Starting phenix.real_space_refine on Thu Oct 10 03:21:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ilp_60672/10_2024/9ilp_60672.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ilp_60672/10_2024/9ilp_60672.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ilp_60672/10_2024/9ilp_60672.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ilp_60672/10_2024/9ilp_60672.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ilp_60672/10_2024/9ilp_60672.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ilp_60672/10_2024/9ilp_60672.cif" } resolution = 3.4 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 ------------------------------------------------------------------------------- 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= 0.007 sd= 2.338 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 252 5.16 5 C 32472 2.51 5 N 8580 2.21 5 O 9876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 51180 Number of models: 1 Model: "" Number of chains: 24 Chain: "a" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain: "b" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain: "c" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain: "d" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain: "e" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain: "f" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain: "g" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain: "h" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain: "i" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain: "j" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain: "k" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain: "l" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain: "A" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2918 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 14, 'TRANS': 352} Chain: "B" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2918 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 14, 'TRANS': 352} Chain: "C" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2918 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 14, 'TRANS': 352} Chain: "D" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2918 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 14, 'TRANS': 352} Chain: "E" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2918 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 14, 'TRANS': 352} Chain: "F" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2918 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 14, 'TRANS': 352} Chain: "G" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2918 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 14, 'TRANS': 352} Chain: "H" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2918 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 14, 'TRANS': 352} Chain: "I" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2918 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 14, 'TRANS': 352} Chain: "J" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2918 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 14, 'TRANS': 352} Chain: "K" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2918 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 14, 'TRANS': 352} Chain: "L" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2918 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 14, 'TRANS': 352} Time building chain proxies: 20.79, per 1000 atoms: 0.41 Number of scatterers: 51180 At special positions: 0 Unit cell: (156.4, 156.4, 163.2, 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 252 16.00 O 9876 8.00 N 8580 7.00 C 32472 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: 8.65 Conformation dependent library (CDL) restraints added in 4.7 seconds 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12144 Finding SS restraints... Secondary structure from input PDB file: 222 helices and 85 sheets defined 47.6% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.50 Creating SS restraints... Processing helix chain 'a' and resid 4 through 13 removed outlier: 3.568A pdb=" N ASP a 8 " --> pdb=" O ILE a 4 " (cutoff:3.500A) Processing helix chain 'a' and resid 21 through 39 removed outlier: 3.804A pdb=" N GLU a 25 " --> pdb=" O GLU a 21 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL a 26 " --> pdb=" O SER a 22 " (cutoff:3.500A) Processing helix chain 'a' and resid 81 through 83 No H-bonds generated for 'chain 'a' and resid 81 through 83' Processing helix chain 'a' and resid 117 through 133 Processing helix chain 'a' and resid 158 through 168 Processing helix chain 'b' and resid 4 through 13 removed outlier: 3.622A pdb=" N ASP b 8 " --> pdb=" O ILE b 4 " (cutoff:3.500A) Processing helix chain 'b' and resid 21 through 39 removed outlier: 3.839A pdb=" N GLU b 25 " --> pdb=" O GLU b 21 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL b 26 " --> pdb=" O SER b 22 " (cutoff:3.500A) Processing helix chain 'b' and resid 81 through 83 No H-bonds generated for 'chain 'b' and resid 81 through 83' Processing helix chain 'b' and resid 117 through 133 removed outlier: 3.593A pdb=" N LYS b 121 " --> pdb=" O PRO b 117 " (cutoff:3.500A) Processing helix chain 'b' and resid 158 through 168 Processing helix chain 'c' and resid 4 through 13 removed outlier: 3.580A pdb=" N ASP c 8 " --> pdb=" O ILE c 4 " (cutoff:3.500A) Processing helix chain 'c' and resid 21 through 39 removed outlier: 3.639A pdb=" N GLU c 25 " --> pdb=" O GLU c 21 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL c 26 " --> pdb=" O SER c 22 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR c 36 " --> pdb=" O ASN c 32 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 83 No H-bonds generated for 'chain 'c' and resid 81 through 83' Processing helix chain 'c' and resid 117 through 133 removed outlier: 3.575A pdb=" N LYS c 121 " --> pdb=" O PRO c 117 " (cutoff:3.500A) Processing helix chain 'c' and resid 158 through 168 Processing helix chain 'd' and resid 4 through 13 removed outlier: 3.565A pdb=" N ASP d 8 " --> pdb=" O ILE d 4 " (cutoff:3.500A) Processing helix chain 'd' and resid 21 through 39 removed outlier: 3.782A pdb=" N GLU d 25 " --> pdb=" O GLU d 21 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL d 26 " --> pdb=" O SER d 22 " (cutoff:3.500A) Processing helix chain 'd' and resid 81 through 83 No H-bonds generated for 'chain 'd' and resid 81 through 83' Processing helix chain 'd' and resid 117 through 133 Processing helix chain 'd' and resid 158 through 168 Processing helix chain 'e' and resid 4 through 14 removed outlier: 3.597A pdb=" N ASP e 8 " --> pdb=" O ILE e 4 " (cutoff:3.500A) Processing helix chain 'e' and resid 21 through 39 removed outlier: 3.816A pdb=" N GLU e 25 " --> pdb=" O GLU e 21 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL e 26 " --> pdb=" O SER e 22 " (cutoff:3.500A) Processing helix chain 'e' and resid 81 through 83 No H-bonds generated for 'chain 'e' and resid 81 through 83' Processing helix chain 'e' and resid 117 through 133 removed outlier: 3.617A pdb=" N LYS e 121 " --> pdb=" O PRO e 117 " (cutoff:3.500A) Processing helix chain 'e' and resid 158 through 168 Processing helix chain 'f' and resid 4 through 13 removed outlier: 3.668A pdb=" N ASP f 8 " --> pdb=" O ILE f 4 " (cutoff:3.500A) Processing helix chain 'f' and resid 21 through 39 removed outlier: 3.632A pdb=" N GLU f 25 " --> pdb=" O GLU f 21 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL f 26 " --> pdb=" O SER f 22 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR f 36 " --> pdb=" O ASN f 32 " (cutoff:3.500A) Processing helix chain 'f' and resid 81 through 83 No H-bonds generated for 'chain 'f' and resid 81 through 83' Processing helix chain 'f' and resid 117 through 133 removed outlier: 3.524A pdb=" N LYS f 121 " --> pdb=" O PRO f 117 " (cutoff:3.500A) Processing helix chain 'f' and resid 158 through 168 Processing helix chain 'g' and resid 4 through 14 removed outlier: 3.570A pdb=" N ASP g 8 " --> pdb=" O ILE g 4 " (cutoff:3.500A) Processing helix chain 'g' and resid 21 through 39 removed outlier: 3.778A pdb=" N GLU g 25 " --> pdb=" O GLU g 21 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL g 26 " --> pdb=" O SER g 22 " (cutoff:3.500A) Processing helix chain 'g' and resid 81 through 83 No H-bonds generated for 'chain 'g' and resid 81 through 83' Processing helix chain 'g' and resid 117 through 133 Processing helix chain 'g' and resid 158 through 168 Processing helix chain 'h' and resid 4 through 13 removed outlier: 3.567A pdb=" N ASP h 8 " --> pdb=" O ILE h 4 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY h 13 " --> pdb=" O TYR h 9 " (cutoff:3.500A) Processing helix chain 'h' and resid 21 through 39 removed outlier: 3.855A pdb=" N GLU h 25 " --> pdb=" O GLU h 21 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL h 26 " --> pdb=" O SER h 22 " (cutoff:3.500A) Processing helix chain 'h' and resid 81 through 83 No H-bonds generated for 'chain 'h' and resid 81 through 83' Processing helix chain 'h' and resid 117 through 133 removed outlier: 3.671A pdb=" N LYS h 121 " --> pdb=" O PRO h 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 158 through 168 Processing helix chain 'i' and resid 4 through 13 removed outlier: 3.635A pdb=" N ASP i 8 " --> pdb=" O ILE i 4 " (cutoff:3.500A) Processing helix chain 'i' and resid 21 through 39 removed outlier: 3.825A pdb=" N GLU i 25 " --> pdb=" O GLU i 21 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL i 26 " --> pdb=" O SER i 22 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR i 36 " --> pdb=" O ASN i 32 " (cutoff:3.500A) Processing helix chain 'i' and resid 81 through 83 No H-bonds generated for 'chain 'i' and resid 81 through 83' Processing helix chain 'i' and resid 117 through 133 removed outlier: 3.610A pdb=" N LYS i 121 " --> pdb=" O PRO i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 158 through 168 Processing helix chain 'j' and resid 4 through 13 removed outlier: 3.563A pdb=" N ASP j 8 " --> pdb=" O ILE j 4 " (cutoff:3.500A) Processing helix chain 'j' and resid 21 through 39 removed outlier: 3.826A pdb=" N GLU j 25 " --> pdb=" O GLU j 21 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL j 26 " --> pdb=" O SER j 22 " (cutoff:3.500A) Processing helix chain 'j' and resid 81 through 83 No H-bonds generated for 'chain 'j' and resid 81 through 83' Processing helix chain 'j' and resid 117 through 133 Processing helix chain 'j' and resid 158 through 168 Processing helix chain 'k' and resid 4 through 13 removed outlier: 3.620A pdb=" N ASP k 8 " --> pdb=" O ILE k 4 " (cutoff:3.500A) Processing helix chain 'k' and resid 21 through 39 removed outlier: 3.832A pdb=" N GLU k 25 " --> pdb=" O GLU k 21 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL k 26 " --> pdb=" O SER k 22 " (cutoff:3.500A) Processing helix chain 'k' and resid 81 through 83 No H-bonds generated for 'chain 'k' and resid 81 through 83' Processing helix chain 'k' and resid 117 through 133 removed outlier: 3.691A pdb=" N LYS k 121 " --> pdb=" O PRO k 117 " (cutoff:3.500A) Processing helix chain 'k' and resid 158 through 168 Processing helix chain 'l' and resid 4 through 13 removed outlier: 3.652A pdb=" N ASP l 8 " --> pdb=" O ILE l 4 " (cutoff:3.500A) Processing helix chain 'l' and resid 21 through 39 removed outlier: 3.634A pdb=" N GLU l 25 " --> pdb=" O GLU l 21 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL l 26 " --> pdb=" O SER l 22 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR l 36 " --> pdb=" O ASN l 32 " (cutoff:3.500A) Processing helix chain 'l' and resid 81 through 83 No H-bonds generated for 'chain 'l' and resid 81 through 83' Processing helix chain 'l' and resid 117 through 133 removed outlier: 3.523A pdb=" N LYS l 121 " --> pdb=" O PRO l 117 " (cutoff:3.500A) Processing helix chain 'l' and resid 158 through 168 Processing helix chain 'A' and resid 14 through 22 removed outlier: 3.587A pdb=" N ILE A 18 " --> pdb=" O GLY A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 42 Processing helix chain 'A' and resid 42 through 59 removed outlier: 3.839A pdb=" N CYS A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 Processing helix chain 'A' and resid 94 through 109 Processing helix chain 'A' and resid 175 through 201 removed outlier: 4.156A pdb=" N THR A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASP A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N SER A 183 " --> pdb=" O THR A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 231 removed outlier: 3.715A pdb=" N ASN A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 278 Processing helix chain 'A' and resid 280 through 286 removed outlier: 3.732A pdb=" N LEU A 284 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 320 Proline residue: A 294 - end of helix Proline residue: A 306 - end of helix removed outlier: 3.717A pdb=" N LEU A 311 " --> pdb=" O MET A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 334 Processing helix chain 'A' and resid 336 through 350 Processing helix chain 'A' and resid 354 through 362 Processing helix chain 'B' and resid 14 through 22 removed outlier: 3.536A pdb=" N ILE B 18 " --> pdb=" O GLY B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 42 through 59 removed outlier: 3.704A pdb=" N THR B 48 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N CYS B 59 " --> pdb=" O SER B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 94 through 109 Processing helix chain 'B' and resid 175 through 181 removed outlier: 3.914A pdb=" N THR B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL B 180 " --> pdb=" O ARG B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 201 Processing helix chain 'B' and resid 215 through 230 Processing helix chain 'B' and resid 262 through 278 Processing helix chain 'B' and resid 280 through 286 removed outlier: 3.719A pdb=" N LEU B 284 " --> pdb=" O PRO B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 320 Proline residue: B 294 - end of helix Proline residue: B 306 - end of helix removed outlier: 3.852A pdb=" N LEU B 311 " --> pdb=" O MET B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 334 Processing helix chain 'B' and resid 336 through 351 Processing helix chain 'B' and resid 354 through 362 Processing helix chain 'C' and resid 14 through 22 removed outlier: 3.585A pdb=" N ILE C 18 " --> pdb=" O GLY C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 42 Processing helix chain 'C' and resid 42 through 59 removed outlier: 3.880A pdb=" N CYS C 59 " --> pdb=" O SER C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 87 Processing helix chain 'C' and resid 94 through 109 Processing helix chain 'C' and resid 175 through 181 removed outlier: 3.931A pdb=" N THR C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL C 180 " --> pdb=" O ARG C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 201 Processing helix chain 'C' and resid 215 through 230 Processing helix chain 'C' and resid 262 through 278 Processing helix chain 'C' and resid 280 through 286 removed outlier: 3.964A pdb=" N LEU C 284 " --> pdb=" O PRO C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 320 removed outlier: 3.998A pdb=" N ARG C 293 " --> pdb=" O ASN C 289 " (cutoff:3.500A) Proline residue: C 294 - end of helix Proline residue: C 306 - end of helix removed outlier: 3.822A pdb=" N LEU C 311 " --> pdb=" O MET C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 334 Processing helix chain 'C' and resid 336 through 351 Processing helix chain 'C' and resid 354 through 362 Processing helix chain 'D' and resid 14 through 22 removed outlier: 3.594A pdb=" N ILE D 18 " --> pdb=" O GLY D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 42 Processing helix chain 'D' and resid 42 through 59 removed outlier: 3.860A pdb=" N CYS D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 87 Processing helix chain 'D' and resid 94 through 109 Processing helix chain 'D' and resid 175 through 181 removed outlier: 4.132A pdb=" N THR D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL D 180 " --> pdb=" O ARG D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 201 Processing helix chain 'D' and resid 215 through 230 Processing helix chain 'D' and resid 262 through 278 Processing helix chain 'D' and resid 280 through 286 removed outlier: 3.731A pdb=" N LEU D 284 " --> pdb=" O PRO D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 320 Proline residue: D 294 - end of helix Proline residue: D 306 - end of helix removed outlier: 3.806A pdb=" N LEU D 311 " --> pdb=" O MET D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 334 Processing helix chain 'D' and resid 336 through 350 Processing helix chain 'D' and resid 354 through 362 Processing helix chain 'E' and resid 14 through 22 removed outlier: 3.535A pdb=" N ILE E 18 " --> pdb=" O GLY E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 42 Processing helix chain 'E' and resid 42 through 59 removed outlier: 3.832A pdb=" N CYS E 59 " --> pdb=" O SER E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 87 Processing helix chain 'E' and resid 94 through 109 Processing helix chain 'E' and resid 175 through 201 removed outlier: 3.969A pdb=" N THR E 179 " --> pdb=" O SER E 175 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL E 180 " --> pdb=" O ARG E 176 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE E 181 " --> pdb=" O VAL E 177 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASP E 182 " --> pdb=" O ALA E 178 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N SER E 183 " --> pdb=" O THR E 179 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU E 184 " --> pdb=" O VAL E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 230 Processing helix chain 'E' and resid 262 through 278 Processing helix chain 'E' and resid 280 through 286 removed outlier: 3.731A pdb=" N LEU E 284 " --> pdb=" O PRO E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 320 Proline residue: E 294 - end of helix Proline residue: E 306 - end of helix removed outlier: 3.822A pdb=" N LEU E 311 " --> pdb=" O MET E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 334 Processing helix chain 'E' and resid 336 through 351 Processing helix chain 'E' and resid 354 through 362 Processing helix chain 'F' and resid 14 through 22 removed outlier: 3.537A pdb=" N ILE F 18 " --> pdb=" O GLY F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 42 through 59 removed outlier: 3.854A pdb=" N CYS F 59 " --> pdb=" O SER F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 86 Processing helix chain 'F' and resid 94 through 109 Processing helix chain 'F' and resid 175 through 201 removed outlier: 3.956A pdb=" N THR F 179 " --> pdb=" O SER F 175 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL F 180 " --> pdb=" O ARG F 176 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE F 181 " --> pdb=" O VAL F 177 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ASP F 182 " --> pdb=" O ALA F 178 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N SER F 183 " --> pdb=" O THR F 179 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU F 185 " --> pdb=" O ILE F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 230 Processing helix chain 'F' and resid 262 through 278 Processing helix chain 'F' and resid 280 through 286 removed outlier: 3.960A pdb=" N LEU F 284 " --> pdb=" O PRO F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 320 removed outlier: 4.002A pdb=" N ARG F 293 " --> pdb=" O ASN F 289 " (cutoff:3.500A) Proline residue: F 294 - end of helix Proline residue: F 306 - end of helix removed outlier: 3.739A pdb=" N LEU F 311 " --> pdb=" O MET F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 334 Processing helix chain 'F' and resid 336 through 351 Processing helix chain 'F' and resid 354 through 362 Processing helix chain 'G' and resid 14 through 22 removed outlier: 3.587A pdb=" N ILE G 18 " --> pdb=" O GLY G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 42 Processing helix chain 'G' and resid 42 through 59 removed outlier: 3.848A pdb=" N CYS G 59 " --> pdb=" O SER G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 