: chain U residue 223 VAL Chi-restraints excluded: chain U residue 297 THR Chi-restraints excluded: chain U residue 319 MET Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain Z residue 81 ASP Chi-restraints excluded: chain Z residue 95 ASP Chi-restraints excluded: chain Z residue 127 SER Chi-restraints excluded: chain M residue 137 VAL Chi-restraints excluded: chain l residue 79 ILE Chi-restraints excluded: chain l residue 139 LEU Chi-restraints excluded: chain o residue 69 SER Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 338 LYS Chi-restraints excluded: chain V residue 86 ILE Chi-restraints excluded: chain V residue 133 LEU Chi-restraints excluded: chain V residue 145 ASN Chi-restraints excluded: chain V residue 223 VAL Chi-restraints excluded: chain V residue 297 THR Chi-restraints excluded: chain a residue 20 THR Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 108 LYS Chi-restraints excluded: chain a residue 127 SER Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 86 ILE Chi-restraints excluded: chain N residue 191 ILE Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain p residue 40 ASP Chi-restraints excluded: chain p residue 69 SER Chi-restraints excluded: chain p residue 77 GLU Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 318 TYR Chi-restraints excluded: chain W residue 86 ILE Chi-restraints excluded: chain W residue 88 THR Chi-restraints excluded: chain W residue 223 VAL Chi-restraints excluded: chain W residue 297 THR Chi-restraints excluded: chain W residue 319 MET Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 81 ASP Chi-restraints excluded: chain b residue 84 ASN Chi-restraints excluded: chain b residue 95 ASP Chi-restraints excluded: chain b residue 127 SER Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain c residue 139 LEU Chi-restraints excluded: chain e residue 40 ASP Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 338 LYS Chi-restraints excluded: chain S residue 352 ILE Chi-restraints excluded: chain T residue 86 ILE Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 133 LEU Chi-restraints excluded: chain T residue 223 VAL Chi-restraints excluded: chain T residue 297 THR Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 108 LYS Chi-restraints excluded: chain X residue 127 SER Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 191 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 288 optimal weight: 30.0000 chunk 789 optimal weight: 10.0000 chunk 810 optimal weight: 0.8980 chunk 867 optimal weight: 20.0000 chunk 174 optimal weight: 7.9990 chunk 378 optimal weight: 20.0000 chunk 869 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 564 optimal weight: 8.9990 chunk 620 optimal weight: 4.9990 chunk 720 optimal weight: 0.0170 overall best weight: 3.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 105 GLN ** P 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 84 ASN G 105 GLN A 41 ASN A 68 ASN ** R 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.125678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.106000 restraints weight = 121043.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.105398 restraints weight = 292679.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.104837 restraints weight = 281407.575| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 77418 Z= 0.188 Angle : 0.510 9.787 104268 Z= 0.273 Chirality : 0.043 0.173 12342 Planarity : 0.003 0.051 13056 Dihedral : 4.315 21.879 10254 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.76 % Favored : 96.20 % Rotamer: Outliers : 2.44 % Allowed : 15.43 % Favored : 82.13 % 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: -0.08 (0.08), residues: 9648 helix: 1.94 (0.10), residues: 2502 sheet: -0.03 (0.11), residues: 2124 loop : -1.13 (0.08), residues: 5022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP W 117 HIS 0.003 0.001 HIS C 250 PHE 0.019 0.001 PHE R 163 TYR 0.020 0.001 TYR M 60 ARG 0.004 0.000 ARG N 221 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 670 time to evaluate : 7.092 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: C 247 ASP cc_start: 0.8310 (m-30) cc_final: 0.8007 (m-30) REVERT: F 103 MET cc_start: 0.4537 (tmm) cc_final: 0.3984 (tpp) REVERT: I 70 GLN cc_start: 0.6701 (OUTLIER) cc_final: 0.6450 (mt0) REVERT: B 226 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8141 (pt) REVERT: P 27 ILE cc_start: 0.7127 (tt) cc_final: 0.6807 (mt) REVERT: P 345 MET cc_start: 0.7024 (ptp) cc_final: 0.6606 (ptp) REVERT: U 103 MET cc_start: 0.4750 (tmm) cc_final: 0.4468 (tpp) REVERT: Z 70 GLN cc_start: 0.6766 (OUTLIER) cc_final: 0.6447 (tt0) REVERT: M 53 LEU cc_start: 0.3725 (OUTLIER) cc_final: 0.3500 (pt) REVERT: M 226 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8173 (pt) REVERT: M 345 MET cc_start: 0.5868 (mtm) cc_final: 0.5553 (mtm) REVERT: g 54 MET cc_start: 0.8599 (mmm) cc_final: 0.8319 (mmt) REVERT: Q 27 ILE cc_start: 0.7126 (tt) cc_final: 0.6829 (mt) REVERT: Q 56 GLU cc_start: 0.5801 (tt0) cc_final: 0.4622 (tp30) REVERT: Q 96 LYS cc_start: 0.6241 (ttpt) cc_final: 0.5663 (mtmm) REVERT: V 146 PHE cc_start: 0.6661 (t80) cc_final: 0.6388 (t80) REVERT: a 70 GLN cc_start: 0.6719 (OUTLIER) cc_final: 0.6409 (tt0) REVERT: N 178 GLN cc_start: 0.5153 (tp40) cc_final: 0.4659 (tp40) REVERT: D 247 ASP cc_start: 0.8331 (m-30) cc_final: 0.8011 (m-30) REVERT: E 30 MET cc_start: 0.6212 (tpp) cc_final: 0.6012 (tpt) REVERT: G 70 GLN cc_start: 0.6723 (OUTLIER) cc_final: 0.6477 (mt0) REVERT: A 226 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8074 (pt) REVERT: R 10 ILE cc_start: 0.8525 (mm) cc_final: 0.8259 (mm) REVERT: R 27 ILE cc_start: 0.7212 (tt) cc_final: 0.6880 (mt) REVERT: R 66 MET cc_start: 0.6047 (ptp) cc_final: 0.5828 (ptm) REVERT: W 103 MET cc_start: 0.4865 (tmm) cc_final: 0.4060 (tpp) REVERT: W 306 LYS cc_start: 0.8264 (tttt) cc_final: 0.7989 (ttmt) REVERT: b 70 GLN cc_start: 0.6694 (OUTLIER) cc_final: 0.6386 (tt0) REVERT: O 30 MET cc_start: 0.6074 (tmm) cc_final: 0.5861 (ttp) REVERT: O 53 LEU cc_start: 0.3400 (OUTLIER) cc_final: 0.3170 (pt) REVERT: O 135 LYS cc_start: 0.6982 (tptp) cc_final: 0.6678 (tttp) REVERT: O 226 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8165 (pt) REVERT: S 3 ILE cc_start: 0.7012 (mm) cc_final: 0.6713 (mm) REVERT: S 27 ILE cc_start: 0.7185 (tt) cc_final: 0.6855 (mt) REVERT: S 56 GLU cc_start: 0.5703 (tt0) cc_final: 0.4472 (tp30) REVERT: S 96 LYS cc_start: 0.6395 (ttpt) cc_final: 0.5792 (mtmm) REVERT: T 103 MET cc_start: 0.4244 (OUTLIER) cc_final: 0.3899 (tpp) REVERT: X 70 GLN cc_start: 0.6724 (OUTLIER) cc_final: 0.6399 (tt0) REVERT: L 178 GLN cc_start: 0.5225 (tp40) cc_final: 0.4692 (tp40) outliers start: 207 outliers final: 141 residues processed: 840 average time/residue: 0.6333 time to fit residues: 947.8782 Evaluate side-chains 752 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 598 time to evaluate : 7.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 79 ILE Chi-restraints excluded: chain h residue 112 ASP Chi-restraints excluded: chain h residue 139 LEU Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain i residue 135 GLU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 25 ARG Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 140 HIS Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 70 GLN Chi-restraints excluded: chain I residue 127 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 139 LEU Chi-restraints excluded: chain n residue 40 ASP Chi-restraints excluded: chain n residue 69 SER Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 56 GLU Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain P residue 203 VAL Chi-restraints excluded: chain P residue 318 TYR Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 88 THR Chi-restraints excluded: chain U residue 181 THR Chi-restraints excluded: chain U residue 223 VAL Chi-restraints excluded: chain U residue 297 THR Chi-restraints excluded: chain U residue 319 MET Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain Z residue 70 GLN Chi-restraints excluded: chain Z residue 81 ASP Chi-restraints excluded: chain Z residue 127 SER Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 226 LEU Chi-restraints excluded: chain l residue 79 ILE Chi-restraints excluded: chain l residue 139 LEU Chi-restraints excluded: chain o residue 69 SER Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 127 VAL Chi-restraints excluded: chain Q residue 338 LYS Chi-restraints excluded: chain Q residue 352 ILE Chi-restraints excluded: chain V residue 86 ILE Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain V residue 133 LEU Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 145 ASN Chi-restraints excluded: chain V residue 223 VAL Chi-restraints excluded: chain V residue 285 GLU Chi-restraints excluded: