Starting phenix.real_space_refine on Tue Dec 31 09:16:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vhp_32002/12_2024/7vhp_32002.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vhp_32002/12_2024/7vhp_32002.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vhp_32002/12_2024/7vhp_32002.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vhp_32002/12_2024/7vhp_32002.map" model { file = "/net/cci-nas-00/data/ceres_data/7vhp_32002/12_2024/7vhp_32002.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vhp_32002/12_2024/7vhp_32002.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 180 5.16 5 C 41784 2.51 5 N 11892 2.21 5 O 12744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 182 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 66600 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "B" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "C" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "D" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "E" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2121 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain: "F" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2121 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain: "G" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2397 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 9, 'TRANS': 289} Chain breaks: 1 Chain: "H" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2397 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 9, 'TRANS': 289} Chain breaks: 1 Chain: "I" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2397 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 9, 'TRANS': 289} Chain breaks: 1 Chain: "U" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2121 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain: "e" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "f" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "W" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "Y" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "a" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "c" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "g" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2121 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain: "i" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2121 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain: "k" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2397 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 9, 'TRANS': 289} Chain breaks: 1 Chain: "m" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2397 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 9, 'TRANS': 289} Chain breaks: 1 Chain: "o" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2397 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 9, 'TRANS': 289} Chain breaks: 1 Chain: "q" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2121 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain: "s" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "u" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "X" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "Z" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "b" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "d" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "h" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2121 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain: "j" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2121 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain: "l" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2397 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 9, 'TRANS': 289} Chain breaks: 1 Chain: "n" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2397 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 9, 'TRANS': 289} Chain breaks: 1 Chain: "p" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2397 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 9, 'TRANS': 289} Chain breaks: 1 Chain: "r" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2121 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain: "t" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "v" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "J" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "K" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "L" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "M" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "N" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2121 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain: "O" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2121 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain: "P" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2397 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 9, 'TRANS': 289} Chain breaks: 1 Chain: "Q" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2397 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 9, 'TRANS': 289} Chain breaks: 1 Chain: "R" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2397 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 9, 'TRANS': 289} Chain breaks: 1 Chain: "S" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2121 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain: "T" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "V" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Time building chain proxies: 29.40, per 1000 atoms: 0.44 Number of scatterers: 66600 At special positions: 0 Unit cell: (225.141, 224.084, 172.291, 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 180 16.00 O 12744 8.00 N 11892 7.00 C 41784 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.09 Conformation dependent library (CDL) restraints added in 6.1 seconds 16368 Ramachandran restraints generated. 8184 Oldfield, 0 Emsley, 8184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15840 Finding SS restraints... Secondary structure from input PDB file: 229 helices and 114 sheets defined 54.8% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.80 Creating SS restraints... Processing helix chain 'A' and resid 33 through 43 Processing helix chain 'A' and resid 75 through 84 removed outlier: 4.118A pdb=" N ASP A 79 " --> pdb=" O PRO A 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 44 Processing helix chain 'B' and resid 76 through 84 Processing helix chain 'C' and resid 33 through 43 Processing helix chain 'C' and resid 74 through 84 removed outlier: 3.936A pdb=" N LEU C 78 " --> pdb=" O ASP C 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 43 Processing helix chain 'D' and resid 75 through 84 removed outlier: 4.102A pdb=" N ASP D 79 " --> pdb=" O PRO D 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 96 Processing helix chain 'E' and resid 169 through 176 removed outlier: 3.554A pdb=" N TYR E 173 " --> pdb=" O ASN E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 199 removed outlier: 3.719A pdb=" N LYS E 198 " --> pdb=" O GLY E 194 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR E 199 " --> pdb=" O VAL E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 206 Processing helix chain 'E' and resid 208 through 224 removed outlier: 4.034A pdb=" N ARG E 213 " --> pdb=" O ARG E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 318 removed outlier: 3.816A pdb=" N ALA E 250 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE E 265 " --> pdb=" O GLU E 261 " (cutoff:3.500A) Proline residue: E 277 - end of helix Proline residue: E 313 - end of helix Processing helix chain 'E' and resid 318 through 338 removed outlier: 3.524A pdb=" N THR E 322 " --> pdb=" O ALA E 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 96 Processing helix chain 'F' and resid 169 through 176 Processing helix chain 'F' and resid 179 through 197 Processing helix chain 'F' and resid 200 through 208 Processing helix chain 'F' and resid 210 through 225 Processing helix chain 'F' and resid 244 through 246 No H-bonds generated for 'chain 'F' and resid 244 through 246' Processing helix chain 'F' and resid 247 through 318 removed outlier: 4.059A pdb=" N ARG F 258 " --> pdb=" O ALA F 254 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU F 259 " --> pdb=" O ILE F 255 " (cutoff:3.500A) Proline residue: F 277 - end of helix Proline residue: F 313 - end of helix removed outlier: 3.750A pdb=" N ALA F 318 " --> pdb=" O GLU F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 337 removed outlier: 3.709A pdb=" N THR F 322 " --> pdb=" O ALA F 318 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 19 removed outlier: 3.505A pdb=" N ILE G 6 " --> pdb=" O ARG G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 107 Processing helix chain 'G' and resid 108 through 110 No H-bonds generated for 'chain 'G' and resid 108 through 110' Processing helix chain 'G' and resid 111 through 133 removed outlier: 3.591A pdb=" N ALA G 115 " --> pdb=" O ASP G 111 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP G 125 " --> pdb=" O ARG G 121 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG G 133 " --> pdb=" O SER G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 142 Processing helix chain 'G' and resid 145 through 157 Processing helix chain 'G' and resid 216 through 289 removed outlier: 3.577A pdb=" N LEU G 282 " --> pdb=" O GLU G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 308 removed outlier: 3.532A pdb=" N TYR G 294 " --> pdb=" O ASP G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 326 removed outlier: 4.487A pdb=" N TYR G 325 " --> pdb=" O PHE G 322 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 19 Processing helix chain 'H' and resid 99 through 107 Processing helix chain 'H' and resid 111 through 134 removed outlier: 4.347A pdb=" N ALA H 115 " --> pdb=" O ASP H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 141 Processing helix chain 'H' and resid 146 through 156 Processing helix chain 'H' and resid 218 through 288 removed outlier: 3.737A pdb=" N VAL H 234 " --> pdb=" O GLU H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 290 through 307 removed outlier: 3.523A pdb=" N TYR H 294 " --> pdb=" O ASP H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 321 through 326 removed outlier: 4.472A pdb=" N TYR H 325 " --> pdb=" O PHE H 322 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 19 Processing helix chain 'I' and resid 99 through 107 Processing helix chain 'I' and resid 111 through 132 removed outlier: 4.438A pdb=" N ALA I 115 " --> pdb=" O ASP I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 147 removed outlier: 3.599A pdb=" N SER I 143 " --> pdb=" O ILE I 139 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ARG I 144 " --> pdb=" O VAL I 140 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY I 145 " --> pdb=" O THR I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 158 Processing helix chain 'I' and resid 216 through 288 removed outlier: 3.563A pdb=" N VAL I 234 " --> pdb=" O GLU I 230 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 307 Processing helix chain 'I' and resid 321 through 326 removed outlier: 4.553A pdb=" N TYR I 325 " --> pdb=" O PHE I 322 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 96 Processing helix chain 'U' and resid 169 through 176 removed outlier: 3.700A pdb=" N TYR U 173 " --> pdb=" O ASN U 169 " (cutoff:3.500A) Processing helix chain 'U' and resid 179 through 199 removed outlier: 4.013A pdb=" N LYS U 198 " --> pdb=" O GLY U 194 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR U 199 " --> pdb=" O VAL U 195 " (cutoff:3.500A) Processing helix chain 'U' and resid 200 through 228 removed outlier: 7.128A pdb=" N ARG U 209 " --> pdb=" O LEU U 205 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N THR U 210 " --> pdb=" O THR U 206 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL U 211 " --> pdb=" O GLU U 207 " (cutoff:3.500A) Proline residue: U 226 - end of helix Processing helix chain 'U' and resid 244 through 318 removed outlier: 4.118A pdb=" N ALA U 249 " --> pdb=" O GLU U 245 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ALA U 250 " --> pdb=" O GLU U 246 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN U 262 " --> pdb=" O ARG U 258 " (cutoff:3.500A) Proline residue: U 277 - end of helix Proline residue: U 313 - end of helix removed outlier: 3.558A pdb=" N ALA U 318 " --> pdb=" O GLU U 314 " (cutoff:3.500A) Processing helix chain 'U' and resid 318 through 338 removed outlier: 3.597A pdb=" N THR U 322 " --> pdb=" O ALA U 318 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR U 338 " --> pdb=" O VAL U 334 " (cutoff:3.500A) Processing helix chain 'e' and resid 33 through 43 removed outlier: 3.593A pdb=" N PHE e 37 " --> pdb=" O ASP e 33 " (cutoff:3.500A) Processing helix chain 'e' and resid 74 through 84 removed outlier: 4.453A pdb=" N LEU e 78 " --> pdb=" O ASP e 74 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASP e 79 " --> pdb=" O PRO e 75 " (cutoff:3.500A) Processing helix chain 'f' and resid 33 through 43 Processing helix chain 'f' and resid 75 through 84 removed outlier: 4.186A pdb=" N ASP f 79 " --> pdb=" O PRO f 75 " (cutoff:3.500A) Processing helix chain 'W' and resid 33 through 43 Processing helix chain 'W' and resid 75 through 84 removed outlier: 4.118A pdb=" N ASP W 79 " --> pdb=" O PRO W 75 " (cutoff:3.500A) Processing helix chain 'Y' and resid 33 through 44 Processing helix chain 'Y' and resid 76 through 84 Processing helix chain 'a' and resid 33 through 43 Processing helix chain 'a' and resid 74 through 84 removed outlier: 3.935A pdb=" N LEU a 78 " --> pdb=" O ASP a 74 " (cutoff:3.500A) Processing helix chain 'c' and resid 33 through 43 Processing helix chain 'c' and resid 75 through 84 removed outlier: 4.101A pdb=" N ASP c 79 " --> pdb=" O PRO c 75 " (cutoff:3.500A) Processing helix chain 'g' and resid 80 through 96 Processing helix chain 'g' and resid 169 through 176 removed outlier: 3.554A pdb=" N TYR g 173 " --> pdb=" O ASN g 169 " (cutoff:3.500A) Processing helix chain 'g' and resid 179 through 199 removed outlier: 3.718A pdb=" N LYS g 198 " --> pdb=" O GLY g 194 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR g 199 " --> pdb=" O VAL g 195 " (cutoff:3.500A) Processing helix chain 'g' and resid 200 through 206 Processing helix chain 'g' and resid 208 through 224 removed outlier: 4.034A pdb=" N ARG g 213 " --> pdb=" O ARG g 209 " (cutoff:3.500A) Processing helix chain 'g' and resid 244 through 318 removed outlier: 3.816A pdb=" N ALA g 250 " --> pdb=" O GLU g 246 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE g 265 " --> pdb=" O GLU g 261 " (cutoff:3.500A) Proline residue: g 277 - end of helix Proline residue: g 313 - end of helix Processing helix chain 'g' and resid 318 through 338 removed outlier: 3.525A pdb=" N THR g 322 " --> pdb=" O ALA g 318 " (cutoff:3.500A) Processing helix chain 'i' and resid 80 through 96 Processing helix chain 'i' and resid 169 through 176 Processing helix chain 'i' and resid 179 through 199 removed outlier: 3.904A pdb=" N TYR i 199 " --> pdb=" O VAL i 195 " (cutoff:3.500A) Processing helix chain 'i' and resid 200 through 228 removed outlier: 5.766A pdb=" N ARG i 209 " --> pdb=" O LEU i 205 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N THR i 210 " --> pdb=" O THR i 206 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN i 217 " --> pdb=" O ARG i 213 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG i 218 " --> pdb=" O SER i 214 " (cutoff:3.500A) Proline residue: i 226 - end of helix Processing helix chain 'i' and resid 244 through 246 No H-bonds generated for 'chain 'i' and resid 244 through 246' Processing helix chain 'i' and resid 247 through 318 removed outlier: 4.058A pdb=" N ARG i 258 " --> pdb=" O ALA i 254 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU i 259 " --> pdb=" O ILE i 255 " (cutoff:3.500A) Proline residue: i 277 - end of helix Proline residue: i 313 - end of helix removed outlier: 3.749A pdb=" N ALA i 318 " --> pdb=" O GLU i 314 " (cutoff:3.500A) Processing helix chain 'i' and resid 318 through 337 removed outlier: 3.709A pdb=" N THR i 322 " --> pdb=" O ALA i 318 " (cutoff:3.500A) Processing helix chain 'k' and resid 2 through 19 removed outlier: 3.504A pdb=" N ILE k 6 " --> pdb=" O ARG k 2 " (cutoff:3.500A) Processing helix chain 'k' and resid 99 through 107 Processing helix chain 'k' and resid 108 through 110 No H-bonds generated for 'chain 'k' and resid 108 through 110' Processing helix chain 'k' and resid 111 through 133 removed outlier: 3.591A pdb=" N ALA k 115 " --> pdb=" O ASP k 111 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP k 125 " --> pdb=" O ARG k 121 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG k 133 " --> pdb=" O SER k 129 " (cutoff:3.500A) Processing helix chain 'k' and resid 135 through 142 Processing helix chain 'k' and resid 145 through 157 Processing helix chain 'k' and resid 216 through 289 removed outlier: 3.577A pdb=" N LEU k 282 " --> pdb=" O GLU k 278 " (cutoff:3.500A) Processing helix chain 'k' and resid 290 through 308 removed outlier: 3.532A pdb=" N TYR k 294 " --> pdb=" O ASP k 290 " (cutoff:3.500A) Processing helix chain 'm' and resid 2 through 19 Processing helix chain 'm' and resid 99 through 107 Processing helix chain 'm' and resid 111 through 134 removed outlier: 4.348A pdb=" N ALA m 115 " --> pdb=" O ASP m 111 " (cutoff:3.500A) Processing helix chain 'm' and resid 135 through 141 Processing helix chain 'm' and resid 146 through 156 Processing helix chain 'm' and resid 218 through 288 removed outlier: 3.737A pdb=" N VAL m 234 " --> pdb=" O GLU m 230 " (cutoff:3.500A) Processing helix chain 'm' and resid 290 through 307 removed outlier: 3.524A pdb=" N TYR m 294 " --> pdb=" O ASP m 290 " (cutoff:3.500A) Processing helix chain 'm' and resid 321 through 326 removed outlier: 4.472A pdb=" N TYR m 325 " --> pdb=" O PHE m 322 " (cutoff:3.500A) Processing helix chain 'o' and resid 2 through 19 Processing helix chain 'o' and resid 99 through 107 Processing helix chain 'o' and resid 111 through 132 removed outlier: 4.438A pdb=" N ALA o 115 " --> pdb=" O ASP o 111 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE o 131 " --> pdb=" O LEU o 127 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY o 132 " --> pdb=" O ARG o 128 " (cutoff:3.500A) Processing helix chain 'o' and resid 135 through 147 removed outlier: 3.599A pdb=" N SER o 143 " --> pdb=" O ILE o 139 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ARG o 144 " --> pdb=" O VAL o 140 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY o 145 " --> pdb=" O THR o 141 " (cutoff:3.500A) Processing helix chain 'o' and resid 147 through 158 Processing helix chain 'o' and resid 216 through 288 removed outlier: 3.563A pdb=" N VAL o 234 " --> pdb=" O GLU o 230 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA o 264 " --> pdb=" O THR o 260 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLN o 267 " --> pdb=" O GLU o 