Processing helix chain 'G' and resid 94 through 109 Processing helix chain 'G' and resid 175 through 181 removed outlier: 4.159A pdb=" N THR G 179 " --> pdb=" O SER G 175 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL G 180 " --> pdb=" O ARG G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 201 removed outlier: 3.501A pdb=" N MET G 190 " --> pdb=" O LYS G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 231 removed outlier: 3.715A pdb=" N ASN G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 262 through 278 Processing helix chain 'G' and resid 280 through 286 removed outlier: 3.727A pdb=" N LEU G 284 " --> pdb=" O PRO G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 320 Proline residue: G 294 - end of helix Proline residue: G 306 - end of helix removed outlier: 3.711A pdb=" N LEU G 311 " --> pdb=" O MET G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 334 Processing helix chain 'G' and resid 336 through 350 Processing helix chain 'G' and resid 354 through 362 Processing helix chain 'H' and resid 14 through 22 removed outlier: 3.539A pdb=" N ILE H 18 " --> pdb=" O GLY H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 42 Processing helix chain 'H' and resid 42 through 59 removed outlier: 3.806A pdb=" N CYS H 59 " --> pdb=" O SER H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 Processing helix chain 'H' and resid 94 through 109 Processing helix chain 'H' and resid 176 through 181 removed outlier: 3.976A pdb=" N VAL H 180 " --> pdb=" O ARG H 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 201 Processing helix chain 'H' and resid 215 through 230 Processing helix chain 'H' and resid 262 through 278 Processing helix chain 'H' and resid 280 through 286 removed outlier: 3.710A pdb=" N LEU H 284 " --> pdb=" O PRO H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 288 through 320 Proline residue: H 294 - end of helix Proline residue: H 306 - end of helix removed outlier: 3.826A pdb=" N LEU H 311 " --> pdb=" O MET H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 330 through 334 Processing helix chain 'H' and resid 336 through 350 Processing helix chain 'H' and resid 354 through 362 Processing helix chain 'I' and resid 14 through 22 removed outlier: 3.517A pdb=" N ILE I 18 " --> pdb=" O GLY I 14 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 42 Processing helix chain 'I' and resid 42 through 59 removed outlier: 3.830A pdb=" N CYS I 59 " --> pdb=" O SER I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 87 Processing helix chain 'I' and resid 94 through 109 Processing helix chain 'I' and resid 175 through 201 removed outlier: 3.942A pdb=" N THR I 179 " --> pdb=" O SER I 175 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL I 180 " --> pdb=" O ARG I 176 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE I 181 " --> pdb=" O VAL I 177 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASP I 182 " --> pdb=" O ALA I 178 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N SER I 183 " --> pdb=" O THR I 179 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS I 189 " --> pdb=" O GLU I 185 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET I 190 " --> pdb=" O LYS I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 215 through 230 Processing helix chain 'I' and resid 262 through 278 Processing helix chain 'I' and resid 280 through 286 removed outlier: 3.921A pdb=" N LEU I 284 " --> pdb=" O PRO I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 288 through 320 Proline residue: I 294 - end of helix Proline residue: I 306 - end of helix removed outlier: 3.818A pdb=" N LEU I 311 " --> pdb=" O MET I 307 " (cutoff:3.500A) Processing helix chain 'I' and resid 330 through 334 Processing helix chain 'I' and resid 336 through 351 Processing helix chain 'I' and resid 354 through 362 Processing helix chain 'J' and resid 14 through 22 removed outlier: 3.574A pdb=" N ILE J 18 " --> pdb=" O GLY J 14 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 42 Processing helix chain 'J' and resid 42 through 59 removed outlier: 4.215A pdb=" N THR J 48 " --> pdb=" O ILE J 44 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N CYS J 59 " --> pdb=" O SER J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 87 Processing helix chain 'J' and resid 94 through 109 Processing helix chain 'J' and resid 176 through 201 removed outlier: 4.003A pdb=" N VAL J 180 " --> pdb=" O ARG J 176 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASP J 182 " --> pdb=" O ALA J 178 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N SER J 183 " --> pdb=" O THR J 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 215 through 231 removed outlier: 3.751A pdb=" N ASN J 231 " --> pdb=" O GLN J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 262 through 278 Processing helix chain 'J' and resid 280 through 286 removed outlier: 3.770A pdb=" N LEU J 284 " --> pdb=" O PRO J 280 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 320 Proline residue: J 294 - end of helix Proline residue: J 306 - end of helix removed outlier: 3.812A pdb=" N LEU J 311 " --> pdb=" O MET J 307 " (cutoff:3.500A) Processing helix chain 'J' and resid 330 through 334 Processing helix chain 'J' and resid 336 through 350 Processing helix chain 'J' and resid 354 through 362 Processing helix chain 'K' and resid 14 through 22 removed outlier: 3.538A pdb=" N ILE K 18 " --> pdb=" O GLY K 14 " (cutoff:3.500A) Processing helix chain 'K' and resid 31 through 42 Processing helix chain 'K' and resid 42 through 59 removed outlier: 3.840A pdb=" N CYS K 59 " --> pdb=" O SER K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 87 Processing helix chain 'K' and resid 94 through 109 Processing helix chain 'K' and resid 176 through 201 removed outlier: 3.829A pdb=" N SER K 183 " --> pdb=" O THR K 179 " (cutoff:3.500A) Processing helix chain 'K' and resid 215 through 230 Processing helix chain 'K' and resid 262 through 278 Processing helix chain 'K' and resid 280 through 286 removed outlier: 3.729A pdb=" N LEU K 284 " --> pdb=" O PRO K 280 " (cutoff:3.500A) Processing helix chain 'K' and resid 288 through 320 Proline residue: K 294 - end of helix Proline residue: K 306 - end of helix removed outlier: 3.819A pdb=" N LEU K 311 " --> pdb=" O MET K 307 " (cutoff:3.500A) Processing helix chain 'K' and resid 330 through 334 Processing helix chain 'K' and resid 336 through 351 Processing helix chain 'K' and resid 354 through 362 Processing helix chain 'L' and resid 14 through 22 removed outlier: 3.510A pdb=" N ILE L 18 " --> pdb=" O GLY L 14 " (cutoff:3.500A) Processing helix chain 'L' and resid 31 through 40 Processing helix chain 'L' and resid 42 through 59 removed outlier: 3.522A pdb=" N ARG L 47 " --> pdb=" O GLU L 43 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N CYS L 59 " --> pdb=" O SER L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 87 Processing helix chain 'L' and resid 94 through 109 Processing helix chain 'L' and resid 175 through 181 removed outlier: 3.903A pdb=" N THR L 179 " --> pdb=" O SER L 175 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL L 180 " --> pdb=" O ARG L 176 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 201 Processing helix chain 'L' and resid 215 through 230 Processing helix chain 'L' and resid 262 through 278 Processing helix chain 'L' and resid 280 through 286 removed outlier: 3.918A pdb=" N LEU L 284 " --> pdb=" O PRO L 280 " (cutoff:3.500A) Processing helix chain 'L' and resid 288 through 320 removed outlier: 3.945A pdb=" N ARG L 293 " --> pdb=" O ASN L 289 " (cutoff:3.500A) Proline residue: L 294 - end of helix Proline residue: L 306 - end of helix removed outlier: 3.820A pdb=" N LEU L 311 " --> pdb=" O MET L 307 " (cutoff:3.500A) Processing helix chain 'L' and resid 330 through 334 Processing helix chain 'L' and resid 336 through 351 Processing helix chain 'L' and resid 354 through 362 Processing sheet with id=AA1, first strand: chain 'a' and resid 46 through 53 removed outlier: 3.759A pdb=" N TYR a 108 " --> pdb=" O VAL a 47 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR a 53 " --> pdb=" O GLY a 102 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY a 102 " --> pdb=" O THR a 53 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N THR a 109 " --> pdb=" O VAL a 70 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL a 70 " --> pdb=" O THR a 109 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 59 through 61 removed outlier: 4.227A pdb=" N LEU a 94 " --> pdb=" O LYS a 86 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS a 86 " --> pdb=" O LEU a 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 139 through 142 removed outlier: 3.531A pdb=" N ALA b 139 " --> pdb=" O THR a 148 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU c 145 " --> pdb=" O ILE c 142 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR c 148 " --> pdb=" O ALA d 139 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA d 139 " --> pdb=" O THR c 148 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA e 139 " --> pdb=" O THR d 148 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR f 148 " --> pdb=" O ALA g 139 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA g 139 " --> pdb=" O THR f 148 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR i 148 " --> pdb=" O ALA j 139 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA j 139 " --> pdb=" O THR i 148 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA k 139 " --> pdb=" O THR j 148 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU l 145 " --> pdb=" O ILE l 142 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR l 148 " --> pdb=" O ALA a 139 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA a 139 " --> pdb=" O THR l 148 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 152 through 153 removed outlier: 3.528A pdb=" N ILE a 156 " --> pdb=" O LYS a 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'b' and resid 46 through 53 removed outlier: 3.670A pdb=" N TYR b 108 " --> pdb=" O VAL b 47 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN b 49 " --> pdb=" O VAL b 106 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL b 106 " --> pdb=" O GLN b 49 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR b 53 " --> pdb=" O GLY b 102 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY b 102 " --> pdb=" O THR b 53 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS b 72 " --> pdb=" O GLU b 107 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N THR b 109 " --> pdb=" O VAL b 70 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL b 70 " --> pdb=" O THR b 109 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 59 through 61 removed outlier: 4.125A pdb=" N LEU b 94 " --> pdb=" O LYS b 86 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS b 86 " --> pdb=" O LEU b 94 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 152 through 153 removed outlier: 3.574A pdb=" N ILE b 156 " --> pdb=" O LYS b 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'c' and resid 46 through 50 removed outlier: 3.591A pdb=" N TYR c 108 " --> pdb=" O VAL c 47 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL c 106 " --> pdb=" O GLN c 49 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS c 72 " --> pdb=" O GLU c 107 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR c 109 " --> pdb=" O VAL c 70 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL c 70 " --> pdb=" O THR c 109 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'c' and resid 59 through 61 Processing sheet with id=AB1, first strand: chain 'c' and resid 152 through 153 removed outlier: 3.564A pdb=" N ILE c 156 " --> pdb=" O LYS c 153 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'd' and resid 46 through 53 removed outlier: 3.506A pdb=" N VAL d 47 " --> pdb=" O TYR d 108 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR d 108 " --> pdb=" O VAL d 47 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR d 53 " --> pdb=" O GLY d 102 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY d 102 " --> pdb=" O THR d 53 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS d 72 " --> pdb=" O GLU d 107 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR d 109 " --> pdb=" O VAL d 70 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL d 70 " --> pdb=" O THR d 109 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'd' and resid 59 through 61 removed outlier: 3.931A pdb=" N LEU d 94 " --> pdb=" O LYS d 86 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS d 86 " --> pdb=" O LEU d 94 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'd' and resid 152 through 153 removed outlier: 3.563A pdb=" N ILE d 156 " --> pdb=" O LYS d 153 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'e' and resid 46 through 53 removed outlier: 3.670A pdb=" N TYR e 108 " --> pdb=" O VAL e 47 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL e 106 " --> pdb=" O GLN e 49 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR e 53 " --> pdb=" O GLY e 102 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY e 102 " --> pdb=" O THR e 53 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THR e 109 " --> pdb=" O VAL e 70 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL e 70 " --> pdb=" O THR e 109 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'e' and resid 59 through 61 removed outlier: 3.997A pdb=" N LEU e 94 " --> pdb=" O LYS e 86 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS e 86 " --> pdb=" O LEU e 94 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'e' and resid 152 through 153 removed outlier: 3.578A pdb=" N ILE e 156 " --> pdb=" O LYS e 153 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'f' and resid 46 through 52 removed outlier: 3.589A pdb=" N TYR f 108 " --> pdb=" O VAL f 47 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL f 106 " --> pdb=" O GLN f 49 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS f 72 " --> pdb=" O GLU f 107 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR f 109 " --> pdb=" O VAL f 70 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL f 70 " --> pdb=" O THR f 109 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'f' and resid 59 through 61 Processing sheet with id=AC1, first strand: chain 'f' and resid 152 through 153 removed outlier: 3.600A pdb=" N ILE f 156 " --> pdb=" O LYS f 153 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'g' and resid 46 through 53 removed outlier: 3.503A pdb=" N VAL g 47 " --> pdb=" O TYR g 108 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR g 108 " --> pdb=" O VAL g 47 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR g 53 " --> pdb=" O GLY g 102 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY g 102 " --> pdb=" O THR g 53 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS g 72 " --> pdb=" O GLU g 107 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR g 109 " --> pdb=" O VAL g 70 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL g 70 " --> pdb=" O THR g 109 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'g' and resid 59 through 61 removed outlier: 3.926A pdb=" N LEU g 94 " --> pdb=" O LYS g 86 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS g 86 " --> pdb=" O LEU g 94 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'g' and resid 152 through 153 removed outlier: 3.521A pdb=" N ILE g 156 " --> pdb=" O LYS g 153 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'h' and resid 46 through 53 removed outlier: 3.666A pdb=" N TYR h 108 " --> pdb=" O VAL h 47 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN h 49 " --> pdb=" O VAL h 106 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL h 106 " --> pdb=" O GLN h 49 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR h 53 " --> pdb=" O GLY h 102 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY h 102 " --> pdb=" O THR h 53 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS h 72 " --> pdb=" O GLU h 107 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N THR h 109 " --> pdb=" O VAL h 70 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL h 70 " --> pdb=" O THR h 109 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'h' and resid 59 through 61 removed outlier: 3.975A pdb=" N LEU h 94 " --> pdb=" O LYS h 86 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS h 86 " --> pdb=" O LEU h 94 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'h' and resid 152 through 153 removed outlier: 3.593A pdb=" N ILE h 156 " --> pdb=" O LYS h 153 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'i' and resid 46 through 52 removed outlier: 3.605A pdb=" N TYR i 108 " --> pdb=" O VAL i 47 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL i 106 " --> pdb=" O GLN i 49 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS i 72 " --> pdb=" O GLU i 107 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR i 109 " --> pdb=" O VAL i 70 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL i 70 " --> pdb=" O THR i 109 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'i' and resid 59 through 61 Processing sheet with id=AD1, first strand: chain 'i' and resid 152 through 153 removed outlier: 3.604A pdb=" N ILE i 156 " --> pdb=" O LYS i 153 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'j' and resid 46 through 53 removed outlier: 3.708A pdb=" N TYR j 108 " --> pdb=" O VAL j 47 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR j 53 " --> pdb=" O GLY j 102 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY j 102 " --> pdb=" O THR j 53 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS j 72 " --> pdb=" O GLU j 107 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR j 109 " --> pdb=" O VAL j 70 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL j 70 " --> pdb=" O THR j 109 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'j' and resid 59 through 61 removed outlier: 4.097A pdb=" N LEU j 94 " --> pdb=" O LYS j 86 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS j 86 " --> pdb=" O LEU j 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'j' and resid 152 through 153 removed outlier: 3.525A pdb=" N ILE j 156 " --> pdb=" O LYS j 153 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'k' and resid 46 through 53 removed outlier: 3.653A pdb=" N TYR k 108 " --> pdb=" O VAL k 47 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL k 106 " --> pdb=" O GLN k 49 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR k 53 " --> pdb=" O GLY k 102 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY k 102 " --> pdb=" O THR k 53 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS k 72 " --> pdb=" O GLU k 107 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THR k 109 " --> pdb=" O VAL k 70 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL k 70 " --> pdb=" O THR k 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'k' and resid 59 through 61 removed outlier: 4.130A pdb=" N LEU k 94 " --> pdb=" O LYS k 86 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS k 86 " --> pdb=" O LEU k 94 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'k' and resid 152 through 153 removed outlier: 3.582A pdb=" N ILE k 156 " --> pdb=" O LYS k 153 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'l' and resid 46 through 50 removed outlier: 3.604A pdb=" N TYR l 108 " --> pdb=" O VAL l 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL l 106 " --> pdb=" O GLN l 49 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS l 72 " --> pdb=" O GLU l 107 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR l 109 " --> pdb=" O VAL l 70 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL l 70 " --> pdb=" O THR l 109 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'l' and resid 59 through 61 Processing sheet with id=AE1, first strand: chain 'l' and resid 152 through 153 removed outlier: 3.589A pdb=" N ILE l 156 " --> pdb=" O LYS l 153 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 60 through 66 removed outlier: 4.674A pdb=" N TYR A 61 " --> pdb=" O ASN A 326 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN A 326 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N VAL A 63 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N THR A 324 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ASP A 65 " --> pdb=" O LYS A 322 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 121 through 124 removed outlier: 3.878A pdb=" N VAL A 124 " --> pdb=" O TYR A 113 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TYR A 113 " --> pdb=" O VAL A 124 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 129 through 133 removed outlier: 3.588A pdb=" N LYS A 141 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 247 through 248 removed outlier: 6.353A pdb=" N LEU A 206 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU B 242 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU A 208 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 239 through 242 Processing sheet with id=AE7, first strand: chain 'B' and resid 60 through 66 removed outlier: 4.629A pdb=" N TYR B 61 " --> pdb=" O ASN B 326 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASN B 326 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL B 63 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N THR B 324 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASP B 65 " --> pdb=" O LYS B 322 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 121 through 124 removed outlier: 3.774A pdb=" N VAL B 124 " --> pdb=" O TYR B 113 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TYR B 113 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 129 through 133 removed outlier: 3.545A pdb=" N LYS B 141 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 247 through 248 removed outlier: 6.359A pdb=" N LEU B 206 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LEU C 242 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU B 208 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 60 through 66 removed outlier: 4.632A pdb=" N TYR C 61 " --> pdb=" O ASN C 326 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASN C 326 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL C 63 " --> pdb=" O THR C 324 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N THR C 324 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASP C 65 " --> pdb=" O LYS C 322 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 121 through 124 removed outlier: 3.713A pdb=" N VAL C 124 " --> pdb=" O TYR C 113 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TYR C 113 " --> pdb=" O VAL C 124 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 129 through 133 removed outlier: 3.566A pdb=" N LYS C 141 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 247 through 248 removed outlier: 6.364A pdb=" N LEU C 206 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LEU D 242 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU C 208 " --> pdb=" O LEU D 242 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 60 through 66 removed outlier: 4.671A pdb=" N TYR D 61 " --> pdb=" O ASN D 326 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ASN D 326 " --> pdb=" O TYR D 61 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL D 63 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N THR D 324 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ASP D 65 " --> pdb=" O LYS D 322 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 121 through 124 removed outlier: 3.861A pdb=" N VAL D 124 " --> pdb=" O TYR D 113 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N TYR D 113 " --> pdb=" O VAL D 124 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 129 through 133 removed outlier: 3.580A pdb=" N LYS D 141 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 247 through 248 removed outlier: 6.357A pdb=" N LEU D 206 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LEU E 242 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU D 208 " --> pdb=" O LEU E 242 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 60 through 66 removed outlier: 4.567A pdb=" N TYR E 61 " --> pdb=" O ASN E 326 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASN E 326 " --> pdb=" O TYR E 61 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N VAL E 63 " --> pdb=" O THR E 324 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N THR E 324 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ASP E 65 " --> pdb=" O LYS E 322 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 121 through 124 removed outlier: 3.764A pdb=" N VAL E 124 " --> pdb=" O TYR E 113 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR E 113 " --> pdb=" O VAL E 124 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 129 through 133 removed outlier: 3.543A pdb=" N LYS E 141 " --> pdb=" O GLU E 132 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 247 through 248 removed outlier: 6.374A pdb=" N LEU E 206 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LEU F 242 " --> pdb=" O LEU E 206 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU E 208 " --> pdb=" O LEU F 242 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 60 through 66 removed outlier: 4.611A pdb=" N TYR F 61 " --> pdb=" O ASN F 326 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASN F 326 " --> pdb=" O TYR F 61 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL F 63 " --> pdb=" O THR F 324 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N THR F 324 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASP F 65 " --> pdb=" O LYS F 322 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 121 through 124 removed outlier: 3.711A pdb=" N VAL F 124 " --> pdb=" O TYR F 113 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR F 113 " --> pdb=" O VAL F 124 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 129 through 133 removed outlier: 3.572A pdb=" N LYS F 141 " --> pdb=" O GLU F 132 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 247 through 248 removed outlier: 6.407A pdb=" N LEU F 206 " --> pdb=" O LEU G 240 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N LEU G 242 " --> pdb=" O LEU F 206 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU F 208 " --> pdb=" O LEU G 242 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 60 through 66 removed outlier: 4.671A pdb=" N TYR G 61 " --> pdb=" O ASN G 326 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ASN G 326 " --> pdb=" O TYR G 61 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N VAL G 63 " --> pdb=" O THR G 324 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N THR G 324 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ASP G 65 " --> pdb=" O LYS G 322 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 121 through 124 removed outlier: 3.875A pdb=" N VAL G 124 " --> pdb=" O TYR G 113 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TYR G 113 " --> pdb=" O VAL G 124 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 129 through 133 removed outlier: 3.586A pdb=" N LYS G 141 " --> pdb=" O GLU G 132 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 247 through 248 removed outlier: 6.361A pdb=" N LEU G 206 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N LEU H 242 " --> pdb=" O LEU G 206 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU G 208 " --> pdb=" O LEU H 242 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 60 through 66 removed outlier: 4.593A pdb=" N TYR H 61 " --> pdb=" O ASN H 326 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ASN H 326 " --> pdb=" O TYR H 61 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL H 63 " --> pdb=" O THR H 324 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N THR H 324 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ASP H 65 " --> pdb=" O LYS H 322 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 121 through 124 removed outlier: 3.743A pdb=" N VAL H 124 " --> pdb=" O TYR H 113 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR H 113 " --> pdb=" O VAL H 124 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'H' and resid 129 through 133 removed outlier: 3.506A pdb=" N LYS H 141 " --> pdb=" O GLU H 132 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'H' and resid 247 through 248 removed outlier: 6.376A pdb=" N LEU H 206 " --> pdb=" O LEU I 240 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N LEU I 242 " --> pdb=" O LEU H 206 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU H 208 " --> pdb=" O LEU I 242 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'I' and resid 60 through 66 removed outlier: 4.620A pdb=" N TYR I 61 " --> pdb=" O ASN I 326 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ASN I 326 " --> pdb=" O TYR I 61 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL I 63 " --> pdb=" O THR I 324 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N THR I 324 " --> pdb=" O VAL I 63 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ASP I 65 " --> pdb=" O LYS I 322 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'I' and resid 121 through 124 removed outlier: 3.710A pdb=" N VAL I 124 " --> pdb=" O TYR I 113 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR I 113 " --> pdb=" O VAL I 124 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'I' and resid 129 through 133 removed outlier: 3.557A pdb=" N LYS I 141 " --> pdb=" O GLU I 132 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'I' and resid 247 through 248 removed outlier: 6.333A pdb=" N LEU I 206 " --> pdb=" O LEU J 240 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LEU J 242 " --> pdb=" O LEU I 206 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU I 208 " --> pdb=" O LEU J 242 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'J' and resid 60 through 66 removed outlier: 4.673A pdb=" N TYR J 61 " --> pdb=" O ASN J 326 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ASN J 326 " --> pdb=" O TYR J 61 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL J 63 " --> pdb=" O THR J 324 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N THR J 324 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASP J 65 " --> pdb=" O LYS J 322 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'J' and resid 121 through 124 removed outlier: 3.803A pdb=" N VAL J 124 " --> pdb=" O TYR J 113 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N TYR J 113 " --> pdb=" O VAL J 124 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'J' and resid 129 through 133 removed outlier: 3.568A pdb=" N LYS J 141 " --> pdb=" O GLU J 132 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'J' and resid 247 through 248 removed outlier: 6.342A pdb=" N LEU J 206 " --> pdb=" O LEU K 240 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N LEU K 242 " --> pdb=" O LEU J 206 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU J 208 " --> pdb=" O LEU K 242 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'K' and resid 60 through 66 removed outlier: 4.608A pdb=" N TYR K 61 " --> pdb=" O ASN K 326 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ASN K 326 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL K 63 " --> pdb=" O THR K 324 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N THR K 324 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASP K 65 " --> pdb=" O LYS K 322 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'K' and resid 121 through 124 removed outlier: 3.742A pdb=" N VAL K 124 " --> pdb=" O TYR K 113 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR K 113 " --> pdb=" O VAL K 124 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'K' and resid 129 through 133 removed outlier: 3.505A pdb=" N LYS K 141 " --> pdb=" O GLU K 132 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'K' and resid 247 through 248 removed outlier: 6.371A pdb=" N LEU K 206 " --> pdb=" O LEU L 240 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU L 242 " --> pdb=" O LEU K 206 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU K 208 " --> pdb=" O LEU L 242 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'L' and resid 60 through 66 removed outlier: 4.619A pdb=" N TYR L 61 " --> pdb=" O ASN L 326 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ASN L 326 " --> pdb=" O TYR L 61 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL L 63 " --> pdb=" O THR L 324 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N THR L 324 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASP L 65 " --> pdb=" O LYS L 322 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'L' and resid 121 through 124 removed outlier: 3.712A pdb=" N VAL L 124 " --> pdb=" O TYR L 113 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR L 113 " --> pdb=" O VAL L 124 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'L' and resid 129 through 133 removed outlier: 3.555A pdb=" N LYS L 141 " --> pdb=" O GLU L 132 " (cutoff:3.500A) 2340 hydrogen bonds defined for protein. 6867 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: 19.00 Time building geometry restraints manager: 10.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 8748 1.28 - 1.41: 12057 1.41 - 1.55: 30803 1.55 - 1.68: 40 1.68 - 1.81: 444 Bond restraints: 52092 Sorted by residual: bond pdb=" C GLU J 43 " pdb=" O GLU J 43 " ideal model delta sigma weight residual 1.236 1.150 0.086 1.15e-02 7.56e+03 5.65e+01 bond pdb=" C LEU e 15 " pdb=" O LEU e 15 " ideal model delta sigma weight residual 1.234 1.150 0.084 1.24e-02 6.50e+03 4.60e+01 bond pdb=" CA SER D 175 " pdb=" C SER D 175 " ideal model delta sigma weight residual 1.523 1.446 0.077 1.24e-02 6.50e+03 3.86e+01 bond pdb=" CA SER A 175 " pdb=" C SER A 175 " ideal model delta sigma weight residual 1.523 1.447 0.077 1.24e-02 6.50e+03 3.83e+01 bond pdb=" CA SER G 175 " pdb=" C SER G 175 " ideal model delta sigma weight residual 1.523 1.449 0.074 1.24e-02 6.50e+03 3.61e+01 ... (remaining 52087 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 69142 2.53 - 5.07: 1117 5.07 - 7.60: 151 7.60 - 10.14: 43 10.14 - 12.67: 11 Bond angle restraints: 70464 Sorted by residual: angle pdb=" N GLU B 43 " pdb=" CA GLU B 43 " pdb=" C GLU B 43 " ideal model delta sigma weight residual 111.28 122.94 -11.66 1.09e+00 8.42e-01 1.14e+02 angle pdb=" N LEU I 214 " pdb=" CA LEU I 214 " pdb=" C LEU I 214 " ideal model delta sigma weight residual 110.65 123.32 -12.67 1.26e+00 6.30e-01 1.01e+02 angle pdb=" N ILE L 292 " pdb=" CA ILE L 292 " pdb=" C ILE L 292 " ideal model delta sigma weight residual 111.05 122.12 -11.07 1.25e+00 6.40e-01 7.85e+01 angle pdb=" N ILE I 292 " pdb=" CA ILE I 292 " pdb=" C ILE I 292 " ideal model delta sigma weight residual 111.09 122.07 -10.98 1.25e+00 6.40e-01 7.72e+01 angle pdb=" N VAL A 180 " pdb=" CA VAL A 180 " pdb=" C VAL A 180 " ideal model delta sigma weight residual 110.53 118.30 -7.77 9.40e-01 1.13e+00 6.83e+01 ... (remaining 70459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 28831 18.00 - 35.99: 2513 35.99 - 53.99: 437 53.99 - 71.99: 82 71.99 - 89.99: 33 Dihedral angle restraints: 31896 sinusoidal: 13056 harmonic: 18840 Sorted by residual: dihedral pdb=" C ILE C 292 " pdb=" N ILE C 292 " pdb=" CA ILE C 292 " pdb=" CB ILE C 292 " ideal model delta harmonic sigma weight residual -122.00 -136.71 14.71 0 2.50e+00 1.60e-01 3.46e+01 dihedral pdb=" C ILE F 292 " pdb=" N ILE F 292 " pdb=" CA ILE F 292 " pdb=" CB ILE F 292 " ideal model delta harmonic sigma weight residual -122.00 -136.33 14.33 0 2.50e+00 1.60e-01 3.29e+01 dihedral pdb=" C ILE L 292 " pdb=" N ILE L 292 " pdb=" CA ILE L 292 " pdb=" CB ILE L 292 " ideal model delta harmonic sigma weight residual -122.00 -135.91 13.91 0 2.50e+00 1.60e-01 3.10e+01 ... (remaining 31893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 7824 0.120 - 0.241: 164 0.241 - 0.361: 34 0.361 - 0.481: 12 0.481 - 0.602: 6 Chirality restraints: 8040 Sorted by residual: chirality pdb=" CA ILE C 292 " pdb=" N ILE C 292 " pdb=" C ILE C 292 " pdb=" CB ILE C 292 " both_signs ideal model delta sigma weight residual False 2.43 1.83 0.60 2.00e-01 2.50e+01 9.05e+00 chirality pdb=" CA ILE F 292 " pdb=" N ILE F 292 " pdb=" C ILE F 292 " pdb=" CB ILE F 292 " both_signs ideal model delta sigma weight residual False 2.43 1.85 0.59 2.00e-01 2.50e+01 8.63e+00 chirality pdb=" CA ILE L 292 " pdb=" N ILE L 292 " pdb=" C ILE L 292 " pdb=" CB ILE L 292 " both_signs ideal model delta sigma weight residual False 2.43 1.86 0.57 2.00e-01 2.50e+01 8.20e+00 ... (remaining 8037 not shown) Planarity restraints: 9096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 174 " 0.021 2.00e-02 2.50e+03 4.39e-02 1.92e+01 pdb=" C GLN D 174 " -0.076 2.00e-02 2.50e+03 pdb=" O GLN D 174 " 0.029 2.00e-02 2.50e+03 pdb=" N SER D 175 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 174 " -0.021 2.00e-02 2.50e+03 4.26e-02 1.82e+01 pdb=" C GLN A 174 " 0.074 2.00e-02 2.50e+03 pdb=" O GLN A 174 " -0.028 2.00e-02 2.50e+03 pdb=" N SER A 175 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU e 11 " 0.020 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C LEU e 11 " -0.068 2.00e-02 2.50e+03 pdb=" O LEU e 11 " 0.025 2.00e-02 2.50e+03 pdb=" N TYR e 12 " 0.023 2.00e-02 2.50e+03 ... (remaining 9093 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4026 2.74 - 3.28: 49077 3.28 - 3.82: 80685 3.82 - 4.36: 95859 4.36 - 4.90: 170744 Nonbonded interactions: 400391 Sorted by model distance: nonbonded pdb=" OG1 THR i 146 " pdb=" OG1 THR j 141 " model vdw 2.197 3.040 nonbonded pdb=" O ARG K 176 " pdb=" OG1 THR K 179 " model vdw 2.201 3.040 nonbonded pdb=" O ASN K 291 " pdb=" ND2 ASN K 295 " model vdw 2.202 3.120 nonbonded pdb=" O ASN H 291 " pdb=" ND2 ASN H 295 " model vdw 2.209 3.120 nonbonded pdb=" O ASN E 291 " pdb=" ND2 ASN E 295 " model vdw 2.212 3.120 ... (remaining 400386 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.320 Check model and map are aligned: 0.280 Set scattering table: 0.340 Process input model: 85.290 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.390 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:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 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 : 0.005 0.090 52092 Z= 0.334 Angle : 0.810 12.673 70464 Z= 0.506 Chirality : 0.053 0.602 8040 Planarity : 0.005 0.061 9096 Dihedral : 13.887 89.986 19752 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 1.17 % Allowed : 7.07 % Favored : 91.76 % Rotamer: Outliers : 0.49 % Allowed : 0.94 % Favored : 98.57 % Cbeta Deviations : 0.10 % 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: -0.33 (0.10), residues: 6396 helix: 1.23 (0.10), residues: 2772 sheet: -0.27 (0.24), residues: 624 loop : -1.65 (0.10), residues: 3000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 131 HIS 0.007 0.002 HIS H 343 PHE 0.024 0.001 PHE I 92 TYR 0.020 0.001 TYR g 12 ARG 0.006 0.000 ARG F 176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1893 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 1865 time to evaluate : 4.