chain V residue 297 THR Chi-restraints excluded: chain a residue 20 THR Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 108 LYS Chi-restraints excluded: chain a residue 127 SER Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 86 ILE Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 191 ILE Chi-restraints excluded: chain N residue 265 VAL Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 70 GLN Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain p residue 40 ASP Chi-restraints excluded: chain p residue 69 SER Chi-restraints excluded: chain p residue 77 GLU Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 56 GLU Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 318 TYR Chi-restraints excluded: chain W residue 86 ILE Chi-restraints excluded: chain W residue 88 THR Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 223 VAL Chi-restraints excluded: chain W residue 297 THR Chi-restraints excluded: chain W residue 319 MET Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 70 GLN Chi-restraints excluded: chain b residue 81 ASP Chi-restraints excluded: chain b residue 84 ASN Chi-restraints excluded: chain b residue 127 SER Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 226 LEU Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain c residue 139 LEU Chi-restraints excluded: chain e residue 40 ASP Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 338 LYS Chi-restraints excluded: chain S residue 352 ILE Chi-restraints excluded: chain T residue 86 ILE Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 103 MET Chi-restraints excluded: chain T residue 133 LEU Chi-restraints excluded: chain T residue 223 VAL Chi-restraints excluded: chain T residue 297 THR Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 70 GLN Chi-restraints excluded: chain X residue 108 LYS Chi-restraints excluded: chain X residue 127 SER Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 191 ILE Chi-restraints excluded: chain L residue 265 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 573 optimal weight: 30.0000 chunk 225 optimal weight: 0.7980 chunk 291 optimal weight: 0.9990 chunk 921 optimal weight: 9.9990 chunk 380 optimal weight: 50.0000 chunk 76 optimal weight: 9.9990 chunk 463 optimal weight: 8.9990 chunk 769 optimal weight: 0.9990 chunk 246 optimal weight: 6.9990 chunk 334 optimal weight: 10.0000 chunk 506 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN ** P 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 84 ASN l 8 ASN Q 99 ASN A 68 ASN ** R 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 84 ASN O 68 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.131169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.112781 restraints weight = 105366.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.111313 restraints weight = 251097.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.110344 restraints weight = 270953.455| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 77418 Z= 0.192 Angle : 0.512 10.135 104268 Z= 0.273 Chirality : 0.043 0.171 12342 Planarity : 0.003 0.051 13056 Dihedral : 4.295 21.939 10254 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.59 % Favored : 96.40 % Rotamer: Outliers : 2.57 % Allowed : 16.35 % Favored : 81.09 % 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: -0.14 (0.08), residues: 9648 helix: 1.94 (0.10), residues: 2502 sheet: -0.10 (0.11), residues: 2124 loop : -1.18 (0.08), residues: 5022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP W 117 HIS 0.003 0.001 HIS D 250 PHE 0.015 0.001 PHE B 92 TYR 0.016 0.001 TYR M 60 ARG 0.003 0.000 ARG E 221 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 660 time to evaluate : 7.181 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: C 66 MET cc_start: 0.6187 (ptp) cc_final: 0.5722 (ttp) REVERT: C 247 ASP cc_start: 0.8356 (m-30) cc_final: 0.8043 (m-30) REVERT: F 156 LYS cc_start: 0.6536 (pttt) cc_final: 0.5691 (tmtt) REVERT: I 70 GLN cc_start: 0.6655 (OUTLIER) cc_final: 0.6453 (mt0) REVERT: B 226 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8107 (pt) REVERT: P 27 ILE cc_start: 0.7058 (tt) cc_final: 0.6755 (mt) REVERT: P 137 VAL cc_start: 0.6333 (OUTLIER) cc_final: 0.5941 (p) REVERT: P 293 GLU cc_start: 0.6572 (tp30) cc_final: 0.6250 (mt-10) REVERT: P 345 MET cc_start: 0.6955 (ptp) cc_final: 0.6607 (ptp) REVERT: U 306 LYS cc_start: 0.8417 (tttt) cc_final: 0.7988 (ttpt) REVERT: U 318 TYR cc_start: 0.5104 (p90) cc_final: 0.4817 (p90) REVERT: Z 70 GLN cc_start: 0.6706 (OUTLIER) cc_final: 0.6396 (tt0) REVERT: M 226 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8196 (pt) REVERT: g 54 MET cc_start: 0.8678 (mmm) cc_final: 0.8428 (mmt) REVERT: Q 5 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.7111 (tt) REVERT: Q 56 GLU cc_start: 0.5760 (tt0) cc_final: 0.4628 (tp30) REVERT: Q 312 LYS cc_start: 0.7499 (mmtp) cc_final: 0.7250 (mmtp) REVERT: V 146 PHE cc_start: 0.6726 (t80) cc_final: 0.6471 (t80) REVERT: a 70 GLN cc_start: 0.6774 (OUTLIER) cc_final: 0.6429 (tt0) REVERT: a 93 VAL cc_start: 0.8733 (OUTLIER) cc_final: 0.8484 (m) REVERT: a 95 ASP cc_start: 0.6309 (m-30) cc_final: 0.5806 (m-30) REVERT: N 178 GLN cc_start: 0.5066 (tp40) cc_final: 0.4852 (mm-40) REVERT: D 247 ASP cc_start: 0.8362 (m-30) cc_final: 0.8035 (m-30) REVERT: G 70 GLN cc_start: 0.6682 (OUTLIER) cc_final: 0.6482 (mt0) REVERT: A 226 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8255 (pt) REVERT: R 10 ILE cc_start: 0.8534 (mm) cc_final: 0.8281 (mm) REVERT: R 27 ILE cc_start: 0.7024 (tt) cc_final: 0.6722 (mt) REVERT: R 137 VAL cc_start: 0.6326 (OUTLIER) cc_final: 0.5953 (p) REVERT: W 103 MET cc_start: 0.4716 (tmm) cc_final: 0.3675 (tpp) REVERT: b 70 GLN cc_start: 0.6627 (OUTLIER) cc_final: 0.6343 (tt0) REVERT: O 30 MET cc_start: 0.6007 (tmm) cc_final: 0.5729 (ttp) REVERT: O 226 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8185 (pt) REVERT: S 3 ILE cc_start: 0.7031 (mm) cc_final: 0.6774 (mm) REVERT: S 5 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7184 (tt) REVERT: S 56 GLU cc_start: 0.5669 (tt0) cc_final: 0.4556 (tp30) REVERT: T 103 MET cc_start: 0.4081 (OUTLIER) cc_final: 0.3757 (tpp) REVERT: X 70 GLN cc_start: 0.6735 (OUTLIER) cc_final: 0.6395 (tt0) REVERT: X 93 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8451 (m) REVERT: X 95 ASP cc_start: 0.6306 (m-30) cc_final: 0.5842 (m-30) REVERT: L 178 GLN cc_start: 0.5134 (tp40) cc_final: 0.4914 (mm-40) outliers start: 218 outliers final: 157 residues processed: 842 average time/residue: 0.6170 time to fit residues: 934.7731 Evaluate side-chains 772 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 598 time to evaluate : 7.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 51 THR Chi-restraints excluded: chain h residue 79 ILE Chi-restraints excluded: chain h residue 112 ASP Chi-restraints excluded: chain h residue 139 LEU Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain i residue 135 GLU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 25 ARG Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 70 GLN Chi-restraints excluded: chain I residue 127 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain k residue 51 THR Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 139 LEU Chi-restraints excluded: chain n residue 40 ASP Chi-restraints excluded: chain n residue 69 SER Chi-restraints excluded: chain n residue 77 GLU Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 56 GLU Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain P residue 203 VAL Chi-restraints excluded: chain P residue 314 VAL Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 88 THR Chi-restraints excluded: chain U residue 102 CYS Chi-restraints excluded: chain U residue 181 THR Chi-restraints excluded: chain U residue 223 VAL Chi-restraints excluded: chain U residue 297 THR Chi-restraints excluded: chain U residue 319 MET Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain Z residue 70 GLN Chi-restraints excluded: chain Z residue 81 ASP Chi-restraints excluded: chain Z residue 127 SER Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 226 LEU Chi-restraints excluded: chain l residue 51 THR Chi-restraints excluded: chain l residue 79 ILE Chi-restraints excluded: chain l residue 139 LEU Chi-restraints excluded: chain o residue 69 SER Chi-restraints excluded: chain o residue 71 MET Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 338 LYS Chi-restraints excluded: chain Q residue 352 ILE Chi-restraints excluded: chain V residue 86 ILE Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain V residue 108 GLU Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 145 ASN Chi-restraints excluded: chain V residue 223 VAL Chi-restraints excluded: chain V residue 297 THR Chi-restraints excluded: chain a residue 20 