263 " (cutoff:3.500A) Processing helix chain 'o' and resid 290 through 307 Processing helix chain 'o' and resid 321 through 326 removed outlier: 4.553A pdb=" N TYR o 325 " --> pdb=" O PHE o 322 " (cutoff:3.500A) Processing helix chain 'q' and resid 80 through 96 Processing helix chain 'q' and resid 169 through 176 removed outlier: 3.700A pdb=" N TYR q 173 " --> pdb=" O ASN q 169 " (cutoff:3.500A) Processing helix chain 'q' and resid 179 through 199 removed outlier: 4.013A pdb=" N LYS q 198 " --> pdb=" O GLY q 194 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR q 199 " --> pdb=" O VAL q 195 " (cutoff:3.500A) Processing helix chain 'q' and resid 200 through 228 removed outlier: 7.128A pdb=" N ARG q 209 " --> pdb=" O LEU q 205 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N THR q 210 " --> pdb=" O THR q 206 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL q 211 " --> pdb=" O GLU q 207 " (cutoff:3.500A) Proline residue: q 226 - end of helix Processing helix chain 'q' and resid 244 through 318 removed outlier: 4.118A pdb=" N ALA q 249 " --> pdb=" O GLU q 245 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ALA q 250 " --> pdb=" O GLU q 246 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN q 262 " --> pdb=" O ARG q 258 " (cutoff:3.500A) Proline residue: q 277 - end of helix Proline residue: q 313 - end of helix removed outlier: 3.558A pdb=" N ALA q 318 " --> pdb=" O GLU q 314 " (cutoff:3.500A) Processing helix chain 'q' and resid 318 through 338 removed outlier: 3.598A pdb=" N THR q 322 " --> pdb=" O ALA q 318 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR q 338 " --> pdb=" O VAL q 334 " (cutoff:3.500A) Processing helix chain 's' and resid 33 through 43 removed outlier: 3.594A pdb=" N PHE s 37 " --> pdb=" O ASP s 33 " (cutoff:3.500A) Processing helix chain 's' and resid 74 through 84 removed outlier: 4.453A pdb=" N LEU s 78 " --> pdb=" O ASP s 74 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASP s 79 " --> pdb=" O PRO s 75 " (cutoff:3.500A) Processing helix chain 'u' and resid 33 through 43 Processing helix chain 'u' and resid 75 through 84 removed outlier: 4.186A pdb=" N ASP u 79 " --> pdb=" O PRO u 75 " (cutoff:3.500A) Processing helix chain 'X' and resid 33 through 43 Processing helix chain 'X' and resid 75 through 84 removed outlier: 4.117A pdb=" N ASP X 79 " --> pdb=" O PRO X 75 " (cutoff:3.500A) Processing helix chain 'Z' and resid 33 through 44 Processing helix chain 'Z' and resid 76 through 84 Processing helix chain 'b' and resid 33 through 43 Processing helix chain 'b' and resid 74 through 84 removed outlier: 3.936A pdb=" N LEU b 78 " --> pdb=" O ASP b 74 " (cutoff:3.500A) Processing helix chain 'd' and resid 33 through 43 Processing helix chain 'd' and resid 75 through 84 removed outlier: 4.102A pdb=" N ASP d 79 " --> pdb=" O PRO d 75 " (cutoff:3.500A) Processing helix chain 'h' and resid 80 through 96 Processing helix chain 'h' and resid 169 through 176 removed outlier: 3.554A pdb=" N TYR h 173 " --> pdb=" O ASN h 169 " (cutoff:3.500A) Processing helix chain 'h' and resid 179 through 199 removed outlier: 3.718A pdb=" N LYS h 198 " --> pdb=" O GLY h 194 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR h 199 " --> pdb=" O VAL h 195 " (cutoff:3.500A) Processing helix chain 'h' and resid 200 through 206 Processing helix chain 'h' and resid 208 through 224 removed outlier: 4.034A pdb=" N ARG h 213 " --> pdb=" O ARG h 209 " (cutoff:3.500A) Processing helix chain 'h' and resid 244 through 318 removed outlier: 3.816A pdb=" N ALA h 250 " --> pdb=" O GLU h 246 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE h 265 " --> pdb=" O GLU h 261 " (cutoff:3.500A) Proline residue: h 277 - end of helix Proline residue: h 313 - end of helix Processing helix chain 'h' and resid 318 through 338 removed outlier: 3.524A pdb=" N THR h 322 " --> pdb=" O ALA h 318 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 96 Processing helix chain 'j' and resid 169 through 176 Processing helix chain 'j' and resid 179 through 197 Processing helix chain 'j' and resid 200 through 224 removed outlier: 5.475A pdb=" N ARG j 209 " --> pdb=" O LEU j 205 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR j 210 " --> pdb=" O THR j 206 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL j 211 " --> pdb=" O GLU j 207 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER j 214 " --> pdb=" O THR j 210 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU j 221 " --> pdb=" O GLN j 217 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU j 222 " --> pdb=" O ARG j 218 " (cutoff:3.500A) Processing helix chain 'j' and resid 244 through 246 No H-bonds generated for 'chain 'j' and resid 244 through 246' Processing helix chain 'j' and resid 247 through 318 removed outlier: 4.059A pdb=" N ARG j 258 " --> pdb=" O ALA j 254 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU j 259 " --> pdb=" O ILE j 255 " (cutoff:3.500A) Proline residue: j 277 - end of helix removed outlier: 3.508A pdb=" N LYS j 310 " --> pdb=" O ALA j 306 " (cutoff:3.500A) Proline residue: j 313 - end of helix removed outlier: 3.750A pdb=" N ALA j 318 " --> pdb=" O GLU j 314 " (cutoff:3.500A) Processing helix chain 'j' and resid 318 through 337 removed outlier: 3.709A pdb=" N THR j 322 " --> pdb=" O ALA j 318 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 19 removed outlier: 3.504A pdb=" N ILE l 6 " --> pdb=" O ARG l 2 " (cutoff:3.500A) Processing helix chain 'l' and resid 99 through 107 Processing helix chain 'l' and resid 108 through 110 No H-bonds generated for 'chain 'l' and resid 108 through 110' Processing helix chain 'l' and resid 111 through 133 removed outlier: 3.591A pdb=" N ALA l 115 " --> pdb=" O ASP l 111 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP l 125 " --> pdb=" O ARG l 121 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG l 133 " --> pdb=" O SER l 129 " (cutoff:3.500A) Processing helix chain 'l' and resid 135 through 142 Processing helix chain 'l' and resid 145 through 157 Processing helix chain 'l' and resid 216 through 289 removed outlier: 3.577A pdb=" N LEU l 282 " --> pdb=" O GLU l 278 " (cutoff:3.500A) Processing helix chain 'l' and resid 290 through 308 removed outlier: 3.532A pdb=" N TYR l 294 " --> pdb=" O ASP l 290 " (cutoff:3.500A) Processing helix chain 'l' and resid 320 through 326 removed outlier: 4.517A pdb=" N TYR l 325 " --> pdb=" O PHE l 322 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 19 Processing helix chain 'n' and resid 99 through 107 Processing helix chain 'n' and resid 111 through 134 removed outlier: 4.348A pdb=" N ALA n 115 " --> pdb=" O ASP n 111 " (cutoff:3.500A) Processing helix chain 'n' and resid 135 through 141 Processing helix chain 'n' and resid 146 through 156 Processing helix chain 'n' and resid 218 through 288 removed outlier: 3.737A pdb=" N VAL n 234 " --> pdb=" O GLU n 230 " (cutoff:3.500A) Processing helix chain 'n' and resid 290 through 307 removed outlier: 3.524A pdb=" N TYR n 294 " --> pdb=" O ASP n 290 " (cutoff:3.500A) Processing helix chain 'n' and resid 321 through 326 removed outlier: 4.472A pdb=" N TYR n 325 " --> pdb=" O PHE n 322 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 19 Processing helix chain 'p' and resid 99 through 107 Processing helix chain 'p' and resid 111 through 132 removed outlier: 4.121A pdb=" N ALA p 115 " --> pdb=" O ASP p 111 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU p 118 " --> pdb=" O GLN p 114 " (cutoff:3.500A) Processing helix chain 'p' and resid 135 through 147 removed outlier: 3.599A pdb=" N SER p 143 " --> pdb=" O ILE p 139 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ARG p 144 " --> pdb=" O VAL p 140 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY p 145 " --> pdb=" O THR p 141 " (cutoff:3.500A) Processing helix chain 'p' and resid 147 through 158 Processing helix chain 'p' and resid 216 through 288 removed outlier: 3.563A pdb=" N VAL p 234 " --> pdb=" O GLU p 230 " (cutoff:3.500A) Processing helix chain 'p' and resid 290 through 307 Processing helix chain 'p' and resid 321 through 326 removed outlier: 4.553A pdb=" N TYR p 325 " --> pdb=" O PHE p 322 " (cutoff:3.500A) Processing helix chain 'r' and resid 80 through 96 Processing helix chain 'r' and resid 169 through 176 removed outlier: 3.699A pdb=" N TYR r 173 " --> pdb=" O ASN r 169 " (cutoff:3.500A) Processing helix chain 'r' and resid 179 through 199 removed outlier: 4.013A pdb=" N LYS r 198 " --> pdb=" O GLY r 194 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR r 199 " --> pdb=" O VAL r 195 " (cutoff:3.500A) Processing helix chain 'r' and resid 200 through 228 removed outlier: 7.128A pdb=" N ARG r 209 " --> pdb=" O LEU r 205 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N THR r 210 " --> pdb=" O THR r 206 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL r 211 " --> pdb=" O GLU r 207 " (cutoff:3.500A) Proline residue: r 226 - end of helix Processing helix chain 'r' and resid 244 through 318 removed outlier: 4.118A pdb=" N ALA r 249 " --> pdb=" O GLU r 245 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ALA r 250 " --> pdb=" O GLU r 246 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN r 262 " --> pdb=" O ARG r 258 " (cutoff:3.500A) Proline residue: r 277 - end of helix Proline residue: r 313 - end of helix removed outlier: 3.558A pdb=" N ALA r 318 " --> pdb=" O GLU r 314 " (cutoff:3.500A) Processing helix chain 'r' and resid 318 through 338 removed outlier: 3.597A pdb=" N THR r 322 " --> pdb=" O ALA r 318 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR r 338 " --> pdb=" O VAL r 334 " (cutoff:3.500A) Processing helix chain 't' and resid 33 through 43 removed outlier: 3.594A pdb=" N PHE t 37 " --> pdb=" O ASP t 33 " (cutoff:3.500A) Processing helix chain 't' and resid 74 through 84 removed outlier: 4.454A pdb=" N LEU t 78 " --> pdb=" O ASP t 74 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASP t 79 " --> pdb=" O PRO t 75 " (cutoff:3.500A) Processing helix chain 'v' and resid 33 through 43 Processing helix chain 'v' and resid 75 through 84 removed outlier: 4.185A pdb=" N ASP v 79 " --> pdb=" O PRO v 75 " (cutoff:3.500A) Processing helix chain 'J' and resid 33 through 43 Processing helix chain 'J' and resid 75 through 84 removed outlier: 4.118A pdb=" N ASP J 79 " --> pdb=" O PRO J 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 33 through 44 Processing helix chain 'K' and resid 76 through 84 Processing helix chain 'L' and resid 33 through 43 Processing helix chain 'L' and resid 74 through 84 removed outlier: 3.936A pdb=" N LEU L 78 " --> pdb=" O ASP L 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 33 through 43 Processing helix chain 'M' and resid 75 through 84 removed outlier: 4.102A pdb=" N ASP M 79 " --> pdb=" O PRO M 75 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 96 Processing helix chain 'N' and resid 169 through 176 removed outlier: 3.554A pdb=" N TYR N 173 " --> pdb=" O ASN N 169 " (cutoff:3.500A) Processing helix chain 'N' and resid 179 through 199 removed outlier: 3.718A pdb=" N LYS N 198 " --> pdb=" O GLY N 194 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR N 199 " --> pdb=" O VAL N 195 " (cutoff:3.500A) Processing helix chain 'N' and resid 200 through 206 Processing helix chain 'N' and resid 208 through 224 removed outlier: 4.035A pdb=" N ARG N 213 " --> pdb=" O ARG N 209 " (cutoff:3.500A) Processing helix chain 'N' and resid 244 through 318 removed outlier: 3.816A pdb=" N ALA N 250 " --> pdb=" O GLU N 246 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE N 265 " --> pdb=" O GLU N 261 " (cutoff:3.500A) Proline residue: N 277 - end of helix Proline residue: N 313 - end of helix Processing helix chain 'N' and resid 318 through 338 removed outlier: 3.524A pdb=" N THR N 322 " --> pdb=" O ALA N 318 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 96 Processing helix chain 'O' and resid 169 through 176 Processing helix chain 'O' and resid 179 through 197 Processing helix chain 'O' and resid 200 through 208 Processing helix chain 'O' and resid 210 through 225 removed outlier: 3.572A pdb=" N THR O 216 " --> pdb=" O ILE O 212 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU O 222 " --> pdb=" O ARG O 218 " (cutoff:3.500A) Processing helix chain 'O' and resid 244 through 246 No H-bonds generated for 'chain 'O' and resid 244 through 246' Processing helix chain 'O' and resid 247 through 318 removed outlier: 4.058A pdb=" N ARG O 258 " --> pdb=" O ALA O 254 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU O 259 " --> pdb=" O ILE O 255 " (cutoff:3.500A) Proline residue: O 277 - end of helix Proline residue: O 313 - end of helix removed outlier: 3.751A pdb=" N ALA O 318 " --> pdb=" O GLU O 314 " (cutoff:3.500A) Processing helix chain 'O' and resid 318 through 337 removed outlier: 3.709A pdb=" N THR O 322 " --> pdb=" O ALA O 318 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 19 removed outlier: 3.504A pdb=" N ILE P 6 " --> pdb=" O ARG P 2 " (cutoff:3.500A) Processing helix chain 'P' and resid 99 through 107 Processing helix chain 'P' and resid 108 through 110 No H-bonds generated for 'chain 'P' and resid 108 through 110' Processing helix chain 'P' and resid 111 through 133 removed outlier: 3.591A pdb=" N ALA P 115 " --> pdb=" O ASP P 111 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP P 125 " --> pdb=" O ARG P 121 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ARG P 133 " --> pdb=" O SER P 129 " (cutoff:3.500A) Processing helix chain 'P' and resid 135 through 142 Processing helix chain 'P' and resid 145 through 157 Processing helix chain 'P' and resid 216 through 289 removed outlier: 3.577A pdb=" N LEU P 282 " --> pdb=" O GLU P 278 " (cutoff:3.500A) Processing helix chain 'P' and resid 290 through 308 removed outlier: 3.533A pdb=" N TYR P 294 " --> pdb=" O ASP P 290 " (cutoff:3.500A) Processing helix chain 'P' and resid 320 through 325 removed outlier: 4.414A pdb=" N TYR P 325 " --> pdb=" O PHE P 322 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 19 Processing helix chain 'Q' and resid 99 through 107 Processing helix chain 'Q' and resid 111 through 134 removed outlier: 4.348A pdb=" N ALA Q 115 " --> pdb=" O ASP Q 111 " (cutoff:3.500A) Processing helix chain 'Q' and resid 135 through 141 Processing helix chain 'Q' and resid 146 through 156 Processing helix chain 'Q' and resid 218 through 288 removed outlier: 3.737A pdb=" N VAL Q 234 " --> pdb=" O GLU Q 230 " (cutoff:3.500A) Processing helix chain 'Q' and resid 290 through 307 removed outlier: 3.523A pdb=" N TYR Q 294 " --> pdb=" O ASP Q 290 " (cutoff:3.500A) Processing helix chain 'Q' and resid 321 through 326 removed outlier: 4.472A pdb=" N TYR Q 325 " --> pdb=" O PHE Q 322 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 19 Processing helix chain 'R' and resid 99 through 107 Processing helix chain 'R' and resid 111 through 132 removed outlier: 4.438A pdb=" N ALA R 115 " --> pdb=" O ASP R 111 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY R 132 " --> pdb=" O ARG R 128 " (cutoff:3.500A) Processing helix chain 'R' and resid 135 through 147 removed outlier: 3.598A pdb=" N SER R 143 " --> pdb=" O ILE R 139 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ARG R 144 " --> pdb=" O VAL R 140 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY R 145 " --> pdb=" O THR R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 158 Processing helix chain 'R' and resid 216 through 288 removed outlier: 3.563A pdb=" N VAL R 234 " --> pdb=" O GLU R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 290 through 307 Processing helix chain 'R' and resid 321 through 326 removed outlier: 4.553A pdb=" N TYR R 325 " --> pdb=" O PHE R 322 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 96 Processing helix chain 'S' and resid 169 through 176 removed outlier: 3.700A pdb=" N TYR S 173 " --> pdb=" O ASN S 169 " (cutoff:3.500A) Processing helix chain 'S' and resid 179 through 199 removed outlier: 4.012A pdb=" N LYS S 198 " --> pdb=" O GLY S 194 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR S 199 " --> pdb=" O VAL S 195 " (cutoff:3.500A) Processing helix chain 'S' and resid 200 through 228 removed outlier: 7.128A pdb=" N ARG S 209 " --> pdb=" O LEU S 205 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N THR S 210 " --> pdb=" O THR S 206 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL S 211 " --> pdb=" O GLU S 207 " (cutoff:3.500A) Proline residue: S 226 - end of helix Processing helix chain 'S' and resid 244 through 318 removed outlier: 4.118A pdb=" N ALA S 249 " --> pdb=" O GLU S 245 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ALA S 250 " --> pdb=" O GLU S 246 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN S 262 " --> pdb=" O ARG S 258 " (cutoff:3.500A) Proline residue: S 277 - end of helix Proline residue: S 313 - end of helix removed outlier: 3.558A pdb=" N ALA S 318 " --> pdb=" O GLU S 314 " (cutoff:3.500A) Processing helix chain 'S' and resid 318 through 338 removed outlier: 3.597A pdb=" N THR S 322 " --> pdb=" O ALA S 318 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR S 338 " --> pdb=" O VAL S 334 " (cutoff:3.500A) Processing helix chain 'T' and resid 33 through 43 removed outlier: 3.593A pdb=" N PHE T 37 " --> pdb=" O ASP T 33 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 84 removed outlier: 4.453A pdb=" N LEU T 78 " --> pdb=" O ASP T 74 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASP T 79 " --> pdb=" O PRO T 75 " (cutoff:3.500A) Processing helix chain 'V' and resid 33 through 43 Processing helix chain 'V' and resid 75 through 84 removed outlier: 4.187A pdb=" N ASP V 79 " --> pdb=" O PRO V 75 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 removed outlier: 4.380A pdb=" N TYR A 69 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU A 48 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG A 47 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL A 89 " --> pdb=" O ARG A 47 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA A 49 " --> pdb=" O VAL A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 65 through 69 removed outlier: 3.776A pdb=" N GLU B 48 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ARG B 47 " --> pdb=" O LYS B 87 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL B 89 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA B 49 " --> pdb=" O VAL B 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 65 through 69 removed outlier: 6.509A pdb=" N ARG C 47 " --> pdb=" O LYS C 87 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL C 89 " --> pdb=" O ARG C 47 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA C 49 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 65 through 69 removed outlier: 6.445A pdb=" N ARG D 47 " --> pdb=" O LYS D 87 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL D 89 " --> pdb=" O ARG D 47 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA D 49 " --> pdb=" O VAL D 89 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 97 through 98 Processing sheet with id=AA6, first strand: chain 'E' and resid 113 through 118 removed outlier: 4.943A pdb=" N PHE E 114 " --> pdb=" O ARG E 110 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ARG E 110 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU E 131 " --> pdb=" O THR E 109 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 141 through 150 removed outlier: 6.751A pdb=" N GLU E 160 " --> pdb=" O GLN E 239 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ARG E 166 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N LEU E 233 " --> pdb=" O ARG E 166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 339 through 341 removed outlier: 5.801A pdb=" N ARG F 339 " --> pdb=" O MET G 314 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LYS E 340 " --> pdb=" O VAL G 313 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL G 315 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LEU E 342 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG E 339 " --> pdb=" O MET H 314 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N MET H 316 " --> pdb=" O ARG E 339 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL E 341 " --> pdb=" O MET H 316 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASP I 312 " --> pdb=" O ARG U 339 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N VAL U 341 " --> pdb=" O ASP I 312 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N MET I 314 " --> pdb=" O VAL U 341 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ARG O 339 " --> pdb=" O MET P 314 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LYS N 340 " --> pdb=" O VAL P 313 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL P 315 " --> pdb=" O LYS N 340 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LEU N 342 " --> pdb=" O VAL P 315 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG N 339 " --> pdb=" O MET Q 314 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N MET Q 316 " --> pdb=" O ARG N 339 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL N 341 " --> pdb=" O MET Q 316 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N MET R 314 " --> pdb=" O VAL S 341 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 97 through 98 Processing sheet with id=AB1, first strand: chain 'F' and resid 113 through 118 removed outlier: 5.042A pdb=" N PHE F 114 " --> pdb=" O ARG F 110 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ARG F 110 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS F 116 " --> pdb=" O VAL F 108 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 141 through 150 removed outlier: 6.662A pdb=" N ARG F 158 " --> pdb=" O ALA F 240 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ALA F 240 " --> pdb=" O ARG F 158 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLU F 160 " --> pdb=" O PHE F 238 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N PHE F 238 " --> pdb=" O GLU F 160 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN F 162 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VAL F 236 " --> pdb=" O ASN F 162 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLN F 164 " --> pdb=" O LEU F 234 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 20 through 22 Processing sheet with id=AB4, first strand: chain 'G' and resid 27 through 33 Processing sheet with id=AB5, first strand: chain 'G' and resid 39 through 40 Processing sheet with id=AB6, first strand: chain 'G' and resid 70 through 80 removed outlier: 4.059A pdb=" N SER G 91 " --> pdb=" O ASN G 74 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA G 76 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL G 89 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG G 78 " --> pdb=" O LEU G 87 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU G 87 " --> pdb=" O ARG G 78 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE G 88 " --> pdb=" O ILE G 213 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE G 213 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASP G 90 " --> pdb=" O LYS G 211 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP G 207 " --> pdb=" O LYS G 94 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG G 96 " --> pdb=" O VAL G 205 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N VAL G 205 " --> pdb=" O ARG G 96 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 21 through 22 Processing sheet with id=AB8, first strand: chain 'H' and resid 47 through 48 Processing sheet with id=AB9, first strand: chain 'H' and resid 39 through 40 removed outlier: 3.638A pdb=" N LYS H 44 " --> pdb=" O ASP H 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 70 through 80 removed outlier: 3.959A pdb=" N ALA H 76 " --> pdb=" O VAL H 89 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N VAL H 89 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ARG H 78 " --> pdb=" O LEU H 87 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU H 87 " --> pdb=" O ARG H 78 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE H 88 " --> pdb=" O GLN H 212 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN H 212 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ASP H 90 " --> pdb=" O ILE H 210 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ILE H 210 " --> pdb=" O ASP H 90 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR H 92 " --> pdb=" O VAL H 208 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N VAL H 208 " --> pdb=" O TYR H 92 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LYS H 94 " --> pdb=" O VAL H 206 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 20 through 21 Processing sheet with id=AC3, first strand: chain 'I' and resid 27 through 28 Processing sheet with id=AC4, first strand: chain 'I' and resid 32 through 33 Processing sheet with id=AC5, first strand: chain 'I' and resid 70 through 74 removed outlier: 3.631A pdb=" N SER I 91 " --> pdb=" O ASN I 74 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 70 through 74 removed outlier: 3.631A pdb=" N SER I 91 " --> pdb=" O ASN I 74 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TYR I 92 " --> pdb=" O ILE I 210 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE I 210 " --> pdb=" O TYR I 92 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LYS I 94 " --> pdb=" O VAL I 208 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N VAL I 208 " --> pdb=" O LYS I 94 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ARG I 96 " --> pdb=" O VAL I 206 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL I 206 " --> pdb=" O ARG I 96 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'U' and resid 97 through 100 Processing sheet with id=AC8, first strand: chain 'U' and resid 116 through 118 Processing sheet with id=AC9, first strand: chain 'U' and resid 141 through 150 removed outlier: 6.651A pdb=" N GLU U 160 " --> pdb=" O GLN U 239 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ARG U 166 " --> pdb=" O LEU U 233 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU U 233 " --> pdb=" O ARG U 166 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'e' and resid 65 through 69 removed outlier: 6.192A pdb=" N ARG e 47 " --> pdb=" O LYS e 87 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL e 89 " --> pdb=" O ARG e 47 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA e 49 " --> pdb=" O VAL e 89 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'f' and resid 65 through 69 removed outlier: 6.488A pdb=" N ARG f 47 " --> pdb=" O LYS f 87 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N VAL f 89 " --> pdb=" O ARG f 47 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA f 49 " --> pdb=" O VAL f 89 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'W' and resid 31 through 32 removed outlier: 4.380A pdb=" N TYR W 69 " --> pdb=" O VAL W 32 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU W 48 " --> pdb=" O THR W 59 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG W 47 " --> pdb=" O LYS W 87 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N VAL W 89 " --> pdb=" O ARG W 47 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ALA W 49 " --> pdb=" O VAL W 89 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Y' and resid 65 through 69 removed outlier: 3.776A pdb=" N GLU Y 48 " --> pdb=" O THR Y 59 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ARG Y 47 " --> pdb=" O LYS Y 87 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL Y 89 " --> pdb=" O ARG Y 47 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA Y 49 " --> pdb=" O VAL Y 89 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'a' and resid 65 through 69 removed outlier: 6.509A pdb=" N ARG a 47 " --> pdb=" O LYS a 87 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL a 89 " --> pdb=" O ARG a 47 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA a 49 " --> pdb=" O VAL a 89 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'c' and resid 65 through 69 removed outlier: 6.445A pdb=" N ARG c 47 " --> pdb=" O LYS c 87 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL c 89 " --> pdb=" O ARG c 47 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA c 49 " --> pdb=" O VAL c 89 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'g' and resid 97 through 98 Processing sheet with id=AD8, first strand: chain 'g' and resid 113 through 118 removed outlier: 4.943A pdb=" N PHE g 114 " --> pdb=" O ARG g 110 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ARG g 110 " --> pdb=" O PHE g 114 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU g 131 " --> pdb=" O THR g 109 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'g' and resid 141 through 150 removed outlier: 6.752A pdb=" N GLU g 160 " --> pdb=" O GLN g 239 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ARG g 166 " --> pdb=" O LEU g 233 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N LEU g 233 " --> pdb=" O ARG g 166 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'o' and resid 313 through 316 removed outlier: 6.387A pdb=" N MET o 314 " --> pdb=" O VAL q 341 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG g 339 " --> pdb=" O MET m 314 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N MET m 316 " --> pdb=" O ARG g 339 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL g 341 " --> pdb=" O MET m 316 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LYS g 340 " --> pdb=" O VAL k 313 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL k 315 " --> pdb=" O LYS g 340 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LEU g 342 " --> pdb=" O VAL k 315 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ARG i 339 " --> pdb=" O MET k 314 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LYS i 340 " --> pdb=" O VAL p 313 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N VAL p 315 " --> pdb=" O LYS i 340 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASP p 312 " --> pdb=" O ARG r 339 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N VAL r 341 " --> pdb=" O ASP p 312 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N MET p 314 " --> pdb=" O VAL r 341 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG h 339 " --> pdb=" O MET n 314 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N MET n 316 " --> pdb=" O ARG h 339 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL h 341 " --> pdb=" O MET n 316 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LYS h 340 " --> pdb=" O VAL l 313 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL l 315 " --> pdb=" O LYS h 340 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LEU h 342 " --> pdb=" O VAL l 315 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ARG j 339 " --> pdb=" O MET l 314 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'i' and resid 97 through 98 Processing sheet with id=AE3, first strand: chain 'i' and resid 113 through 118 removed outlier: 5.042A pdb=" N PHE i 114 " --> pdb=" O ARG i 110 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ARG i 110 " --> pdb=" O PHE i 114 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS i 116 " --> pdb=" O VAL i 108 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'i' and resid 141 through 150 removed outlier: 3.810A pdb=" N ALA i 240 " --> pdb=" O GLU i 160 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASN i 162 " --> pdb=" O PHE i 238 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N PHE i 238 " --> pdb=" O ASN i 162 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N GLN i 164 " --> pdb=" O VAL i 236 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N VAL i 236 " --> pdb=" O GLN i 164 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ARG i 166 " --> pdb=" O LEU i 234 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU i 234 " --> pdb=" O ARG i 166 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'k' and resid 20 through 22 Processing sheet with id=AE6, first strand: chain 'k' and resid 27 through 33 Processing sheet with id=AE7, first strand: chain 'k' and resid 39 through 40 Processing sheet with id=AE8, first strand: chain 'k' and resid 70 through 80 removed outlier: 4.058A pdb=" N SER k 91 " --> pdb=" O ASN k 74 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ALA k 76 " --> pdb=" O VAL k 89 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL k 89 " --> pdb=" O ALA k 76 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG k 78 " --> pdb=" O LEU k 87 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU k 87 " --> pdb=" O ARG k 78 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE k 88 " --> pdb=" O ILE k 213 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE k 213 " --> pdb=" O ILE k 88 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASP k 90 " --> pdb=" O LYS k 211 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP k 207 " --> pdb=" O LYS k 94 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG k 96 " --> pdb=" O VAL k 205 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N VAL k 205 " --> pdb=" O ARG k 96 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'm' and resid 21 through 22 Processing sheet with id=AF1, first strand: chain 'm' and resid 47 through 48 Processing sheet with id=AF2, first strand: chain 'm' and resid 39 through 40 removed outlier: 3.637A pdb=" N LYS m 44 " --> pdb=" O ASP m 40 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'm' and resid 70 through 80 removed outlier: 3.959A pdb=" N ALA m 76 " --> pdb=" O VAL m 89 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N VAL m 89 " --> pdb=" O ALA m 76 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ARG m 78 " --> pdb=" O LEU m 87 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU m 87 " --> pdb=" O ARG m 78 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE m 88 " --> pdb=" O GLN m 212 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN m 212 " --> pdb=" O ILE m 88 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ASP m 90 " --> pdb=" O ILE m 210 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ILE m 210 " --> pdb=" O ASP m 90 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR m 92 " --> pdb=" O VAL m 208 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N VAL m 208 " --> pdb=" O TYR m 92 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LYS m 94 " --> pdb=" O VAL m 206 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'o' and resid 20 through 21 Processing sheet with id=AF5, first strand: chain 'o' and resid 27 through 28 Processing sheet with id=AF6, first strand: chain 'o' and resid 32 through 33 Processing sheet with id=AF7, first strand: chain 'o' and resid 70 through 74 removed outlier: 3.632A pdb=" N SER o 91 " --> pdb=" O ASN o 74 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'o' and resid 70 through 74 removed outlier: 3.632A pdb=" N SER o 91 " --> pdb=" O ASN o 74 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TYR o 92 " --> pdb=" O ILE o 210 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE o 210 " --> pdb=" O TYR o 92 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LYS o 94 " --> pdb=" O VAL o 208 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N VAL o 208 " --> pdb=" O LYS o 94 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ARG o 96 " --> pdb=" O VAL o 206 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL o 206 " --> pdb=" O ARG o 96 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'q' and resid 97 through 100 Processing sheet with id=AG1, first strand: chain 'q' and resid 116 through 118 Processing sheet with id=AG2, first strand: chain 'q' and resid 141 through 150 removed outlier: 6.651A pdb=" N GLU q 160 " --> pdb=" O GLN q 239 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ARG q 166 " --> pdb=" O LEU q 233 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU q 233 " --> pdb=" O ARG q 166 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 's' and resid 65 through 69 removed outlier: 6.192A pdb=" N ARG s 47 " --> pdb=" O LYS s 87 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL s 89 " --> pdb=" O ARG s 47 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA s 49 " --> pdb=" O VAL s 89 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'u' and resid 65 through 69 removed outlier: 6.487A pdb=" N ARG u 47 " --> pdb=" O LYS u 87 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N VAL u 89 " --> pdb=" O ARG u 47 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA u 49 " --> pdb=" O VAL u 89 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 31 through 32 removed outlier: 4.380A pdb=" N TYR X 69 " --> pdb=" O VAL X 32 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU X 48 " --> pdb=" O THR X 59 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG X 47 " --> pdb=" O LYS X 87 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL X 89 " --> pdb=" O ARG X 47 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA X 49 " --> pdb=" O VAL X 89 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Z' and resid 65 through 69 removed outlier: 3.776A pdb=" N GLU Z 48 " --> pdb=" O THR Z 59 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ARG Z 47 " --> pdb=" O LYS Z 87 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL Z 89 " --> pdb=" O ARG Z 47 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA Z 49 " --> pdb=" O VAL Z 89 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'b' and resid 65 through 69 removed outlier: 6.508A pdb=" N ARG b 47 " --> pdb=" O LYS b 87 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL b 89 " --> pdb=" O ARG b 47 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA b 49 " --> pdb=" O VAL b 89 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'd' and resid 65 through 69 removed outlier: 6.445A pdb=" N ARG d 47 " --> pdb=" O LYS d 87 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL d 89 " --> pdb=" O ARG d 47 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA d 49 " --> pdb=" O VAL d 89 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'h' and resid 97 through 98 Processing sheet with id=AH1, first strand: chain 'h' and resid 113 through 118 removed outlier: 4.943A pdb=" N PHE h 114 " --> pdb=" O ARG h 110 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ARG h 110 " --> pdb=" O PHE h 114 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU h 131 " --> pdb=" O THR h 109 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'h' and resid 141 through 150 removed outlier: 6.751A pdb=" N GLU h 160 " --> pdb=" O GLN h 239 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ARG h 166 " --> pdb=" O LEU h 233 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N LEU h 233 " --> pdb=" O ARG h 166 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'j' and resid 97 through 98 Processing sheet with id=AH4, first strand: chain 'j' and resid 113 through 118 removed outlier: 5.042A pdb=" N PHE j 114 " --> pdb=" O ARG j 110 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ARG j 110 " --> pdb=" O PHE j 114 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS j 116 " --> pdb=" O VAL j 108 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'j' and resid 141 through 150 removed outlier: 6.662A pdb=" N ARG j 158 " --> pdb=" O ALA j 240 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ALA j 240 " --> pdb=" O ARG j 158 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLU j 160 " --> pdb=" O PHE j 238 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N PHE j 238 " --> pdb=" O GLU j 160 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASN j 162 " --> pdb=" O VAL j 236 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VAL j 236 " --> pdb=" O ASN j 162 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLN j 164 " --> pdb=" O LEU j 234 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'l' and resid 20 through 22 Processing sheet with id=AH7, first strand: chain 'l' and resid 27 through 33 Processing sheet with id=AH8, first strand: chain 'l' and resid 39 through 40 Processing sheet with id=AH9, first strand: chain 'l' and resid 70 through 80 removed outlier: 4.059A pdb=" N SER l 91 " --> pdb=" O ASN l 74 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA l 76 " --> pdb=" O VAL l 89 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL l 89 " --> pdb=" O ALA l 76 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG l 78 " --> pdb=" O LEU l 87 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU l 87 " --> pdb=" O ARG l 78 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE l 88 " --> pdb=" O ILE l 213 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE l 213 " --> pdb=" O ILE l 88 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASP l 90 " --> pdb=" O LYS l 211 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP l 207 " --> pdb=" O LYS l 94 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG l 96 " --> pdb=" O VAL l 205 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N VAL l 205 " --> pdb=" O ARG l 96 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'n' and resid 21 through 22 Processing sheet with id=AI2, first strand: chain 'n' and resid 47 through 48 Processing sheet with id=AI3, first strand: chain 'n' and resid 39 through 40 removed outlier: 3.637A pdb=" N LYS n 44 " --> pdb=" O ASP n 40 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'n' and resid 70 through 80 removed outlier: 3.958A pdb=" N ALA n 76 " --> pdb=" O VAL n 89 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N VAL n 89 " --> pdb=" O ALA n 76 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ARG n 78 " --> pdb=" O LEU n 87 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU n 87 " --> pdb=" O ARG n 78 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE n 88 " --> pdb=" O GLN n 212 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLN n 212 " --> pdb=" O ILE n 88 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ASP n 90 " --> pdb=" O ILE n 210 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ILE n 210 " --> pdb=" O ASP n 90 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR n 92 " --> pdb=" O VAL n 208 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N VAL n 208 " --> pdb=" O TYR n 92 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LYS n 94 " --> pdb=" O VAL n 206 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'p' and resid 20 through 21 Processing sheet with id=AI6, first strand: chain 'p' and resid 27 through 28 Processing sheet with id=AI7, first strand: chain 'p' and resid 32 through 33 Processing sheet with id=AI8, first strand: chain 'p' and resid 70 through 74 removed outlier: 3.631A pdb=" N SER p 91 " --> pdb=" O ASN p 74 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'p' and resid 70 through 74 removed outlier: 3.631A pdb=" N SER p 91 " --> pdb=" O ASN p 74 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TYR p 92 " --> pdb=" O ILE p 210 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE p 210 " --> pdb=" O TYR p 92 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LYS p 94 " --> pdb=" O VAL p 208 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N VAL p 208 " --> pdb=" O LYS p 94 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ARG p 96 " --> pdb=" O VAL p 206 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL p 206 " --> pdb=" O ARG p 96 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'r' and resid 97 through 100 Processing sheet with id=AJ2, first strand: chain 'r' and resid 116 through 118 Processing sheet with id=AJ3, first strand: chain 'r' and resid 141 through 150 removed outlier: 6.651A pdb=" N GLU r 160 " --> pdb=" O GLN r 239 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG r 166 " --> pdb=" O LEU r 233 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU r 233 " --> pdb=" O ARG r 166 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 't' and resid 65 through 69 removed outlier: 6.192A pdb=" N ARG t 47 " --> pdb=" O LYS t 87 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL t 89 " --> pdb=" O ARG t 47 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA t 49 " --> pdb=" O VAL t 89 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'v' and resid 65 through 69 removed outlier: 6.488A pdb=" N ARG v 47 " --> pdb=" O LYS v 87 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N VAL v 89 " --> pdb=" O ARG v 47 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA v 49 " --> pdb=" O VAL v 89 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'J' and resid 31 through 32 removed outlier: 4.380A pdb=" N TYR J 69 " --> pdb=" O VAL J 32 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU J 48 " --> pdb=" O THR J 59 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG J 47 " --> pdb=" O LYS J 87 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL J 89 " --> pdb=" O ARG J 47 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ALA J 49 " --> pdb=" O VAL J 89 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'K' and resid 65 through 69 removed outlier: 3.776A pdb=" N GLU K 48 " --> pdb=" O THR K 59 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ARG K 47 " --> pdb=" O LYS K 87 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL K 89 " --> pdb=" O ARG K 47 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA K 49 " --> pdb=" O VAL K 89 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'L' and resid 65 through 69 removed outlier: 6.509A pdb=" N ARG L 47 " --> pdb=" O LYS L 87 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N VAL L 89 " --> pdb=" O ARG L 47 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA L 49 " --> pdb=" O VAL L 89 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'M' and resid 65 through 69 removed outlier: 6.444A pdb=" N ARG M 47 " --> pdb=" O LYS M 87 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL M 89 " --> pdb=" O ARG M 47 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA M 49 " --> pdb=" O VAL M 89 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'N' and resid 97 through 98 Processing sheet with id=AK2, first strand: chain 'N' and resid 113 through 118 removed outlier: 4.943A pdb=" N PHE N 114 " --> pdb=" O ARG N 110 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ARG N 110 " --> pdb=" O PHE N 114 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU N 131 " --> pdb=" O THR N 109 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'N' and resid 141 through 150 removed outlier: 6.751A pdb=" N GLU N 160 " --> pdb=" O GLN N 239 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ARG N 166 " --> pdb=" O LEU N 233 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N LEU N 233 " --> pdb=" O ARG N 166 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'O' and resid 97 through 98 Processing sheet with id=AK5, first strand: chain 'O' and resid 113 through 118 removed outlier: 5.042A pdb=" N PHE O 114 " --> pdb=" O ARG O 110 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ARG O 110 " --> pdb=" O PHE O 114 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS O 116 " --> pdb=" O VAL O 108 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'O' and resid 141 through 150 removed outlier: 6.662A pdb=" N ARG O 158 " --> pdb=" O ALA O 240 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA O 240 " --> pdb=" O ARG O 158 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N GLU O 160 " --> pdb=" O PHE O 238 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N PHE O 238 " --> pdb=" O GLU O 160 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN O 162 " --> pdb=" O VAL O 236 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL O 236 " --> pdb=" O ASN O 162 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLN O 164 " --> pdb=" O LEU O 234 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'P' and resid 20 through 22 Processing sheet with id=AK8, first strand: chain 'P' and resid 27 through 33 Processing sheet with id=AK9, first strand: chain 'P' and resid 39 through 40 Processing sheet with id=AL1, first strand: chain 'P' and resid 70 through 80 removed outlier: 4.059A pdb=" N SER P 91 " --> pdb=" O ASN P 74 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ALA P 76 " --> pdb=" O VAL P 89 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL P 89 " --> pdb=" O ALA P 76 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG P 78 " --> pdb=" O LEU P 87 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU P 87 " --> pdb=" O ARG P 78 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE P 88 " --> pdb=" O ILE P 213 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE P 213 " --> pdb=" O ILE P 88 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASP P 90 " --> pdb=" O LYS P 211 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP P 207 " --> pdb=" O LYS P 94 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG P 96 " --> pdb=" O VAL P 205 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N VAL P 205 " --> pdb=" O ARG P 96 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'Q' and resid 21 through 22 Processing sheet with id=AL3, first strand: chain 'Q' and resid 47 through 48 Processing sheet with id=AL4, first strand: chain 'Q' and resid 39 through 40 removed outlier: 3.637A pdb=" N LYS Q 44 " --> pdb=" O ASP Q 40 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'Q' and resid 70 through 80 removed outlier: 3.959A pdb=" N ALA Q 76 " --> pdb=" O VAL Q 89 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N VAL Q 89 " --> pdb=" O ALA Q 76 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ARG Q 78 " --> pdb=" O LEU Q 87 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU Q 87 " --> pdb=" O ARG Q 78 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE Q 88 " --> pdb=" O GLN Q 212 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN Q 212 " --> pdb=" O ILE Q 88 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ASP Q 90 " --> pdb=" O ILE Q 210 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ILE Q 210 " --> pdb=" O ASP Q 90 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR Q 92 " --> pdb=" O VAL Q 208 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N VAL Q 208 " --> pdb=" O TYR Q 92 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LYS Q 94 " --> pdb=" O VAL Q 206 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'R' and resid 20 through 21 Processing sheet with id=AL7, first strand: chain 'R' and resid 27 through 28 Processing sheet with id=AL8, first strand: chain 'R' and resid 32 through 33 Processing sheet with id=AL9, first strand: chain 'R' and resid 70 through 74 removed outlier: 3.631A pdb=" N SER R 91 " --> pdb=" O ASN R 74 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'R' and resid 70 through 74 removed outlier: 3.631A pdb=" N SER R 91 " --> pdb=" O ASN R 74 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TYR R 92 " --> pdb=" O ILE R 210 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE R 210 " --> pdb=" O TYR R 92 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N LYS R 94 " --> pdb=" O VAL R 208 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N VAL R 208 " --> pdb=" O LYS R 94 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ARG R 96 " --> pdb=" O VAL R 206 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL R 206 " --> pdb=" O ARG R 96 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'S' and resid 97 through 100 Processing sheet with id=AM3, first strand: chain 'S' and resid 116 through 118 Processing sheet with id=AM4, first strand: chain 'S' and resid 141 through 150 removed outlier: 6.651A pdb=" N GLU S 160 " --> pdb=" O GLN S 239 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG S 166 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU S 233 " --> pdb=" O ARG S 166 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'T' and resid 65 through 69 removed outlier: 6.192A pdb=" N ARG T 47 " --> pdb=" O LYS T 87 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL T 89 " --> pdb=" O ARG T 47 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA T 49 " --> pdb=" O VAL T 89 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'V' and resid 65 through 69 removed outlier: 6.488A pdb=" N ARG V 47 " --> pdb=" O LYS V 87 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N VAL V 89 " --> pdb=" O ARG V 47 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA V 49 " --> pdb=" O VAL V 89 " (cutoff:3.500A) 4158 hydrogen bonds defined for protein. 12114 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 26.69 Time building geometry restraints manager: 14.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 12369 1.32 - 1.45: 15764 1.45 - 1.57: 39067 1.57 - 1.69: 0 1.69 - 1.81: 360 Bond restraints: 67560 Sorted by residual: bond pdb=" C ILE F 212 " pdb=" O ILE F 212 " ideal model delta sigma weight residual 1.237 1.202 0.034 1.13e-02 7.83e+03 9.25e+00 bond pdb=" C ARG F 213 " pdb=" O ARG F 213 " ideal model delta sigma weight residual 1.237 1.203 0.034 1.19e-02 7.06e+03 8.15e+00 bond pdb=" CA ILE F 212 " pdb=" C ILE F 212 " ideal model delta sigma weight residual 1.524 1.496 0.028 1.22e-02 6.72e+03 5.36e+00 bond pdb=" C SER F 214 " pdb=" O SER F 214 " ideal model delta sigma weight residual 1.237 1.210 0.027 1.19e-02 7.06e+03 4.99e+00 bond pdb=" C ASP F 215 " pdb=" O ASP F 215 " ideal model delta sigma weight residual 1.237 1.211 0.025 1.17e-02 7.31e+03 4.67e+00 ... (remaining 67555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 90111 2.36 - 4.72: 985 4.72 - 7.08: 102 7.08 - 9.45: 13 9.45 - 11.81: 1 Bond angle restraints: 91212 Sorted by residual: angle pdb=" N ILE O 212 " pdb=" CA ILE O 212 " pdb=" C ILE O 212 " ideal model delta sigma weight residual 110.53 117.22 -6.69 9.40e-01 1.13e+00 5.07e+01 angle pdb=" N ILE p 112 " pdb=" CA ILE p 112 " pdb=" C ILE p 112 " ideal model delta sigma weight residual 110.62 117.64 -7.02 1.02e+00 9.61e-01 4.74e+01 angle pdb=" N ALA o 264 " pdb=" CA ALA o 264 " pdb=" C ALA o 264 " ideal model delta sigma weight residual 110.80 98.99 11.81 2.13e+00 2.20e-01 3.07e+01 angle pdb=" N ILE i 224 " pdb=" CA ILE i 224 " pdb=" C ILE i 224 " ideal model delta sigma weight residual 110.72 116.21 -5.49 1.01e+00 9.80e-01 2.95e+01 angle pdb=" N ILE I 131 " pdb=" CA ILE I 131 " pdb=" C ILE I 131 " ideal model delta sigma weight residual 110.72 115.86 -5.14 1.01e+00 9.80e-01 2.59e+01 ... (remaining 91207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 37488 17.00 - 34.00: 3716 34.00 - 51.00: 609 51.00 - 68.00: 67 68.00 - 85.00: 60 Dihedral angle restraints: 41940 sinusoidal: 17532 harmonic: 24408 Sorted by residual: dihedral pdb=" CA GLY q 208 " pdb=" C GLY q 208 " pdb=" N ARG q 209 " pdb=" CA ARG q 209 " ideal model delta harmonic sigma weight residual -180.00 -156.39 -23.61 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA GLY U 208 " pdb=" C GLY U 208 " pdb=" N ARG U 209 " pdb=" CA ARG U 209 " ideal model delta harmonic sigma weight residual -180.00 -156.40 -23.60 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA GLY S 208 " pdb=" C GLY S 208 " pdb=" N ARG S 209 " pdb=" CA ARG S 209 " ideal model delta harmonic sigma weight residual -180.00 -156.41 -23.59 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 41937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 8608 0.059 - 0.117: 1539 0.117 - 0.176: 192 0.176 - 0.235: 16 0.235 - 0.293: 1 Chirality restraints: 10356 Sorted by residual: chirality pdb=" CA ALA o 264 " pdb=" N ALA o 264 " pdb=" C ALA o 264 " pdb=" CB ALA o 264 " both_signs ideal model delta sigma weight residual False 2.48 2.78 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA ILE j 298 " pdb=" N ILE j 298 " pdb=" C ILE j 298 " pdb=" CB ILE j 298 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ASP j 228 " pdb=" N ASP j 228 " pdb=" C ASP j 228 " pdb=" CB ASP j 228 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 10353 not shown) Planarity restraints: 11940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY O 208 " -0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C GLY O 208 " 0.063 2.00e-02 2.50e+03 pdb=" O GLY O 208 " -0.024 2.00e-02 2.50e+03 pdb=" N ARG O 209 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN o 194 " 0.050 5.00e-02 4.00e+02 7.57e-02 9.18e+00 pdb=" N PRO o 195 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO o 195 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO o 195 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN I 194 " 0.050 5.00e-02 4.00e+02 7.56e-02 9.15e+00 pdb=" N PRO I 195 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO I 195 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO I 195 " 0.041 5.00e-02 4.00e+02 ... (remaining 11937 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.90: 39 1.90 - 2.65: 988 2.65 - 3.40: 94770 3.40 - 4.15: 152189 4.15 - 4.90: 281621 Nonbonded interactions: 529607 Sorted by model distance: nonbonded pdb=" O GLU p 263 " pdb=" CD GLN p 267 " model vdw 1.149 3.270 nonbonded pdb=" OE2 GLU i 221 " pdb=" NH1 ARG i 225 " model vdw 1.151 3.120 nonbonded pdb=" CG2 VAL j 195 " pdb=" OD2 ASP j 215 " model vdw 1.301 3.460 nonbonded pdb=" CE1 TYR j 227 " pdb=" CD LYS l 94 " model vdw 1.301 3.740 nonbonded pdb=" OE1 GLU i 221 " pdb=" NH2 ARG i 225 " model vdw 1.309 3.120 ... (remaining 529602 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 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'N' selection = chain 'O' selection = chain 'S' selection = chain 'U' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'q' selection = chain 'r' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' } 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: 3.