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 3 ILE cc_start: 0.8317 (mt) cc_final: 0.8074 (mt) REVERT: a 8 ASP cc_start: 0.8123 (m-30) cc_final: 0.7923 (m-30) REVERT: a 60 TYR cc_start: 0.8864 (m-80) cc_final: 0.8609 (m-80) REVERT: a 96 LYS cc_start: 0.8161 (mttm) cc_final: 0.7921 (mmtt) REVERT: b 2 GLN cc_start: 0.7465 (tt0) cc_final: 0.7225 (tt0) REVERT: b 41 MET cc_start: 0.8213 (mtm) cc_final: 0.7944 (mpp) REVERT: b 58 LYS cc_start: 0.8710 (mtpt) cc_final: 0.8402 (mtmm) REVERT: b 96 LYS cc_start: 0.8118 (mttp) cc_final: 0.7716 (mmtm) REVERT: c 167 TYR cc_start: 0.7790 (m-80) cc_final: 0.7580 (m-80) REVERT: d 8 ASP cc_start: 0.8088 (m-30) cc_final: 0.7831 (m-30) REVERT: d 49 GLN cc_start: 0.8463 (tt0) cc_final: 0.8214 (tt0) REVERT: d 60 TYR cc_start: 0.8850 (m-80) cc_final: 0.8607 (m-80) REVERT: d 96 LYS cc_start: 0.8399 (mttm) cc_final: 0.7957 (mmtt) REVERT: e 58 LYS cc_start: 0.8719 (mtpt) cc_final: 0.8391 (mtmm) REVERT: e 68 THR cc_start: 0.7963 (p) cc_final: 0.7594 (p) REVERT: e 96 LYS cc_start: 0.8044 (mttp) cc_final: 0.7576 (mmtm) REVERT: f 8 ASP cc_start: 0.7611 (m-30) cc_final: 0.7337 (m-30) REVERT: f 16 LYS cc_start: 0.6011 (OUTLIER) cc_final: 0.4874 (pttp) REVERT: f 49 GLN cc_start: 0.8130 (tt0) cc_final: 0.7678 (tt0) REVERT: g 3 ILE cc_start: 0.8247 (mt) cc_final: 0.7934 (mt) REVERT: g 49 GLN cc_start: 0.8408 (tt0) cc_final: 0.8200 (tt0) REVERT: g 60 TYR cc_start: 0.8836 (m-80) cc_final: 0.8633 (m-80) REVERT: g 96 LYS cc_start: 0.8372 (mttm) cc_final: 0.8027 (mmtt) REVERT: g 142 ILE cc_start: 0.7153 (mt) cc_final: 0.6939 (pt) REVERT: h 2 GLN cc_start: 0.7580 (tt0) cc_final: 0.7133 (tt0) REVERT: h 58 LYS cc_start: 0.8710 (mtpt) cc_final: 0.8333 (mtmm) REVERT: h 96 LYS cc_start: 0.7877 (mttp) cc_final: 0.7458 (mmtm) REVERT: h 146 THR cc_start: 0.9128 (m) cc_final: 0.8896 (m) REVERT: i 16 LYS cc_start: 0.6151 (OUTLIER) cc_final: 0.5066 (pttp) REVERT: j 60 TYR cc_start: 0.8806 (m-80) cc_final: 0.8604 (m-80) REVERT: j 96 LYS cc_start: 0.8037 (mttm) cc_final: 0.7489 (mmtt) REVERT: k 49 GLN cc_start: 0.8026 (tt0) cc_final: 0.7808 (tt0) REVERT: k 58 LYS cc_start: 0.8685 (mtpt) cc_final: 0.8353 (mtmm) REVERT: k 96 LYS cc_start: 0.7913 (mttp) cc_final: 0.7549 (mmtm) REVERT: l 2 GLN cc_start: 0.6815 (tt0) cc_final: 0.6614 (tt0) REVERT: l 49 GLN cc_start: 0.8270 (tt0) cc_final: 0.7878 (tt0) REVERT: l 167 TYR cc_start: 0.7877 (m-80) cc_final: 0.7605 (m-80) REVERT: A 21 MET cc_start: 0.6711 (mmp) cc_final: 0.6270 (tpp) REVERT: A 22 GLU cc_start: 0.7371 (tp30) cc_final: 0.6895 (tp30) REVERT: A 188 SER cc_start: 0.8269 (p) cc_final: 0.8066 (t) REVERT: B 79 LYS cc_start: 0.7114 (mtpt) cc_final: 0.6752 (mmmt) REVERT: C 31 LYS cc_start: 0.8242 (mttt) cc_final: 0.8012 (mtmt) REVERT: C 50 ASN cc_start: 0.8910 (m-40) cc_final: 0.8580 (m-40) REVERT: C 130 GLN cc_start: 0.7930 (tt0) cc_final: 0.7534 (tt0) REVERT: C 188 SER cc_start: 0.8312 (p) cc_final: 0.8059 (t) REVERT: C 291 ASN cc_start: 0.7866 (OUTLIER) cc_final: 0.7102 (m-40) REVERT: C 297 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7740 (mt-10) REVERT: D 22 GLU cc_start: 0.7346 (tp30) cc_final: 0.6852 (tp30) REVERT: D 188 SER cc_start: 0.8317 (p) cc_final: 0.8097 (t) REVERT: E 31 LYS cc_start: 0.8409 (mttt) cc_final: 0.8160 (mttt) REVERT: E 79 LYS cc_start: 0.7020 (mtpt) cc_final: 0.6686 (mmmt) REVERT: F 20 ASP cc_start: 0.6919 (m-30) cc_final: 0.6553 (m-30) REVERT: F 50 ASN cc_start: 0.8906 (m-40) cc_final: 0.8279 (m-40) REVERT: F 188 SER cc_start: 0.8287 (p) cc_final: 0.7920 (t) REVERT: F 203 VAL cc_start: 0.8690 (m) cc_final: 0.8219 (t) REVERT: F 291 ASN cc_start: 0.7851 (OUTLIER) cc_final: 0.7055 (m-40) REVERT: G 21 MET cc_start: 0.6699 (mmp) cc_final: 0.6246 (tpp) REVERT: G 22 GLU cc_start: 0.7066 (tp30) cc_final: 0.6663 (tp30) REVERT: G 50 ASN cc_start: 0.8844 (m-40) cc_final: 0.8635 (m110) REVERT: G 188 SER cc_start: 0.8312 (p) cc_final: 0.7978 (t) REVERT: H 26 HIS cc_start: 0.6869 (m90) cc_final: 0.6633 (m-70) REVERT: H 41 LYS cc_start: 0.7743 (mttt) cc_final: 0.7361 (mttt) REVERT: H 79 LYS cc_start: 0.7127 (mtpt) cc_final: 0.6786 (mmmt) REVERT: H 297 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7317 (mt-10) REVERT: I 20 ASP cc_start: 0.7244 (m-30) cc_final: 0.7008 (m-30) REVERT: I 31 LYS cc_start: 0.8377 (mttt) cc_final: 0.8150 (mtmt) REVERT: I 61 TYR cc_start: 0.8022 (m-80) cc_final: 0.7794 (m-80) REVERT: I 136 ASN cc_start: 0.7964 (m-40) cc_final: 0.7401 (m-40) REVERT: I 227 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8400 (tm-30) REVERT: I 297 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7677 (mt-10) REVERT: J 21 MET cc_start: 0.6668 (mmp) cc_final: 0.6189 (tpp) REVERT: J 31 LYS cc_start: 0.8581 (mttt) cc_final: 0.8276 (mtmt) REVERT: J 50 ASN cc_start: 0.8992 (m-40) cc_final: 0.8786 (m110) REVERT: J 188 SER cc_start: 0.8318 (p) cc_final: 0.8104 (t) REVERT: K 26 HIS cc_start: 0.6853 (m90) cc_final: 0.6571 (m-70) REVERT: K 31 LYS cc_start: 0.8321 (mttt) cc_final: 0.7951 (mttt) REVERT: K 79 LYS cc_start: 0.7185 (mtpt) cc_final: 0.6805 (mmmt) REVERT: L 31 LYS cc_start: 0.8246 (mttt) cc_final: 0.8008 (mtmt) REVERT: L 188 SER cc_start: 0.8307 (p) cc_final: 0.7956 (t) REVERT: L 227 GLN cc_start: 0.8673 (tm-30) cc_final: 0.8439 (tm-30) REVERT: L 297 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7741 (mt-10) outliers start: 28 outliers final: 14 residues processed: 1879 average time/residue: 0.5058 time to fit residues: 1559.2386 Evaluate side-chains 1202 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1184 time to evaluate : 4.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 15 LEU Chi-restraints excluded: chain f residue 16 LYS Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 291 ASN Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 291 ASN Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 291 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 537 optimal weight: 0.7980 chunk 482 optimal weight: 2.9990 chunk 267 optimal weight: 0.9990 chunk 164 optimal weight: 0.0870 chunk 325 optimal weight: 4.9990 chunk 257 optimal weight: 1.9990 chunk 498 optimal weight: 0.3980 chunk 192 optimal weight: 10.0000 chunk 303 optimal weight: 5.9990 chunk 371 optimal weight: 9.9990 chunk 577 optimal weight: 10.0000 overall best weight: 0.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 151 ASN b 138 GLN c 151 ASN ** c 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 151 ASN ** f 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 138 GLN i 151 ASN ** i 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 151 ASN k 138 GLN l 151 ASN ** l 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 37 GLN A 223 GLN A 326 ASN ** A 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 ASN B 90 ASN B 146 ASN B 174 GLN B 295 ASN B 326 ASN ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 ASN C 37 GLN C 90 ASN C 174 GLN C 326 ASN ** C 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 373 ASN D 37 GLN ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 GLN D 326 ASN ** D 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 ASN ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 ASN E 174 GLN E 223 GLN E 326 ASN E 343 HIS E 373 ASN F 90 ASN F 174 GLN F 281 GLN F 326 ASN ** F 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 373 ASN G 37 GLN ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 223 GLN G 231 ASN G 326 ASN ** G 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 373 ASN ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 146 ASN H 326 ASN ** H 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 373 ASN I 37 GLN I 90 ASN I 174 GLN I 281 GLN I 326 ASN ** I 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN J 223 GLN J 231 ASN J 326 ASN ** J 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 373 ASN K 90 ASN K 146 ASN K 295 ASN K 326 ASN K 343 HIS K 373 ASN L 37 GLN L 90 ASN L 130 GLN L 174 GLN L 223 GLN L 326 ASN L 373 ASN Total number of N/Q/H flips: 70 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 52092 Z= 0.180 Angle : 0.597 8.394 70464 Z= 0.318 Chirality : 0.043 0.317 8040 Planarity : 0.005 0.051 9096 Dihedral : 5.251 55.200 7029 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.84 % Allowed : 6.74 % Favored : 92.42 % Rotamer: Outliers : 2.25 % Allowed : 9.49 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.11), residues: 6396 helix: 1.63 (0.10), residues: 2772 sheet: 0.93 (0.21), residues: 792 loop : -1.75 (0.11), residues: 2832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 131 HIS 0.006 0.001 HIS H 343 PHE 0.014 0.001 PHE K 92 TYR 0.013 0.001 TYR I 300 ARG 0.003 0.000 ARG c 140 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1387 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1258 time to evaluate : 5.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 49 GLN cc_start: 0.8548 (tt0) cc_final: 0.8273 (tt0) REVERT: a 60 TYR cc_start: 0.9011 (m-80) cc_final: 0.8749 (m-80) REVERT: a 96 LYS cc_start: 0.8254 (mttm) cc_final: 0.8012 (mmtt) REVERT: b 2 GLN cc_start: 0.7506 (tt0) cc_final: 0.7260 (tt0) REVERT: b 41 MET cc_start: 0.8434 (mtm) cc_final: 0.8138 (mpp) REVERT: b 96 LYS cc_start: 0.8289 (mttp) cc_final: 0.7808 (mmtm) REVERT: d 8 ASP cc_start: 0.8063 (m-30) cc_final: 0.7827 (m-30) REVERT: d 60 TYR cc_start: 0.9033 (m-80) cc_final: 0.8706 (m-80) REVERT: d 96 LYS cc_start: 0.8396 (mttm) cc_final: 0.8066 (mmtt) REVERT: e 2 GLN cc_start: 0.7254 (tt0) cc_final: 0.7031 (tt0) REVERT: e 96 LYS cc_start: 0.8035 (mttp) cc_final: 0.7603 (mmtm) REVERT: f 5 THR cc_start: 0.7921 (p) cc_final: 0.7562 (t) REVERT: f 16 LYS cc_start: 0.6354 (OUTLIER) cc_final: 0.5214 (pttp) REVERT: f 116 MET cc_start: 0.8241 (tpt) cc_final: 0.7995 (tpt) REVERT: g 49 GLN cc_start: 0.8747 (tt0) cc_final: 0.8228 (tt0) REVERT: g 60 TYR cc_start: 0.8967 (m-80) cc_final: 0.8764 (m-80) REVERT: g 96 LYS cc_start: 0.8440 (mttm) cc_final: 0.8101 (mmtt) REVERT: h 96 LYS cc_start: 0.8043 (mttp) cc_final: 0.7561 (mmtm) REVERT: i 5 THR cc_start: 0.7782 (p) cc_final: 0.7403 (t) REVERT: i 8 ASP cc_start: 0.7912 (m-30) cc_final: 0.7309 (m-30) REVERT: i 16 LYS cc_start: 0.6407 (OUTLIER) cc_final: 0.5316 (pttp) REVERT: j 49 GLN cc_start: 0.8557 (tt0) cc_final: 0.8214 (tt0) REVERT: j 60 TYR cc_start: 0.9066 (m-80) cc_final: 0.8830 (m-80) REVERT: j 96 LYS cc_start: 0.8181 (mttm) cc_final: 0.7559 (mmtt) REVERT: k 2 GLN cc_start: 0.7348 (tt0) cc_final: 0.7050 (tt0) REVERT: k 73 MET cc_start: 0.8525 (ttm) cc_final: 0.8306 (ttm) REVERT: k 96 LYS cc_start: 0.7998 (mttp) cc_final: 0.7603 (mmtm) REVERT: l 5 THR cc_start: 0.7997 (p) cc_final: 0.7497 (t) REVERT: l 8 ASP cc_start: 0.7885 (m-30) cc_final: 0.7247 (m-30) REVERT: l 16 LYS cc_start: 0.6956 (OUTLIER) cc_final: 0.5372 (pttm) REVERT: l 167 TYR cc_start: 0.8277 (m-80) cc_final: 0.8045 (m-80) REVERT: A 21 MET cc_start: 0.6706 (mmp) cc_final: 0.6325 (tpp) REVERT: A 31 LYS cc_start: 0.8621 (mtmt) cc_final: 0.8110 (mtpt) REVERT: B 41 LYS cc_start: 0.7902 (mttt) cc_final: 0.7558 (mttt) REVERT: B 79 LYS cc_start: 0.7151 (mtpt) cc_final: 0.6746 (mmmt) REVERT: C 37 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7794 (mp10) REVERT: C 61 TYR cc_start: 0.8040 (m-80) cc_final: 0.7746 (m-80) REVERT: C 271 LYS cc_start: 0.8372 (mmtp) cc_final: 0.8045 (mmmt) REVERT: C 297 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7733 (mt-10) REVERT: D 21 MET cc_start: 0.7166 (mmm) cc_final: 0.5843 (tpp) REVERT: D 31 LYS cc_start: 0.8587 (mtmt) cc_final: 0.8373 (mtmt) REVERT: D 79 LYS cc_start: 0.8114 (mmmt) cc_final: 0.7481 (tptp) REVERT: D 225 GLU cc_start: 0.7347 (tt0) cc_final: 0.6942 (tt0) REVERT: E 50 ASN cc_start: 0.8739 (m110) cc_final: 0.8514 (m110) REVERT: E 79 LYS cc_start: 0.7143 (mtpt) cc_final: 0.6734 (mmmt) REVERT: E 192 ASN cc_start: 0.8475 (m-40) cc_final: 0.8267 (m110) REVERT: F 61 TYR cc_start: 0.7988 (m-80) cc_final: 0.7680 (m-80) REVERT: F 291 ASN cc_start: 0.7989 (OUTLIER) cc_final: 0.7608 (m-40) REVERT: G 17 ILE cc_start: 0.8537 (mp) cc_final: 0.8177 (mm) REVERT: G 21 MET cc_start: 0.6703 (mmp) cc_final: 0.6180 (tpp) REVERT: G 50 ASN cc_start: 0.8928 (m-40) cc_final: 0.8502 (m110) REVERT: G 188 SER cc_start: 0.8243 (p) cc_final: 0.8019 (t) REVERT: H 26 HIS cc_start: 0.6981 (m90) cc_final: 0.6676 (m-70) REVERT: H 41 LYS cc_start: 0.7664 (mttt) cc_final: 0.7455 (mttt) REVERT: H 51 MET cc_start: 0.8699 (ttm) cc_final: 0.8404 (mtp) REVERT: H 79 LYS cc_start: 0.7191 (mtpt) cc_final: 0.6770 (mmmt) REVERT: H 180 VAL cc_start: 0.8464 (OUTLIER) cc_final: 0.8192 (t) REVERT: H 297 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7606 (mt-10) REVERT: I 61 TYR cc_start: 0.8001 (m-80) cc_final: 0.7710 (m-80) REVERT: I 267 GLU cc_start: 0.6868 (mt-10) cc_final: 0.6656 (mt-10) REVERT: I 297 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7661 (mt-10) REVERT: J 21 MET cc_start: 0.6680 (mmp) cc_final: 0.6305 (tpp) REVERT: J 31 LYS cc_start: 0.8647 (mttt) cc_final: 0.8008 (mtpt) REVERT: J 50 ASN cc_start: 0.8944 (m-40) cc_final: 0.8592 (m110) REVERT: J 119 THR cc_start: 0.8030 (p) cc_final: 0.7691 (p) REVERT: K 26 HIS cc_start: 0.6893 (m90) cc_final: 0.6633 (m-70) REVERT: K 31 LYS cc_start: 0.8573 (mttt) cc_final: 0.8240 (mttt) REVERT: K 79 LYS cc_start: 0.7233 (mtpt) cc_final: 0.6791 (mmmt) REVERT: K 300 TYR cc_start: 0.8310 (OUTLIER) cc_final: 0.7569 (t80) REVERT: L 61 TYR cc_start: 0.8130 (m-80) cc_final: 0.7758 (m-80) REVERT: L 79 LYS cc_start: 0.8011 (mmmt) cc_final: 0.7673 (mmmt) REVERT: L 267 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6727 (mt-10) REVERT: L 297 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7702 (mt-10) outliers start: 129 outliers final: 72 residues processed: 1343 average time/residue: 0.4909 time to fit residues: 1103.3918 Evaluate side-chains 1203 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 1125 time to evaluate : 4.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 142 ILE Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain b residue 63 SER Chi-restraints excluded: chain b residue 156 ILE Chi-restraints excluded: chain c residue 69 SER Chi-restraints excluded: chain c residue 98 ASN Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain c residue 156 ILE Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain d residue 156 ILE Chi-restraints excluded: chain e residue 15 LEU Chi-restraints excluded: chain e residue 63 SER Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain e residue 156 ILE Chi-restraints excluded: chain e residue 166 VAL Chi-restraints excluded: chain f residue 16 LYS Chi-restraints excluded: chain f residue 69 SER Chi-restraints excluded: chain f residue 98 ASN Chi-restraints excluded: chain f residue 141 THR Chi-restraints excluded: chain f residue 156 ILE Chi-restraints excluded: chain g residue 109 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 156 ILE Chi-restraints excluded: chain h residue 63 SER Chi-restraints excluded: chain h residue 156 ILE Chi-restraints excluded: chain h residue 166 VAL Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 63 SER Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain i residue 98 ASN Chi-restraints excluded: chain i residue 141 THR Chi-restraints excluded: chain i residue 156 ILE Chi-restraints excluded: chain j residue 35 ILE Chi-restraints excluded: chain j residue 53 THR Chi-restraints excluded: chain j residue 69 SER Chi-restraints excluded: chain j residue 156 ILE Chi-restraints excluded: chain k residue 63 SER Chi-restraints excluded: chain k residue 156 ILE Chi-restraints excluded: chain l residue 16 LYS Chi-restraints excluded: chain l residue 69 SER Chi-restraints excluded: chain l residue 98 ASN Chi-restraints excluded: chain l residue 141 THR Chi-restraints excluded: chain l residue 156 ILE Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 291 ASN Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 296 ILE Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 217 LYS Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain K residue 43 GLU Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 296 ILE Chi-restraints excluded: chain K residue 300 TYR Chi-restraints excluded: chain L residue 43 GLU Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 217 LYS Chi-restraints excluded: chain L residue 300 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 320 optimal weight: 0.0270 chunk 179 optimal weight: 0.3980 chunk 480 optimal weight: 8.9990 chunk 393 optimal weight: 7.9990 chunk 159 optimal weight: 5.9990 chunk 578 optimal weight: 4.9990 chunk 625 optimal weight: 7.9990 chunk 515 optimal weight: 7.9990 chunk 573 optimal weight: 8.9990 chunk 197 optimal weight: 9.9990 chunk 464 optimal weight: 1.9990 overall best weight: 2.6844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 151 ASN c 151 ASN ** c 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 151 ASN ** f 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 151 ASN i 159 HIS j 151 ASN l 151 ASN ** l 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 ASN A 343 HIS ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 ASN B 343 HIS C 161 ASN C 326 ASN C 371 GLN D 326 ASN D 343 HIS ** E 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 326 ASN F 37 GLN ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 ASN F 326 ASN G 326 ASN G 343 HIS ** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 291 ASN H 326 ASN H 343 HIS I 37 GLN I 326 ASN I 371 GLN ** J 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 326 ASN ** K 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 291 ASN K 326 ASN L 37 GLN L 223 GLN L 326 ASN L 371 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 52092 Z= 0.292 Angle : 0.659 8.264 70464 Z= 0.347 Chirality : 0.045 0.285 8040 Planarity : 0.005 0.051 9096 Dihedral : 5.397 51.871 7009 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.94 % Allowed : 7.10 % Favored : 91.96 % Rotamer: Outliers : 3.09 % Allowed : 11.90 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.11), residues: 6396 helix: 1.42 (0.10), residues: 2796 sheet: 1.03 (0.21), residues: 816 loop : -1.85 (0.11), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP L 116 HIS 0.007 0.002 HIS C 343 PHE 0.016 0.002 PHE B 277 TYR 0.022 0.002 TYR I 300 ARG 0.004 0.001 ARG H 176 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1327 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 1150 time to evaluate : 4.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 49 GLN cc_start: 0.8733 (tt0) cc_final: 0.8403 (tt0) REVERT: a 96 LYS cc_start: 0.8481 (mttm) cc_final: 0.8136 (mmtt) REVERT: b 96 LYS cc_start: 0.8361 (mttp) cc_final: 0.7998 (mmtm) REVERT: c 41 MET cc_start: 0.8151 (mtt) cc_final: 0.7813 (mmm) REVERT: c 167 TYR cc_start: 0.8314 (m-80) cc_final: 0.8080 (m-80) REVERT: d 8 ASP cc_start: 0.8207 (m-30) cc_final: 0.7989 (m-30) REVERT: d 49 GLN cc_start: 0.8438 (tt0) cc_final: 0.8196 (tt0) REVERT: d 96 LYS cc_start: 0.8450 (mttm) cc_final: 0.7998 (mmtt) REVERT: e 2 GLN cc_start: 0.7736 (tt0) cc_final: 0.7518 (tt0) REVERT: e 83 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6833 (mp0) REVERT: e 96 LYS cc_start: 0.8354 (mttp) cc_final: 0.7949 (mmtm) REVERT: f 5 THR cc_start: 0.8176 (p) cc_final: 0.7767 (t) REVERT: f 16 LYS cc_start: 0.6333 (OUTLIER) cc_final: 0.5204 (pttp) REVERT: f 41 MET cc_start: 0.8042 (mtt) cc_final: 0.7740 (mmm) REVERT: g 49 GLN cc_start: 0.8775 (tt0) cc_final: 0.8317 (tt0) REVERT: g 96 LYS cc_start: 0.8450 (mttm) cc_final: 0.8027 (mmtt) REVERT: h 96 LYS cc_start: 0.8219 (mttp) cc_final: 0.7878 (mmtm) REVERT: i 5 THR cc_start: 0.8184 (p) cc_final: 0.7756 (t) REVERT: i 16 LYS cc_start: 0.6452 (OUTLIER) cc_final: 0.5231 (pttp) REVERT: j 49 GLN cc_start: 0.8741 (tt0) cc_final: 0.8395 (tt0) REVERT: j 96 LYS cc_start: 0.8472 (mttm) cc_final: 0.7783 (mmtt) REVERT: k 73 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.8270 (ttm) REVERT: k 96 LYS cc_start: 0.8262 (mttp) cc_final: 0.7902 (mmtm) REVERT: l 5 THR cc_start: 0.8303 (p) cc_final: 0.7888 (t) REVERT: l 16 LYS cc_start: 0.7039 (OUTLIER) cc_final: 0.5370 (pttm) REVERT: l 83 GLU cc_start: 0.5584 (mp0) cc_final: 0.5112 (mp0) REVERT: A 21 MET cc_start: 0.6866 (mmp) cc_final: 0.6208 (tpp) REVERT: A 105 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8182 (m-30) REVERT: A 272 SER cc_start: 0.8830 (t) cc_final: 0.8618 (p) REVERT: B 41 LYS cc_start: 0.8237 (mttt) cc_final: 0.7979 (mttt) REVERT: B 79 LYS cc_start: 0.7142 (mtpt) cc_final: 0.6706 (mmmt) REVERT: B 146 ASN cc_start: 0.5859 (m-40) cc_final: 0.5630 (m110) REVERT: C 203 VAL cc_start: 0.8817 (m) cc_final: 0.8234 (t) REVERT: C 271 LYS cc_start: 0.8406 (mmtp) cc_final: 0.8063 (mmmt) REVERT: D 21 MET cc_start: 0.7311 (mmm) cc_final: 0.6903 (tpt) REVERT: D 31 LYS cc_start: 0.8725 (mtmt) cc_final: 0.8349 (mtpt) REVERT: D 79 LYS cc_start: 0.8173 (mmmt) cc_final: 0.7630 (tptp) REVERT: E 42 ILE cc_start: 0.8186 (mm) cc_final: 0.7946 (mm) REVERT: E 79 LYS cc_start: 0.7127 (mtpt) cc_final: 0.6704 (mmmt) REVERT: E 146 ASN cc_start: 0.5899 (m-40) cc_final: 0.5697 (m110) REVERT: F 203 VAL cc_start: 0.8812 (m) cc_final: 0.8172 (t) REVERT: G 21 MET cc_start: 0.6776 (mmp) cc_final: 0.6142 (tpp) REVERT: H 79 LYS cc_start: 0.7178 (mtpt) cc_final: 0.6738 (mmmt) REVERT: H 146 ASN cc_start: 0.5846 (m-40) cc_final: 0.5604 (m110) REVERT: H 180 VAL cc_start: 0.8824 (OUTLIER) cc_final: 0.8481 (t) REVERT: H 297 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7609 (mt-10) REVERT: I 79 LYS cc_start: 0.7894 (mmmt) cc_final: 0.7448 (pttt) REVERT: I 203 VAL cc_start: 0.8789 (m) cc_final: 0.8219 (t) REVERT: J 21 MET cc_start: 0.6858 (mmp) cc_final: 0.6276 (tpp) REVERT: J 31 LYS cc_start: 0.8818 (mttt) cc_final: 0.8370 (mtpt) REVERT: J 119 THR cc_start: 0.8504 (OUTLIER) cc_final: 0.8257 (p) REVERT: J 148 ILE cc_start: 0.7295 (mm) cc_final: 0.7005 (mm) REVERT: K 31 LYS cc_start: 0.8716 (mttt) cc_final: 0.8324 (mttt) REVERT: K 50 ASN cc_start: 0.9017 (m-40) cc_final: 0.8695 (m110) REVERT: K 79 LYS cc_start: 0.7167 (mtpt) cc_final: 0.6717 (mmmt) REVERT: K 146 ASN cc_start: 0.5972 (m-40) cc_final: 0.5715 (m110) REVERT: K 300 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.7839 (t80) REVERT: L 79 LYS cc_start: 0.8104 (mmmt) cc_final: 0.7768 (mmmt) REVERT: L 271 LYS cc_start: 0.8432 (mmtp) cc_final: 0.8169 (mmmt) outliers start: 177 outliers final: 130 residues processed: 1232 average time/residue: 0.5068 time to fit residues: 1051.8266 Evaluate side-chains 1232 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1094 time to evaluate : 4.