THR Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 108 LYS Chi-restraints excluded: chain a residue 127 SER Chi-restraints excluded: chain a residue 138 MET Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 86 ILE Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 191 ILE Chi-restraints excluded: chain N residue 265 VAL Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 70 GLN Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain m residue 51 THR Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain m residue 139 LEU Chi-restraints excluded: chain p residue 40 ASP Chi-restraints excluded: chain p residue 64 LEU Chi-restraints excluded: chain p residue 69 SER Chi-restraints excluded: chain p residue 77 GLU Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 56 GLU Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain W residue 86 ILE Chi-restraints excluded: chain W residue 88 THR Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 223 VAL Chi-restraints excluded: chain W residue 297 THR Chi-restraints excluded: chain W residue 319 MET Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 70 GLN Chi-restraints excluded: chain b residue 81 ASP Chi-restraints excluded: chain b residue 127 SER Chi-restraints excluded: chain O residue 68 ASN Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 226 LEU Chi-restraints excluded: chain O residue 320 THR Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain c residue 139 LEU Chi-restraints excluded: chain e residue 40 ASP Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 338 LYS Chi-restraints excluded: chain S residue 352 ILE Chi-restraints excluded: chain T residue 30 MET Chi-restraints excluded: chain T residue 86 ILE Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 103 MET Chi-restraints excluded: chain T residue 133 LEU Chi-restraints excluded: chain T residue 136 VAL Chi-restraints excluded: chain T residue 223 VAL Chi-restraints excluded: chain T residue 285 GLU Chi-restraints excluded: chain T residue 297 THR Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 70 GLN Chi-restraints excluded: chain X residue 83 LEU Chi-restraints excluded: chain X residue 93 VAL Chi-restraints excluded: chain X residue 108 LYS Chi-restraints excluded: chain X residue 127 SER Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 191 ILE Chi-restraints excluded: chain L residue 265 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 21 optimal weight: 0.9980 chunk 254 optimal weight: 8.9990 chunk 247 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 952 optimal weight: 7.9990 chunk 432 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 748 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 664 optimal weight: 9.9990 chunk 158 optimal weight: 7.9990 overall best weight: 4.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 123 ASN B 68 ASN Q 99 ASN A 68 ASN R 68 ASN ** S 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.132342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.113309 restraints weight = 160028.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.111578 restraints weight = 320734.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.112043 restraints weight = 314080.783| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 77418 Z= 0.250 Angle : 0.544 10.040 104268 Z= 0.292 Chirality : 0.044 0.165 12342 Planarity : 0.004 0.053 13056 Dihedral : 4.489 22.405 10254 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.17 % Favored : 95.82 % Rotamer: Outliers : 2.94 % Allowed : 16.96 % Favored : 80.10 % 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: -0.38 (0.08), residues: 9648 helix: 1.78 (0.10), residues: 2496 sheet: -0.31 (0.11), residues: 2136 loop : -1.31 (0.08), residues: 5016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP U 117 HIS 0.008 0.001 HIS U 140 PHE 0.014 0.001 PHE V 98 TYR 0.020 0.001 TYR W 318 ARG 0.003 0.000 ARG V 221 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 893 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 250 poor density : 643 time to evaluate : 7.084 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: h 54 MET cc_start: 0.8846 (mmm) cc_final: 0.8349 (mmt) REVERT: C 66 MET cc_start: 0.6767 (ptp) cc_final: 0.6285 (ttp) REVERT: C 247 ASP cc_start: 0.8360 (m-30) cc_final: 0.8061 (m-30) REVERT: F 30 MET cc_start: 0.3777 (tpt) cc_final: 0.3477 (mmm) REVERT: F 156 LYS cc_start: 0.6818 (pttt) cc_final: 0.5953 (tmtt) REVERT: B 226 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8090 (pt) REVERT: P 66 MET cc_start: 0.6485 (ptt) cc_final: 0.5789 (ptp) REVERT: P 137 VAL cc_start: 0.6447 (OUTLIER) cc_final: 0.6058 (p) REVERT: P 345 MET cc_start: 0.7031 (ptp) cc_final: 0.6676 (ptp) REVERT: U 306 LYS cc_start: 0.8262 (tttt) cc_final: 0.8032 (ttpt) REVERT: Z 70 GLN cc_start: 0.6729 (OUTLIER) cc_final: 0.6420 (tt0) REVERT: M 226 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8175 (pt) REVERT: g 54 MET cc_start: 0.8716 (mmm) cc_final: 0.8463 (mmt) REVERT: Q 5 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7173 (tt) REVERT: Q 56 GLU cc_start: 0.5990 (tt0) cc_final: 0.4677 (tp30) REVERT: Q 312 LYS cc_start: 0.7460 (mmtp) cc_final: 0.7147 (mmtp) REVERT: a 70 GLN cc_start: 0.6853 (OUTLIER) cc_final: 0.6495 (tt0) REVERT: a 93 VAL cc_start: 0.8805 (OUTLIER) cc_final: 0.8573 (m) REVERT: J 54 MET cc_start: 0.8801 (mmm) cc_final: 0.8176 (mmt) REVERT: D 247 ASP cc_start: 0.8356 (m-30) cc_final: 0.8042 (m-30) REVERT: A 226 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8228 (pt) REVERT: R 137 VAL cc_start: 0.6352 (OUTLIER) cc_final: 0.5951 (p) REVERT: W 103 MET cc_start: 0.4702 (tmm) cc_final: 0.3941 (tpp) REVERT: W 306 LYS cc_start: 0.8392 (tttt) cc_final: 0.8098 (ttpt) REVERT: b 70 GLN cc_start: 0.6728 (OUTLIER) cc_final: 0.6421 (tt0) REVERT: O 226 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8177 (pt) REVERT: S 5 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7188 (tt) REVERT: S 56 GLU cc_start: 0.5947 (tt0) cc_final: 0.4576 (tp30) REVERT: S 312 LYS cc_start: 0.7472 (mmtp) cc_final: 0.7158 (mmtp) REVERT: T 103 MET cc_start: 0.4526 (OUTLIER) cc_final: 0.4088 (tpp) REVERT: X 70 GLN cc_start: 0.6830 (OUTLIER) cc_final: 0.6454 (tt0) REVERT: L 194 MET cc_start: 0.4399 (ptm) cc_final: 0.3838 (ppp) outliers start: 250 outliers final: 186 residues processed: 856 average time/residue: 0.6274 time to fit residues: 958.4022 Evaluate side-chains 784 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 584 time to evaluate : 7.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 51 THR Chi-restraints excluded: chain h residue 79 ILE Chi-restraints excluded: chain h residue 112 ASP Chi-restraints excluded: chain h residue 139 LEU Chi-restraints excluded: chain d residue 34 MET Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain i residue 77 GLU Chi-restraints excluded: chain i residue 135 GLU Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 25 ARG Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 140 HIS Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 127 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 202 ARG Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain k residue 51 THR Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 139 LEU Chi-restraints excluded: chain n residue 40 ASP Chi-restraints excluded: chain n residue 64 LEU Chi-restraints excluded: chain n residue 69 SER Chi-restraints excluded: chain n residue 77 GLU Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 56 GLU Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain P residue 203 VAL Chi-restraints excluded: chain P residue 314 VAL Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 88 THR Chi-restraints excluded: chain U residue 102 CYS Chi-restraints excluded: chain U residue 136 VAL Chi-restraints excluded: chain U residue 145 ASN Chi-restraints excluded: chain U residue 160 VAL Chi-restraints excluded: chain U residue 181 THR Chi-restraints excluded: chain U residue 223 VAL Chi-restraints excluded: chain U residue 228 GLU Chi-restraints excluded: chain U residue 297 THR Chi-restraints excluded: chain U residue 319 MET Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain Z residue 70 GLN Chi-restraints excluded: chain Z residue 81 ASP Chi-restraints excluded: chain Z residue 84 ASN Chi-restraints excluded: chain Z residue 95 ASP Chi-restraints excluded: chain Z residue 127 SER Chi-restraints excluded: chain M residue 86 ILE Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 170 LEU Chi-restraints excluded: chain M residue 226 LEU Chi-restraints excluded: chain M residue 320 THR Chi-restraints excluded: chain l residue 51 THR Chi-restraints excluded: chain l residue 62 ILE Chi-restraints excluded: chain l residue 79 ILE Chi-restraints excluded: chain l residue 139 