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 1.950 Check model and map are aligned: 0.370 Set scattering table: 0.450 Process input model: 113.180 Find NCS groups from input model: 2.330 Set up NCS constraints: 0.590 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:2.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 67560 Z= 0.202 Angle : 0.632 11.808 91212 Z= 0.375 Chirality : 0.045 0.293 10356 Planarity : 0.004 0.076 11940 Dihedral : 13.465 85.002 26100 Min Nonbonded Distance : 1.149 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.13 % Favored : 96.84 % Rotamer: Outliers : 0.32 % Allowed : 0.55 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.09), residues: 8184 helix: 2.46 (0.08), residues: 4148 sheet: 0.93 (0.15), residues: 1368 loop : -0.71 (0.12), residues: 2668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP U 92 HIS 0.002 0.001 HIS Q 53 PHE 0.023 0.001 PHE G 287 TYR 0.020 0.001 TYR Q 17 ARG 0.011 0.000 ARG M 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16368 Ramachandran restraints generated. 8184 Oldfield, 0 Emsley, 8184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16368 Ramachandran restraints generated. 8184 Oldfield, 0 Emsley, 8184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1940 residues out of total 7224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 1917 time to evaluate : 5.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 ASN cc_start: 0.4997 (m-40) cc_final: 0.4672 (m-40) REVERT: B 70 ILE cc_start: 0.7879 (mt) cc_final: 0.7436 (pt) REVERT: B 78 LEU cc_start: 0.6665 (pp) cc_final: 0.6422 (tt) REVERT: D 91 GLU cc_start: 0.6862 (mm-30) cc_final: 0.6569 (mt-10) REVERT: E 242 ARG cc_start: 0.7265 (mmm-85) cc_final: 0.6795 (ptp-110) REVERT: E 252 ASP cc_start: 0.7306 (m-30) cc_final: 0.6000 (m-30) REVERT: E 345 ASP cc_start: 0.6389 (m-30) cc_final: 0.5980 (m-30) REVERT: F 131 GLU cc_start: 0.6628 (tp30) cc_final: 0.6397 (mp0) REVERT: F 158 ARG cc_start: 0.7151 (mmm-85) cc_final: 0.6858 (tpp80) REVERT: F 214 SER cc_start: 0.7548 (t) cc_final: 0.7216 (p) REVERT: F 344 ASN cc_start: 0.8178 (t0) cc_final: 0.7830 (t0) REVERT: H 319 ASP cc_start: 0.8146 (t70) cc_final: 0.7930 (t0) REVERT: I 18 MET cc_start: 0.6600 (tpt) cc_final: 0.6365 (mmp) REVERT: I 84 LYS cc_start: 0.7925 (mtmt) cc_final: 0.7584 (mptt) REVERT: I 125 ASP cc_start: 0.7814 (t0) cc_final: 0.7362 (m-30) REVERT: I 232 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7821 (mm-30) REVERT: I 316 MET cc_start: 0.7340 (mtm) cc_final: 0.7135 (mtp) REVERT: U 148 VAL cc_start: 0.8408 (t) cc_final: 0.8153 (m) REVERT: U 162 ASN cc_start: 0.7860 (m-40) cc_final: 0.7453 (m-40) REVERT: U 164 GLN cc_start: 0.8239 (mt0) cc_final: 0.7916 (mt0) REVERT: e 31 LYS cc_start: 0.7172 (tppt) cc_final: 0.6864 (tptt) REVERT: e 43 ASN cc_start: 0.7474 (t0) cc_final: 0.7156 (m-40) REVERT: e 76 LYS cc_start: 0.5960 (mmmt) cc_final: 0.5693 (ptmt) REVERT: f 76 LYS cc_start: 0.8455 (mmmt) cc_final: 0.7685 (ptmm) REVERT: f 77 LEU cc_start: 0.8005 (tt) cc_final: 0.7598 (tt) REVERT: W 76 LYS cc_start: 0.4857 (ptmt) cc_final: 0.4549 (mtpt) REVERT: Y 57 ASN cc_start: 0.5566 (m-40) cc_final: 0.4662 (m-40) REVERT: Y 69 TYR cc_start: 0.6086 (m-80) cc_final: 0.5882 (m-80) REVERT: Y 70 ILE cc_start: 0.7303 (mt) cc_final: 0.6899 (pt) REVERT: a 40 GLU cc_start: 0.5082 (tt0) cc_final: 0.4711 (tt0) REVERT: c 34 TYR cc_start: 0.5267 (t80) cc_final: 0.4987 (t80) REVERT: c 65 ARG cc_start: 0.6486 (mtp-110) cc_final: 0.6153 (ptm-80) REVERT: c 70 ILE cc_start: 0.5886 (mp) cc_final: 0.5278 (mp) REVERT: i 132 VAL cc_start: 0.6650 (p) cc_final: 0.6444 (p) REVERT: i 146 SER cc_start: 0.6845 (t) cc_final: 0.6600 (p) REVERT: i 162 ASN cc_start: 0.8631 (m-40) cc_final: 0.8362 (m-40) REVERT: i 237 ASN cc_start: 0.7799 (p0) cc_final: 0.7122 (p0) REVERT: k 18 MET cc_start: 0.5515 (mmp) cc_final: 0.5281 (mtt) REVERT: k 74 ASN cc_start: 0.7598 (m110) cc_final: 0.7298 (m110) REVERT: k 265 GLU cc_start: 0.8009 (tp30) cc_final: 0.7765 (tp30) REVERT: k 314 MET cc_start: 0.8273 (ttt) cc_final: 0.7838 (ttm) REVERT: m 120 LYS cc_start: 0.8229 (ttmm) cc_final: 0.7978 (mttt) REVERT: m 198 MET cc_start: 0.7348 (mmt) cc_final: 0.6971 (mmt) REVERT: m 319 ASP cc_start: 0.8330 (t70) cc_final: 0.8084 (t0) REVERT: q 100 ILE cc_start: 0.7504 (mt) cc_final: 0.7133 (tt) REVERT: q 153 ASP cc_start: 0.7896 (m-30) cc_final: 0.7649 (p0) REVERT: q 210 THR cc_start: 0.7227 (p) cc_final: 0.6868 (p) REVERT: q 248 LYS cc_start: 0.7728 (ttmt) cc_final: 0.7196 (ttmm) REVERT: q 267 GLU cc_start: 0.7799 (tp30) cc_final: 0.7583 (tp30) REVERT: s 38 LEU cc_start: 0.8125 (mt) cc_final: 0.7885 (tt) REVERT: s 47 ARG cc_start: 0.7156 (ttm170) cc_final: 0.6826 (ttp-170) REVERT: s 79 ASP cc_start: 0.6790 (m-30) cc_final: 0.6495 (t70) REVERT: u 50 ARG cc_start: 0.7823 (mtm110) cc_final: 0.7594 (mtp85) REVERT: u 76 LYS cc_start: 0.8291 (mmmt) cc_final: 0.7510 (ptmt) REVERT: u 80 ASN cc_start: 0.8145 (t0) cc_final: 0.7857 (t0) REVERT: X 76 LYS cc_start: 0.4770 (ptmt) cc_final: 0.4426 (tptt) REVERT: Z 57 ASN cc_start: 0.5614 (m-40) cc_final: 0.4464 (m110) REVERT: Z 70 ILE cc_start: 0.7505 (mt) cc_final: 0.7218 (pt) REVERT: h 274 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7857 (tt0) REVERT: j 162 ASN cc_start: 0.8469 (m-40) cc_final: 0.7842 (m110) REVERT: j 344 ASN cc_start: 0.8479 (t0) cc_final: 0.8250 (t0) REVERT: l 74 ASN cc_start: 0.7554 (m110) cc_final: 0.7128 (m110) REVERT: l 212 GLN cc_start: 0.7476 (pt0) cc_final: 0.7268 (pm20) REVERT: l 314 MET cc_start: 0.8522 (ttt) cc_final: 0.8156 (ttm) REVERT: l 321 ASP cc_start: 0.7531 (m-30) cc_final: 0.7231 (p0) REVERT: n 198 MET cc_start: 0.7335 (mmt) cc_final: 0.7025 (tpp) REVERT: n 227 MET cc_start: 0.8387 (mtm) cc_final: 0.8163 (mtp) REVERT: n 316 MET cc_start: 0.7998 (mtm) cc_final: 0.7463 (mtm) REVERT: n 319 ASP cc_start: 0.8285 (t70) cc_final: 0.7943 (t0) REVERT: p 125 ASP cc_start: 0.7523 (t0) cc_final: 0.7208 (m-30) REVERT: p 314 MET cc_start: 0.8088 (ttm) cc_final: 0.7582 (mtp) REVERT: r 149 MET cc_start: 0.6860 (mmm) cc_final: 0.6050 (mpp) REVERT: r 153 ASP cc_start: 0.7912 (m-30) cc_final: 0.7618 (p0) REVERT: r 161 MET cc_start: 0.7749 (mmt) cc_final: 0.7483 (mmm) REVERT: r 186 GLN cc_start: 0.7805 (mt0) cc_final: 0.7603 (mm-40) REVERT: r 210 THR cc_start: 0.6957 (p) cc_final: 0.6726 (p) REVERT: r 238 PHE cc_start: 0.8249 (t80) cc_final: 0.7792 (t80) REVERT: r 248 LYS cc_start: 0.7505 (ttmt) cc_final: 0.6782 (ttmm) REVERT: r 331 MET cc_start: 0.7396 (mmm) cc_final: 0.7142 (mmm) REVERT: t 56 ILE cc_start: 0.8773 (mt) cc_final: 0.8571 (mp) REVERT: v 76 LYS cc_start: 0.8651 (mmmt) cc_final: 0.8045 (ptmt) REVERT: J 34 TYR cc_start: 0.5304 (t80) cc_final: 0.5034 (t80) REVERT: J 76 LYS cc_start: 0.5415 (ptmt) cc_final: 0.5126 (ptmm) REVERT: K 39 GLN cc_start: 0.7101 (tp40) cc_final: 0.6861 (tp40) REVERT: K 62 ASP cc_start: 0.6284 (p0) cc_final: 0.6005 (p0) REVERT: K 70 ILE cc_start: 0.7272 (mt) cc_final: 0.6687 (pt) REVERT: L 40 GLU cc_start: 0.5737 (tt0) cc_final: 0.5453 (tt0) REVERT: M 70 ILE cc_start: 0.6100 (mp) cc_final: 0.5896 (mp) REVERT: M 87 LYS cc_start: 0.6989 (ttmm) cc_final: 0.6364 (tppt) REVERT: N 198 LYS cc_start: 0.8528 (mtmm) cc_final: 0.8280 (pttt) REVERT: O 160 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7261 (mt-10) REVERT: P 240 SER cc_start: 0.7937 (t) cc_final: 0.7719 (m) REVERT: P 310 ASN cc_start: 0.6645 (t0) cc_final: 0.6179 (t0) REVERT: Q 70 GLN cc_start: 0.8150 (mt0) cc_final: 0.7903 (mt0) REVERT: Q 214 ASN cc_start: 0.8232 (m-40) cc_final: 0.7932 (t0) REVERT: R 18 MET cc_start: 0.6125 (tpt) cc_final: 0.5823 (mmp) REVERT: R 96 ARG cc_start: 0.7743 (ttp-110) cc_final: 0.7416 (ttp-170) REVERT: S 161 MET cc_start: 0.7997 (mmt) cc_final: 0.7743 (mmm) REVERT: S 248 LYS cc_start: 0.7919 (ttmt) cc_final: 0.7533 (ttmm) REVERT: T 47 ARG cc_start: 0.7598 (ttm170) cc_final: 0.7085 (ttp-170) REVERT: T 48 GLU cc_start: 0.7663 (tt0) cc_final: 0.7355 (mp0) REVERT: T 79 ASP cc_start: 0.6886 (m-30) cc_final: 0.6273 (t70) REVERT: V 76 LYS cc_start: 0.8588 (mmmt) cc_final: 0.7821 (ptmm) REVERT: V 77 LEU cc_start: 0.8100 (tt) cc_final: 0.7827 (tt) REVERT: V 80 ASN cc_start: 0.8539 (t0) cc_final: 0.8276 (t0) outliers start: 23 outliers final: 6 residues processed: 1932 average time/residue: 0.6828 time to fit residues: 2154.1880 Evaluate side-chains 948 residues out of total 7224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 942 time to evaluate : 5.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain i residue 195 VAL Chi-restraints excluded: chain j residue 213 ARG Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain O residue 223 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 678 optimal weight: 1.9990 chunk 609 optimal weight: 10.0000 chunk 338 optimal weight: 10.0000 chunk 208 optimal weight: 6.9990 chunk 411 optimal weight: 10.0000 chunk 325 optimal weight: 5.9990 chunk 630 optimal weight: 8.9990 chunk 243 optimal weight: 2.9990 chunk 383 optimal weight: 0.7980 chunk 469 optimal weight: 6.9990 chunk 730 optimal weight: 0.8980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 57 ASN E 260 ASN F 116 HIS F 155 ASN G 310 ASN I 70 GLN e 64 ASN W 52 ASN a 42 ASN g 260 ASN m 75 GLN o 114 GLN o 310 ASN q 217 GLN X 52 ASN ** b 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 337 ASN l 74 ASN p 114 GLN p 156 ASN p 310 ASN t 64 ASN v 39 GLN K 39 GLN L 42 ASN V 43 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 67560 Z= 0.349 Angle : 0.654 13.047 91212 Z= 0.355 Chirality : 0.047 0.190 10356 Planarity : 0.005 0.053 11940 Dihedral : 4.537 38.547 9334 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.13 % Favored : 96.86 % Rotamer: Outliers : 1.99 % Allowed : 11.25 % Favored : 86.75 % 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: 1.50 (0.09), residues: 8184 helix: 2.11 (0.08), residues: 4256 sheet: 0.71 (0.13), residues: 1504 loop : -0.83 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP U 92 HIS 0.007 0.001 HIS F 116 PHE 0.029 0.002 PHE l 287 TYR 0.022 0.002 TYR I 224 ARG 0.010 0.001 ARG K 30 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16368 Ramachandran restraints generated. 8184 Oldfield, 0 Emsley, 8184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16368 Ramachandran restraints generated. 8184 Oldfield, 0 Emsley, 8184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1167 residues out of total 7224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 1023 time to evaluate : 5.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.6420 (pp) cc_final: 0.6079 (mt) REVERT: B 43 ASN cc_start: 0.7007 (t0) cc_final: 0.6489 (t0) REVERT: D 89 VAL cc_start: 0.5546 (t) cc_final: 0.5261 (p) REVERT: E 242 ARG cc_start: 0.7495 (mmm-85) cc_final: 0.6940 (ptp-110) REVERT: F 131 GLU cc_start: 0.6600 (tp30) cc_final: 0.6239 (mp0) REVERT: F 343 VAL cc_start: 0.9629 (m) cc_final: 0.9340 (t) REVERT: G 86 ASP cc_start: 0.7633 (t0) cc_final: 0.7412 (t0) REVERT: H 198 MET cc_start: 0.7387 (mtp) cc_final: 0.6943 (tpp) REVERT: I 27 GLU cc_start: 0.6924 (pm20) cc_final: 0.6672 (pm20) REVERT: I 84 LYS cc_start: 0.7904 (mtmt) cc_final: 0.7611 (mppt) REVERT: I 232 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7750 (tt0) REVERT: U 148 VAL cc_start: 0.8646 (t) cc_final: 0.8321 (m) REVERT: U 149 MET cc_start: 0.7075 (mmt) cc_final: 0.6859 (mtt) REVERT: e 42 ASN cc_start: 0.7925 (t0) cc_final: 0.7632 (t0) REVERT: f 76 LYS cc_start: 0.8475 (mmmt) cc_final: 0.7637 (ptmm) REVERT: W 76 LYS cc_start: 0.4552 (ptmt) cc_final: 0.4309 (ptpt) REVERT: Y 43 ASN cc_start: 0.7294 (t0) cc_final: 0.6694 (t0) REVERT: Y 45 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.7129 (mp10) REVERT: Y 69 TYR cc_start: 0.6329 (m-80) cc_final: 0.6033 (m-80) REVERT: Y 87 LYS cc_start: 0.6728 (OUTLIER) cc_final: 0.6349 (mtpt) REVERT: a 81 LEU cc_start: 0.7067 (mp) cc_final: 0.6548 (tt) REVERT: c 34 TYR cc_start: 0.5431 (t80) cc_final: 0.5024 (t80) REVERT: c 46 VAL cc_start: 0.6754 (p) cc_final: 0.6355 (m) REVERT: c 59 THR cc_start: 0.6219 (m) cc_final: 0.5430 (p) REVERT: c 70 ILE cc_start: 0.5346 (mp) cc_final: 0.4664 (mp) REVERT: c 84 LYS cc_start: 0.6389 (mmtt) cc_final: 0.6129 (tttt) REVERT: g 331 MET cc_start: 0.8320 (mmm) cc_final: 0.7951 (mmm) REVERT: i 287 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8312 (mt) REVERT: k 314 MET cc_start: 0.8497 (ttt) cc_final: 0.8206 (ttm) REVERT: m 120 LYS cc_start: 0.8294 (ttmm) cc_final: 0.8000 (mttm) REVERT: m 319 ASP cc_start: 0.8436 (t70) cc_final: 0.8223 (t0) REVERT: o 84 LYS cc_start: 0.7808 (mtmt) cc_final: 0.7596 (mppt) REVERT: q 100 ILE cc_start: 0.7405 (mt) cc_final: 0.7164 (tt) REVERT: q 238 PHE cc_start: 0.8341 (t80) cc_final: 0.8082 (t80) REVERT: q 267 GLU cc_start: 0.7727 (tp30) cc_final: 0.7402 (tp30) REVERT: s 48 GLU cc_start: 0.7294 (mp0) cc_final: 0.7082 (tt0) REVERT: s 76 LYS cc_start: 0.5697 (ptmt) cc_final: 0.5041 (tmtt) REVERT: s 79 ASP cc_start: 0.7085 (m-30) cc_final: 0.6353 (t70) REVERT: u 76 LYS cc_start: 0.8507 (mmmt) cc_final: 0.7774 (ptmt) REVERT: X 76 LYS cc_start: 0.5038 (ptmt) cc_final: 0.4616 (tptt) REVERT: Z 43 ASN cc_start: 0.7819 (t0) cc_final: 0.7222 (t0) REVERT: d 47 ARG cc_start: 0.6301 (tmm-80) cc_final: 0.6053 (tmm160) REVERT: d 70 ILE cc_start: 0.5553 (mp) cc_final: 0.5038 (mm) REVERT: d 89 VAL cc_start: 0.6074 (t) cc_final: 0.5805 (p) REVERT: h 331 MET cc_start: 0.8248 (mmm) cc_final: 0.7697 (mmm) REVERT: j 233 LEU cc_start: 0.8102 (tp) cc_final: 0.7886 (tp) REVERT: l 18 MET cc_start: 0.6716 (tpp) cc_final: 0.5224 (mtt) REVERT: l 135 ASP cc_start: 0.7190 (m-30) cc_final: 0.6946 (m-30) REVERT: l 237 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7254 (ttm170) REVERT: l 240 SER cc_start: 0.8224 (t) cc_final: 0.8019 (m) REVERT: l 241 GLN cc_start: 0.7905 (tm-30) cc_final: 0.7626 (tm-30) REVERT: l 314 MET cc_start: 0.8629 (ttt) cc_final: 0.8274 (ttm) REVERT: n 316 MET cc_start: 0.8179 (mtm) cc_final: 0.7597 (mtm) REVERT: n 319 ASP cc_start: 0.8353 (t70) cc_final: 0.8104 (t0) REVERT: p 84 LYS cc_start: 0.7935 (mtmt) cc_final: 0.7529 (mppt) REVERT: r 160 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7404 (mp0) REVERT: r 161 MET cc_start: 0.7989 (mmt) cc_final: 0.7602 (mmm) REVERT: r 186 GLN cc_start: 0.8255 (mt0) cc_final: 0.7966 (mm-40) REVERT: r 238 PHE cc_start: 0.8188 (t80) cc_final: 0.7846 (t80) REVERT: r 331 MET cc_start: 0.7964 (mmm) cc_final: 0.7632 (mmm) REVERT: t 87 LYS cc_start: 0.7742 (tptp) cc_final: 0.7454 (ttpt) REVERT: v 76 LYS cc_start: 0.8724 (mmmt) cc_final: 0.8070 (ptmt) REVERT: J 37 PHE cc_start: 0.6192 (t80) cc_final: 0.5872 (t80) REVERT: J 76 LYS cc_start: 0.5483 (ptmt) cc_final: 0.5171 (ptmm) REVERT: K 43 ASN cc_start: 0.7519 (t0) cc_final: 0.7061 (t0) REVERT: K 55 GLU cc_start: 0.4940 (tp30) cc_final: 0.4622 (tp30) REVERT: L 74 ASP cc_start: 0.4656 (OUTLIER) cc_final: 0.4352 (m-30) REVERT: L 81 LEU cc_start: 0.7392 (mp) cc_final: 0.6937 (tt) REVERT: L 82 LEU cc_start: 0.6114 (mt) cc_final: 0.5814 (mp) REVERT: M 34 TYR cc_start: 0.6199 (t80) cc_final: 0.5751 (t80) REVERT: M 89 VAL cc_start: 0.6260 (t) cc_final: 0.5798 (p) REVERT: N 242 ARG cc_start: 0.7579 (ptt90) cc_final: 0.7314 (ptm-80) REVERT: N 331 MET cc_start: 0.8426 (mmm) cc_final: 0.8054 (mmm) REVERT: P 240 SER cc_start: 0.8153 (t) cc_final: 0.7840 (m) REVERT: P 241 GLN cc_start: 0.8148 (tm-30) cc_final: 0.7621 (tm-30) REVERT: Q 70 GLN cc_start: 0.8524 (mt0) cc_final: 0.7937 (mp10) REVERT: Q 120 LYS cc_start: 0.8195 (ttmm) cc_final: 0.7822 (mttm) REVERT: R 18 MET cc_start: 0.5876 (tpt) cc_final: 0.5562 (tpp) REVERT: R 21 PHE cc_start: 0.5520 (t80) cc_final: 0.5238 (t80) REVERT: R 84 LYS cc_start: 0.8467 (mtmt) cc_final: 0.8068 (mttp) REVERT: R 96 ARG cc_start: 0.7807 (ttp-110) cc_final: 0.7417 (ttp-170) REVERT: R 129 SER cc_start: 0.8272 (t) cc_final: 0.7980 (m) REVERT: R 290 ASP cc_start: 0.7996 (t0) cc_final: 0.7771 (t70) REVERT: T 40 GLU cc_start: 0.7883 (tt0) cc_final: 0.7571 (tt0) REVERT: T 79 ASP cc_start: 0.7209 (m-30) cc_final: 0.6747 (t70) REVERT: V 52 ASN cc_start: 0.6328 (p0) cc_final: 0.5934 (p0) REVERT: V 64 ASN cc_start: 0.7865 (m110) cc_final: 0.7581 (m-40) REVERT: V 65 ARG cc_start: 0.8081 (ptp90) cc_final: 0.7774 (ptp90) REVERT: V 76 LYS cc_start: 0.8900 (mmmt) cc_final: 0.8045 (ptmm) outliers start: 144 outliers final: 89 residues processed: 1111 average time/residue: 0.6213 time to fit residues: 1168.7107 Evaluate side-chains 913 residues out of total 7224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 819 time to evaluate : 5.