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 52 THR Chi-restraints excluded: chain a residue 69 SER Chi-restraints excluded: chain a residue 109 THR Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 166 VAL Chi-restraints excluded: chain b residue 87 LEU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 156 ILE Chi-restraints excluded: chain b residue 166 VAL Chi-restraints excluded: chain c residue 69 SER Chi-restraints excluded: chain c residue 70 VAL Chi-restraints excluded: chain c residue 98 ASN Chi-restraints excluded: chain c residue 105 ASP Chi-restraints excluded: chain c residue 109 THR Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain c residue 156 ILE Chi-restraints excluded: chain c residue 166 VAL Chi-restraints excluded: chain d residue 69 SER Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain d residue 156 ILE Chi-restraints excluded: chain d residue 166 VAL Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain e residue 70 VAL Chi-restraints excluded: chain e residue 156 ILE Chi-restraints excluded: chain e residue 166 VAL Chi-restraints excluded: chain f residue 16 LYS Chi-restraints excluded: chain f residue 69 SER Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 98 ASN Chi-restraints excluded: chain f residue 105 ASP Chi-restraints excluded: chain f residue 109 THR Chi-restraints excluded: chain f residue 141 THR Chi-restraints excluded: chain f residue 156 ILE Chi-restraints excluded: chain f residue 166 VAL Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 109 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 156 ILE Chi-restraints excluded: chain g residue 164 ILE Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain h residue 63 SER Chi-restraints excluded: chain h residue 69 SER Chi-restraints excluded: chain h residue 109 THR Chi-restraints excluded: chain h residue 156 ILE Chi-restraints excluded: chain h residue 166 VAL Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 63 SER Chi-restraints excluded: chain i residue 66 SER Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain i residue 70 VAL Chi-restraints excluded: chain i residue 98 ASN Chi-restraints excluded: chain i residue 105 ASP Chi-restraints excluded: chain i residue 109 THR Chi-restraints excluded: chain i residue 141 THR Chi-restraints excluded: chain i residue 156 ILE Chi-restraints excluded: chain i residue 166 VAL Chi-restraints excluded: chain j residue 63 SER Chi-restraints excluded: chain j residue 69 SER Chi-restraints excluded: chain j residue 109 THR Chi-restraints excluded: chain j residue 156 ILE Chi-restraints excluded: chain j residue 166 VAL Chi-restraints excluded: chain k residue 63 SER Chi-restraints excluded: chain k residue 69 SER Chi-restraints excluded: chain k residue 73 MET Chi-restraints excluded: chain k residue 156 ILE Chi-restraints excluded: chain k residue 166 VAL Chi-restraints excluded: chain l residue 16 LYS Chi-restraints excluded: chain l residue 69 SER Chi-restraints excluded: chain l residue 98 ASN Chi-restraints excluded: chain l residue 105 ASP Chi-restraints excluded: chain l residue 109 THR Chi-restraints excluded: chain l residue 141 THR Chi-restraints excluded: chain l residue 156 ILE Chi-restraints excluded: chain l residue 166 VAL Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 300 TYR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 288 ASN Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 105 ASP Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 298 LEU Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 326 ASN Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 105 ASP Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 298 LEU Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 300 TYR Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 326 ASN Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 300 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 571 optimal weight: 4.9990 chunk 435 optimal weight: 8.9990 chunk 300 optimal weight: 0.8980 chunk 64 optimal weight: 10.0000 chunk 276 optimal weight: 5.9990 chunk 388 optimal weight: 0.7980 chunk 580 optimal weight: 6.9990 chunk 614 optimal weight: 0.9980 chunk 303 optimal weight: 1.9990 chunk 550 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 151 ASN b 110 GLN d 151 ASN j 151 ASN k 110 GLN l 2 GLN ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 ASN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 ASN C 37 GLN C 130 GLN C 326 ASN C 343 HIS C 371 GLN ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 ASN D 371 GLN ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 ASN E 326 ASN F 281 GLN F 326 ASN F 343 HIS G 149 ASN G 161 ASN G 326 ASN H 50 ASN H 161 ASN H 326 ASN I 37 GLN ** I 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 326 ASN I 343 HIS I 371 GLN J 161 ASN J 326 ASN J 343 HIS K 161 ASN K 174 GLN K 326 ASN L 161 ASN L 326 ASN L 343 HIS Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 52092 Z= 0.186 Angle : 0.585 8.957 70464 Z= 0.306 Chirality : 0.043 0.243 8040 Planarity : 0.004 0.046 9096 Dihedral : 5.150 50.659 7002 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.80 % Allowed : 6.77 % Favored : 92.43 % Rotamer: Outliers : 3.41 % Allowed : 13.16 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.11), residues: 6396 helix: 1.61 (0.10), residues: 2772 sheet: 1.07 (0.21), residues: 816 loop : -1.77 (0.11), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 116 HIS 0.007 0.001 HIS G 343 PHE 0.014 0.001 PHE K 92 TYR 0.013 0.001 TYR a 88 ARG 0.002 0.000 ARG E 176 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1320 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 1125 time to evaluate : 4.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 49 GLN cc_start: 0.8712 (tt0) cc_final: 0.8400 (tt0) REVERT: a 96 LYS cc_start: 0.8544 (mttm) cc_final: 0.8177 (mmtt) REVERT: b 96 LYS cc_start: 0.8399 (mttp) cc_final: 0.8074 (mmtm) REVERT: b 110 GLN cc_start: 0.7366 (mt0) cc_final: 0.7041 (mt0) REVERT: c 41 MET cc_start: 0.8270 (mtt) cc_final: 0.8019 (mtt) REVERT: c 165 GLU cc_start: 0.8362 (tp30) cc_final: 0.7689 (mm-30) REVERT: c 167 TYR cc_start: 0.7986 (m-80) cc_final: 0.7757 (m-10) REVERT: d 49 GLN cc_start: 0.8511 (tt0) cc_final: 0.8308 (tt0) REVERT: d 96 LYS cc_start: 0.8563 (mttm) cc_final: 0.8135 (mmtt) REVERT: e 2 GLN cc_start: 0.7723 (tt0) cc_final: 0.7494 (tt0) REVERT: e 83 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6796 (mp0) REVERT: e 96 LYS cc_start: 0.8325 (mttp) cc_final: 0.7986 (mmtm) REVERT: e 110 GLN cc_start: 0.7126 (mt0) cc_final: 0.6728 (mt0) REVERT: f 5 THR cc_start: 0.8118 (p) cc_final: 0.7672 (t) REVERT: f 16 LYS cc_start: 0.6290 (OUTLIER) cc_final: 0.5092 (pttp) REVERT: f 116 MET cc_start: 0.8330 (tpt) cc_final: 0.8129 (tpt) REVERT: g 49 GLN cc_start: 0.8709 (tt0) cc_final: 0.8384 (tt0) REVERT: g 96 LYS cc_start: 0.8531 (mttm) cc_final: 0.8090 (mmtt) REVERT: h 96 LYS cc_start: 0.8303 (mttp) cc_final: 0.7980 (mmtm) REVERT: i 5 THR cc_start: 0.8072 (p) cc_final: 0.7645 (t) REVERT: i 16 LYS cc_start: 0.6298 (OUTLIER) cc_final: 0.5235 (pttp) REVERT: j 49 GLN cc_start: 0.8723 (tt0) cc_final: 0.8418 (tt0) REVERT: j 96 LYS cc_start: 0.8480 (mttm) cc_final: 0.7810 (mmtt) REVERT: k 73 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8241 (ttm) REVERT: k 96 LYS cc_start: 0.8335 (mttp) cc_final: 0.8020 (mmtm) REVERT: k 110 GLN cc_start: 0.7205 (mt0) cc_final: 0.6933 (mt0) REVERT: l 5 THR cc_start: 0.8203 (p) cc_final: 0.7809 (t) REVERT: l 16 LYS cc_start: 0.6890 (OUTLIER) cc_final: 0.5313 (pttm) REVERT: l 165 GLU cc_start: 0.8358 (tp30) cc_final: 0.7744 (mm-30) REVERT: A 21 MET cc_start: 0.6835 (mmp) cc_final: 0.6223 (tpp) REVERT: A 105 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.8065 (m-30) REVERT: A 272 SER cc_start: 0.8840 (t) cc_final: 0.8562 (p) REVERT: B 41 LYS cc_start: 0.8247 (mttt) cc_final: 0.7980 (mttt) REVERT: B 79 LYS cc_start: 0.7145 (mtpt) cc_final: 0.6690 (mmmt) REVERT: B 146 ASN cc_start: 0.5893 (m-40) cc_final: 0.5662 (m110) REVERT: C 146 ASN cc_start: 0.5644 (m-40) cc_final: 0.5287 (m-40) REVERT: C 152 VAL cc_start: 0.6901 (OUTLIER) cc_final: 0.6631 (t) REVERT: C 171 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7512 (pt) REVERT: C 203 VAL cc_start: 0.8802 (m) cc_final: 0.8178 (t) REVERT: C 271 LYS cc_start: 0.8336 (mmtp) cc_final: 0.7995 (mmmt) REVERT: D 21 MET cc_start: 0.7317 (mmm) cc_final: 0.6937 (tpt) REVERT: D 31 LYS cc_start: 0.8692 (mttt) cc_final: 0.8281 (mtpt) REVERT: D 79 LYS cc_start: 0.8178 (mmmt) cc_final: 0.7641 (tptp) REVERT: E 50 ASN cc_start: 0.8930 (m110) cc_final: 0.8701 (m110) REVERT: E 79 LYS cc_start: 0.7114 (mtpt) cc_final: 0.6677 (mmmt) REVERT: E 182 ASP cc_start: 0.7239 (t0) cc_final: 0.6795 (m-30) REVERT: F 152 VAL cc_start: 0.6874 (OUTLIER) cc_final: 0.6599 (t) REVERT: F 271 LYS cc_start: 0.7821 (mmtt) cc_final: 0.7546 (tptt) REVERT: G 17 ILE cc_start: 0.8642 (mp) cc_final: 0.8302 (mm) REVERT: G 21 MET cc_start: 0.6753 (mmp) cc_final: 0.6112 (tpp) REVERT: H 79 LYS cc_start: 0.7156 (mtpt) cc_final: 0.6711 (mmmt) REVERT: H 146 ASN cc_start: 0.5964 (m-40) cc_final: 0.5720 (m110) REVERT: H 180 VAL cc_start: 0.8755 (OUTLIER) cc_final: 0.8416 (t) REVERT: H 297 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7789 (mt-10) REVERT: I 79 LYS cc_start: 0.7788 (mmmt) cc_final: 0.7261 (pttt) REVERT: I 152 VAL cc_start: 0.6988 (OUTLIER) cc_final: 0.6714 (t) REVERT: I 171 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.7727 (pt) REVERT: J 21 MET cc_start: 0.6841 (mmp) cc_final: 0.6259 (tpp) REVERT: J 31 LYS cc_start: 0.8826 (mttt) cc_final: 0.8311 (mtpt) REVERT: J 119 THR cc_start: 0.8444 (OUTLIER) cc_final: 0.8185 (p) REVERT: K 26 HIS cc_start: 0.7100 (m90) cc_final: 0.6887 (m90) REVERT: K 31 LYS cc_start: 0.8708 (mttt) cc_final: 0.8291 (mttt) REVERT: K 79 LYS cc_start: 0.7148 (mtpt) cc_final: 0.6693 (mmmt) REVERT: K 300 TYR cc_start: 0.8361 (OUTLIER) cc_final: 0.7663 (t80) REVERT: L 79 LYS cc_start: 0.8082 (mmmt) cc_final: 0.7402 (pttt) REVERT: L 152 VAL cc_start: 0.7009 (OUTLIER) cc_final: 0.6741 (t) REVERT: L 171 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.7711 (pt) REVERT: L 271 LYS cc_start: 0.8404 (mmtp) cc_final: 0.8114 (mmmt) outliers start: 195 outliers final: 120 residues processed: 1227 average time/residue: 0.4822 time to fit residues: 992.8998 Evaluate side-chains 1228 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1093 time to evaluate : 4.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 35 ILE Chi-restraints excluded: chain a residue 69 SER Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 164 ILE Chi-restraints excluded: chain a residue 166 VAL Chi-restraints excluded: chain b residue 20 LEU Chi-restraints excluded: chain b residue 156 ILE Chi-restraints excluded: chain c residue 59 LYS Chi-restraints excluded: chain c residue 69 SER Chi-restraints excluded: chain c residue 98 ASN Chi-restraints excluded: chain c residue 109 THR Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain c residue 156 ILE Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain d residue 110 GLN Chi-restraints excluded: chain d residue 156 ILE Chi-restraints excluded: chain e residue 15 LEU Chi-restraints excluded: chain e residue 70 VAL Chi-restraints excluded: chain e residue 98 ASN Chi-restraints excluded: chain e residue 156 ILE Chi-restraints excluded: chain f residue 16 LYS Chi-restraints excluded: chain f residue 69 SER Chi-restraints excluded: chain f residue 98 ASN Chi-restraints excluded: chain f residue 105 ASP Chi-restraints excluded: chain f residue 109 THR Chi-restraints excluded: chain f residue 141 THR Chi-restraints excluded: chain f residue 156 ILE Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 109 THR Chi-restraints excluded: chain g residue 110 GLN Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 156 ILE Chi-restraints excluded: chain g residue 159 HIS Chi-restraints excluded: chain h residue 69 SER Chi-restraints excluded: chain h residue 98 ASN Chi-restraints excluded: chain h residue 109 THR Chi-restraints excluded: chain h residue 156 ILE Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 63 SER Chi-restraints excluded: chain i residue 98 ASN Chi-restraints excluded: chain i residue 105 ASP Chi-restraints excluded: chain i residue 109 THR Chi-restraints excluded: chain i residue 141 THR Chi-restraints excluded: chain i residue 156 ILE Chi-restraints excluded: chain j residue 35 ILE Chi-restraints excluded: chain j residue 109 THR Chi-restraints excluded: chain j residue 156 ILE Chi-restraints excluded: chain j residue 166 VAL Chi-restraints excluded: chain k residue 69 SER Chi-restraints excluded: chain k residue 73 MET Chi-restraints excluded: chain k residue 109 THR Chi-restraints excluded: chain k residue 156 ILE Chi-restraints excluded: chain l residue 16 LYS Chi-restraints excluded: chain l residue 98 ASN Chi-restraints excluded: chain l residue 109 THR Chi-restraints excluded: chain l residue 141 THR Chi-restraints excluded: chain l residue 156 ILE Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 300 TYR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 300 TYR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 105 ASP Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 171 ILE Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 105 ASP Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 188 SER Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 300 TYR Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain L residue 31 LYS Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 171 ILE Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 300 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 511 optimal weight: 4.9990 chunk 348 optimal weight: 5.9990 chunk 8 optimal weight: 0.0020 chunk 457 optimal weight: 10.0000 chunk 253 optimal weight: 7.9990 chunk 524 optimal weight: 5.9990 chunk 424 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 313 optimal weight: 0.4980 chunk 551 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 overall best weight: 2.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 151 ASN d 151 ASN e 138 GLN j 151 ASN ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 ASN A 326 ASN B 50 ASN B 161 ASN B 326 ASN C 37 GLN C 326 ASN D 146 ASN ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 ASN ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 ASN E 161 ASN E 326 ASN F 326 ASN G 149 ASN G 161 ASN G 326 ASN G 371 GLN H 161 ASN H 326 ASN I 37 GLN I 130 GLN I 326 ASN I 371 GLN J 161 ASN J 326 ASN K 50 ASN K 161 ASN K 326 ASN L 326 ASN L 371 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 52092 Z= 0.237 Angle : 0.608 11.014 70464 Z= 0.316 Chirality : 0.044 0.235 8040 Planarity : 0.004 0.044 9096 Dihedral : 5.183 50.046 7000 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.70 % Allowed : 7.02 % Favored : 92.28 % Rotamer: Outliers : 3.95 % Allowed : 14.10 % Favored : 81.95 % 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: 0.05 (0.11), residues: 6396 helix: 1.55 (0.10), residues: 2796 sheet: 0.73 (0.20), residues: 888 loop : -1.94 (0.11), residues: 2712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 116 HIS 0.008 0.002 HIS I 343 PHE 0.014 0.001 PHE H 277 TYR 0.018 0.001 TYR a 88 ARG 0.003 0.000 ARG l 168 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1366 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1140 time to evaluate : 4.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 41 MET cc_start: 0.8055 (mtt) cc_final: 0.7713 (mtt) REVERT: a 49 GLN cc_start: 0.8734 (tt0) cc_final: 0.8474 (tt0) REVERT: a 96 LYS cc_start: 0.8548 (mttm) cc_final: 0.8192 (mmtt) REVERT: b 96 LYS cc_start: 0.8360 (mttp) cc_final: 0.8050 (mmtm) REVERT: c 165 GLU cc_start: 0.8323 (tp30) cc_final: 0.7670 (mm-30) REVERT: d 8 ASP cc_start: 0.7928 (m-30) cc_final: 0.7670 (m-30) REVERT: d 41 MET cc_start: 0.8154 (mtt) cc_final: 0.7947 (mtt) REVERT: d 49 GLN cc_start: 0.8539 (tt0) cc_final: 0.8287 (tt0) REVERT: d 96 LYS cc_start: 0.8595 (mttm) cc_final: 0.8339 (mmtt) REVERT: e 83 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6760 (mp0) REVERT: e 96 LYS cc_start: 0.8313 (mttp) cc_final: 0.8045 (mmtm) REVERT: e 110 GLN cc_start: 0.7168 (mt0) cc_final: 0.6609 (mt0) REVERT: f 5 THR cc_start: 0.8218 (p) cc_final: 0.7747 (t) REVERT: f 16 LYS cc_start: 0.6248 (OUTLIER) cc_final: 0.5231 (pttp) REVERT: f 27 MET cc_start: 0.8628 (mtt) cc_final: 0.8335 (mtt) REVERT: f 165 GLU cc_start: 0.8316 (tp30) cc_final: 0.7596 (mm-30) REVERT: g 49 GLN cc_start: 0.8731 (tt0) cc_final: 0.8414 (tt0) REVERT: g 96 LYS cc_start: 0.8586 (mttm) cc_final: 0.8215 (mmtt) REVERT: h 96 LYS cc_start: 0.8417 (mttp) cc_final: 0.8152 (mmtm) REVERT: i 5 THR cc_start: 0.8187 (p) cc_final: 0.7751 (t) REVERT: i 16 LYS cc_start: 0.6353 (OUTLIER) cc_final: 0.5353 (pttp) REVERT: j 49 GLN cc_start: 0.8779 (tt0) cc_final: 0.8439 (tt0) REVERT: j 96 LYS cc_start: 0.8547 (mttm) cc_final: 0.7870 (mmtt) REVERT: k 25 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7172 (mm-30) REVERT: k 73 MET cc_start: 0.8472 (ttm) cc_final: 0.8206 (ttm) REVERT: k 96 LYS cc_start: 0.8358 (mttp) cc_final: 0.8098 (mmtm) REVERT: k 110 GLN cc_start: 0.7294 (mt0) cc_final: 0.7044 (mt0) REVERT: k 165 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7609 (mm-30) REVERT: l 5 THR cc_start: 0.8282 (p) cc_final: 0.7812 (t) REVERT: l 16 LYS cc_start: 0.6984 (OUTLIER) cc_final: 0.5379 (pttm) REVERT: l 165 GLU cc_start: 0.8308 (tp30) cc_final: 0.7683 (mm-30) REVERT: A 79 LYS cc_start: 0.8119 (mmmt) cc_final: 0.7596 (tptp) REVERT: A 195 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8187 (tt0) REVERT: B 41 LYS cc_start: 0.8356 (mttt) cc_final: 0.8095 (mttt) REVERT: B 79 LYS cc_start: 0.7159 (mtpt) cc_final: 0.6701 (mmmt) REVERT: C 152 VAL cc_start: 0.7365 (OUTLIER) cc_final: 0.7143 (t) REVERT: C 171 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7520 (pt) REVERT: C 203 VAL cc_start: 0.8829 (m) cc_final: 0.8227 (t) REVERT: C 271 LYS cc_start: 0.8358 (mmtp) cc_final: 0.8048 (mmmt) REVERT: D 79 LYS cc_start: 0.8184 (mmmt) cc_final: 0.7657 (tptp) REVERT: E 50 ASN cc_start: 0.9006 (m110) cc_final: 0.8790 (m110) REVERT: E 79 LYS cc_start: 0.7179 (mtpt) cc_final: 0.6669 (mmmt) REVERT: F 152 VAL cc_start: 0.7335 (OUTLIER) cc_final: 0.7080 (t) REVERT: F 171 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7713 (pt) REVERT: F 203 VAL cc_start: 0.8795 (m) cc_final: 0.8166 (t) REVERT: G 21 MET cc_start: 0.6820 (mmp) cc_final: 0.6229 (tpp) REVERT: G 189 LYS cc_start: 0.8613 (mtpt) cc_final: 0.8004 (mtpt) REVERT: G 195 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8086 (tt0) REVERT: H 50 ASN cc_start: 0.8965 (m-40) cc_final: 0.8721 (m110) REVERT: H 79 LYS cc_start: 0.7213 (mtpt) cc_final: 0.6698 (mmmt) REVERT: H 180 VAL cc_start: 0.8860 (OUTLIER) cc_final: 0.8551 (t) REVERT: I 79 LYS cc_start: 0.7830 (mmmt) cc_final: 0.7249 (pttt) REVERT: I 152 VAL cc_start: 0.7397 (OUTLIER) cc_final: 0.7149 (t) REVERT: I 171 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.7786 (pt) REVERT: I 203 VAL cc_start: 0.8778 (m) cc_final: 0.8217 (t) REVERT: J 21 MET cc_start: 0.6859 (mmp) cc_final: 0.6525 (tpt) REVERT: J 31 LYS cc_start: 0.8805 (mttt) cc_final: 0.8335 (mtpt) REVERT: J 148 ILE cc_start: 0.7355 (mm) cc_final: 0.7134 (mm) REVERT: K 31 LYS cc_start: 0.8740 (mttt) cc_final: 0.8325 (mttt) REVERT: K 79 LYS cc_start: 0.7207 (mtpt) cc_final: 0.6681 (mmmt) REVERT: K 146 ASN cc_start: 0.5435 (m-40) cc_final: 0.5125 (m110) REVERT: K 300 TYR cc_start: 0.8409 (OUTLIER) cc_final: 0.7762 (t80) REVERT: L 79 LYS cc_start: 0.8092 (mmmt) cc_final: 0.7380 (pttt) REVERT: L 152 VAL cc_start: 0.7412 (OUTLIER) cc_final: 0.7166 (t) REVERT: L 171 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.7771 (pt) REVERT: L 271 LYS cc_start: 0.8409 (mmtp) cc_final: 0.8159 (mmmt) outliers start: 226 outliers final: 172 residues processed: 1253 average time/residue: 0.4856 time to fit residues: 1017.4787 Evaluate side-chains 1275 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1088 time to evaluate : 4.