LEU Chi-restraints excluded: chain o residue 69 SER Chi-restraints excluded: chain o residue 71 MET Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 118 ILE Chi-restraints excluded: chain Q residue 141 GLU Chi-restraints excluded: chain Q residue 338 LYS Chi-restraints excluded: chain Q residue 352 ILE Chi-restraints excluded: chain V residue 86 ILE Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 145 ASN Chi-restraints excluded: chain V residue 223 VAL Chi-restraints excluded: chain V residue 285 GLU Chi-restraints excluded: chain V residue 297 THR Chi-restraints excluded: chain a residue 20 THR Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 83 LEU Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 108 LYS Chi-restraints excluded: chain a residue 127 SER Chi-restraints excluded: chain a residue 138 MET Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 86 ILE Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 191 ILE Chi-restraints excluded: chain N residue 265 VAL Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain m residue 51 THR Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain m residue 139 LEU Chi-restraints excluded: chain p residue 40 ASP Chi-restraints excluded: chain p residue 64 LEU Chi-restraints excluded: chain p residue 69 SER Chi-restraints excluded: chain p residue 77 GLU Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 56 GLU Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain W residue 86 ILE Chi-restraints excluded: chain W residue 88 THR Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain W residue 136 VAL Chi-restraints excluded: chain W residue 160 VAL Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 223 VAL Chi-restraints excluded: chain W residue 228 GLU Chi-restraints excluded: chain W residue 297 THR Chi-restraints excluded: chain W residue 319 MET Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 70 GLN Chi-restraints excluded: chain b residue 81 ASP Chi-restraints excluded: chain b residue 127 SER Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 86 ILE Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 226 LEU Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 62 ILE Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain c residue 139 LEU Chi-restraints excluded: chain e residue 40 ASP Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 118 ILE Chi-restraints excluded: chain S residue 141 GLU Chi-restraints excluded: chain S residue 338 LYS Chi-restraints excluded: chain S residue 352 ILE Chi-restraints excluded: chain T residue 30 MET Chi-restraints excluded: chain T residue 86 ILE Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 103 MET Chi-restraints excluded: chain T residue 136 VAL Chi-restraints excluded: chain T residue 223 VAL Chi-restraints excluded: chain T residue 285 GLU Chi-restraints excluded: chain T residue 297 THR Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain X residue 70 GLN Chi-restraints excluded: chain X residue 83 LEU Chi-restraints excluded: chain X residue 108 LYS Chi-restraints excluded: chain X residue 127 SER Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 191 ILE Chi-restraints excluded: chain L residue 265 VAL Chi-restraints excluded: chain L residue 320 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 185 optimal weight: 5.9990 chunk 559 optimal weight: 2.9990 chunk 826 optimal weight: 10.0000 chunk 645 optimal weight: 10.0000 chunk 859 optimal weight: 8.9990 chunk 869 optimal weight: 10.0000 chunk 462 optimal weight: 20.0000 chunk 510 optimal weight: 6.9990 chunk 420 optimal weight: 9.9990 chunk 596 optimal weight: 0.7980 chunk 900 optimal weight: 4.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 HIS Z 84 ASN ** Q 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 99 ASN N 41 ASN ** S 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.133547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.115171 restraints weight = 159925.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.114824 restraints weight = 344710.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.114169 restraints weight = 314956.424| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 77418 Z= 0.231 Angle : 0.537 9.831 104268 Z= 0.286 Chirality : 0.044 0.166 12342 Planarity : 0.003 0.054 13056 Dihedral : 4.465 22.271 10254 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.92 % Favored : 96.07 % Rotamer: Outliers : 2.85 % Allowed : 18.13 % Favored : 79.03 % 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: -0.44 (0.08), residues: 9648 helix: 1.69 (0.10), residues: 2526 sheet: -0.39 (0.11), residues: 2136 loop : -1.33 (0.08), residues: 4986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP T 117 HIS 0.004 0.001 HIS E 140 PHE 0.015 0.001 PHE F 98 TYR 0.014 0.001 TYR M 60 ARG 0.003 0.000 ARG P 166 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 242 poor density : 617 time to evaluate : 7.130 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: h 54 MET cc_start: 0.8801 (mmm) cc_final: 0.8297 (mmt) REVERT: C 247 ASP cc_start: 0.8373 (m-30) cc_final: 0.8044 (m-30) REVERT: F 156 LYS cc_start: 0.6512 (pttt) cc_final: 0.5827 (tmtt) REVERT: B 226 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8100 (pt) REVERT: P 137 VAL cc_start: 0.6449 (OUTLIER) cc_final: 0.6042 (p) REVERT: P 345 MET cc_start: 0.7030 (ptp) cc_final: 0.6658 (ptp) REVERT: U 306 LYS cc_start: 0.8290 (tttt) cc_final: 0.8082 (ttpt) REVERT: Z 70 GLN cc_start: 0.6786 (OUTLIER) cc_final: 0.6467 (tt0) REVERT: M 226 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8188 (pt) REVERT: g 54 MET cc_start: 0.8658 (mmm) cc_final: 0.8396 (mmt) REVERT: Q 56 GLU cc_start: 0.5802 (tt0) cc_final: 0.4479 (tp30) REVERT: Q 312 LYS cc_start: 0.7526 (mmtp) cc_final: 0.7233 (mmtp) REVERT: V 170 LEU cc_start: 0.6034 (tp) cc_final: 0.5770 (tp) REVERT: a 70 GLN cc_start: 0.6811 (OUTLIER) cc_final: 0.6437 (tt0) REVERT: a 93 VAL cc_start: 0.8819 (OUTLIER) cc_final: 0.8593 (m) REVERT: J 54 MET cc_start: 0.8752 (mmm) cc_final: 0.8127 (mmt) REVERT: D 68 ASN cc_start: 0.6857 (OUTLIER) cc_final: 0.6579 (p0) REVERT: D 247 ASP cc_start: 0.8365 (m-30) cc_final: 0.8043 (m-30) REVERT: A 226 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8238 (pt) REVERT: R 137 VAL cc_start: 0.6455 (OUTLIER) cc_final: 0.6041 (p) REVERT: W 103 MET cc_start: 0.4786 (tmm) cc_final: 0.4099 (tpp) REVERT: W 306 LYS cc_start: 0.8384 (tttt) cc_final: 0.8105 (ttpt) REVERT: b 70 GLN cc_start: 0.6765 (OUTLIER) cc_final: 0.6460 (tt0) REVERT: O 226 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8189 (pt) REVERT: Y 54 MET cc_start: 0.8943 (mmm) cc_final: 0.8660 (mmt) REVERT: S 56 GLU cc_start: 0.5876 (tt0) cc_final: 0.4486 (tp30) REVERT: S 312 LYS cc_start: 0.7532 (mmtp) cc_final: 0.7219 (mmtp) REVERT: T 103 MET cc_start: 0.4575 (OUTLIER) cc_final: 0.4164 (tpp) REVERT: T 170 LEU cc_start: 0.6277 (tp) cc_final: 0.6011 (tp) REVERT: X 70 GLN cc_start: 0.6816 (OUTLIER) cc_final: 0.6447 (tt0) outliers start: 242 outliers final: 197 residues processed: 819 average time/residue: 0.6267 time to fit residues: 916.7152 Evaluate side-chains 793 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 583 time to evaluate : 7.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 51 THR Chi-restraints excluded: chain h residue 79 ILE Chi-restraints excluded: chain h residue 112 ASP Chi-restraints excluded: chain h residue 139 LEU Chi-restraints excluded: chain d residue 34 MET Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain i residue 77 GLU Chi-restraints excluded: chain i residue 135 GLU Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 25 ARG Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 140 HIS Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 127 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain k residue 51 THR Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 139 LEU Chi-restraints excluded: chain n residue 40 ASP Chi-restraints excluded: chain n residue 64 LEU Chi-restraints excluded: chain n residue 69 SER Chi-restraints excluded: chain n residue 77 GLU Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 56 GLU Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain P residue 203 VAL Chi-restraints excluded: chain P residue 314 VAL Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 88 THR Chi-restraints excluded: chain U residue 102 CYS Chi-restraints excluded: chain U residue 140 HIS Chi-restraints excluded: chain U residue 145 ASN Chi-restraints excluded: chain U residue 160 VAL Chi-restraints excluded: chain U residue 181 THR Chi-restraints excluded: chain U residue 223 VAL Chi-restraints excluded: chain U residue 228 GLU Chi-restraints excluded: chain U residue 297 THR Chi-restraints excluded: chain U residue 319 