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 57 ASN Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain U residue 143 LEU Chi-restraints excluded: chain U residue 190 SER Chi-restraints excluded: chain e residue 77 LEU Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Y residue 58 VAL Chi-restraints excluded: chain Y residue 77 LEU Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain c residue 88 VAL Chi-restraints excluded: chain g residue 143 LEU Chi-restraints excluded: chain g residue 149 MET Chi-restraints excluded: chain g residue 338 THR Chi-restraints excluded: chain g residue 343 VAL Chi-restraints excluded: chain i residue 114 PHE Chi-restraints excluded: chain i residue 184 LEU Chi-restraints excluded: chain i residue 216 THR Chi-restraints excluded: chain i residue 220 LEU Chi-restraints excluded: chain i residue 287 LEU Chi-restraints excluded: chain m residue 85 LYS Chi-restraints excluded: chain o residue 236 ARG Chi-restraints excluded: chain o residue 285 ASP Chi-restraints excluded: chain q residue 143 LEU Chi-restraints excluded: chain q residue 196 ILE Chi-restraints excluded: chain q residue 217 GLN Chi-restraints excluded: chain s residue 31 LYS Chi-restraints excluded: chain u residue 33 ASP Chi-restraints excluded: chain u residue 68 THR Chi-restraints excluded: chain u residue 72 VAL Chi-restraints excluded: chain u residue 77 LEU Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Z residue 58 VAL Chi-restraints excluded: chain Z residue 77 LEU Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain d residue 68 THR Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain h residue 108 VAL Chi-restraints excluded: chain h residue 201 MET Chi-restraints excluded: chain h residue 231 ILE Chi-restraints excluded: chain h residue 332 GLU Chi-restraints excluded: chain j residue 95 SER Chi-restraints excluded: chain j residue 133 LYS Chi-restraints excluded: chain j residue 176 SER Chi-restraints excluded: chain l residue 27 GLU Chi-restraints excluded: chain l residue 30 ILE Chi-restraints excluded: chain l residue 237 ARG Chi-restraints excluded: chain n residue 71 THR Chi-restraints excluded: chain p residue 118 LEU Chi-restraints excluded: chain r residue 100 ILE Chi-restraints excluded: chain r residue 143 LEU Chi-restraints excluded: chain r residue 201 MET Chi-restraints excluded: chain t residue 62 ASP Chi-restraints excluded: chain v residue 77 LEU Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain L residue 74 ASP Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 201 MET Chi-restraints excluded: chain N residue 332 GLU Chi-restraints excluded: chain N residue 343 VAL Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 142 GLU Chi-restraints excluded: chain O residue 184 LEU Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain P residue 14 VAL Chi-restraints excluded: chain P residue 237 ARG Chi-restraints excluded: chain P residue 321 ASP Chi-restraints excluded: chain Q residue 14 VAL Chi-restraints excluded: chain Q residue 314 MET Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain S residue 288 GLU Chi-restraints excluded: chain T residue 62 ASP Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 68 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 405 optimal weight: 0.5980 chunk 226 optimal weight: 9.9990 chunk 607 optimal weight: 3.9990 chunk 497 optimal weight: 3.9990 chunk 201 optimal weight: 10.0000 chunk 731 optimal weight: 0.9980 chunk 790 optimal weight: 0.9990 chunk 651 optimal weight: 0.7980 chunk 725 optimal weight: 0.5980 chunk 249 optimal weight: 1.9990 chunk 586 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 260 ASN G 310 ASN I 114 GLN I 156 ASN I 214 ASN U 162 ASN U 217 GLN U 239 GLN e 64 ASN e 85 ASN Y 39 GLN g 260 ASN o 310 ASN q 217 GLN s 42 ASN s 85 ASN u 39 GLN Z 57 ASN d 64 ASN h 239 GLN j 239 GLN l 74 ASN p 310 ASN t 64 ASN v 39 GLN M 57 ASN P 74 ASN P 75 GLN P 310 ASN Q 75 GLN R 310 ASN V 42 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 67560 Z= 0.173 Angle : 0.541 11.419 91212 Z= 0.292 Chirality : 0.043 0.170 10356 Planarity : 0.004 0.045 11940 Dihedral : 4.212 23.462 9325 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.91 % Favored : 97.08 % Rotamer: Outliers : 2.13 % Allowed : 13.46 % Favored : 84.41 % 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: 1.73 (0.09), residues: 8184 helix: 2.33 (0.08), residues: 4308 sheet: 0.70 (0.13), residues: 1504 loop : -0.78 (0.12), residues: 2372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP U 92 HIS 0.002 0.001 HIS U 116 PHE 0.020 0.001 PHE S 238 TYR 0.018 0.001 TYR D 34 ARG 0.006 0.000 ARG r 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16368 Ramachandran restraints generated. 8184 Oldfield, 0 Emsley, 8184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16368 Ramachandran restraints generated. 8184 Oldfield, 0 Emsley, 8184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1082 residues out of total 7224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 928 time to evaluate : 5.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.5601 (t80) cc_final: 0.5337 (t80) REVERT: A 77 LEU cc_start: 0.6529 (pp) cc_final: 0.6219 (mt) REVERT: B 43 ASN cc_start: 0.7013 (t0) cc_final: 0.6503 (t0) REVERT: B 47 ARG cc_start: 0.7121 (mtm110) cc_final: 0.6581 (mtm180) REVERT: D 89 VAL cc_start: 0.5811 (t) cc_final: 0.5400 (p) REVERT: E 242 ARG cc_start: 0.7478 (mmm-85) cc_final: 0.7019 (ptp-110) REVERT: F 131 GLU cc_start: 0.6720 (tp30) cc_final: 0.6341 (mp0) REVERT: F 149 MET cc_start: 0.7663 (mmm) cc_final: 0.7271 (mpp) REVERT: F 160 GLU cc_start: 0.7339 (mt-10) cc_final: 0.7013 (mt-10) REVERT: G 71 THR cc_start: 0.8250 (m) cc_final: 0.8045 (p) REVERT: H 36 LYS cc_start: 0.6685 (tttt) cc_final: 0.6314 (pttt) REVERT: H 198 MET cc_start: 0.7361 (mtp) cc_final: 0.6904 (tpp) REVERT: I 27 GLU cc_start: 0.7116 (pm20) cc_final: 0.6788 (pm20) REVERT: I 84 LYS cc_start: 0.7939 (mtmt) cc_final: 0.7645 (mppt) REVERT: e 42 ASN cc_start: 0.7961 (t0) cc_final: 0.7644 (t0) REVERT: e 76 LYS cc_start: 0.6750 (pttp) cc_final: 0.6053 (tptp) REVERT: f 76 LYS cc_start: 0.8400 (mmmt) cc_final: 0.7644 (pttp) REVERT: W 76 LYS cc_start: 0.4490 (ptmt) cc_final: 0.4214 (ptpt) REVERT: Y 43 ASN cc_start: 0.7326 (t0) cc_final: 0.6673 (t0) REVERT: Y 45 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.6964 (mp10) REVERT: Y 60 LYS cc_start: 0.7272 (ttmt) cc_final: 0.6974 (ttmt) REVERT: Y 69 TYR cc_start: 0.6041 (m-80) cc_final: 0.5765 (m-10) REVERT: Y 87 LYS cc_start: 0.6731 (OUTLIER) cc_final: 0.6290 (mtpt) REVERT: a 81 LEU cc_start: 0.7048 (mp) cc_final: 0.6616 (tt) REVERT: a 82 LEU cc_start: 0.5621 (tp) cc_final: 0.5340 (mp) REVERT: c 46 VAL cc_start: 0.6818 (p) cc_final: 0.6609 (t) REVERT: c 59 THR cc_start: 0.6092 (m) cc_final: 0.5401 (p) REVERT: c 70 ILE cc_start: 0.5586 (mp) cc_final: 0.4858 (mp) REVERT: c 80 ASN cc_start: 0.6718 (m110) cc_final: 0.6087 (p0) REVERT: c 84 LYS cc_start: 0.6428 (mmtt) cc_final: 0.6125 (tttt) REVERT: g 149 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7921 (mtm) REVERT: g 331 MET cc_start: 0.8219 (mmm) cc_final: 0.7914 (mmm) REVERT: k 75 GLN cc_start: 0.8281 (mm-40) cc_final: 0.8052 (mp10) REVERT: k 310 ASN cc_start: 0.6939 (t0) cc_final: 0.6681 (t0) REVERT: k 314 MET cc_start: 0.8424 (ttt) cc_final: 0.8080 (ttm) REVERT: m 120 LYS cc_start: 0.8290 (ttmm) cc_final: 0.7929 (mttm) REVERT: m 319 ASP cc_start: 0.8417 (t70) cc_final: 0.8188 (t0) REVERT: o 290 ASP cc_start: 0.7902 (t0) cc_final: 0.7583 (t70) REVERT: q 238 PHE cc_start: 0.8307 (t80) cc_final: 0.8021 (t80) REVERT: q 267 GLU cc_start: 0.7691 (tp30) cc_final: 0.7479 (tp30) REVERT: s 76 LYS cc_start: 0.5826 (ptmt) cc_final: 0.5090 (tmtt) REVERT: s 79 ASP cc_start: 0.7099 (m-30) cc_final: 0.6389 (t70) REVERT: u 74 ASP cc_start: 0.6709 (t0) cc_final: 0.6433 (t70) REVERT: u 76 LYS cc_start: 0.8523 (mmmt) cc_final: 0.7769 (ptmt) REVERT: u 80 ASN cc_start: 0.7996 (t0) cc_final: 0.7788 (t0) REVERT: X 55 GLU cc_start: 0.4696 (tp30) cc_final: 0.4201 (tp30) REVERT: X 76 LYS cc_start: 0.4798 (ptmt) cc_final: 0.4313 (tptt) REVERT: Z 43 ASN cc_start: 0.7879 (t0) cc_final: 0.7088 (t0) REVERT: d 30 ARG cc_start: 0.5411 (ttm170) cc_final: 0.4837 (ttm110) REVERT: d 34 TYR cc_start: 0.5714 (t80) cc_final: 0.5273 (t80) REVERT: d 70 ILE cc_start: 0.5453 (mp) cc_final: 0.5018 (mm) REVERT: d 89 VAL cc_start: 0.5979 (t) cc_final: 0.5767 (p) REVERT: d 91 GLU cc_start: 0.6751 (mm-30) cc_final: 0.5844 (mt-10) REVERT: h 331 MET cc_start: 0.8274 (mmm) cc_final: 0.7855 (mmm) REVERT: j 149 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7274 (mpp) REVERT: l 135 ASP cc_start: 0.7176 (m-30) cc_final: 0.6936 (m-30) REVERT: l 237 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7321 (ttm170) REVERT: l 241 GLN cc_start: 0.7890 (tm-30) cc_final: 0.7636 (tm-30) REVERT: l 314 MET cc_start: 0.8609 (ttt) cc_final: 0.8320 (ttm) REVERT: n 311 GLN cc_start: 0.7314 (mp10) cc_final: 0.7095 (mp10) REVERT: n 319 ASP cc_start: 0.8286 (t70) cc_final: 0.8034 (t0) REVERT: p 84 LYS cc_start: 0.7991 (mtmt) cc_final: 0.7607 (mppt) REVERT: p 125 ASP cc_start: 0.7087 (t0) cc_final: 0.6800 (m-30) REVERT: p 146 ARG cc_start: 0.7775 (mmm-85) cc_final: 0.7296 (mtp85) REVERT: r 160 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7461 (mp0) REVERT: r 161 MET cc_start: 0.8118 (mmt) cc_final: 0.7792 (mmm) REVERT: r 238 PHE cc_start: 0.8169 (t80) cc_final: 0.7957 (t80) REVERT: t 87 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7495 (ttpt) REVERT: v 76 LYS cc_start: 0.8749 (mmmt) cc_final: 0.8078 (ptmt) REVERT: J 55 GLU cc_start: 0.5494 (tp30) cc_final: 0.5255 (tp30) REVERT: J 76 LYS cc_start: 0.5356 (ptmt) cc_final: 0.5038 (ptmm) REVERT: K 43 ASN cc_start: 0.7562 (t0) cc_final: 0.6957 (t0) REVERT: L 81 LEU cc_start: 0.7195 (mp) cc_final: 0.6764 (tt) REVERT: M 34 TYR cc_start: 0.6128 (t80) cc_final: 0.5495 (t80) REVERT: M 70 ILE cc_start: 0.6068 (mp) cc_final: 0.5535 (mm) REVERT: O 142 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7086 (tt0) REVERT: O 232 THR cc_start: 0.7811 (OUTLIER) cc_final: 0.7547 (p) REVERT: P 212 GLN cc_start: 0.7975 (pt0) cc_final: 0.7480 (pp30) REVERT: P 240 SER cc_start: 0.8021 (t) cc_final: 0.7810 (m) REVERT: P 241 GLN cc_start: 0.7950 (tm-30) cc_final: 0.7448 (tm-30) REVERT: Q 70 GLN cc_start: 0.8377 (mt0) cc_final: 0.7850 (mp10) REVERT: Q 120 LYS cc_start: 0.8052 (ttmm) cc_final: 0.7759 (mttm) REVERT: R 18 MET cc_start: 0.5937 (tpt) cc_final: 0.5604 (tpp) REVERT: R 38 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.6875 (tt) REVERT: R 84 LYS cc_start: 0.8431 (mtmt) cc_final: 0.8023 (mttp) REVERT: R 290 ASP cc_start: 0.7826 (t0) cc_final: 0.7544 (t0) REVERT: S 124 TRP cc_start: 0.6181 (t60) cc_final: 0.5911 (t60) REVERT: T 69 TYR cc_start: 0.6961 (m-10) cc_final: 0.6652 (m-10) REVERT: T 79 ASP cc_start: 0.7232 (m-30) cc_final: 0.6629 (t70) REVERT: V 52 ASN cc_start: 0.6472 (p0) cc_final: 0.5355 (p0) REVERT: V 55 GLU cc_start: 0.7537 (tt0) cc_final: 0.7111 (tt0) REVERT: V 64 ASN cc_start: 0.7683 (m110) cc_final: 0.7430 (m-40) REVERT: V 76 LYS cc_start: 0.8882 (mmmt) cc_final: 0.8012 (ptmm) outliers start: 154 outliers final: 67 residues processed: 1025 average time/residue: 0.6104 time to fit residues: 1062.8379 Evaluate side-chains 889 residues out of total 7224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 813 time to evaluate : 6.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 181 ASP Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 285 ASP Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain U residue 190 SER Chi-restraints excluded: chain U residue 217 GLN Chi-restraints excluded: chain e residue 39 GLN Chi-restraints excluded: chain f residue 33 ASP Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Y residue 58 VAL Chi-restraints excluded: chain Y residue 77 LEU Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain g residue 149 MET Chi-restraints excluded: chain g residue 343 VAL Chi-restraints excluded: chain i residue 184 LEU Chi-restraints excluded: chain i residue 224 ILE Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 321 ASP Chi-restraints excluded: chain o residue 131 ILE Chi-restraints excluded: chain o residue 265 GLU Chi-restraints excluded: chain s residue 31 LYS Chi-restraints excluded: chain s residue 62 ASP Chi-restraints excluded: chain u residue 33 ASP Chi-restraints excluded: chain u residue 72 VAL Chi-restraints excluded: chain u residue 77 LEU Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Z residue 58 VAL Chi-restraints excluded: chain d residue 68 THR Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain h residue 201 MET Chi-restraints excluded: chain h residue 332 GLU Chi-restraints excluded: chain j residue 149 MET Chi-restraints excluded: chain j residue 184 LEU Chi-restraints excluded: chain j residue 189 ASP Chi-restraints excluded: chain l residue 27 GLU Chi-restraints excluded: chain l residue 71 THR Chi-restraints excluded: chain l residue 237 ARG Chi-restraints excluded: chain p residue 86 ASP Chi-restraints excluded: chain p residue 118 LEU Chi-restraints excluded: chain p residue 285 ASP Chi-restraints excluded: chain p residue 310 ASN Chi-restraints excluded: chain r residue 100 ILE Chi-restraints excluded: chain r residue 201 MET Chi-restraints excluded: chain r residue 237 ASN Chi-restraints excluded: chain t residue 62 ASP Chi-restraints excluded: chain t residue 87 LYS Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 332 GLU Chi-restraints excluded: chain N residue 343 VAL Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 142 GLU Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain Q residue 14 VAL Chi-restraints excluded: chain Q residue 314 MET Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 310 LYS Chi-restraints excluded: chain T residue 39 GLN Chi-restraints excluded: chain T residue 62 ASP Chi-restraints excluded: chain V residue 77 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 722 optimal weight: 0.2980 chunk 549 optimal weight: 2.9990 chunk 379 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 349 optimal weight: 0.7980 chunk 491 optimal weight: 6.9990 chunk 734 optimal weight: 1.9990 chunk 777 optimal weight: 0.0270 chunk 383 optimal weight: 3.9990 chunk 695 optimal weight: 0.0070 chunk 209 optimal weight: 7.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 162 ASN F 186 GLN I 114 GLN U 162 ASN U 239 GLN Y 39 GLN ** c 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 310 ASN u 39 GLN l 310 ASN t 64 ASN v 39 GLN M 42 ASN P 310 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.112 67560 Z= 0.160 Angle : 0.524 16.004 91212 Z= 0.281 Chirality : 0.043 0.173 10356 Planarity : 0.004 0.041 11940 Dihedral : 4.103 24.558 9325 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.83 % Favored : 97.15 % Rotamer: Outliers : 2.19 % Allowed : 14.73 % Favored : 83.08 % 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: 1.88 (0.09), residues: 8184 helix: 2.43 (0.08), residues: 4328 sheet: 0.75 (0.13), residues: 1504 loop : -0.71 (0.12), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP U 92 HIS 0.002 0.001 HIS m 53 PHE 0.025 0.001 PHE D 37 TYR 0.022 0.001 TYR c 34 ARG 0.006 0.000 ARG c 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16368 Ramachandran restraints generated. 8184 Oldfield, 0 Emsley, 8184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16368 Ramachandran restraints generated. 8184 Oldfield, 0 Emsley, 8184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1039 residues out of total 7224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 881 time to evaluate : 5.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.6578 (pp) cc_final: 0.6278 (mt) REVERT: B 43 ASN cc_start: 0.7112 (t0) cc_final: 0.6598 (t0) REVERT: B 47 ARG cc_start: 0.7058 (mtm110) cc_final: 0.6539 (mtm180) REVERT: B 50 ARG cc_start: 0.5435 (mtt90) cc_final: 0.4844 (mtp180) REVERT: D 41 VAL cc_start: 0.7705 (t) cc_final: 0.7406 (p) REVERT: D 70 ILE cc_start: 0.5504 (mm) cc_final: 0.4954 (mm) REVERT: D 89 VAL cc_start: 0.5922 (t) cc_final: 0.5680 (p) REVERT: E 242 ARG cc_start: 0.7458 (mmm-85) cc_final: 0.7052 (ptp-110) REVERT: F 104 GLU cc_start: 0.6643 (OUTLIER) cc_final: 0.6070 (pm20) REVERT: F 131 GLU cc_start: 0.6764 (tp30) cc_final: 0.6381 (mp0) REVERT: G 274 GLU cc_start: 0.7409 (tp30) cc_final: 0.7209 (tp30) REVERT: H 198 MET cc_start: 0.7336 (mtp) cc_final: 0.6982 (tpp) REVERT: I 84 LYS cc_start: 0.7944 (mtmt) cc_final: 0.7646 (mppt) REVERT: U 149 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6892 (mtp) REVERT: e 38 LEU cc_start: 0.8089 (tp) cc_final: 0.7887 (tt) REVERT: e 42 ASN cc_start: 0.7947 (t0) cc_final: 0.7644 (t0) REVERT: e 76 LYS cc_start: 0.6737 (pttp) cc_final: 0.6231 (tptp) REVERT: e 77 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7754 (tp) REVERT: f 76 LYS cc_start: 0.8457 (mmmt) cc_final: 0.7509 (ptmm) REVERT: W 76 LYS cc_start: 0.4366 (ptmt) cc_final: 0.4115 (ptpt) REVERT: Y 43 ASN cc_start: 0.7176 (t0) cc_final: 0.6523 (t0) REVERT: Y 45 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.6950 (mp10) REVERT: Y 69 TYR cc_start: 0.6012 (m-80) cc_final: 0.5668 (m-80) REVERT: Y 87 LYS cc_start: 0.6750 (OUTLIER) cc_final: 0.6369 (ttmt) REVERT: a 81 LEU cc_start: 0.7076 (mp) cc_final: 0.6666 (tt) REVERT: a 82 LEU cc_start: 0.5661 (tp) cc_final: 0.5371 (mp) REVERT: c 34 TYR cc_start: 0.4669 (t80) cc_final: 0.4212 (t80) REVERT: c 59 THR cc_start: 0.6195 (m) cc_final: 0.5566 (p) REVERT: g 149 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7917 (mtm) REVERT: g 331 MET cc_start: 0.8279 (mmm) cc_final: 0.7956 (mmm) REVERT: k 75 GLN cc_start: 0.8144 (mm-40) cc_final: 0.7906 (mp10) REVERT: k 77 ASP cc_start: 0.7945 (p0) cc_final: 0.6873 (t0) REVERT: k 314 MET cc_start: 0.8429 (ttt) cc_final: 0.8111 (ttm) REVERT: m 100 PHE cc_start: 0.7868 (m-80) cc_final: 0.7659 (m-80) REVERT: m 120 LYS cc_start: 0.8177 (ttmm) cc_final: 0.7870 (mttm) REVERT: m 319 ASP cc_start: 0.8402 (t70) cc_final: 0.8183 (t0) REVERT: o 236 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7394 (ptp-110) REVERT: o 290 ASP cc_start: 0.7868 (t0) cc_final: 0.7523 (t70) REVERT: q 149 MET cc_start: 0.7011 (mtp) cc_final: 0.6656 (mtp) REVERT: q 217 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.6743 (tp40) REVERT: q 267 GLU cc_start: 0.7696 (tp30) cc_final: 0.7482 (tp30) REVERT: s 70 ILE cc_start: 0.7238 (OUTLIER) cc_final: 0.6841 (mm) REVERT: s 76 LYS cc_start: 0.5775 (ptmt) cc_final: 0.5097 (tmtt) REVERT: s 79 ASP cc_start: 0.7134 (m-30) cc_final: 0.6432 (t70) REVERT: u 76 LYS cc_start: 0.8582 (mmmt) cc_final: 0.7825 (ptmt) REVERT: u 80 ASN cc_start: 0.7947 (t0) cc_final: 0.7716 (t0) REVERT: X 76 LYS cc_start: 0.4914 (ptmt) cc_final: 0.4383 (tptt) REVERT: Z 43 ASN cc_start: 0.7605 (t0) cc_final: 0.6775 (t0) REVERT: Z 55 GLU cc_start: 0.5763 (tp30) cc_final: 0.5254 (tp30) REVERT: Z 76 LYS cc_start: 0.4706 (pttt) cc_final: 0.4500 (pttm) REVERT: d 30 ARG cc_start: 0.5655 (ttm170) cc_final: 0.5213 (ttm110) REVERT: d 34 TYR cc_start: 0.5608 (t80) cc_final: 0.5306 (t80) REVERT: d 59 THR cc_start: 0.5970 (m) cc_final: 0.5529 (p) REVERT: d 70 ILE cc_start: 0.5627 (mp) cc_final: 0.5264 (mm) REVERT: d 89 VAL cc_start: 0.6074 (t) cc_final: 0.5528 (p) REVERT: d 91 GLU cc_start: 0.6653 (mm-30) cc_final: 0.6439 (pm20) REVERT: h 149 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7399 (mmm) REVERT: h 331 MET cc_start: 0.8253 (mmm) cc_final: 0.7936 (mmm) REVERT: j 160 GLU cc_start: 0.7343 (mt-10) cc_final: 0.7128 (mp0) REVERT: l 74 ASN cc_start: 0.7913 (m-40) cc_final: 0.7654 (m110) REVERT: l 135 ASP cc_start: 0.7144 (m-30) cc_final: 0.6857 (m-30) REVERT: l 237 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7402 (ttm170) REVERT: l 314 MET cc_start: 0.8581 (ttt) cc_final: 0.8281 (ttm) REVERT: n 311 GLN cc_start: 0.7433 (mp10) cc_final: 0.7208 (mp10) REVERT: n 319 ASP cc_start: 0.8268 (t70) cc_final: 0.8022 (t0) REVERT: p 84 LYS cc_start: 0.7951 (mtmt) cc_final: 0.7611 (mppt) REVERT: p 125 ASP cc_start: 0.7149 (t70) cc_final: 0.6842 (m-30) REVERT: p 146 ARG cc_start: 0.7756 (mmm-85) cc_final: 0.7368 (mtp85) REVERT: r 160 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7509 (mp0) REVERT: r 161 MET cc_start: 0.8129 (mmt) cc_final: 0.7791 (mmm) REVERT: r 238 PHE cc_start: 0.8204 (t80) cc_final: 0.7837 (t80) REVERT: t 85 ASN cc_start: 0.7495 (t0) cc_final: 0.7289 (t0) REVERT: v 76 LYS cc_start: 0.8786 (mmmt) cc_final: 0.8100 (ptmt) REVERT: J 76 LYS cc_start: 0.5220 (ptmt) cc_final: 0.4891 (ptmm) REVERT: K 43 ASN cc_start: 0.7553 (t0) cc_final: 0.6908 (t0) REVERT: L 81 LEU cc_start: 0.7143 (mp) cc_final: 0.6787 (tt) REVERT: L 82 LEU cc_start: 0.6105 (mt) cc_final: 0.5877 (mp) REVERT: M 34 TYR cc_start: 0.6140 (t80) cc_final: 0.5890 (t80) REVERT: M 91 GLU cc_start: 0.5585 (mm-30) cc_final: 0.5381 (mt-10) REVERT: O 142 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7164 (tt0) REVERT: O 232 THR cc_start: 0.7618 (OUTLIER) cc_final: 0.7340 (p) REVERT: P 212 GLN cc_start: 0.7906 (pt0) cc_final: 0.7554 (pp30) REVERT: P 241 GLN cc_start: 0.7932 (tm-30) cc_final: 0.7440 (tm-30) REVERT: Q 70 GLN cc_start: 0.8292 (mt0) cc_final: 0.7792 (mp10) REVERT: Q 120 LYS cc_start: 0.8085 (ttmm) cc_final: 0.7753 (mttm) REVERT: R 18 MET cc_start: 0.5927 (tpt) cc_final: 0.5632 (tpp) REVERT: R 84 LYS cc_start: 0.8422 (mtmt) cc_final: 0.8037 (mppt) REVERT: R 144 ARG cc_start: 0.7490 (tpt170) cc_final: 0.7241 (tpt90) REVERT: R 290 ASP cc_start: 0.7698 (t0) cc_final: 0.7393 (t0) REVERT: S 124 TRP cc_start: 0.6207 (t60) cc_final: 0.5938 (t60) REVERT: S 161 MET cc_start: 0.7857 (mmt) cc_final: 0.7546 (mmt) REVERT: T 79 ASP cc_start: 0.7319 (m-30) cc_final: 0.6671 (t70) REVERT: V 52 ASN cc_start: 0.6540 (p0) cc_final: 0.5485 (p0) REVERT: V 55 GLU cc_start: 0.7521 (tt0) cc_final: 0.7091 (tt0) REVERT: V 76 LYS cc_start: 0.8859 (mmmt) cc_final: 0.8010 (ptmm) outliers start: 158 outliers final: 86 residues processed: 965 average time/residue: 0.6102 time to fit residues: 1001.6237 Evaluate side-chains 906 residues out of total 7224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 807 time to evaluate : 5.