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 7 GLU Chi-restraints excluded: chain a residue 35 ILE Chi-restraints excluded: chain a residue 69 SER Chi-restraints excluded: chain a residue 109 THR Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 159 HIS Chi-restraints excluded: chain a residue 166 VAL Chi-restraints excluded: chain b residue 20 LEU Chi-restraints excluded: chain b residue 69 SER Chi-restraints excluded: chain b residue 98 ASN Chi-restraints excluded: chain b residue 156 ILE Chi-restraints excluded: chain b residue 162 THR Chi-restraints excluded: chain c residue 69 SER Chi-restraints excluded: chain c residue 70 VAL Chi-restraints excluded: chain c residue 98 ASN Chi-restraints excluded: chain c residue 109 THR Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain c residue 156 ILE Chi-restraints excluded: chain d residue 69 SER Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain d residue 110 GLN Chi-restraints excluded: chain d residue 156 ILE Chi-restraints excluded: chain d residue 164 ILE Chi-restraints excluded: chain d residue 166 VAL Chi-restraints excluded: chain e residue 15 LEU Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain e residue 70 VAL Chi-restraints excluded: chain e residue 98 ASN Chi-restraints excluded: chain e residue 156 ILE Chi-restraints excluded: chain f residue 16 LYS Chi-restraints excluded: chain f residue 66 SER Chi-restraints excluded: chain f residue 69 SER Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 98 ASN Chi-restraints excluded: chain f residue 109 THR Chi-restraints excluded: chain f residue 141 THR Chi-restraints excluded: chain f residue 156 ILE Chi-restraints excluded: chain f residue 166 VAL Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 109 THR Chi-restraints excluded: chain g residue 110 GLN Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 145 GLU Chi-restraints excluded: chain g residue 156 ILE Chi-restraints excluded: chain g residue 159 HIS Chi-restraints excluded: chain g residue 164 ILE Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain h residue 69 SER Chi-restraints excluded: chain h residue 98 ASN Chi-restraints excluded: chain h residue 109 THR Chi-restraints excluded: chain h residue 156 ILE Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 63 SER Chi-restraints excluded: chain i residue 66 SER Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain i residue 70 VAL Chi-restraints excluded: chain i residue 98 ASN Chi-restraints excluded: chain i residue 105 ASP Chi-restraints excluded: chain i residue 109 THR Chi-restraints excluded: chain i residue 141 THR Chi-restraints excluded: chain i residue 156 ILE Chi-restraints excluded: chain i residue 159 HIS Chi-restraints excluded: chain i residue 166 VAL Chi-restraints excluded: chain j residue 35 ILE Chi-restraints excluded: chain j residue 69 SER Chi-restraints excluded: chain j residue 109 THR Chi-restraints excluded: chain j residue 156 ILE Chi-restraints excluded: chain j residue 159 HIS Chi-restraints excluded: chain j residue 166 VAL Chi-restraints excluded: chain k residue 69 SER Chi-restraints excluded: chain k residue 109 THR Chi-restraints excluded: chain k residue 156 ILE Chi-restraints excluded: chain k residue 162 THR Chi-restraints excluded: chain l residue 16 LYS Chi-restraints excluded: chain l residue 70 VAL Chi-restraints excluded: chain l residue 98 ASN Chi-restraints excluded: chain l residue 105 ASP Chi-restraints excluded: chain l residue 109 THR Chi-restraints excluded: chain l residue 141 THR Chi-restraints excluded: chain l residue 156 ILE Chi-restraints excluded: chain l residue 166 VAL Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 300 TYR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain E residue 343 HIS Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 300 TYR Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 195 GLU Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 298 LEU Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 326 ASN Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 171 ILE Chi-restraints excluded: chain I residue 259 ASP Chi-restraints excluded: chain I residue 300 TYR Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 105 ASP Chi-restraints excluded: chain J residue 161 ASN Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 298 LEU Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 161 ASN Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 188 SER Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 300 TYR Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 326 ASN Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 154 GLU Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 171 ILE Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 224 GLU Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 300 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 206 optimal weight: 6.9990 chunk 553 optimal weight: 10.0000 chunk 121 optimal weight: 0.0980 chunk 360 optimal weight: 10.0000 chunk 151 optimal weight: 9.9990 chunk 615 optimal weight: 10.0000 chunk 510 optimal weight: 6.9990 chunk 284 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 203 optimal weight: 4.9990 chunk 323 optimal weight: 3.9990 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 151 ASN d 151 ASN f 2 GLN h 110 GLN i 2 GLN j 151 ASN l 2 GLN ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 ASN A 326 ASN A 371 GLN B 161 ASN B 326 ASN C 37 GLN C 326 ASN ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 ASN D 371 GLN ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 ASN E 326 ASN F 326 ASN F 371 GLN G 149 ASN G 161 ASN G 326 ASN G 371 GLN H 161 ASN H 326 ASN I 37 GLN I 326 ASN I 371 GLN J 161 ASN J 326 ASN K 26 HIS K 161 ASN K 326 ASN L 326 ASN L 371 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 52092 Z= 0.419 Angle : 0.728 15.562 70464 Z= 0.380 Chirality : 0.048 0.249 8040 Planarity : 0.005 0.046 9096 Dihedral : 5.614 47.089 6997 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.81 % Allowed : 7.02 % Favored : 92.17 % Rotamer: Outliers : 4.44 % Allowed : 14.73 % Favored : 80.84 % 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: -0.32 (0.10), residues: 6396 helix: 1.23 (0.09), residues: 2784 sheet: 0.62 (0.19), residues: 864 loop : -2.11 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP L 116 HIS 0.010 0.003 HIS D 343 PHE 0.018 0.002 PHE F 277 TYR 0.027 0.002 TYR a 88 ARG 0.006 0.001 ARG E 176 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1366 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 1112 time to evaluate : 4.498 Fit side-chains REVERT: a 10 ARG cc_start: 0.8003 (ttm170) cc_final: 0.7711 (ttm-80) REVERT: a 49 GLN cc_start: 0.8855 (tt0) cc_final: 0.8575 (tt0) REVERT: a 96 LYS cc_start: 0.8660 (mttm) cc_final: 0.8343 (mmtt) REVERT: b 96 LYS cc_start: 0.8463 (mttp) cc_final: 0.8175 (mmtm) REVERT: d 41 MET cc_start: 0.8222 (mtt) cc_final: 0.7976 (mtt) REVERT: d 49 GLN cc_start: 0.8568 (tt0) cc_final: 0.8293 (tt0) REVERT: d 96 LYS cc_start: 0.8620 (mttm) cc_final: 0.8281 (mmtt) REVERT: e 83 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6492 (mp0) REVERT: f 16 LYS cc_start: 0.6360 (OUTLIER) cc_final: 0.5182 (pttp) REVERT: g 49 GLN cc_start: 0.8880 (tt0) cc_final: 0.8400 (tt0) REVERT: g 96 LYS cc_start: 0.8595 (mttm) cc_final: 0.8269 (mmtt) REVERT: h 96 LYS cc_start: 0.8465 (mttp) cc_final: 0.8245 (mmtm) REVERT: i 5 THR cc_start: 0.8349 (p) cc_final: 0.7922 (t) REVERT: i 16 LYS cc_start: 0.6184 (OUTLIER) cc_final: 0.4891 (pttp) REVERT: j 49 GLN cc_start: 0.8801 (tt0) cc_final: 0.8485 (tt0) REVERT: j 96 LYS cc_start: 0.8595 (mttm) cc_final: 0.7951 (mmtt) REVERT: j 118 GLU cc_start: 0.7182 (mp0) cc_final: 0.6779 (mp0) REVERT: k 3 ILE cc_start: 0.8618 (mt) cc_final: 0.8394 (mt) REVERT: k 8 ASP cc_start: 0.8321 (m-30) cc_final: 0.8101 (m-30) REVERT: k 25 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7297 (mm-30) REVERT: k 96 LYS cc_start: 0.8487 (mttp) cc_final: 0.8258 (mmtm) REVERT: k 110 GLN cc_start: 0.7373 (mt0) cc_final: 0.7109 (mt0) REVERT: l 16 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.5391 (pttm) REVERT: A 79 LYS cc_start: 0.8177 (mmmt) cc_final: 0.7666 (tptp) REVERT: A 195 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8236 (tt0) REVERT: B 41 LYS cc_start: 0.8464 (mttt) cc_final: 0.8195 (mttt) REVERT: B 79 LYS cc_start: 0.7241 (mtpt) cc_final: 0.6703 (mmmt) REVERT: B 326 ASN cc_start: 0.7339 (OUTLIER) cc_final: 0.6976 (t0) REVERT: C 152 VAL cc_start: 0.7420 (OUTLIER) cc_final: 0.7144 (t) REVERT: C 203 VAL cc_start: 0.8871 (m) cc_final: 0.8365 (t) REVERT: C 271 LYS cc_start: 0.8562 (mmtp) cc_final: 0.8343 (mmmt) REVERT: D 79 LYS cc_start: 0.8187 (mmmt) cc_final: 0.7708 (tptp) REVERT: D 255 SER cc_start: 0.8489 (m) cc_final: 0.8184 (p) REVERT: E 15 GLN cc_start: 0.8385 (tp-100) cc_final: 0.8126 (tp-100) REVERT: E 79 LYS cc_start: 0.7206 (mtpt) cc_final: 0.6692 (mmmt) REVERT: E 130 GLN cc_start: 0.8126 (tt0) cc_final: 0.7916 (tt0) REVERT: E 326 ASN cc_start: 0.7314 (OUTLIER) cc_final: 0.6994 (t0) REVERT: F 79 LYS cc_start: 0.7597 (mmmt) cc_final: 0.7092 (pttt) REVERT: F 90 ASN cc_start: 0.8004 (m-40) cc_final: 0.7802 (m-40) REVERT: F 152 VAL cc_start: 0.7340 (OUTLIER) cc_final: 0.7105 (t) REVERT: F 203 VAL cc_start: 0.8798 (m) cc_final: 0.8261 (t) REVERT: F 271 LYS cc_start: 0.8044 (mmtt) cc_final: 0.7691 (tptt) REVERT: G 21 MET cc_start: 0.6930 (mmp) cc_final: 0.6354 (tpp) REVERT: G 26 HIS cc_start: 0.7453 (m90) cc_final: 0.7234 (m170) REVERT: G 105 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.8034 (m-30) REVERT: G 195 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8061 (tt0) REVERT: H 15 GLN cc_start: 0.8419 (tp-100) cc_final: 0.8132 (tp-100) REVERT: H 31 LYS cc_start: 0.8788 (mttt) cc_final: 0.8445 (mttt) REVERT: H 79 LYS cc_start: 0.7244 (mtpt) cc_final: 0.6719 (mmmt) REVERT: H 180 VAL cc_start: 0.8843 (OUTLIER) cc_final: 0.8513 (t) REVERT: H 326 ASN cc_start: 0.7322 (OUTLIER) cc_final: 0.6993 (t0) REVERT: I 152 VAL cc_start: 0.7414 (OUTLIER) cc_final: 0.7170 (t) REVERT: I 182 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.6953 (m-30) REVERT: I 203 VAL cc_start: 0.8804 (m) cc_final: 0.8300 (t) REVERT: I 212 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6488 (mt-10) REVERT: I 275 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8689 (tp) REVERT: J 31 LYS cc_start: 0.8877 (mttt) cc_final: 0.8436 (mtpt) REVERT: J 105 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.8020 (m-30) REVERT: K 15 GLN cc_start: 0.8408 (tp-100) cc_final: 0.8099 (tp-100) REVERT: K 31 LYS cc_start: 0.8873 (mttt) cc_final: 0.8384 (mttt) REVERT: K 79 LYS cc_start: 0.7237 (mtpt) cc_final: 0.6716 (mmmt) REVERT: K 300 TYR cc_start: 0.8421 (OUTLIER) cc_final: 0.7896 (t80) REVERT: K 326 ASN cc_start: 0.7260 (OUTLIER) cc_final: 0.6966 (t0) REVERT: L 79 LYS cc_start: 0.7983 (mmmt) cc_final: 0.7210 (pttt) REVERT: L 152 VAL cc_start: 0.7418 (OUTLIER) cc_final: 0.7171 (t) REVERT: L 203 VAL cc_start: 0.8857 (m) cc_final: 0.8326 (t) REVERT: L 275 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8727 (tp) outliers start: 254 outliers final: 180 residues processed: 1256 average time/residue: 0.5013 time to fit residues: 1043.9592 Evaluate side-chains 1267 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1066 time to evaluate : 4.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 69 SER Chi-restraints excluded: chain a residue 109 THR Chi-restraints excluded: chain a residue 110 GLN Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 159 HIS Chi-restraints excluded: chain a residue 166 VAL Chi-restraints excluded: chain b residue 20 LEU Chi-restraints excluded: chain b residue 69 SER Chi-restraints excluded: chain b residue 87 LEU Chi-restraints excluded: chain b residue 98 ASN Chi-restraints excluded: chain b residue 147 VAL Chi-restraints excluded: chain b residue 156 ILE Chi-restraints excluded: chain b residue 162 THR Chi-restraints excluded: chain b residue 166 VAL Chi-restraints excluded: chain c residue 66 SER Chi-restraints excluded: chain c residue 69 SER Chi-restraints excluded: chain c residue 70 VAL Chi-restraints excluded: chain c residue 98 ASN Chi-restraints excluded: chain c residue 105 ASP Chi-restraints excluded: chain c residue 109 THR Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain c residue 156 ILE Chi-restraints excluded: chain c residue 166 VAL Chi-restraints excluded: chain d residue 69 SER Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain d residue 110 GLN Chi-restraints excluded: chain d residue 147 VAL Chi-restraints excluded: chain d residue 156 ILE Chi-restraints excluded: chain d residue 166 VAL Chi-restraints excluded: chain e residue 15 LEU Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain e residue 70 VAL Chi-restraints excluded: chain e residue 98 ASN Chi-restraints excluded: chain e residue 147 VAL Chi-restraints excluded: chain e residue 156 ILE Chi-restraints excluded: chain e residue 162 THR Chi-restraints excluded: chain f residue 16 LYS Chi-restraints excluded: chain f residue 66 SER Chi-restraints excluded: chain f residue 69 SER Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 98 ASN Chi-restraints excluded: chain f residue 105 ASP Chi-restraints excluded: chain f residue 109 THR Chi-restraints excluded: chain f residue 141 THR Chi-restraints excluded: chain f residue 156 ILE Chi-restraints excluded: chain f residue 166 VAL Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 109 THR Chi-restraints excluded: chain g residue 110 GLN Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 145 GLU Chi-restraints excluded: chain g residue 156 ILE Chi-restraints excluded: chain g residue 159 HIS Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain h residue 69 SER Chi-restraints excluded: chain h residue 98 ASN Chi-restraints excluded: chain h residue 109 THR Chi-restraints excluded: chain h residue 147 VAL Chi-restraints excluded: chain h residue 156 ILE Chi-restraints excluded: chain h residue 162 THR Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 42 ASP Chi-restraints excluded: chain i residue 63 SER Chi-restraints excluded: chain i residue 66 SER Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain i residue 70 VAL Chi-restraints excluded: chain i residue 98 ASN Chi-restraints excluded: chain i residue 105 ASP Chi-restraints excluded: chain i residue 109 THR Chi-restraints excluded: chain i residue 141 THR Chi-restraints excluded: chain i residue 156 ILE Chi-restraints excluded: chain i residue 166 VAL Chi-restraints excluded: chain j residue 69 SER Chi-restraints excluded: chain j residue 109 THR Chi-restraints excluded: chain j residue 145 GLU Chi-restraints excluded: chain j residue 156 ILE Chi-restraints excluded: chain j residue 166 VAL Chi-restraints excluded: chain k residue 69 SER Chi-restraints excluded: chain k residue 109 THR Chi-restraints excluded: chain k residue 147 VAL Chi-restraints excluded: chain k residue 156 ILE Chi-restraints excluded: chain k residue 162 THR Chi-restraints excluded: chain l residue 16 LYS Chi-restraints excluded: chain l residue 42 ASP Chi-restraints excluded: chain l residue 69 SER Chi-restraints excluded: chain l residue 70 VAL Chi-restraints excluded: chain l residue 93 ILE Chi-restraints excluded: chain l residue 98 ASN Chi-restraints excluded: chain l residue 105 ASP Chi-restraints excluded: chain l residue 109 THR Chi-restraints excluded: chain l residue 141 THR Chi-restraints excluded: chain l residue 156 ILE Chi-restraints excluded: chain l residue 162 THR Chi-restraints excluded: chain l residue 166 VAL Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 161 ASN Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 TYR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 300 TYR Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 105 ASP Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 161 ASN Chi-restraints excluded: chain G residue 195 GLU Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 298 LEU Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain H residue 326 ASN Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 182 ASP Chi-restraints excluded: chain I residue 212 GLU Chi-restraints excluded: chain I residue 259 ASP Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 300 TYR Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain J residue 16 ARG Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 105 ASP Chi-restraints excluded: chain J residue 154 GLU Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 298 LEU Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 161 ASN Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 188 SER Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 300 TYR Chi-restraints excluded: chain K residue 326 ASN Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 154 GLU Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 224 GLU Chi-restraints excluded: chain L residue 275 LEU Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 300 TYR Chi-restraints excluded: chain L residue 324 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 593 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 350 optimal weight: 0.9990 chunk 449 optimal weight: 1.9990 chunk 348 optimal weight: 0.8980 chunk 518 optimal weight: 0.8980 chunk 343 optimal weight: 4.9990 chunk 613 optimal weight: 0.9980 chunk 383 optimal weight: 4.9990 chunk 373 optimal weight: 5.9990 chunk 283 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 151 ASN d 151 ASN h 110 GLN h 132 HIS i 2 GLN j 110 GLN j 151 ASN k 2 GLN ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 ASN A 326 ASN A 371 GLN B 161 ASN B 326 ASN C 37 GLN ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN C 326 ASN ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 ASN D 371 GLN ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 ASN E 161 ASN E 326 ASN F 326 ASN F 371 GLN G 149 ASN G 161 ASN G 326 ASN G 371 GLN H 161 ASN H 291 ASN H 326 ASN I 326 ASN J 161 ASN J 326 ASN K 161 ASN K 291 ASN K 326 ASN L 326 ASN L 371 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 52092 Z= 0.171 Angle : 0.587 10.101 70464 Z= 0.305 Chirality : 0.043 0.400 8040 Planarity : 0.004 0.042 9096 Dihedral : 5.222 45.354 6997 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.66 % Allowed : 7.25 % Favored : 92.09 % Rotamer: Outliers : 3.51 % Allowed : 16.42 % Favored : 80.07 % 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: 0.01 (0.11), residues: 6396 helix: 1.59 (0.10), residues: 2772 sheet: 0.63 (0.19), residues: 864 loop : -1.97 (0.11), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP j 131 HIS 0.006 0.001 HIS C 343 PHE 0.011 0.001 PHE K 277 TYR 0.027 0.001 TYR b 88 ARG 0.005 0.000 ARG k 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1319 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1118 