MET Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 70 GLN Chi-restraints excluded: chain Z residue 81 ASP Chi-restraints excluded: chain Z residue 84 ASN Chi-restraints excluded: chain Z residue 127 SER Chi-restraints excluded: chain M residue 86 ILE Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 226 LEU Chi-restraints excluded: chain M residue 320 THR Chi-restraints excluded: chain l residue 51 THR Chi-restraints excluded: chain l residue 62 ILE Chi-restraints excluded: chain l residue 79 ILE Chi-restraints excluded: chain l residue 139 LEU Chi-restraints excluded: chain o residue 69 SER Chi-restraints excluded: chain o residue 71 MET Chi-restraints excluded: chain o residue 142 ILE Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 118 ILE Chi-restraints excluded: chain Q residue 141 GLU Chi-restraints excluded: chain Q residue 338 LYS Chi-restraints excluded: chain V residue 86 ILE Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 145 ASN Chi-restraints excluded: chain V residue 160 VAL Chi-restraints excluded: chain V residue 223 VAL Chi-restraints excluded: chain V residue 297 THR Chi-restraints excluded: chain a residue 20 THR Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 83 LEU Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 108 LYS Chi-restraints excluded: chain a residue 127 SER Chi-restraints excluded: chain a residue 138 MET Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 86 ILE Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 191 ILE Chi-restraints excluded: chain N residue 289 SER Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 140 HIS Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain m residue 51 THR Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain m residue 139 LEU Chi-restraints excluded: chain p residue 40 ASP Chi-restraints excluded: chain p residue 64 LEU Chi-restraints excluded: chain p residue 69 SER Chi-restraints excluded: chain p residue 77 GLU Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 56 GLU Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 86 ILE Chi-restraints excluded: chain W residue 88 THR Chi-restraints excluded: chain W residue 140 HIS Chi-restraints excluded: chain W residue 151 VAL Chi-restraints excluded: chain W residue 160 VAL Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 223 VAL Chi-restraints excluded: chain W residue 228 GLU Chi-restraints excluded: chain W residue 297 THR Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 70 GLN Chi-restraints excluded: chain b residue 81 ASP Chi-restraints excluded: chain b residue 127 SER Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 86 ILE Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 226 LEU Chi-restraints excluded: chain O residue 320 THR Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 62 ILE Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain c residue 139 LEU Chi-restraints excluded: chain e residue 40 ASP Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain e residue 142 ILE Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 118 ILE Chi-restraints excluded: chain S residue 141 GLU Chi-restraints excluded: chain S residue 338 LYS Chi-restraints excluded: chain S residue 352 ILE Chi-restraints excluded: chain T residue 30 MET Chi-restraints excluded: chain T residue 86 ILE Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 103 MET Chi-restraints excluded: chain T residue 136 VAL Chi-restraints excluded: chain T residue 160 VAL Chi-restraints excluded: chain T residue 223 VAL Chi-restraints excluded: chain T residue 285 GLU Chi-restraints excluded: chain T residue 297 THR Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain X residue 70 GLN Chi-restraints excluded: chain X residue 83 LEU Chi-restraints excluded: chain X residue 95 ASP Chi-restraints excluded: chain X residue 108 LYS Chi-restraints excluded: chain X residue 127 SER Chi-restraints excluded: chain X residue 138 MET Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 191 ILE Chi-restraints excluded: chain L residue 265 VAL Chi-restraints excluded: chain L residue 289 SER Chi-restraints excluded: chain L residue 320 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 901 optimal weight: 10.0000 chunk 863 optimal weight: 20.0000 chunk 686 optimal weight: 20.0000 chunk 510 optimal weight: 5.9990 chunk 107 optimal weight: 0.5980 chunk 438 optimal weight: 5.9990 chunk 856 optimal weight: 6.9990 chunk 402 optimal weight: 30.0000 chunk 252 optimal weight: 6.9990 chunk 742 optimal weight: 10.0000 chunk 94 optimal weight: 20.0000 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 99 ASN ** V 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 105 GLN A 68 ASN ** S 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.117247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.096767 restraints weight = 147441.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.096161 restraints weight = 375569.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.096258 restraints weight = 302128.276| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 77418 Z= 0.273 Angle : 0.565 9.451 104268 Z= 0.301 Chirality : 0.045 0.215 12342 Planarity : 0.004 0.054 13056 Dihedral : 4.599 22.475 10254 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.43 % Favored : 95.56 % Rotamer: Outliers : 3.27 % Allowed : 18.13 % Favored : 78.60 % 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: -0.60 (0.08), residues: 9648 helix: 1.58 (0.10), residues: 2526 sheet: -0.46 (0.11), residues: 2076 loop : -1.44 (0.08), residues: 5046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP V 117 HIS 0.004 0.001 HIS f 66 PHE 0.016 0.001 PHE F 98 TYR 0.018 0.002 TYR l 99 ARG 0.003 0.000 ARG O 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 887 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 278 poor density : 609 time to evaluate : 7.306 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: h 54 MET cc_start: 0.8958 (mmm) cc_final: 0.8360 (mmt) REVERT: C 68 ASN cc_start: 0.6750 (p0) cc_final: 0.6444 (p0) REVERT: F 156 LYS cc_start: 0.6714 (pttt) cc_final: 0.5905 (tmtt) REVERT: B 226 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7942 (pt) REVERT: P 137 VAL cc_start: 0.6534 (OUTLIER) cc_final: 0.6093 (p) REVERT: P 345 MET cc_start: 0.7080 (ptp) cc_final: 0.6725 (ptp) REVERT: U 30 MET cc_start: 0.5029 (tpp) cc_final: 0.4618 (tpt) REVERT: Z 70 GLN cc_start: 0.6850 (OUTLIER) cc_final: 0.6532 (tt0) REVERT: M 226 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8179 (pt) REVERT: g 54 MET cc_start: 0.8674 (mmm) cc_final: 0.8395 (mmt) REVERT: Q 56 GLU cc_start: 0.6048 (tt0) cc_final: 0.4610 (tp30) REVERT: Q 312 LYS cc_start: 0.7511 (mmtp) cc_final: 0.7202 (mmtp) REVERT: V 316 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8307 (pp) REVERT: a 70 GLN cc_start: 0.6831 (OUTLIER) cc_final: 0.6439 (tt0) REVERT: a 93 VAL cc_start: 0.8864 (OUTLIER) cc_final: 0.8633 (m) REVERT: N 163 PHE cc_start: 0.5507 (t80) cc_final: 0.5230 (t80) REVERT: J 54 MET cc_start: 0.8956 (mmm) cc_final: 0.8245 (mmt) REVERT: D 247 ASP cc_start: 0.8377 (m-30) cc_final: 0.8019 (m-30) REVERT: D 320 THR cc_start: 0.5208 (OUTLIER) cc_final: 0.4757 (t) REVERT: A 226 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8225 (pt) REVERT: R 137 VAL cc_start: 0.6313 (OUTLIER) cc_final: 0.5901 (p) REVERT: W 103 MET cc_start: 0.4680 (tmm) cc_final: 0.3943 (tpp) REVERT: W 306 LYS cc_start: 0.8389 (tttt) cc_final: 0.8105 (ttpt) REVERT: b 70 GLN cc_start: 0.6830 (OUTLIER) cc_final: 0.6512 (tt0) REVERT: O 226 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8168 (pt) REVERT: Y 54 MET cc_start: 0.8871 (mmm) cc_final: 0.8569 (mmt) REVERT: S 56 GLU cc_start: 0.6086 (tt0) cc_final: 0.4616 (tp30) REVERT: S 312 LYS cc_start: 0.7469 (mmtp) cc_final: 0.7161 (mmtp) REVERT: T 103 MET cc_start: 0.4526 (OUTLIER) cc_final: 0.4058 (tpp) REVERT: X 70 GLN cc_start: 0.6841 (OUTLIER) cc_final: 0.6448 (tt0) REVERT: X 95 ASP cc_start: 0.6818 (OUTLIER) cc_final: 0.6613 (m-30) REVERT: L 163 PHE cc_start: 0.5434 (t80) cc_final: 0.5152 (t80) outliers start: 278 outliers final: 216 residues processed: 852 average time/residue: 0.6674 time to fit residues: 1019.2652 Evaluate side-chains 807 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 231 poor density : 576 time to evaluate : 7.