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 253 ASP Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain I residue 48 TYR Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 274 GLU Chi-restraints excluded: chain I residue 285 ASP Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain U residue 143 LEU Chi-restraints excluded: chain U residue 149 MET Chi-restraints excluded: chain U residue 190 SER Chi-restraints excluded: chain e residue 39 GLN Chi-restraints excluded: chain e residue 77 LEU Chi-restraints excluded: chain e residue 82 LEU Chi-restraints excluded: chain f residue 33 ASP Chi-restraints excluded: chain W residue 72 VAL Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Y residue 77 LEU Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain g residue 149 MET Chi-restraints excluded: chain g residue 343 VAL Chi-restraints excluded: chain i residue 114 PHE Chi-restraints excluded: chain i residue 184 LEU Chi-restraints excluded: chain i residue 196 ILE Chi-restraints excluded: chain i residue 220 LEU Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 321 ASP Chi-restraints excluded: chain m residue 241 GLN Chi-restraints excluded: chain o residue 131 ILE Chi-restraints excluded: chain o residue 236 ARG Chi-restraints excluded: chain o residue 265 GLU Chi-restraints excluded: chain q residue 100 ILE Chi-restraints excluded: chain q residue 196 ILE Chi-restraints excluded: chain q residue 217 GLN Chi-restraints excluded: chain s residue 31 LYS Chi-restraints excluded: chain s residue 62 ASP Chi-restraints excluded: chain s residue 70 ILE Chi-restraints excluded: chain u residue 33 ASP Chi-restraints excluded: chain u residue 72 VAL Chi-restraints excluded: chain u residue 77 LEU Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Z residue 32 VAL Chi-restraints excluded: chain Z residue 58 VAL Chi-restraints excluded: chain Z residue 77 LEU Chi-restraints excluded: chain b residue 56 ILE Chi-restraints excluded: chain d residue 68 THR Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain h residue 149 MET Chi-restraints excluded: chain h residue 201 MET Chi-restraints excluded: chain h residue 332 GLU Chi-restraints excluded: chain j residue 176 SER Chi-restraints excluded: chain j residue 184 LEU Chi-restraints excluded: chain j residue 189 ASP Chi-restraints excluded: chain l residue 27 GLU Chi-restraints excluded: chain l residue 71 THR Chi-restraints excluded: chain l residue 237 ARG Chi-restraints excluded: chain l residue 326 MET Chi-restraints excluded: chain p residue 86 ASP Chi-restraints excluded: chain p residue 118 LEU Chi-restraints excluded: chain p residue 285 ASP Chi-restraints excluded: chain r residue 100 ILE Chi-restraints excluded: chain r residue 201 MET Chi-restraints excluded: chain r residue 237 ASN Chi-restraints excluded: chain t residue 62 ASP Chi-restraints excluded: chain v residue 77 LEU Chi-restraints excluded: chain v residue 91 GLU Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 332 GLU Chi-restraints excluded: chain N residue 343 VAL Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 142 GLU Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain O residue 272 THR Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 316 MET Chi-restraints excluded: chain Q residue 14 VAL Chi-restraints excluded: chain Q residue 314 MET Chi-restraints excluded: chain R residue 86 ASP Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain T residue 39 GLN Chi-restraints excluded: chain T residue 62 ASP Chi-restraints excluded: chain V residue 77 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 647 optimal weight: 2.9990 chunk 441 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 578 optimal weight: 6.9990 chunk 320 optimal weight: 8.9990 chunk 663 optimal weight: 6.9990 chunk 537 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 396 optimal weight: 7.9990 chunk 697 optimal weight: 0.9980 chunk 196 optimal weight: 5.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 ASN D 57 ASN E 260 ASN F 155 ASN U 162 ASN U 239 GLN W 73 GLN Y 39 GLN c 52 ASN g 260 ASN k 74 ASN k 310 ASN o 74 ASN o 310 ASN u 39 GLN ** b 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 42 ASN j 186 GLN j 217 GLN l 310 ASN p 212 GLN t 64 ASN v 39 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.150 67560 Z= 0.450 Angle : 0.669 16.274 91212 Z= 0.359 Chirality : 0.048 0.251 10356 Planarity : 0.005 0.046 11940 Dihedral : 4.635 27.016 9325 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.56 % Favored : 96.43 % Rotamer: Outliers : 3.32 % Allowed : 15.53 % Favored : 81.15 % 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: 1.13 (0.09), residues: 8184 helix: 1.83 (0.08), residues: 4308 sheet: 0.36 (0.13), residues: 1548 loop : -0.98 (0.12), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP U 92 HIS 0.007 0.002 HIS G 238 PHE 0.020 0.002 PHE S 238 TYR 0.026 0.002 TYR X 34 ARG 0.010 0.001 ARG p 121 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16368 Ramachandran restraints generated. 8184 Oldfield, 0 Emsley, 8184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16368 Ramachandran restraints generated. 8184 Oldfield, 0 Emsley, 8184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1056 residues out of total 7224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 240 poor density : 816 time to evaluate : 5.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.5580 (t80) cc_final: 0.5228 (t80) REVERT: A 37 PHE cc_start: 0.7347 (t80) cc_final: 0.7126 (t80) REVERT: A 77 LEU cc_start: 0.6216 (pp) cc_final: 0.5944 (mt) REVERT: B 43 ASN cc_start: 0.6828 (t0) cc_final: 0.6301 (t0) REVERT: B 76 LYS cc_start: 0.4588 (OUTLIER) cc_final: 0.4319 (pptt) REVERT: D 41 VAL cc_start: 0.7545 (t) cc_final: 0.7232 (p) REVERT: D 70 ILE cc_start: 0.5543 (mm) cc_final: 0.5065 (mm) REVERT: E 131 GLU cc_start: 0.7150 (tp30) cc_final: 0.6922 (tp30) REVERT: E 201 MET cc_start: 0.8229 (ttp) cc_final: 0.7996 (ttp) REVERT: E 242 ARG cc_start: 0.7643 (mmm-85) cc_final: 0.7075 (ptp-110) REVERT: F 131 GLU cc_start: 0.6724 (tp30) cc_final: 0.6140 (mp0) REVERT: G 75 GLN cc_start: 0.8269 (mm-40) cc_final: 0.7989 (mp10) REVERT: G 218 GLU cc_start: 0.7261 (pm20) cc_final: 0.7005 (pm20) REVERT: G 241 GLN cc_start: 0.8085 (tm-30) cc_final: 0.7796 (tm-30) REVERT: G 267 GLN cc_start: 0.8431 (mt0) cc_final: 0.8127 (mm-40) REVERT: I 84 LYS cc_start: 0.7914 (mtmt) cc_final: 0.7689 (mppt) REVERT: U 149 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.7017 (mtt) REVERT: U 289 GLU cc_start: 0.7853 (tt0) cc_final: 0.7621 (tt0) REVERT: U 305 VAL cc_start: 0.8704 (OUTLIER) cc_final: 0.8501 (t) REVERT: e 38 LEU cc_start: 0.8143 (tp) cc_final: 0.7935 (tt) REVERT: e 70 ILE cc_start: 0.8160 (mt) cc_final: 0.7923 (mt) REVERT: e 76 LYS cc_start: 0.6749 (pttp) cc_final: 0.6479 (tptp) REVERT: e 79 ASP cc_start: 0.7826 (m-30) cc_final: 0.6976 (t70) REVERT: f 76 LYS cc_start: 0.8621 (mmmt) cc_final: 0.7544 (ptmm) REVERT: W 76 LYS cc_start: 0.4540 (ptmt) cc_final: 0.4268 (ptpt) REVERT: Y 43 ASN cc_start: 0.7197 (t0) cc_final: 0.6609 (t0) REVERT: Y 69 TYR cc_start: 0.6331 (m-80) cc_final: 0.6070 (m-80) REVERT: c 47 ARG cc_start: 0.6580 (tmm-80) cc_final: 0.6379 (tmm160) REVERT: c 91 GLU cc_start: 0.6357 (mm-30) cc_final: 0.5936 (mt-10) REVERT: g 331 MET cc_start: 0.8254 (mmm) cc_final: 0.8042 (mmm) REVERT: i 149 MET cc_start: 0.8044 (mtp) cc_final: 0.7840 (mtp) REVERT: k 241 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7821 (tm-30) REVERT: k 314 MET cc_start: 0.8395 (ttt) cc_final: 0.8082 (ttm) REVERT: m 75 GLN cc_start: 0.7037 (mm110) cc_final: 0.6624 (mm110) REVERT: m 120 LYS cc_start: 0.8367 (ttmm) cc_final: 0.8012 (mttm) REVERT: o 150 GLU cc_start: 0.6610 (mm-30) cc_final: 0.6313 (tp30) REVERT: q 201 MET cc_start: 0.8514 (ttp) cc_final: 0.8264 (ttp) REVERT: q 238 PHE cc_start: 0.8378 (t80) cc_final: 0.8040 (t80) REVERT: q 267 GLU cc_start: 0.7634 (tp30) cc_final: 0.7317 (tp30) REVERT: s 76 LYS cc_start: 0.5470 (ptmt) cc_final: 0.5020 (tmtt) REVERT: u 74 ASP cc_start: 0.6673 (t0) cc_final: 0.6445 (t70) REVERT: u 76 LYS cc_start: 0.8681 (mmmt) cc_final: 0.7861 (ptmt) REVERT: X 55 GLU cc_start: 0.4335 (tp30) cc_final: 0.4004 (tp30) REVERT: Z 43 ASN cc_start: 0.7645 (t0) cc_final: 0.6850 (t0) REVERT: b 51 ILE cc_start: 0.5674 (tp) cc_final: 0.4928 (pt) REVERT: d 30 ARG cc_start: 0.5633 (ttm170) cc_final: 0.5174 (ttm110) REVERT: d 70 ILE cc_start: 0.5621 (mp) cc_final: 0.5107 (mm) REVERT: d 89 VAL cc_start: 0.6029 (t) cc_final: 0.5739 (p) REVERT: h 149 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7324 (mmm) REVERT: l 237 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7319 (ttm170) REVERT: l 314 MET cc_start: 0.8580 (ttt) cc_final: 0.8230 (ttm) REVERT: n 311 GLN cc_start: 0.7408 (mp10) cc_final: 0.7177 (mp10) REVERT: p 72 MET cc_start: 0.7292 (OUTLIER) cc_final: 0.6931 (ptm) REVERT: p 84 LYS cc_start: 0.7745 (mtmt) cc_final: 0.7330 (mppt) REVERT: r 160 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7533 (mp0) REVERT: r 161 MET cc_start: 0.8006 (mmt) cc_final: 0.7617 (mmm) REVERT: r 238 PHE cc_start: 0.8415 (t80) cc_final: 0.8199 (t80) REVERT: t 79 ASP cc_start: 0.7664 (m-30) cc_final: 0.7089 (t70) REVERT: v 64 ASN cc_start: 0.7831 (m110) cc_final: 0.7423 (m-40) REVERT: v 76 LYS cc_start: 0.8892 (mmmt) cc_final: 0.8055 (ptmt) REVERT: J 76 LYS cc_start: 0.5295 (ptmt) cc_final: 0.4946 (ptmm) REVERT: K 43 ASN cc_start: 0.7319 (t0) cc_final: 0.6526 (t0) REVERT: L 81 LEU cc_start: 0.7189 (mp) cc_final: 0.6696 (tt) REVERT: L 82 LEU cc_start: 0.6272 (mt) cc_final: 0.6022 (mp) REVERT: M 34 TYR cc_start: 0.6317 (t80) cc_final: 0.6087 (t80) REVERT: M 84 LYS cc_start: 0.7011 (mttp) cc_final: 0.6450 (mmmm) REVERT: M 91 GLU cc_start: 0.6185 (mm-30) cc_final: 0.5761 (mt-10) REVERT: P 212 GLN cc_start: 0.7889 (pt0) cc_final: 0.7463 (pt0) REVERT: P 241 GLN cc_start: 0.8185 (tm-30) cc_final: 0.7667 (tm-30) REVERT: Q 70 GLN cc_start: 0.8454 (mt0) cc_final: 0.7899 (mp10) REVERT: Q 100 PHE cc_start: 0.7636 (m-80) cc_final: 0.7342 (m-80) REVERT: R 18 MET cc_start: 0.6081 (tpt) cc_final: 0.5719 (tpp) REVERT: R 21 PHE cc_start: 0.5625 (t80) cc_final: 0.5334 (t80) REVERT: R 38 LEU cc_start: 0.7566 (pp) cc_final: 0.7204 (tp) REVERT: R 129 SER cc_start: 0.8310 (t) cc_final: 0.8076 (m) REVERT: R 144 ARG cc_start: 0.7315 (tpt170) cc_final: 0.7017 (tpt90) REVERT: T 45 GLN cc_start: 0.7199 (pm20) cc_final: 0.6895 (pm20) REVERT: V 52 ASN cc_start: 0.6670 (p0) cc_final: 0.6422 (p0) REVERT: V 64 ASN cc_start: 0.7782 (m110) cc_final: 0.7470 (m-40) REVERT: V 76 LYS cc_start: 0.8952 (mmmt) cc_final: 0.7998 (ptmm) outliers start: 240 outliers final: 154 residues processed: 971 average time/residue: 0.6062 time to fit residues: 1009.2189 Evaluate side-chains 910 residues out of total 7224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 750 time to evaluate : 5.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain F residue 181 ASP Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 274 GLU Chi-restraints excluded: chain I residue 285 ASP Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain U residue 143 LEU Chi-restraints excluded: chain U residue 149 MET Chi-restraints excluded: chain U residue 190 SER Chi-restraints excluded: chain U residue 210 THR Chi-restraints excluded: chain U residue 217 GLN Chi-restraints excluded: chain U residue 305 VAL Chi-restraints excluded: chain e residue 39 GLN Chi-restraints excluded: chain e residue 64 ASN Chi-restraints excluded: chain e residue 82 LEU Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain Y residue 32 VAL Chi-restraints excluded: chain Y residue 58 VAL Chi-restraints excluded: chain Y residue 77 LEU Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain g residue 143 LEU Chi-restraints excluded: chain g residue 149 MET Chi-restraints excluded: chain g residue 167 VAL Chi-restraints excluded: chain g residue 343 VAL Chi-restraints excluded: chain i residue 114 PHE Chi-restraints excluded: chain i residue 184 LEU Chi-restraints excluded: chain i residue 196 ILE Chi-restraints excluded: chain i residue 220 LEU Chi-restraints excluded: chain i residue 272 THR Chi-restraints excluded: chain i residue 275 VAL Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 149 LEU Chi-restraints excluded: chain k residue 321 ASP Chi-restraints excluded: chain m residue 241 GLN Chi-restraints excluded: chain o residue 148 THR Chi-restraints excluded: chain o residue 192 VAL Chi-restraints excluded: chain o residue 217 THR Chi-restraints excluded: chain o residue 236 ARG Chi-restraints excluded: chain o residue 258 THR Chi-restraints excluded: chain o residue 265 GLU Chi-restraints excluded: chain o residue 285 ASP Chi-restraints excluded: chain q residue 100 ILE Chi-restraints excluded: chain q residue 143 LEU Chi-restraints excluded: chain q residue 196 ILE Chi-restraints excluded: chain q residue 210 THR Chi-restraints excluded: chain q residue 217 GLN Chi-restraints excluded: chain q residue 342 LEU Chi-restraints excluded: chain s residue 31 LYS Chi-restraints excluded: chain s residue 62 ASP Chi-restraints excluded: chain u residue 33 ASP Chi-restraints excluded: chain u residue 41 VAL Chi-restraints excluded: chain u residue 68 THR Chi-restraints excluded: chain u residue 70 ILE Chi-restraints excluded: chain u residue 72 VAL Chi-restraints excluded: chain u residue 77 LEU Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 80 ASN Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Z residue 58 VAL Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain Z residue 77 LEU Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain d residue 68 THR Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain h residue 149 MET Chi-restraints excluded: chain h residue 167 VAL Chi-restraints excluded: chain h residue 332 GLU Chi-restraints excluded: chain j residue 114 PHE Chi-restraints excluded: chain j residue 117 LEU Chi-restraints excluded: chain j residue 176 SER Chi-restraints excluded: chain j residue 184 LEU Chi-restraints excluded: chain j residue 189 ASP Chi-restraints excluded: chain j residue 223 THR Chi-restraints excluded: chain j residue 236 VAL Chi-restraints excluded: chain j residue 275 VAL Chi-restraints excluded: chain l residue 27 GLU Chi-restraints excluded: chain l residue 71 THR Chi-restraints excluded: chain l residue 237 ARG Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 58 PHE Chi-restraints excluded: chain n residue 87 LEU Chi-restraints excluded: chain n residue 119 LEU Chi-restraints excluded: chain n residue 314 MET Chi-restraints excluded: chain p residue 37 VAL Chi-restraints excluded: chain p residue 72 MET Chi-restraints excluded: chain p residue 86 ASP Chi-restraints excluded: chain p residue 118 LEU Chi-restraints excluded: chain p residue 148 THR Chi-restraints excluded: chain p residue 201 LEU Chi-restraints excluded: chain p residue 217 THR Chi-restraints excluded: chain p residue 285 ASP Chi-restraints excluded: chain r residue 90 ILE Chi-restraints excluded: chain r residue 100 ILE Chi-restraints excluded: chain r residue 132 VAL Chi-restraints excluded: chain r residue 143 LEU Chi-restraints excluded: chain r residue 201 MET Chi-restraints excluded: chain r residue 305 VAL Chi-restraints excluded: chain t residue 62 ASP Chi-restraints excluded: chain v residue 77 LEU Chi-restraints excluded: chain v residue 91 GLU Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 201 MET Chi-restraints excluded: chain N residue 332 GLU Chi-restraints excluded: chain N residue 334 VAL Chi-restraints excluded: chain N residue 343 VAL Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 142 GLU Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain O residue 184 LEU Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain O residue 272 THR Chi-restraints excluded: chain O residue 342 LEU Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 237 ARG Chi-restraints excluded: chain P residue 316 MET Chi-restraints excluded: chain P residue 321 ASP Chi-restraints excluded: chain Q residue 14 VAL Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 314 MET Chi-restraints excluded: chain R residue 86 ASP Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain S residue 288 GLU Chi-restraints excluded: chain S residue 305 VAL Chi-restraints excluded: chain S residue 310 LYS Chi-restraints excluded: chain T residue 39 GLN Chi-restraints excluded: chain T residue 62 ASP Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 87 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 261 optimal weight: 0.7980 chunk 699 optimal weight: 3.9990 chunk 153 optimal weight: 0.6980 chunk 456 optimal weight: 6.9990 chunk 191 optimal weight: 6.9990 chunk 777 optimal weight: 0.7980 chunk 645 optimal weight: 0.7980 chunk 360 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 257 optimal weight: 3.9990 chunk 408 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 64 ASN E 260 ASN g 260 ASN k 310 ASN o 310 ASN u 39 GLN b 45 GLN j 116 HIS p 310 ASN v 39 GLN R 310 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.133 67560 Z= 0.170 Angle : 0.535 17.708 91212 Z= 0.285 Chirality : 0.043 0.299 10356 Planarity : 0.004 0.044 11940 Dihedral : 4.224 30.719 9325 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.03 % Favored : 96.96 % Rotamer: Outliers : 2.19 % Allowed : 17.05 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.58 (0.09), residues: 8184 helix: 2.26 (0.08), residues: 4324 sheet: 0.41 (0.13), residues: 1536 loop : -0.84 (0.12), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP i 92 HIS 0.004 0.001 HIS j 116 PHE 0.023 0.001 PHE U 238 TYR 0.025 0.001 TYR J 66 ARG 0.008 0.000 ARG M 65 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16368 Ramachandran restraints generated. 