time to evaluate : 4.378 Fit side-chains REVERT: a 41 MET cc_start: 0.7977 (mtt) cc_final: 0.7664 (mtt) REVERT: a 49 GLN cc_start: 0.8770 (tt0) cc_final: 0.8522 (tt0) REVERT: b 96 LYS cc_start: 0.8425 (mttp) cc_final: 0.8217 (mmtm) REVERT: d 41 MET cc_start: 0.8107 (mtt) cc_final: 0.7873 (mtt) REVERT: d 49 GLN cc_start: 0.8568 (tt0) cc_final: 0.8343 (tt0) REVERT: d 96 LYS cc_start: 0.8599 (mttm) cc_final: 0.8285 (mmtt) REVERT: e 83 GLU cc_start: 0.6576 (mt-10) cc_final: 0.6213 (mp0) REVERT: e 110 GLN cc_start: 0.7418 (mt0) cc_final: 0.7015 (mt0) REVERT: f 5 THR cc_start: 0.8060 (p) cc_final: 0.7644 (t) REVERT: f 16 LYS cc_start: 0.6210 (OUTLIER) cc_final: 0.5284 (pttp) REVERT: f 27 MET cc_start: 0.8629 (mtt) cc_final: 0.8340 (mtt) REVERT: f 167 TYR cc_start: 0.8049 (m-80) cc_final: 0.7773 (m-10) REVERT: g 49 GLN cc_start: 0.8793 (tt0) cc_final: 0.8522 (tt0) REVERT: g 96 LYS cc_start: 0.8565 (mttm) cc_final: 0.8267 (mmtt) REVERT: i 5 THR cc_start: 0.8078 (p) cc_final: 0.7675 (t) REVERT: i 16 LYS cc_start: 0.6340 (OUTLIER) cc_final: 0.5394 (pttp) REVERT: i 116 MET cc_start: 0.8480 (tpp) cc_final: 0.8121 (tpp) REVERT: j 49 GLN cc_start: 0.8750 (tt0) cc_final: 0.8522 (tt0) REVERT: j 96 LYS cc_start: 0.8548 (mttm) cc_final: 0.7932 (mmtt) REVERT: k 25 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7138 (mm-30) REVERT: k 96 LYS cc_start: 0.8410 (mttp) cc_final: 0.8209 (mmtm) REVERT: k 110 GLN cc_start: 0.7272 (mt0) cc_final: 0.6983 (mt0) REVERT: l 16 LYS cc_start: 0.6978 (OUTLIER) cc_final: 0.5353 (pttm) REVERT: A 79 LYS cc_start: 0.8165 (mmmt) cc_final: 0.7629 (tptp) REVERT: B 41 LYS cc_start: 0.8348 (mttt) cc_final: 0.8082 (mttt) REVERT: B 79 LYS cc_start: 0.7190 (mtpt) cc_final: 0.6653 (mmmt) REVERT: B 300 TYR cc_start: 0.8089 (OUTLIER) cc_final: 0.7830 (t80) REVERT: C 79 LYS cc_start: 0.7695 (mmmt) cc_final: 0.7151 (pttt) REVERT: C 171 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7473 (pt) REVERT: C 203 VAL cc_start: 0.8848 (m) cc_final: 0.8209 (t) REVERT: D 79 LYS cc_start: 0.8184 (mmmt) cc_final: 0.7665 (tptp) REVERT: D 171 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7692 (pt) REVERT: E 43 GLU cc_start: 0.7344 (pm20) cc_final: 0.7114 (pm20) REVERT: E 50 ASN cc_start: 0.8936 (m110) cc_final: 0.8692 (m110) REVERT: E 79 LYS cc_start: 0.7186 (mtpt) cc_final: 0.6656 (mmmt) REVERT: E 146 ASN cc_start: 0.5665 (m-40) cc_final: 0.5447 (m110) REVERT: E 300 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.7744 (t80) REVERT: F 79 LYS cc_start: 0.7591 (mmmt) cc_final: 0.7077 (pttt) REVERT: F 146 ASN cc_start: 0.5205 (m-40) cc_final: 0.4999 (m110) REVERT: F 171 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7528 (pt) REVERT: F 271 LYS cc_start: 0.7596 (mmtt) cc_final: 0.7260 (tptt) REVERT: G 21 MET cc_start: 0.6875 (mmp) cc_final: 0.6325 (tpp) REVERT: G 26 HIS cc_start: 0.7467 (m90) cc_final: 0.7222 (m170) REVERT: G 243 ASP cc_start: 0.7588 (p0) cc_final: 0.7229 (p0) REVERT: H 31 LYS cc_start: 0.8782 (mttt) cc_final: 0.8477 (mttt) REVERT: H 50 ASN cc_start: 0.8929 (m-40) cc_final: 0.8689 (m110) REVERT: H 79 LYS cc_start: 0.7189 (mtpt) cc_final: 0.6668 (mmmt) REVERT: H 275 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8691 (tt) REVERT: H 300 TYR cc_start: 0.8103 (OUTLIER) cc_final: 0.7805 (t80) REVERT: I 79 LYS cc_start: 0.7700 (mmmt) cc_final: 0.7207 (pttt) REVERT: I 146 ASN cc_start: 0.4981 (m-40) cc_final: 0.4770 (m110) REVERT: I 152 VAL cc_start: 0.7370 (OUTLIER) cc_final: 0.7100 (t) REVERT: I 171 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.7746 (pt) REVERT: I 203 VAL cc_start: 0.8781 (m) cc_final: 0.8157 (t) REVERT: J 31 LYS cc_start: 0.8829 (mttt) cc_final: 0.8346 (mtpt) REVERT: J 171 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7704 (pt) REVERT: J 243 ASP cc_start: 0.7538 (p0) cc_final: 0.7159 (p0) REVERT: K 26 HIS cc_start: 0.6885 (m90) cc_final: 0.6638 (m-70) REVERT: K 31 LYS cc_start: 0.8851 (mttt) cc_final: 0.8325 (mttt) REVERT: K 79 LYS cc_start: 0.7184 (mtpt) cc_final: 0.6661 (mmmt) REVERT: K 171 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7578 (pt) REVERT: K 272 SER cc_start: 0.9156 (t) cc_final: 0.8906 (p) REVERT: K 300 TYR cc_start: 0.8285 (OUTLIER) cc_final: 0.7744 (t80) REVERT: L 79 LYS cc_start: 0.7965 (mmmt) cc_final: 0.7125 (pttt) REVERT: L 146 ASN cc_start: 0.4974 (m-40) cc_final: 0.4764 (m110) REVERT: L 152 VAL cc_start: 0.7390 (OUTLIER) cc_final: 0.7126 (t) REVERT: L 171 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7559 (pt) outliers start: 201 outliers final: 123 residues processed: 1232 average time/residue: 0.4922 time to fit residues: 1009.9775 Evaluate side-chains 1205 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 1065 time to evaluate : 4.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 7 GLU Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 159 HIS Chi-restraints excluded: chain a residue 166 VAL Chi-restraints excluded: chain b residue 20 LEU Chi-restraints excluded: chain b residue 69 SER Chi-restraints excluded: chain b residue 98 ASN Chi-restraints excluded: chain b residue 156 ILE Chi-restraints excluded: chain b residue 166 VAL Chi-restraints excluded: chain c residue 66 SER Chi-restraints excluded: chain c residue 70 VAL Chi-restraints excluded: chain c residue 98 ASN Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain c residue 156 ILE Chi-restraints excluded: chain d residue 147 VAL Chi-restraints excluded: chain d residue 156 ILE Chi-restraints excluded: chain d residue 159 HIS Chi-restraints excluded: chain e residue 15 LEU Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain e residue 70 VAL Chi-restraints excluded: chain e residue 109 THR Chi-restraints excluded: chain e residue 156 ILE Chi-restraints excluded: chain f residue 16 LYS Chi-restraints excluded: chain f residue 98 ASN Chi-restraints excluded: chain f residue 105 ASP Chi-restraints excluded: chain f residue 141 THR Chi-restraints excluded: chain f residue 156 ILE Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 156 ILE Chi-restraints excluded: chain g residue 159 HIS Chi-restraints excluded: chain h residue 69 SER Chi-restraints excluded: chain h residue 98 ASN Chi-restraints excluded: chain h residue 109 THR Chi-restraints excluded: chain h residue 156 ILE Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 63 SER Chi-restraints excluded: chain i residue 66 SER Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain i residue 98 ASN Chi-restraints excluded: chain i residue 141 THR Chi-restraints excluded: chain i residue 156 ILE Chi-restraints excluded: chain i residue 159 HIS Chi-restraints excluded: chain j residue 35 ILE Chi-restraints excluded: chain j residue 69 SER Chi-restraints excluded: chain j residue 156 ILE Chi-restraints excluded: chain j residue 159 HIS Chi-restraints excluded: chain k residue 95 LEU Chi-restraints excluded: chain k residue 156 ILE Chi-restraints excluded: chain l residue 16 LYS Chi-restraints excluded: chain l residue 98 ASN Chi-restraints excluded: chain l residue 105 ASP Chi-restraints excluded: chain l residue 141 THR Chi-restraints excluded: chain l residue 156 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 300 TYR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 300 TYR Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 300 TYR Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 105 ASP Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain H residue 300 TYR Chi-restraints excluded: chain H residue 326 ASN Chi-restraints excluded: chain I residue 16 ARG Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain I residue 171 ILE Chi-restraints excluded: chain I residue 259 ASP Chi-restraints excluded: chain I residue 300 TYR Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain J residue 16 ARG Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 105 ASP Chi-restraints excluded: chain J residue 171 ILE Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 171 ILE Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 188 SER Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 300 TYR Chi-restraints excluded: chain K residue 326 ASN Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 154 GLU Chi-restraints excluded: chain L residue 171 ILE Chi-restraints excluded: chain L residue 181 ILE Chi-restraints excluded: chain L residue 182 ASP Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 224 GLU Chi-restraints excluded: chain L residue 300 TYR Chi-restraints excluded: chain L residue 324 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 379 optimal weight: 0.2980 chunk 244 optimal weight: 1.9990 chunk 366 optimal weight: 4.9990 chunk 184 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 chunk 389 optimal weight: 9.9990 chunk 417 optimal weight: 4.9990 chunk 303 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 chunk 481 optimal weight: 7.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 151 ASN b 2 GLN d 151 ASN f 2 GLN i 2 GLN j 151 ASN k 2 GLN l 2 GLN ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 ASN A 295 ASN A 326 ASN A 371 GLN B 161 ASN ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 ASN C 371 GLN ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 ASN D 326 ASN ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 ASN F 326 ASN F 371 GLN G 149 ASN G 161 ASN G 295 ASN G 326 ASN G 371 GLN H 161 ASN I 326 ASN I 371 GLN J 161 ASN J 295 ASN J 326 ASN J 371 GLN K 26 HIS K 161 ASN L 326 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 52092 Z= 0.246 Angle : 0.625 11.850 70464 Z= 0.321 Chirality : 0.044 0.383 8040 Planarity : 0.004 0.041 9096 Dihedral : 5.225 48.232 6997 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.66 % Allowed : 7.10 % Favored : 92.25 % Rotamer: Outliers : 3.56 % Allowed : 16.54 % Favored : 79.89 % 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: -0.12 (0.10), residues: 6396 helix: 1.49 (0.10), residues: 2796 sheet: 0.57 (0.19), residues: 864 loop : -2.08 (0.11), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP F 116 HIS 0.007 0.002 HIS C 343 PHE 0.012 0.001 PHE L 277 TYR 0.028 0.002 TYR e 88 ARG 0.003 0.000 ARG d 161 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1299 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1095 time to evaluate : 4.414 Fit side-chains REVERT: a 49 GLN cc_start: 0.8794 (tt0) cc_final: 0.8545 (tt0) REVERT: a 165 GLU cc_start: 0.7974 (tp30) cc_final: 0.7766 (mm-30) REVERT: b 96 LYS cc_start: 0.8452 (mttp) cc_final: 0.8240 (mmtm) REVERT: c 165 GLU cc_start: 0.8323 (tp30) cc_final: 0.8046 (mm-30) REVERT: d 41 MET cc_start: 0.8163 (mtt) cc_final: 0.7886 (mtt) REVERT: d 58 LYS cc_start: 0.8715 (mtmm) cc_final: 0.8497 (mtmm) REVERT: d 96 LYS cc_start: 0.8625 (mttm) cc_final: 0.8292 (mmtt) REVERT: d 165 GLU cc_start: 0.7682 (tp30) cc_final: 0.7350 (mm-30) REVERT: e 83 GLU cc_start: 0.6585 (mt-10) cc_final: 0.6203 (mp0) REVERT: e 110 GLN cc_start: 0.7459 (mt0) cc_final: 0.7046 (mt0) REVERT: f 16 LYS cc_start: 0.6265 (OUTLIER) cc_final: 0.5370 (pttp) REVERT: f 167 TYR cc_start: 0.8286 (m-80) cc_final: 0.7989 (m-10) REVERT: g 49 GLN cc_start: 0.8827 (tt0) cc_final: 0.8537 (tt0) REVERT: g 96 LYS cc_start: 0.8603 (mttm) cc_final: 0.8276 (mmtt) REVERT: h 165 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7610 (mm-30) REVERT: i 16 LYS cc_start: 0.6413 (OUTLIER) cc_final: 0.5480 (pttp) REVERT: j 49 GLN cc_start: 0.8839 (tt0) cc_final: 0.8552 (tt0) REVERT: j 96 LYS cc_start: 0.8560 (mttm) cc_final: 0.7945 (mmtt) REVERT: j 118 GLU cc_start: 0.7111 (mp0) cc_final: 0.6651 (mp0) REVERT: k 25 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7176 (mm-30) REVERT: k 96 LYS cc_start: 0.8457 (mttp) cc_final: 0.8233 (mmtm) REVERT: k 110 GLN cc_start: 0.7208 (mt0) cc_final: 0.6995 (mt0) REVERT: k 118 GLU cc_start: 0.7245 (mp0) cc_final: 0.6510 (mp0) REVERT: l 16 LYS cc_start: 0.7005 (OUTLIER) cc_final: 0.5306 (pttm) REVERT: l 165 GLU cc_start: 0.8202 (tp30) cc_final: 0.7602 (mm-30) REVERT: A 79 LYS cc_start: 0.8175 (mmmt) cc_final: 0.7656 (tptp) REVERT: B 79 LYS cc_start: 0.7214 (mtpt) cc_final: 0.6680 (mmmt) REVERT: B 151 ARG cc_start: 0.7073 (mtp-110) cc_final: 0.6798 (ttm170) REVERT: B 300 TYR cc_start: 0.8125 (OUTLIER) cc_final: 0.7865 (t80) REVERT: C 171 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7544 (pt) REVERT: C 203 VAL cc_start: 0.8839 (m) cc_final: 0.8231 (t) REVERT: D 79 LYS cc_start: 0.8184 (mmmt) cc_final: 0.7672 (tptp) REVERT: D 171 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7714 (pt) REVERT: E 43 GLU cc_start: 0.7459 (pm20) cc_final: 0.7223 (pm20) REVERT: E 50 ASN cc_start: 0.8971 (m110) cc_final: 0.8735 (m110) REVERT: E 79 LYS cc_start: 0.7214 (mtpt) cc_final: 0.6675 (mmmt) REVERT: E 151 ARG cc_start: 0.7104 (mtp-110) cc_final: 0.6593 (ttm170) REVERT: E 300 TYR cc_start: 0.8184 (OUTLIER) cc_final: 0.7847 (t80) REVERT: F 79 LYS cc_start: 0.7609 (mmmt) cc_final: 0.7077 (pttt) REVERT: F 203 VAL cc_start: 0.8821 (m) cc_final: 0.8164 (t) REVERT: F 271 LYS cc_start: 0.7724 (mmtt) cc_final: 0.7388 (tptt) REVERT: G 21 MET cc_start: 0.6885 (mmp) cc_final: 0.6335 (tpp) REVERT: H 15 GLN cc_start: 0.8423 (tp-100) cc_final: 0.8096 (tp-100) REVERT: H 31 LYS cc_start: 0.8785 (mttt) cc_final: 0.8469 (mttt) REVERT: H 50 ASN cc_start: 0.8988 (m-40) cc_final: 0.8741 (m110) REVERT: H 79 LYS cc_start: 0.7215 (mtpt) cc_final: 0.6698 (mmmt) REVERT: H 151 ARG cc_start: 0.6990 (mtp-110) cc_final: 0.6708 (ttm170) REVERT: H 300 TYR cc_start: 0.8146 (OUTLIER) cc_final: 0.7782 (t80) REVERT: I 79 LYS cc_start: 0.7740 (mmmt) cc_final: 0.7195 (pttt) REVERT: I 152 VAL cc_start: 0.7464 (OUTLIER) cc_final: 0.7194 (t) REVERT: I 171 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.7743 (pt) REVERT: I 203 VAL cc_start: 0.8782 (m) cc_final: 0.8196 (t) REVERT: J 31 LYS cc_start: 0.8838 (mttt) cc_final: 0.8365 (mtpt) REVERT: J 171 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7651 (pt) REVERT: K 15 GLN cc_start: 0.8421 (tp-100) cc_final: 0.8118 (tp-100) REVERT: K 31 LYS cc_start: 0.8833 (mttt) cc_final: 0.8338 (mttt) REVERT: K 79 LYS cc_start: 0.7214 (mtpt) cc_final: 0.6693 (mmmt) REVERT: K 130 GLN cc_start: 0.7953 (tt0) cc_final: 0.7655 (tt0) REVERT: K 151 ARG cc_start: 0.7161 (mtp-110) cc_final: 0.6641 (ttm170) REVERT: K 171 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7568 (pt) REVERT: K 300 TYR cc_start: 0.8367 (OUTLIER) cc_final: 0.7855 (t80) REVERT: L 79 LYS cc_start: 0.7971 (mmmt) cc_final: 0.7166 (pttt) REVERT: L 152 VAL cc_start: 0.7468 (OUTLIER) cc_final: 0.7217 (t) REVERT: L 171 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.7706 (pt) REVERT: L 212 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6534 (mt-10) outliers start: 204 outliers final: 148 residues processed: 1202 average time/residue: 0.4944 time to fit residues: 986.9190 Evaluate side-chains 1240 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1076 time to evaluate : 4.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 7 GLU Chi-restraints excluded: chain a residue 110 GLN Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 159 HIS Chi-restraints excluded: chain a residue 166 VAL Chi-restraints excluded: chain b residue 69 SER Chi-restraints excluded: chain b residue 98 ASN Chi-restraints excluded: chain b residue 141 THR Chi-restraints excluded: chain b residue 156 ILE Chi-restraints excluded: chain b residue 166 VAL Chi-restraints excluded: chain c residue 66 SER Chi-restraints excluded: chain c residue 70 VAL Chi-restraints excluded: chain c residue 98 ASN Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain c residue 156 ILE Chi-restraints excluded: chain c residue 166 VAL Chi-restraints excluded: chain d residue 147 VAL Chi-restraints excluded: chain d residue 156 ILE Chi-restraints excluded: chain d residue 159 HIS Chi-restraints excluded: chain e residue 15 LEU Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain e residue 70 VAL Chi-restraints excluded: chain e residue 141 THR Chi-restraints excluded: chain e residue 156 ILE Chi-restraints excluded: chain f residue 16 LYS Chi-restraints excluded: chain f residue 66 SER Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 98 ASN Chi-restraints excluded: chain f residue 105 ASP Chi-restraints excluded: chain f residue 141 THR Chi-restraints excluded: chain f residue 156 ILE Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 110 GLN Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 156 ILE Chi-restraints excluded: chain g residue 159 HIS Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain h residue 69 SER Chi-restraints excluded: chain h residue 98 ASN Chi-restraints excluded: chain h residue 109 THR Chi-restraints excluded: chain h residue 156 ILE Chi-restraints excluded: chain h residue 166 VAL Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 63 SER Chi-restraints excluded: chain i residue 66 SER Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain i residue 70 VAL Chi-restraints excluded: chain i residue 98 ASN Chi-restraints excluded: chain i residue 141 THR Chi-restraints excluded: chain i residue 156 ILE Chi-restraints excluded: chain i residue 159 HIS Chi-restraints excluded: chain j residue 69 SER Chi-restraints excluded: chain j residue 156 ILE Chi-restraints excluded: chain j residue 159 HIS Chi-restraints excluded: chain k residue 156 ILE Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 16 LYS Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 70 VAL Chi-restraints excluded: chain l residue 98 ASN Chi-restraints excluded: chain l residue 105 ASP Chi-restraints excluded: chain l residue 141 THR Chi-restraints excluded: chain l residue 156 ILE Chi-restraints excluded: chain l residue 166 VAL Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 161 ASN Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 300 TYR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 300 TYR Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 300 TYR Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 105 ASP Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain H residue 300 TYR Chi-restraints excluded: chain H residue 326 ASN Chi-restraints excluded: chain I residue 16 ARG Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain I residue 171 ILE Chi-restraints excluded: chain I residue 259 ASP Chi-restraints excluded: chain I residue 300 TYR Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 105 ASP Chi-restraints excluded: chain J residue 161 ASN Chi-restraints excluded: chain J residue 171 ILE Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 298 LEU Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 161 ASN Chi-restraints excluded: chain K residue 171 ILE Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 188 SER Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 300 TYR Chi-restraints excluded: chain K residue 326 ASN Chi-restraints excluded: chain K residue 343 HIS Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 154 GLU Chi-restraints excluded: chain L residue 171 ILE Chi-restraints excluded: chain L residue 181 ILE Chi-restraints excluded: chain L residue 182 ASP Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 224 GLU Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 300 TYR Chi-restraints excluded: chain L residue 324 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 557 optimal weight: 1.9990 chunk 587 optimal weight: 8.9990 chunk 535 optimal weight: 0.4980 chunk 571 optimal weight: 0.5980 chunk 343 optimal weight: 0.9980 chunk 248 optimal weight: 0.3980 chunk 448 optimal weight: 0.7980 chunk 175 optimal weight: 6.9990 chunk 516 optimal weight: 1.9990 chunk 540 optimal weight: 7.9990 chunk 569 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 151 ASN b 2 GLN d 151 ASN e 132 HIS f 2 GLN i 2 GLN j 151 ASN l 2 GLN ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 ASN A 326 ASN A 371 GLN B 161 ASN B 326 ASN ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 ASN C 371 GLN ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 ASN D 371 GLN ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 ASN E 326 ASN F 326 