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 51 THR Chi-restraints excluded: chain h residue 79 ILE Chi-restraints excluded: chain h residue 112 ASP Chi-restraints excluded: chain h residue 139 LEU Chi-restraints excluded: chain d residue 34 MET Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain i residue 77 GLU Chi-restraints excluded: chain i residue 135 GLU Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 25 ARG Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 140 HIS Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 127 SER Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 202 ARG Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain k residue 51 THR Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 139 LEU Chi-restraints excluded: chain n residue 40 ASP Chi-restraints excluded: chain n residue 64 LEU Chi-restraints excluded: chain n residue 69 SER Chi-restraints excluded: chain n residue 77 GLU Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 56 GLU Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain P residue 203 VAL Chi-restraints excluded: chain P residue 314 VAL Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 88 THR Chi-restraints excluded: chain U residue 102 CYS Chi-restraints excluded: chain U residue 140 HIS Chi-restraints excluded: chain U residue 145 ASN Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 160 VAL Chi-restraints excluded: chain U residue 181 THR Chi-restraints excluded: chain U residue 223 VAL Chi-restraints excluded: chain U residue 228 GLU Chi-restraints excluded: chain U residue 297 THR Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 70 GLN Chi-restraints excluded: chain Z residue 81 ASP Chi-restraints excluded: chain Z residue 127 SER Chi-restraints excluded: chain Z residue 138 MET Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 160 VAL Chi-restraints excluded: chain M residue 226 LEU Chi-restraints excluded: chain M residue 320 THR Chi-restraints excluded: chain l residue 51 THR Chi-restraints excluded: chain l residue 62 ILE Chi-restraints excluded: chain l residue 79 ILE Chi-restraints excluded: chain l residue 139 LEU Chi-restraints excluded: chain o residue 64 LEU Chi-restraints excluded: chain o residue 69 SER Chi-restraints excluded: chain o residue 71 MET Chi-restraints excluded: chain o residue 142 ILE Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 118 ILE Chi-restraints excluded: chain Q residue 141 GLU Chi-restraints excluded: chain Q residue 258 ILE Chi-restraints excluded: chain Q residue 338 LYS Chi-restraints excluded: chain V residue 86 ILE Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 145 ASN Chi-restraints excluded: chain V residue 160 VAL Chi-restraints excluded: chain V residue 208 LEU Chi-restraints excluded: chain V residue 223 VAL Chi-restraints excluded: chain V residue 285 GLU Chi-restraints excluded: chain V residue 297 THR Chi-restraints excluded: chain V residue 316 LEU Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 83 LEU Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 105 GLN Chi-restraints excluded: chain a residue 108 LYS Chi-restraints excluded: chain a residue 127 SER Chi-restraints excluded: chain a residue 138 MET Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 86 ILE Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 191 ILE Chi-restraints excluded: chain N residue 265 VAL Chi-restraints excluded: chain N residue 289 SER Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 140 ASP Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 140 HIS Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain m residue 51 THR Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain m residue 139 LEU Chi-restraints excluded: chain p residue 40 ASP Chi-restraints excluded: chain p residue 64 LEU Chi-restraints excluded: chain p residue 69 SER Chi-restraints excluded: chain p residue 77 GLU Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 56 GLU Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 86 ILE Chi-restraints excluded: chain W residue 88 THR Chi-restraints excluded: chain W residue 140 HIS Chi-restraints excluded: chain W residue 151 VAL Chi-restraints excluded: chain W residue 160 VAL Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 223 VAL Chi-restraints excluded: chain W residue 228 GLU Chi-restraints excluded: chain W residue 297 THR Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 54 THR Chi-restraints excluded: chain b residue 70 GLN Chi-restraints excluded: chain b residue 81 ASP Chi-restraints excluded: chain b residue 127 SER Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 86 ILE Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 226 LEU Chi-restraints excluded: chain O residue 320 THR Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 62 ILE Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain c residue 139 LEU Chi-restraints excluded: chain e residue 40 ASP Chi-restraints excluded: chain e residue 64 LEU Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain e residue 142 ILE Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 118 ILE Chi-restraints excluded: chain S residue 141 GLU Chi-restraints excluded: chain S residue 258 ILE Chi-restraints excluded: chain S residue 338 LYS Chi-restraints excluded: chain S residue 352 ILE Chi-restraints excluded: chain T residue 30 MET Chi-restraints excluded: chain T residue 86 ILE Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 103 MET Chi-restraints excluded: chain T residue 136 VAL Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain T residue 160 VAL Chi-restraints excluded: chain T residue 223 VAL Chi-restraints excluded: chain T residue 285 GLU Chi-restraints excluded: chain T residue 297 THR Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain X residue 70 GLN Chi-restraints excluded: chain X residue 83 LEU Chi-restraints excluded: chain X residue 95 ASP Chi-restraints excluded: chain X residue 108 LYS Chi-restraints excluded: chain X residue 127 SER Chi-restraints excluded: chain X residue 138 MET Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 191 ILE Chi-restraints excluded: chain L residue 265 VAL Chi-restraints excluded: chain L residue 289 SER Chi-restraints excluded: chain L residue 320 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 153 optimal weight: 6.9990 chunk 894 optimal weight: 9.9990 chunk 619 optimal weight: 7.9990 chunk 425 optimal weight: 7.9990 chunk 586 optimal weight: 20.0000 chunk 826 optimal weight: 10.0000 chunk 798 optimal weight: 9.9990 chunk 476 optimal weight: 10.0000 chunk 23 optimal weight: 0.7980 chunk 319 optimal weight: 7.9990 chunk 853 optimal weight: 0.6980 overall best weight: 4.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 99 ASN ** D 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 41 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.119894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.098756 restraints weight = 137298.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.097276 restraints weight = 361963.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.097357 restraints weight = 276047.921| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 77418 Z= 0.253 Angle : 0.555 10.928 104268 Z= 0.295 Chirality : 0.044 0.206 12342 Planarity : 0.004 0.055 13056 Dihedral : 4.566 22.464 10254 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.27 % Favored : 95.72 % Rotamer: Outliers : 3.11 % Allowed : 18.50 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.08), residues: 9648 helix: 1.55 (0.10), residues: 2526 sheet: -0.52 (0.11), residues: 2076 loop : -1.48 (0.08), residues: 5046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP T 117 HIS 0.004 0.001 HIS f 66 PHE 0.026 0.001 PHE E 146 TYR 0.018 0.001 TYR M 60 ARG 0.004 0.000 ARG M 218 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 264 poor density : 603 time to evaluate : 7.072 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: h 54 MET cc_start: 0.8910 (mmm) cc_final: 0.8303 (mmt) REVERT: C 68 ASN cc_start: 0.6844 (p0) cc_final: 0.6583 (p0) REVERT: F 117 TRP cc_start: 0.6681 (t60) cc_final: 0.6262 (t60) REVERT: F 156 LYS cc_start: 0.6540 (pttt) cc_final: 0.5761 (tmtt) REVERT: F 319 MET cc_start: 0.6807 (ttp) cc_final: 0.6341 (ptm) REVERT: B 226 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7930 (pt) REVERT: P 137 VAL cc_start: 0.6386 (OUTLIER) cc_final: 0.5963 (p) REVERT: P 345 MET cc_start: 0.7118 (ptp) cc_final: 0.6756 (ptp) REVERT: U 30 MET cc_start: 0.5302 (tpp) cc_final: 0.4965 (tpt) REVERT: Z 70 GLN cc_start: 0.6924 (OUTLIER) cc_final: 0.6614 (tt0) REVERT: M 226 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8107 (pt) REVERT: g 54 MET cc_start: 0.8618 (mmm) cc_final: 0.8388 (mmt) REVERT: Q 56 GLU cc_start: 0.6155 (tt0) cc_final: 0.4666 (tp30) REVERT: Q 312 LYS cc_start: 0.7509 (mmtp) cc_final: 0.7219 (mmtp) REVERT: V 316 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8336 (pp) REVERT: a 70 GLN cc_start: 0.6884 (OUTLIER) cc_final: 0.6493 (tt0) REVERT: a 93 VAL cc_start: 0.8885 (OUTLIER) cc_final: 0.8629 (m) REVERT: N 163 PHE cc_start: 0.5478 (t80) cc_final: 0.5220 (t80) REVERT: J 54 MET cc_start: 0.8960 (mmm) cc_final: 0.8219 (mmt) REVERT: D 247 ASP cc_start: 0.8481 (m-30) cc_final: 0.8114 (m-30) REVERT: D 320 THR cc_start: 0.5296 (OUTLIER) cc_final: 0.4864 (t) REVERT: A 226 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8039 (pt) REVERT: R 137 VAL cc_start: 0.6309 (OUTLIER) cc_final: 0.5886 (p) REVERT: W 103 MET cc_start: 0.4808 (tmm) cc_final: 0.4123 (tpp) REVERT: W 306 LYS cc_start: 0.8388 (tttt) cc_final: 0.8112 (ttpt) REVERT: b 70 GLN cc_start: 0.6878 (OUTLIER) cc_final: 0.6582 (tt0) REVERT: O 226 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8129 (pt) REVERT: Y 54 MET cc_start: 0.8784 (mmm) cc_final: 0.8487 (mmt) REVERT: S 56 GLU cc_start: 0.6181 (tt0) cc_final: 0.4676 (tp30) REVERT: S 312 LYS cc_start: 0.7512 (mmtp) cc_final: 0.7224 (mmtp) REVERT: T 103 MET cc_start: 0.4668 (OUTLIER) cc_final: 0.4129 (tpp) REVERT: T 146 PHE cc_start: 0.7048 (t80) cc_final: 0.6720 (t80) REVERT: T 194 MET cc_start: 0.5742 (ttp) cc_final: 0.5438 (ttp) REVERT: X 70 GLN cc_start: 0.6906 (OUTLIER) cc_final: 0.6518 (tt0) REVERT: L 163 PHE cc_start: 0.5465 (t80) cc_final: 0.5167 (t80) outliers start: 264 outliers final: 217 residues processed: 827 average time/residue: 0.6376 time to fit residues: 936.5223 Evaluate side-chains 796 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 231 poor density : 565 time to evaluate : 7.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 51 THR Chi-restraints excluded: chain h residue 79 ILE Chi-restraints excluded: chain h residue 112 ASP Chi-restraints excluded: chain h residue 139 LEU Chi-restraints excluded: chain d residue 34 MET Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain i residue 77 GLU Chi-restraints excluded: chain i residue 135 GLU Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 25 ARG Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 140 HIS Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 127 SER Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 202 ARG Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain k residue 51 THR Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 139 LEU Chi-restraints excluded: chain n residue 40 ASP Chi-restraints excluded: chain n residue 64 LEU Chi-restraints excluded: chain n residue 69 SER Chi-restraints excluded: chain n residue 77 GLU Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 56 GLU Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain P residue 203 VAL Chi-restraints excluded: chain P residue 211 ILE Chi-restraints excluded: chain P residue 314 VAL Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 88 THR Chi-restraints excluded: chain U residue 102 CYS Chi-restraints excluded: chain U residue 140 HIS Chi-restraints excluded: chain U residue 145 ASN Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 160 VAL Chi-restraints excluded: chain U residue 181 THR Chi-restraints excluded: chain U residue 223 VAL Chi-restraints excluded: chain U residue 297 THR Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 70 GLN Chi-restraints excluded: chain Z residue 81 ASP Chi-restraints excluded: chain Z residue 127 SER Chi-restraints excluded: chain Z residue 138 MET Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 160 VAL Chi-restraints excluded: chain M residue 226 LEU Chi-restraints excluded: chain M residue 320 THR Chi-restraints excluded: chain l residue 51 THR Chi-restraints excluded: chain l residue 62 ILE Chi-restraints excluded: chain l residue 79 ILE Chi-restraints excluded: chain l residue 139 LEU Chi-restraints excluded: chain o residue 64 LEU Chi-restraints excluded: chain o residue 69 SER Chi-restraints excluded: chain o residue 71 MET Chi-restraints excluded: chain o residue 142 ILE Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 118 ILE Chi-restraints excluded: chain Q residue 141 GLU Chi-restraints excluded: chain Q residue 258 ILE Chi-restraints excluded: chain Q residue 338 LYS Chi-restraints excluded: chain V residue 86 ILE Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 145 ASN Chi-restraints excluded: chain V residue 160 VAL Chi-restraints excluded: chain V residue 208 LEU Chi-restraints excluded: chain V residue 223 VAL Chi-restraints excluded: chain V residue 253 ILE Chi-restraints excluded: chain V residue 285 GLU Chi-restraints excluded: chain V residue 297 THR Chi-restraints excluded: chain V residue 316 LEU Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 83 LEU Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 108 LYS Chi-restraints excluded: chain a residue 127 SER Chi-restraints excluded: chain a residue 138 MET Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 191 ILE Chi-restraints excluded: chain N residue 265 VAL Chi-restraints excluded: chain N residue 289 SER Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 140 HIS Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain m residue 51 THR Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain m residue 139 LEU Chi-restraints excluded: chain p residue 40 ASP Chi-restraints excluded: chain p residue 64 LEU Chi-restraints excluded: chain p residue 69 SER Chi-restraints excluded: chain p residue 77 GLU Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 56 GLU Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 86 ILE Chi-restraints excluded: chain W residue 88 THR Chi-restraints excluded: chain W residue 140 HIS Chi-restraints excluded: chain W residue 151 VAL Chi-restraints excluded: chain W residue 160 VAL Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 223 VAL Chi-restraints excluded: chain W residue 228 GLU Chi-restraints excluded: chain W residue 297 THR Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 54 THR Chi-restraints excluded: chain b residue 70 GLN Chi-restraints excluded: chain b residue 81 ASP Chi-restraints excluded: chain b residue 127 SER Chi-restraints excluded: chain b residue 138 MET Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 226 LEU Chi-restraints excluded: chain O residue 320 THR Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 62 ILE Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain c residue 139 LEU Chi-restraints excluded: chain e residue 40 ASP Chi-restraints excluded: chain e residue 64 LEU Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain e residue 142 ILE Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 118 ILE Chi-restraints excluded: chain S residue 141 GLU Chi-restraints excluded: chain S residue 258 ILE Chi-restraints excluded: chain S residue 338 LYS Chi-restraints excluded: chain S residue 352 ILE Chi-restraints excluded: chain T residue 30 MET Chi-restraints excluded: chain T residue 86 ILE Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 103 MET Chi-restraints excluded: chain T residue 136 VAL Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain T residue 160 VAL Chi-restraints excluded: chain T residue 223 VAL Chi-restraints excluded: chain T residue 253 ILE Chi-restraints excluded: chain T residue 285 GLU Chi-restraints excluded: chain T residue 297 THR Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain X residue 70 GLN Chi-restraints excluded: chain X residue 83 LEU Chi-restraints excluded: chain X residue 108 LYS Chi-restraints excluded: chain X residue 127 SER Chi-restraints excluded: chain X residue 138 MET Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 191 ILE Chi-restraints excluded: chain L residue 265 VAL Chi-restraints excluded: chain L residue 289 SER Chi-restraints excluded: chain L residue 320 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 547 optimal weight: 0.8980 chunk 340 optimal weight: 4.9990 chunk 683 optimal weight: 10.0000 chunk 447 optimal weight: 20.0000 chunk 779 optimal weight: 10.0000 chunk 810 optimal weight: 1.9990 chunk 918 optimal weight: 10.0000 chunk 830 optimal weight: 6.9990 chunk 895 optimal weight: 3.9990 chunk 819 optimal weight: 0.7980 chunk 405 optimal weight: 0.0020 overall best weight: 1.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 123 ASN ** P 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 41 ASN M 41 ASN ** Q 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.135136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.117371 restraints weight = 158848.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.115966 restraints weight = 260152.