ASN G 161 ASN G 326 ASN G 371 GLN H 161 ASN H 326 ASN I 326 ASN J 161 ASN J 326 ASN J 371 GLN K 161 ASN K 326 ASN L 326 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 52092 Z= 0.151 Angle : 0.564 11.526 70464 Z= 0.292 Chirality : 0.042 0.356 8040 Planarity : 0.004 0.040 9096 Dihedral : 4.892 36.723 6994 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.47 % Favored : 92.07 % Rotamer: Outliers : 2.71 % Allowed : 17.71 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.10), residues: 6396 helix: 1.70 (0.10), residues: 2784 sheet: 1.21 (0.21), residues: 648 loop : -1.80 (0.11), residues: 2964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 131 HIS 0.005 0.001 HIS F 343 PHE 0.011 0.001 PHE G 197 TYR 0.023 0.001 TYR G 150 ARG 0.006 0.000 ARG G 151 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1275 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1120 time to evaluate : 4.551 Fit side-chains REVERT: a 41 MET cc_start: 0.7895 (mtt) cc_final: 0.7551 (mtt) REVERT: a 49 GLN cc_start: 0.8751 (tt0) cc_final: 0.8500 (tt0) REVERT: b 54 LYS cc_start: 0.8428 (mmmt) cc_final: 0.8063 (mtpt) REVERT: b 96 LYS cc_start: 0.8418 (mttp) cc_final: 0.8175 (mmtm) REVERT: c 27 MET cc_start: 0.8650 (mtt) cc_final: 0.8439 (mtt) REVERT: d 96 LYS cc_start: 0.8639 (mttm) cc_final: 0.8284 (mmtt) REVERT: d 165 GLU cc_start: 0.7856 (tp30) cc_final: 0.7343 (mm-30) REVERT: e 83 GLU cc_start: 0.6420 (mt-10) cc_final: 0.6088 (mp0) REVERT: e 110 GLN cc_start: 0.7419 (mt0) cc_final: 0.7027 (mt0) REVERT: f 16 LYS cc_start: 0.6487 (OUTLIER) cc_final: 0.5299 (pttp) REVERT: f 27 MET cc_start: 0.8608 (mtt) cc_final: 0.8297 (mtt) REVERT: f 165 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7510 (mm-30) REVERT: f 167 TYR cc_start: 0.7848 (m-80) cc_final: 0.7575 (m-10) REVERT: g 41 MET cc_start: 0.7903 (mtt) cc_final: 0.7549 (mtt) REVERT: g 49 GLN cc_start: 0.8735 (tt0) cc_final: 0.8514 (tt0) REVERT: g 96 LYS cc_start: 0.8622 (mttm) cc_final: 0.8287 (mmtt) REVERT: g 118 GLU cc_start: 0.7084 (mp0) cc_final: 0.6677 (mp0) REVERT: i 16 LYS cc_start: 0.6623 (OUTLIER) cc_final: 0.5053 (pttm) REVERT: j 49 GLN cc_start: 0.8806 (tt0) cc_final: 0.8560 (tt0) REVERT: j 96 LYS cc_start: 0.8529 (mttm) cc_final: 0.7925 (mmtt) REVERT: j 118 GLU cc_start: 0.7129 (mp0) cc_final: 0.6703 (mp0) REVERT: k 21 GLU cc_start: 0.6862 (tm-30) cc_final: 0.6628 (tm-30) REVERT: k 25 GLU cc_start: 0.7325 (mm-30) cc_final: 0.6995 (mm-30) REVERT: k 110 GLN cc_start: 0.7220 (mt0) cc_final: 0.6958 (mt0) REVERT: l 16 LYS cc_start: 0.6767 (OUTLIER) cc_final: 0.5125 (pttm) REVERT: l 27 MET cc_start: 0.8629 (mtt) cc_final: 0.8373 (mtt) REVERT: A 79 LYS cc_start: 0.8165 (mmmt) cc_final: 0.7624 (tptp) REVERT: B 79 LYS cc_start: 0.7181 (mtpt) cc_final: 0.6636 (mmmt) REVERT: B 151 ARG cc_start: 0.7056 (mtp-110) cc_final: 0.6746 (ttm170) REVERT: B 300 TYR cc_start: 0.8132 (OUTLIER) cc_final: 0.7767 (t80) REVERT: C 79 LYS cc_start: 0.7695 (mmmt) cc_final: 0.7131 (pttt) REVERT: C 146 ASN cc_start: 0.6253 (m-40) cc_final: 0.6042 (m110) REVERT: C 171 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7416 (pt) REVERT: C 203 VAL cc_start: 0.8838 (m) cc_final: 0.8149 (t) REVERT: D 79 LYS cc_start: 0.8180 (mmmt) cc_final: 0.7661 (tptp) REVERT: D 171 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7574 (pt) REVERT: D 368 ASP cc_start: 0.6648 (t0) cc_final: 0.5631 (p0) REVERT: E 50 ASN cc_start: 0.8827 (m110) cc_final: 0.8597 (m110) REVERT: E 79 LYS cc_start: 0.7180 (mtpt) cc_final: 0.6638 (mmmt) REVERT: E 151 ARG cc_start: 0.6998 (mtp-110) cc_final: 0.6696 (ttm170) REVERT: E 300 TYR cc_start: 0.8082 (OUTLIER) cc_final: 0.7727 (t80) REVERT: F 79 LYS cc_start: 0.7620 (mmmt) cc_final: 0.7065 (pttt) REVERT: F 171 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7626 (pt) REVERT: G 17 ILE cc_start: 0.8431 (mp) cc_final: 0.8140 (mm) REVERT: H 31 LYS cc_start: 0.8752 (mttt) cc_final: 0.8471 (mttt) REVERT: H 50 ASN cc_start: 0.8876 (m-40) cc_final: 0.8645 (m110) REVERT: H 79 LYS cc_start: 0.7183 (mtpt) cc_final: 0.6657 (mmmt) REVERT: H 151 ARG cc_start: 0.6981 (mtp-110) cc_final: 0.6604 (ttm170) REVERT: H 300 TYR cc_start: 0.8012 (OUTLIER) cc_final: 0.7722 (t80) REVERT: I 79 LYS cc_start: 0.7734 (mmmt) cc_final: 0.7182 (pttt) REVERT: I 171 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7522 (pt) REVERT: I 275 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8285 (tp) REVERT: J 31 LYS cc_start: 0.8779 (mttt) cc_final: 0.8254 (mtpt) REVERT: J 171 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7588 (pt) REVERT: J 368 ASP cc_start: 0.6789 (t0) cc_final: 0.5890 (p0) REVERT: K 31 LYS cc_start: 0.8712 (mttt) cc_final: 0.8283 (mttt) REVERT: K 50 ASN cc_start: 0.8653 (m-40) cc_final: 0.8404 (m110) REVERT: K 79 LYS cc_start: 0.7170 (mtpt) cc_final: 0.6643 (mmmt) REVERT: K 151 ARG cc_start: 0.6913 (mtp-110) cc_final: 0.6613 (ttm170) REVERT: K 300 TYR cc_start: 0.8193 (OUTLIER) cc_final: 0.7494 (t80) REVERT: L 79 LYS cc_start: 0.7965 (mmmt) cc_final: 0.7112 (pttt) REVERT: L 171 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7425 (pt) outliers start: 155 outliers final: 95 residues processed: 1201 average time/residue: 0.4939 time to fit residues: 988.6351 Evaluate side-chains 1174 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 1065 time to evaluate : 4.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 35 ILE Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 159 HIS Chi-restraints excluded: chain b residue 98 ASN Chi-restraints excluded: chain b residue 141 THR Chi-restraints excluded: chain b residue 156 ILE Chi-restraints excluded: chain c residue 98 ASN Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain c residue 156 ILE Chi-restraints excluded: chain d residue 69 SER Chi-restraints excluded: chain d residue 147 VAL Chi-restraints excluded: chain d residue 156 ILE Chi-restraints excluded: chain d residue 159 HIS Chi-restraints excluded: chain e residue 15 LEU Chi-restraints excluded: chain e residue 70 VAL Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 141 THR Chi-restraints excluded: chain e residue 156 ILE Chi-restraints excluded: chain f residue 16 LYS Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 98 ASN Chi-restraints excluded: chain f residue 141 THR Chi-restraints excluded: chain f residue 156 ILE Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 156 ILE Chi-restraints excluded: chain g residue 159 HIS Chi-restraints excluded: chain h residue 109 THR Chi-restraints excluded: chain h residue 156 ILE Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 42 ASP Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain i residue 98 ASN Chi-restraints excluded: chain i residue 141 THR Chi-restraints excluded: chain i residue 156 ILE Chi-restraints excluded: chain i residue 159 HIS Chi-restraints excluded: chain j residue 35 ILE Chi-restraints excluded: chain j residue 69 SER Chi-restraints excluded: chain j residue 156 ILE Chi-restraints excluded: chain j residue 159 HIS Chi-restraints excluded: chain k residue 95 LEU Chi-restraints excluded: chain k residue 156 ILE Chi-restraints excluded: chain l residue 16 LYS Chi-restraints excluded: chain l residue 98 ASN Chi-restraints excluded: chain l residue 141 THR Chi-restraints excluded: chain l residue 156 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 300 TYR Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 300 TYR Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 300 TYR Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 326 ASN Chi-restraints excluded: chain G residue 105 ASP Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain H residue 300 TYR Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain I residue 171 ILE Chi-restraints excluded: chain I residue 259 ASP Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 300 TYR Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 326 ASN Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 171 ILE Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 188 SER Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 275 LEU Chi-restraints excluded: chain K residue 298 LEU Chi-restraints excluded: chain K residue 300 TYR Chi-restraints excluded: chain K residue 343 HIS Chi-restraints excluded: chain L residue 154 GLU Chi-restraints excluded: chain L residue 171 ILE Chi-restraints excluded: chain L residue 181 ILE Chi-restraints excluded: chain L residue 182 ASP Chi-restraints excluded: chain L residue 300 TYR Chi-restraints excluded: chain L residue 324 THR Chi-restraints excluded: chain L residue 326 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 375 optimal weight: 5.9990 chunk 604 optimal weight: 3.9990 chunk 368 optimal weight: 0.0970 chunk 286 optimal weight: 0.9980 chunk 419 optimal weight: 5.9990 chunk 633 optimal weight: 5.9990 chunk 583 optimal weight: 8.9990 chunk 504 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 389 optimal weight: 9.9990 chunk 309 optimal weight: 2.9990 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 151 ASN d 151 ASN f 2 GLN g 2 GLN i 2 GLN j 151 ASN A 50 ASN ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 ASN A 326 ASN B 161 ASN B 326 ASN C 161 ASN ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 ASN C 371 GLN D 50 ASN ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 ASN D 326 ASN ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 ASN E 326 ASN F 326 ASN F 371 GLN G 161 ASN G 295 ASN G 326 ASN G 371 GLN H 161 ASN H 326 ASN I 326 ASN J 295 ASN J 326 ASN K 26 HIS K 161 ASN K 326 ASN L 161 ASN L 326 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 52092 Z= 0.287 Angle : 0.647 12.171 70464 Z= 0.329 Chirality : 0.045 0.374 8040 Planarity : 0.004 0.040 9096 Dihedral : 5.010 30.353 6992 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.21 % Favored : 92.32 % Rotamer: Outliers : 2.57 % Allowed : 18.12 % Favored : 79.32 % 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: -0.02 (0.10), residues: 6396 helix: 1.59 (0.10), residues: 2784 sheet: 0.54 (0.19), residues: 864 loop : -2.00 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP I 116 HIS 0.007 0.002 HIS C 343 PHE 0.013 0.002 PHE K 157 TYR 0.022 0.002 TYR h 88 ARG 0.004 0.000 ARG c 161 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1249 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1102 time to evaluate : 4.331 Fit side-chains revert: symmetry clash REVERT: a 49 GLN cc_start: 0.8795 (tt0) cc_final: 0.8548 (tt0) REVERT: b 96 LYS cc_start: 0.8463 (mttp) cc_final: 0.8231 (mmtm) REVERT: c 27 MET cc_start: 0.8711 (mtt) cc_final: 0.8505 (mtt) REVERT: d 58 LYS cc_start: 0.8714 (mtmm) cc_final: 0.8479 (mtmm) REVERT: d 96 LYS cc_start: 0.8655 (mttm) cc_final: 0.8280 (mmtt) REVERT: d 118 GLU cc_start: 0.6905 (mp0) cc_final: 0.6638 (mp0) REVERT: d 165 GLU cc_start: 0.7970 (tp30) cc_final: 0.7471 (mm-30) REVERT: e 83 GLU cc_start: 0.6445 (mt-10) cc_final: 0.6194 (mp0) REVERT: f 16 LYS cc_start: 0.6522 (OUTLIER) cc_final: 0.5333 (pttp) REVERT: f 27 MET cc_start: 0.8681 (mtt) cc_final: 0.8375 (mtt) REVERT: f 167 TYR cc_start: 0.8322 (m-80) cc_final: 0.8038 (m-10) REVERT: g 49 GLN cc_start: 0.8786 (tt0) cc_final: 0.8559 (tt0) REVERT: g 96 LYS cc_start: 0.8637 (mttm) cc_final: 0.8287 (mmtt) REVERT: g 118 GLU cc_start: 0.7034 (mp0) cc_final: 0.6752 (mp0) REVERT: h 165 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7592 (mm-30) REVERT: i 16 LYS cc_start: 0.6557 (OUTLIER) cc_final: 0.5391 (pttp) REVERT: i 116 MET cc_start: 0.8479 (tpp) cc_final: 0.8119 (tpp) REVERT: j 49 GLN cc_start: 0.8861 (tt0) cc_final: 0.8566 (tt0) REVERT: j 96 LYS cc_start: 0.8578 (mttm) cc_final: 0.7963 (mmtt) REVERT: k 21 GLU cc_start: 0.6941 (tm-30) cc_final: 0.6672 (tm-30) REVERT: k 25 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7133 (mm-30) REVERT: k 110 GLN cc_start: 0.7219 (mt0) cc_final: 0.6993 (mt0) REVERT: A 79 LYS cc_start: 0.8184 (mmmt) cc_final: 0.7658 (tptp) REVERT: B 79 LYS cc_start: 0.7225 (mtpt) cc_final: 0.6679 (mmmt) REVERT: B 151 ARG cc_start: 0.7248 (mtp-110) cc_final: 0.6795 (ttm170) REVERT: B 300 TYR cc_start: 0.8219 (OUTLIER) cc_final: 0.7861 (t80) REVERT: C 171 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7521 (pt) REVERT: C 203 VAL cc_start: 0.8838 (m) cc_final: 0.8229 (t) REVERT: D 31 LYS cc_start: 0.8868 (mtmt) cc_final: 0.8462 (mtpt) REVERT: D 79 LYS cc_start: 0.8195 (mmmt) cc_final: 0.7680 (tptp) REVERT: D 171 ILE cc_start: 0.7994 (OUTLIER) cc_final: 0.7653 (pt) REVERT: D 225 GLU cc_start: 0.7331 (tt0) cc_final: 0.6942 (tt0) REVERT: D 255 SER cc_start: 0.8538 (m) cc_final: 0.8192 (p) REVERT: E 50 ASN cc_start: 0.9021 (m110) cc_final: 0.8784 (m110) REVERT: E 79 LYS cc_start: 0.7234 (mtpt) cc_final: 0.6684 (mmmt) REVERT: E 151 ARG cc_start: 0.7209 (mtp-110) cc_final: 0.6755 (ttm170) REVERT: E 236 GLN cc_start: 0.8008 (tt0) cc_final: 0.7727 (tt0) REVERT: E 300 TYR cc_start: 0.8187 (OUTLIER) cc_final: 0.7833 (t80) REVERT: F 79 LYS cc_start: 0.7633 (mmmt) cc_final: 0.7074 (pttt) REVERT: F 203 VAL cc_start: 0.8823 (m) cc_final: 0.8154 (t) REVERT: G 31 LYS cc_start: 0.8882 (mttt) cc_final: 0.8394 (mtpt) REVERT: G 105 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.8046 (m-30) REVERT: H 15 GLN cc_start: 0.8357 (tp-100) cc_final: 0.8078 (tp-100) REVERT: H 31 LYS cc_start: 0.8768 (mttt) cc_final: 0.8445 (mttt) REVERT: H 50 ASN cc_start: 0.8981 (m-40) cc_final: 0.8740 (m110) REVERT: H 79 LYS cc_start: 0.7227 (mtpt) cc_final: 0.6695 (mmmt) REVERT: H 151 ARG cc_start: 0.7427 (mtp-110) cc_final: 0.6816 (ttm170) REVERT: H 300 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.7781 (t80) REVERT: I 79 LYS cc_start: 0.7768 (mmmt) cc_final: 0.7193 (pttt) REVERT: I 171 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7627 (pt) REVERT: I 203 VAL cc_start: 0.8801 (m) cc_final: 0.8218 (t) REVERT: I 275 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8561 (tp) REVERT: J 31 LYS cc_start: 0.8801 (mttt) cc_final: 0.8352 (mtpt) REVERT: J 171 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7607 (pt) REVERT: J 182 ASP cc_start: 0.7868 (t70) cc_final: 0.7427 (t70) REVERT: K 31 LYS cc_start: 0.8746 (mttt) cc_final: 0.8336 (mttt) REVERT: K 79 LYS cc_start: 0.7222 (mtpt) cc_final: 0.6700 (mmmt) REVERT: K 151 ARG cc_start: 0.7247 (mtp-110) cc_final: 0.6775 (ttm170) REVERT: K 300 TYR cc_start: 0.8362 (OUTLIER) cc_final: 0.7837 (t80) REVERT: L 79 LYS cc_start: 0.7995 (mmmt) cc_final: 0.7118 (pttt) REVERT: L 171 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7554 (pt) outliers start: 147 outliers final: 106 residues processed: 1180 average time/residue: 0.5006 time to fit residues: 978.5039 Evaluate side-chains 1211 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 1092 time to evaluate : 4.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 7 GLU Chi-restraints excluded: chain a residue 69 SER Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 159 HIS Chi-restraints excluded: chain b residue 98 ASN Chi-restraints excluded: chain b residue 141 THR Chi-restraints excluded: chain b residue 156 ILE Chi-restraints excluded: chain c residue 98 ASN Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain c residue 156 ILE Chi-restraints excluded: chain d residue 69 SER Chi-restraints excluded: chain d residue 147 VAL Chi-restraints excluded: chain d residue 156 ILE Chi-restraints excluded: chain d residue 159 HIS Chi-restraints excluded: chain e residue 15 LEU Chi-restraints excluded: chain e residue 70 VAL Chi-restraints excluded: chain e residue 141 THR Chi-restraints excluded: chain e residue 156 ILE Chi-restraints excluded: chain f residue 16 LYS Chi-restraints excluded: chain f residue 69 SER Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 98 ASN Chi-restraints excluded: chain f residue 141 THR Chi-restraints excluded: chain f residue 156 ILE Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 110 GLN Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 156 ILE Chi-restraints excluded: chain g residue 159 HIS Chi-restraints excluded: chain h residue 109 THR Chi-restraints excluded: chain h residue 156 ILE Chi-restraints excluded: chain h residue 166 VAL Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 42 ASP Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain i residue 70 VAL Chi-restraints excluded: chain i residue 98 ASN Chi-restraints excluded: chain i residue 141 THR Chi-restraints excluded: chain i residue 156 ILE Chi-restraints excluded: chain i residue 159 HIS Chi-restraints excluded: chain i residue 166 VAL Chi-restraints excluded: chain j residue 7 GLU Chi-restraints excluded: chain j residue 69 SER Chi-restraints excluded: chain j residue 156 ILE Chi-restraints excluded: chain j residue 159 HIS Chi-restraints excluded: chain k residue 95 LEU Chi-restraints excluded: chain k residue 156 ILE Chi-restraints excluded: chain l residue 70 VAL Chi-restraints excluded: chain l residue 98 ASN Chi-restraints excluded: chain l residue 141 THR Chi-restraints excluded: chain l residue 156 ILE Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 161 ASN Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 300 TYR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 300 TYR Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 300 TYR Chi-restraints excluded: chain G residue 105 ASP Chi-restraints excluded: chain G residue 161 ASN Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 300 TYR Chi-restraints excluded: chain H residue 326 ASN Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 171 ILE Chi-restraints excluded: chain I residue 259 ASP Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 300 TYR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 171 ILE Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain K residue 161 ASN Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 188 SER Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 275 LEU Chi-restraints excluded: chain K residue 300 TYR Chi-restraints excluded: chain K residue 326 ASN Chi-restraints excluded: chain K residue 343 HIS Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 171 ILE Chi-restraints excluded: chain L residue 181 ILE Chi-restraints excluded: chain L residue 182 ASP Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 224 GLU Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 300 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 400 optimal weight: 6.9990 chunk 537 optimal weight: 7.9990 chunk 154 optimal weight: 2.9990 chunk 465 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 505 optimal weight: 0.9990 chunk 211 optimal weight: 3.9990 chunk 518 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 151 ASN d 151 ASN f 2 GLN g 2 GLN i 2 GLN j 151 ASN l 2 GLN ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 ASN A 371 GLN B 161 ASN C 50 ASN C 326 ASN C 371 GLN ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 ASN D 371 GLN ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 326 ASN F 326 ASN G 326 ASN G 371 GLN H 161 ASN I 326 ASN J 326 ASN K 161 ASN L 50 ASN L 326 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.117390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.103728 restraints weight = 68242.750| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.43 r_work: 0.2845 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.142 52092 Z= 0.324 Angle : 1.000 59.200 70464 Z= 0.585 Chirality : 0.048 0.871 8040 Planarity : 0.005 0.147 9096 Dihedral : 5.106 31.800 6992 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.18 % Favored : 92.37 % Rotamer: Outliers : 2.66 % Allowed : 18.20 % Favored : 79.14 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.05 (0.10), residues: 6396 helix: 1.56 (0.10), residues: 2784 sheet: 0.51 (0.19), residues: 864 loop : -2.01 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP I 116 HIS 0.007 0.002 HIS F 343 PHE 0.013 0.002 PHE F 262 TYR 0.018 0.002 TYR j 88 ARG 0.007 0.000 ARG i 161 =============================================================================== Job complete usr+sys time: 14867.08 seconds wall clock time: 261 minutes 5.17 seconds (15665.17 seconds total)