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.115044 restraints weight = 250047.551| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 77418 Z= 0.131 Angle : 0.494 12.643 104268 Z= 0.261 Chirality : 0.042 0.165 12342 Planarity : 0.003 0.057 13056 Dihedral : 4.139 21.176 10254 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.78 % Allowed : 19.92 % Favored : 78.31 % 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: -0.35 (0.08), residues: 9648 helix: 1.89 (0.10), residues: 2532 sheet: -0.34 (0.11), residues: 2184 loop : -1.36 (0.08), residues: 4932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP V 117 HIS 0.003 0.001 HIS e 72 PHE 0.022 0.001 PHE E 146 TYR 0.024 0.001 TYR M 60 ARG 0.007 0.000 ARG X 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 643 time to evaluate : 7.139 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: h 54 MET cc_start: 0.8884 (mmm) cc_final: 0.8351 (mmt) REVERT: C 68 ASN cc_start: 0.6523 (p0) cc_final: 0.6252 (p0) REVERT: F 117 TRP cc_start: 0.6518 (t60) cc_final: 0.6248 (t60) REVERT: F 146 PHE cc_start: 0.6339 (OUTLIER) cc_final: 0.6059 (t80) REVERT: F 158 TYR cc_start: 0.6837 (m-80) cc_final: 0.6620 (m-80) REVERT: F 318 TYR cc_start: 0.4661 (p90) cc_final: 0.4147 (p90) REVERT: F 319 MET cc_start: 0.6145 (ttp) cc_final: 0.5028 (ptm) REVERT: B 226 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8220 (pt) REVERT: n 40 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7608 (t0) REVERT: P 27 ILE cc_start: 0.7102 (tt) cc_final: 0.6898 (mt) REVERT: P 137 VAL cc_start: 0.6555 (OUTLIER) cc_final: 0.6140 (p) REVERT: U 30 MET cc_start: 0.4443 (tpp) cc_final: 0.4163 (tpt) REVERT: Z 27 ASP cc_start: 0.7592 (t70) cc_final: 0.7185 (t0) REVERT: Z 70 GLN cc_start: 0.6776 (OUTLIER) cc_final: 0.6496 (tt0) REVERT: Z 76 MET cc_start: 0.8406 (ttm) cc_final: 0.8154 (ttm) REVERT: M 226 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8160 (pt) REVERT: g 54 MET cc_start: 0.8546 (mmm) cc_final: 0.8323 (mmt) REVERT: Q 56 GLU cc_start: 0.5735 (tt0) cc_final: 0.4477 (tp30) REVERT: Q 312 LYS cc_start: 0.7429 (mmtp) cc_final: 0.7173 (mmtp) REVERT: V 145 ASN cc_start: 0.4842 (OUTLIER) cc_final: 0.4455 (p0) REVERT: a 70 GLN cc_start: 0.6786 (OUTLIER) cc_final: 0.6362 (tt0) REVERT: a 93 VAL cc_start: 0.8807 (OUTLIER) cc_final: 0.8575 (m) REVERT: N 163 PHE cc_start: 0.4737 (t80) cc_final: 0.4472 (t80) REVERT: J 54 MET cc_start: 0.8872 (mmm) cc_final: 0.8209 (mmt) REVERT: D 247 ASP cc_start: 0.8467 (m-30) cc_final: 0.8081 (m-30) REVERT: E 30 MET cc_start: 0.4916 (tpp) cc_final: 0.4572 (tpt) REVERT: E 318 TYR cc_start: 0.4590 (p90) cc_final: 0.4068 (p90) REVERT: A 226 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8242 (pt) REVERT: p 40 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7589 (t0) REVERT: R 27 ILE cc_start: 0.7082 (tt) cc_final: 0.6880 (mt) REVERT: R 137 VAL cc_start: 0.6522 (OUTLIER) cc_final: 0.6095 (p) REVERT: W 103 MET cc_start: 0.4591 (tmm) cc_final: 0.3965 (tpp) REVERT: W 306 LYS cc_start: 0.8373 (tttt) cc_final: 0.8048 (ttpt) REVERT: b 27 ASP cc_start: 0.7661 (t70) cc_final: 0.7233 (t0) REVERT: b 70 GLN cc_start: 0.6768 (OUTLIER) cc_final: 0.6486 (tt0) REVERT: b 76 MET cc_start: 0.8416 (ttm) cc_final: 0.8184 (ttm) REVERT: O 226 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8192 (pt) REVERT: Y 54 MET cc_start: 0.8757 (mmm) cc_final: 0.8474 (mmt) REVERT: S 56 GLU cc_start: 0.5685 (tt0) cc_final: 0.4395 (tp30) REVERT: S 96 LYS cc_start: 0.6266 (ttpt) cc_final: 0.5612 (mtmm) REVERT: S 312 LYS cc_start: 0.7465 (mmtp) cc_final: 0.7048 (mmtp) REVERT: T 103 MET cc_start: 0.4555 (OUTLIER) cc_final: 0.4024 (tpp) REVERT: X 70 GLN cc_start: 0.6804 (OUTLIER) cc_final: 0.6372 (tt0) REVERT: L 163 PHE cc_start: 0.4702 (t80) cc_final: 0.4468 (t80) outliers start: 151 outliers final: 113 residues processed: 771 average time/residue: 0.6353 time to fit residues: 871.2020 Evaluate side-chains 716 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 587 time to evaluate : 7.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain i residue 77 GLU Chi-restraints excluded: chain i residue 135 GLU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 25 ARG Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 140 HIS Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 127 SER Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain n residue 40 ASP Chi-restraints excluded: chain n residue 64 LEU Chi-restraints excluded: chain n residue 69 SER Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 56 GLU Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain P residue 203 VAL Chi-restraints excluded: chain P residue 314 VAL Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 102 CYS Chi-restraints excluded: chain U residue 145 ASN Chi-restraints excluded: chain U residue 160 VAL Chi-restraints excluded: chain U residue 228 GLU Chi-restraints excluded: chain U residue 297 THR Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 70 GLN Chi-restraints excluded: chain Z residue 81 ASP Chi-restraints excluded: chain Z residue 127 SER Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 226 LEU Chi-restraints excluded: chain M residue 320 THR Chi-restraints excluded: chain l residue 51 THR Chi-restraints excluded: chain l residue 79 ILE Chi-restraints excluded: chain o residue 71 MET Chi-restraints excluded: chain o residue 142 ILE Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 118 ILE Chi-restraints excluded: chain Q residue 141 GLU Chi-restraints excluded: chain Q residue 338 LYS Chi-restraints excluded: chain V residue 86 ILE Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 145 ASN Chi-restraints excluded: chain V residue 160 VAL Chi-restraints excluded: chain V residue 297 THR Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 127 SER Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 140 HIS Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain m residue 139 LEU Chi-restraints excluded: chain p residue 40 ASP Chi-restraints excluded: chain p residue 69 SER Chi-restraints excluded: chain p residue 77 GLU Chi-restraints excluded: chain R residue 56 GLU Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 86 ILE Chi-restraints excluded: chain W residue 145 ASN Chi-restraints excluded: chain W residue 160 VAL Chi-restraints excluded: chain W residue 228 GLU Chi-restraints excluded: chain W residue 297 THR Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 54 THR Chi-restraints excluded: chain b residue 70 GLN Chi-restraints excluded: chain b residue 81 ASP Chi-restraints excluded: chain b residue 127 SER Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 226 LEU Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain e residue 40 ASP Chi-restraints excluded: chain e residue 142 ILE Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain S residue 118 ILE Chi-restraints excluded: chain S residue 338 LYS Chi-restraints excluded: chain S residue 352 ILE Chi-restraints excluded: chain T residue 30 MET Chi-restraints excluded: chain T residue 86 ILE Chi-restraints excluded: chain T residue 103 MET Chi-restraints excluded: chain T residue 136 VAL Chi-restraints excluded: chain T residue 160 VAL Chi-restraints excluded: chain T residue 297 THR Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 70 GLN Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 265 VAL Chi-restraints excluded: chain L residue 320 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 808 optimal weight: 10.0000 chunk 944 optimal weight: 20.0000 chunk 534 optimal weight: 20.0000 chunk 297 optimal weight: 20.0000 chunk 384 optimal weight: 4.9990 chunk 196 optimal weight: 20.0000 chunk 152 optimal weight: 9.9990 chunk 428 optimal weight: 6.9990 chunk 338 optimal weight: 9.9990 chunk 448 optimal weight: 30.0000 chunk 510 optimal weight: 5.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 328 ASN I 123 ASN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 224 ASN U 328 ASN Z 123 ASN M 41 ASN ** M 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 99 ASN V 328 ASN a 105 GLN a 123 ASN ** D 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 ASN G 123 ASN A 140 HIS b 123 ASN Y 66 HIS T 328 ASN X 105 GLN X 123 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.116106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.095079 restraints weight = 146830.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.094489 restraints weight = 405550.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.095238 restraints weight = 277637.511| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 77418 Z= 0.377 Angle : 0.646 11.364 104268 Z= 0.342 Chirality : 0.047 0.328 12342 Planarity : 0.004 0.052 13056 Dihedral : 4.863 27.776 10254 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.08 % Allowed : 20.23 % Favored : 77.68 % 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: -0.82 (0.08), residues: 9648 helix: 1.42 (0.10), residues: 2520 sheet: -0.56 (0.11), residues: 2028 loop : -1.60 (0.08), residues: 5100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 117 HIS 0.008 0.002 HIS l 66 PHE 0.035 0.002 PHE W 146 TYR 0.023 0.002 TYR W 269 ARG 0.005 0.001 ARG O 218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19915.05 seconds wall clock time: 349 minutes 0.14 seconds (20940.14 seconds total)