8184 Oldfield, 0 Emsley, 8184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16368 Ramachandran restraints generated. 8184 Oldfield, 0 Emsley, 8184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1013 residues out of total 7224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 855 time to evaluate : 5.901 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: A 34 TYR cc_start: 0.5651 (t80) cc_final: 0.5329 (t80) REVERT: A 77 LEU cc_start: 0.6042 (pp) cc_final: 0.5783 (mt) REVERT: B 43 ASN cc_start: 0.6862 (t0) cc_final: 0.6372 (t0) REVERT: B 45 GLN cc_start: 0.7340 (mt0) cc_final: 0.7033 (mt0) REVERT: D 41 VAL cc_start: 0.7670 (t) cc_final: 0.7373 (p) REVERT: D 89 VAL cc_start: 0.6028 (t) cc_final: 0.5729 (p) REVERT: E 131 GLU cc_start: 0.7153 (tp30) cc_final: 0.6804 (tp30) REVERT: E 242 ARG cc_start: 0.7562 (mmm-85) cc_final: 0.7063 (ptp-110) REVERT: F 104 GLU cc_start: 0.6618 (OUTLIER) cc_final: 0.6074 (pm20) REVERT: F 131 GLU cc_start: 0.6776 (tp30) cc_final: 0.6297 (mp0) REVERT: G 75 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7880 (mp10) REVERT: G 241 GLN cc_start: 0.7969 (tm-30) cc_final: 0.7659 (tm-30) REVERT: G 267 GLN cc_start: 0.8357 (mt0) cc_final: 0.8096 (mm-40) REVERT: G 274 GLU cc_start: 0.7362 (tp30) cc_final: 0.7149 (tp30) REVERT: I 84 LYS cc_start: 0.8036 (mtmt) cc_final: 0.7668 (mppt) REVERT: U 149 MET cc_start: 0.7310 (OUTLIER) cc_final: 0.7021 (mtt) REVERT: e 38 LEU cc_start: 0.8182 (tp) cc_final: 0.7970 (tt) REVERT: e 76 LYS cc_start: 0.6740 (pttp) cc_final: 0.6475 (tmtt) REVERT: f 76 LYS cc_start: 0.8608 (mmmt) cc_final: 0.7492 (ptmm) REVERT: W 76 LYS cc_start: 0.4487 (ptmt) cc_final: 0.4265 (ptpt) REVERT: Y 43 ASN cc_start: 0.7240 (t0) cc_final: 0.6580 (t0) REVERT: Y 87 LYS cc_start: 0.6879 (OUTLIER) cc_final: 0.6449 (mtpt) REVERT: c 59 THR cc_start: 0.6279 (m) cc_final: 0.5572 (p) REVERT: g 149 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7523 (mtt) REVERT: g 331 MET cc_start: 0.8165 (mmm) cc_final: 0.7943 (mmm) REVERT: k 241 GLN cc_start: 0.8049 (tm-30) cc_final: 0.7754 (tm-30) REVERT: k 314 MET cc_start: 0.8446 (ttt) cc_final: 0.8115 (ttm) REVERT: m 120 LYS cc_start: 0.8256 (ttmm) cc_final: 0.7937 (mttm) REVERT: o 290 ASP cc_start: 0.7893 (t0) cc_final: 0.7562 (t70) REVERT: q 201 MET cc_start: 0.8515 (ttp) cc_final: 0.8289 (ttp) REVERT: q 217 GLN cc_start: 0.7293 (OUTLIER) cc_final: 0.6688 (tp40) REVERT: q 238 PHE cc_start: 0.8340 (t80) cc_final: 0.8003 (t80) REVERT: q 267 GLU cc_start: 0.7673 (tp30) cc_final: 0.7462 (tp30) REVERT: u 74 ASP cc_start: 0.6537 (t0) cc_final: 0.6322 (t70) REVERT: u 76 LYS cc_start: 0.8657 (mmmt) cc_final: 0.7840 (ptmt) REVERT: X 55 GLU cc_start: 0.4927 (tp30) cc_final: 0.4674 (tp30) REVERT: Z 43 ASN cc_start: 0.7738 (t0) cc_final: 0.6947 (t0) REVERT: d 30 ARG cc_start: 0.5656 (ttm170) cc_final: 0.5280 (ttm110) REVERT: d 34 TYR cc_start: 0.6113 (t80) cc_final: 0.5758 (t80) REVERT: d 70 ILE cc_start: 0.5802 (mp) cc_final: 0.5259 (mm) REVERT: d 89 VAL cc_start: 0.6032 (t) cc_final: 0.5762 (p) REVERT: d 91 GLU cc_start: 0.6511 (mm-30) cc_final: 0.6087 (mt-10) REVERT: h 149 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7292 (mmm) REVERT: l 74 ASN cc_start: 0.7851 (m-40) cc_final: 0.7629 (m110) REVERT: l 237 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7407 (ttm170) REVERT: l 312 ASP cc_start: 0.8522 (p0) cc_final: 0.8216 (p0) REVERT: l 314 MET cc_start: 0.8581 (ttt) cc_final: 0.8281 (ttm) REVERT: p 84 LYS cc_start: 0.7843 (mtmt) cc_final: 0.7444 (mppt) REVERT: r 100 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7359 (mt) REVERT: r 160 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7502 (mp0) REVERT: r 161 MET cc_start: 0.8018 (mmt) cc_final: 0.7613 (mmm) REVERT: r 201 MET cc_start: 0.8490 (ttt) cc_final: 0.8238 (ttp) REVERT: t 38 LEU cc_start: 0.8278 (mt) cc_final: 0.7881 (tt) REVERT: t 48 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7998 (tm-30) REVERT: t 79 ASP cc_start: 0.7659 (m-30) cc_final: 0.7019 (t70) REVERT: v 76 LYS cc_start: 0.8881 (mmmt) cc_final: 0.7985 (ptmm) REVERT: J 55 GLU cc_start: 0.5734 (tp30) cc_final: 0.5098 (tp30) REVERT: J 76 LYS cc_start: 0.5321 (ptmt) cc_final: 0.5105 (ptmm) REVERT: K 43 ASN cc_start: 0.7314 (t0) cc_final: 0.6499 (t0) REVERT: K 87 LYS cc_start: 0.7583 (mmtt) cc_final: 0.7168 (tppt) REVERT: L 81 LEU cc_start: 0.7199 (mp) cc_final: 0.6828 (tt) REVERT: L 82 LEU cc_start: 0.6290 (mt) cc_final: 0.6052 (mp) REVERT: N 335 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8372 (mp) REVERT: P 212 GLN cc_start: 0.7995 (pt0) cc_final: 0.7445 (pt0) REVERT: P 241 GLN cc_start: 0.7982 (tm-30) cc_final: 0.7536 (tm-30) REVERT: Q 70 GLN cc_start: 0.8298 (mt0) cc_final: 0.7896 (mp10) REVERT: Q 100 PHE cc_start: 0.7584 (m-80) cc_final: 0.7052 (m-80) REVERT: Q 120 LYS cc_start: 0.8154 (ttmm) cc_final: 0.7830 (mttm) REVERT: R 18 MET cc_start: 0.6089 (tpt) cc_final: 0.5732 (tpp) REVERT: R 38 LEU cc_start: 0.7514 (pp) cc_final: 0.7142 (tp) REVERT: R 144 ARG cc_start: 0.7298 (tpt170) cc_final: 0.7030 (tpt90) REVERT: R 290 ASP cc_start: 0.7825 (t0) cc_final: 0.7517 (t0) REVERT: T 45 GLN cc_start: 0.7042 (pm20) cc_final: 0.6559 (pm20) REVERT: V 44 ASP cc_start: 0.7500 (OUTLIER) cc_final: 0.7241 (t0) REVERT: V 64 ASN cc_start: 0.7800 (m110) cc_final: 0.7515 (m-40) REVERT: V 76 LYS cc_start: 0.8931 (mmmt) cc_final: 0.8148 (pttt) outliers start: 158 outliers final: 95 residues processed: 951 average time/residue: 0.6107 time to fit residues: 988.1467 Evaluate side-chains 876 residues out of total 7224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 771 time to evaluate : 5.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain I residue 274 GLU Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain U residue 149 MET Chi-restraints excluded: chain U residue 190 SER Chi-restraints excluded: chain U residue 217 GLN Chi-restraints excluded: chain e residue 39 GLN Chi-restraints excluded: chain W residue 80 ASN Chi-restraints excluded: chain Y residue 58 VAL Chi-restraints excluded: chain Y residue 77 LEU Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain a residue 56 ILE Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain g residue 143 LEU Chi-restraints excluded: chain g residue 149 MET Chi-restraints excluded: chain g residue 167 VAL Chi-restraints excluded: chain i residue 114 PHE Chi-restraints excluded: chain i residue 184 LEU Chi-restraints excluded: chain i residue 196 ILE Chi-restraints excluded: chain i residue 220 LEU Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain o residue 131 ILE Chi-restraints excluded: chain o residue 192 VAL Chi-restraints excluded: chain o residue 265 GLU Chi-restraints excluded: chain q residue 100 ILE Chi-restraints excluded: chain q residue 132 VAL Chi-restraints excluded: chain q residue 217 GLN Chi-restraints excluded: chain s residue 31 LYS Chi-restraints excluded: chain s residue 62 ASP Chi-restraints excluded: chain u residue 33 ASP Chi-restraints excluded: chain u residue 72 VAL Chi-restraints excluded: chain u residue 77 LEU Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain Z residue 32 VAL Chi-restraints excluded: chain Z residue 58 VAL Chi-restraints excluded: chain Z residue 77 LEU Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain d residue 68 THR Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain h residue 149 MET Chi-restraints excluded: chain h residue 221 GLU Chi-restraints excluded: chain h residue 332 GLU Chi-restraints excluded: chain j residue 184 LEU Chi-restraints excluded: chain j residue 189 ASP Chi-restraints excluded: chain j residue 236 VAL Chi-restraints excluded: chain l residue 22 VAL Chi-restraints excluded: chain l residue 27 GLU Chi-restraints excluded: chain l residue 71 THR Chi-restraints excluded: chain l residue 237 ARG Chi-restraints excluded: chain n residue 58 PHE Chi-restraints excluded: chain p residue 93 ILE Chi-restraints excluded: chain p residue 118 LEU Chi-restraints excluded: chain p residue 201 LEU Chi-restraints excluded: chain p residue 310 ASN Chi-restraints excluded: chain r residue 100 ILE Chi-restraints excluded: chain r residue 237 ASN Chi-restraints excluded: chain t residue 62 ASP Chi-restraints excluded: chain v residue 77 LEU Chi-restraints excluded: chain v residue 91 GLU Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain N residue 107 VAL Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 332 GLU Chi-restraints excluded: chain N residue 335 LEU Chi-restraints excluded: chain N residue 343 VAL Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain O residue 184 LEU Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain O residue 272 THR Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 316 MET Chi-restraints excluded: chain Q residue 14 VAL Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 271 MET Chi-restraints excluded: chain R residue 138 ASP Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain T residue 62 ASP Chi-restraints excluded: chain V residue 40 GLU Chi-restraints excluded: chain V residue 44 ASP Chi-restraints excluded: chain V residue 77 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 749 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 443 optimal weight: 0.9980 chunk 568 optimal weight: 0.9990 chunk 440 optimal weight: 0.1980 chunk 654 optimal weight: 9.9990 chunk 434 optimal weight: 6.9990 chunk 774 optimal weight: 5.9990 chunk 484 optimal weight: 10.0000 chunk 472 optimal weight: 2.9990 chunk 357 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 ASN ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 310 ASN o 156 ASN o 267 GLN u 39 GLN l 114 GLN p 156 ASN p 310 ASN v 39 GLN v 42 ASN L 64 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 67560 Z= 0.205 Angle : 0.555 20.325 91212 Z= 0.293 Chirality : 0.044 0.321 10356 Planarity : 0.004 0.043 11940 Dihedral : 4.171 30.308 9325 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.34 % Favored : 96.65 % Rotamer: Outliers : 2.52 % Allowed : 17.44 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.62 (0.09), residues: 8184 helix: 2.30 (0.08), residues: 4332 sheet: 0.41 (0.13), residues: 1532 loop : -0.83 (0.12), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP i 92 HIS 0.004 0.001 HIS i 116 PHE 0.022 0.001 PHE r 238 TYR 0.020 0.001 TYR X 34 ARG 0.007 0.000 ARG m 237 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16368 Ramachandran restraints generated. 8184 Oldfield, 0 Emsley, 8184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16368 Ramachandran restraints generated. 8184 Oldfield, 0 Emsley, 8184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 983 residues out of total 7224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 801 time to evaluate : 5.757 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: A 34 TYR cc_start: 0.5938 (t80) cc_final: 0.5615 (t80) REVERT: A 77 LEU cc_start: 0.6052 (pp) cc_final: 0.5797 (mt) REVERT: B 43 ASN cc_start: 0.6889 (t0) cc_final: 0.6332 (t0) REVERT: B 45 GLN cc_start: 0.7354 (mt0) cc_final: 0.6973 (mt0) REVERT: D 41 VAL cc_start: 0.7667 (t) cc_final: 0.7293 (p) REVERT: D 70 ILE cc_start: 0.5680 (mm) cc_final: 0.5216 (mm) REVERT: D 89 VAL cc_start: 0.6247 (t) cc_final: 0.5988 (p) REVERT: D 91 GLU cc_start: 0.5783 (OUTLIER) cc_final: 0.5284 (mp0) REVERT: E 131 GLU cc_start: 0.7189 (tp30) cc_final: 0.6837 (tp30) REVERT: E 179 SER cc_start: 0.8390 (t) cc_final: 0.8013 (p) REVERT: E 242 ARG cc_start: 0.7561 (mmm-85) cc_final: 0.7060 (ptp-110) REVERT: F 131 GLU cc_start: 0.6711 (tp30) cc_final: 0.6248 (mp0) REVERT: F 343 VAL cc_start: 0.9645 (m) cc_final: 0.9380 (t) REVERT: G 75 GLN cc_start: 0.8167 (mm-40) cc_final: 0.7882 (mp10) REVERT: G 241 GLN cc_start: 0.8000 (tm-30) cc_final: 0.7681 (tm-30) REVERT: G 311 GLN cc_start: 0.8103 (mp10) cc_final: 0.7887 (mp10) REVERT: H 321 ASP cc_start: 0.7566 (t0) cc_final: 0.7284 (t70) REVERT: I 84 LYS cc_start: 0.8021 (mtmt) cc_final: 0.7662 (mppt) REVERT: U 149 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.7014 (mtt) REVERT: e 76 LYS cc_start: 0.6690 (pttp) cc_final: 0.6468 (tmtt) REVERT: f 76 LYS cc_start: 0.8585 (mmmt) cc_final: 0.7431 (ptmm) REVERT: Y 43 ASN cc_start: 0.7244 (t0) cc_final: 0.6646 (t0) REVERT: Y 87 LYS cc_start: 0.6985 (OUTLIER) cc_final: 0.6467 (mtpt) REVERT: c 47 ARG cc_start: 0.6351 (tmm-80) cc_final: 0.6070 (tmm160) REVERT: g 331 MET cc_start: 0.8187 (mmm) cc_final: 0.7965 (mmm) REVERT: k 48 TYR cc_start: 0.5699 (OUTLIER) cc_final: 0.4964 (m-10) REVERT: k 77 ASP cc_start: 0.8115 (p0) cc_final: 0.7151 (t0) REVERT: k 314 MET cc_start: 0.8410 (ttt) cc_final: 0.8021 (ttm) REVERT: m 87 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8144 (pp) REVERT: m 120 LYS cc_start: 0.8298 (ttmm) cc_final: 0.7964 (mttm) REVERT: o 267 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7548 (pt0) REVERT: o 290 ASP cc_start: 0.7919 (t0) cc_final: 0.7574 (t70) REVERT: q 217 GLN cc_start: 0.7322 (OUTLIER) cc_final: 0.6715 (tp40) REVERT: q 267 GLU cc_start: 0.7611 (tp30) cc_final: 0.7405 (tp30) REVERT: u 74 ASP cc_start: 0.6627 (t0) cc_final: 0.6413 (t70) REVERT: u 76 LYS cc_start: 0.8678 (mmmt) cc_final: 0.7836 (ptmt) REVERT: u 80 ASN cc_start: 0.7946 (t0) cc_final: 0.7742 (t0) REVERT: X 55 GLU cc_start: 0.4985 (tp30) cc_final: 0.4665 (tp30) REVERT: Z 43 ASN cc_start: 0.7722 (t0) cc_final: 0.6922 (t0) REVERT: d 34 TYR cc_start: 0.6259 (t80) cc_final: 0.5930 (t80) REVERT: d 70 ILE cc_start: 0.5804 (mp) cc_final: 0.5442 (mm) REVERT: d 89 VAL cc_start: 0.5979 (t) cc_final: 0.5748 (p) REVERT: d 91 GLU cc_start: 0.6500 (mm-30) cc_final: 0.6142 (mt-10) REVERT: h 149 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7346 (mmm) REVERT: l 74 ASN cc_start: 0.7891 (m-40) cc_final: 0.7626 (m110) REVERT: l 237 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7332 (ttm170) REVERT: l 312 ASP cc_start: 0.8512 (p0) cc_final: 0.8246 (p0) REVERT: l 314 MET cc_start: 0.8552 (ttt) cc_final: 0.8247 (ttm) REVERT: n 72 MET cc_start: 0.8706 (ptm) cc_final: 0.8432 (ptm) REVERT: p 84 LYS cc_start: 0.7836 (mtmt) cc_final: 0.7419 (mppt) REVERT: r 160 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7586 (mp0) REVERT: r 201 MET cc_start: 0.8529 (ttt) cc_final: 0.8289 (ttp) REVERT: t 38 LEU cc_start: 0.8273 (mt) cc_final: 0.8000 (tt) REVERT: t 48 GLU cc_start: 0.8260 (tm-30) cc_final: 0.8051 (tm-30) REVERT: t 79 ASP cc_start: 0.7624 (m-30) cc_final: 0.7065 (t70) REVERT: v 48 GLU cc_start: 0.7817 (pt0) cc_final: 0.7594 (pt0) REVERT: v 76 LYS cc_start: 0.8876 (mmmt) cc_final: 0.8018 (pttp) REVERT: J 55 GLU cc_start: 0.5446 (tp30) cc_final: 0.4795 (tp30) REVERT: K 43 ASN cc_start: 0.7361 (t0) cc_final: 0.6527 (t0) REVERT: L 81 LEU cc_start: 0.6867 (mp) cc_final: 0.6476 (tt) REVERT: L 82 LEU cc_start: 0.6218 (mt) cc_final: 0.6004 (mp) REVERT: M 47 ARG cc_start: 0.7153 (tmm-80) cc_final: 0.6928 (tmm-80) REVERT: M 70 ILE cc_start: 0.6019 (mp) cc_final: 0.5424 (mm) REVERT: M 84 LYS cc_start: 0.6934 (mttp) cc_final: 0.6508 (mttm) REVERT: N 335 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8296 (mp) REVERT: P 212 GLN cc_start: 0.7936 (pt0) cc_final: 0.7443 (pt0) REVERT: P 241 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7578 (tm-30) REVERT: Q 70 GLN cc_start: 0.8281 (mt0) cc_final: 0.7884 (mp10) REVERT: Q 100 PHE cc_start: 0.7562 (m-80) cc_final: 0.7100 (m-80) REVERT: Q 120 LYS cc_start: 0.8160 (ttmm) cc_final: 0.7857 (mttm) REVERT: R 18 MET cc_start: 0.6047 (tpt) cc_final: 0.5708 (tpp) REVERT: R 38 LEU cc_start: 0.7552 (pp) cc_final: 0.7098 (tp) REVERT: R 144 ARG cc_start: 0.7196 (tpt170) cc_final: 0.6945 (tpt90) REVERT: R 290 ASP cc_start: 0.7816 (t0) cc_final: 0.7474 (t0) REVERT: T 45 GLN cc_start: 0.7239 (pm20) cc_final: 0.6774 (pm20) REVERT: V 33 ASP cc_start: 0.7480 (p0) cc_final: 0.7145 (p0) REVERT: V 64 ASN cc_start: 0.7729 (m110) cc_final: 0.7459 (m-40) REVERT: V 76 LYS cc_start: 0.8933 (mmmt) cc_final: 0.8161 (pttt) outliers start: 182 outliers final: 138 residues processed: 921 average time/residue: 0.6430 time to fit residues: 1023.8848 Evaluate side-chains 916 residues out of total 7224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 768 time to evaluate : 5.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 181 ASP Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain I residue 274 GLU Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain U residue 135 VAL Chi-restraints excluded: chain U residue 143 LEU Chi-restraints excluded: chain U residue 149 MET Chi-restraints excluded: chain U residue 190 SER Chi-restraints excluded: chain U residue 217 GLN Chi-restraints excluded: chain U residue 342 LEU Chi-restraints excluded: chain e residue 39 GLN Chi-restraints excluded: chain f residue 33 ASP Chi-restraints excluded: chain W residue 72 VAL Chi-restraints excluded: chain W residue 80 ASN Chi-restraints excluded: chain Y residue 58 VAL Chi-restraints excluded: chain Y residue 77 LEU Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain a residue 56 ILE Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain g residue 143 LEU Chi-restraints excluded: chain g residue 149 MET Chi-restraints excluded: chain g residue 167 VAL Chi-restraints excluded: chain g residue 343 VAL Chi-restraints excluded: chain i residue 114 PHE Chi-restraints excluded: chain i residue 184 LEU Chi-restraints excluded: chain i residue 196 ILE Chi-restraints excluded: chain i residue 220 LEU Chi-restraints excluded: chain i residue 275 VAL Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 48 TYR Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain m residue 87 LEU Chi-restraints excluded: chain o residue 22 VAL Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain o residue 131 ILE Chi-restraints excluded: chain o residue 192 VAL Chi-restraints excluded: chain o residue 217 THR Chi-restraints excluded: chain o residue 265 GLU Chi-restraints excluded: chain o residue 267 GLN Chi-restraints excluded: chain q residue 100 ILE Chi-restraints excluded: chain q residue 132 VAL Chi-restraints excluded: chain q residue 217 GLN Chi-restraints excluded: chain s residue 31 LYS Chi-restraints excluded: chain s residue 62 ASP Chi-restraints excluded: chain u residue 33 ASP Chi-restraints excluded: chain u residue 68 THR Chi-restraints excluded: chain u residue 72 VAL Chi-restraints excluded: chain u residue 77 LEU Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain Z residue 32 VAL Chi-restraints excluded: chain Z residue 58 VAL Chi-restraints excluded: chain Z residue 77 LEU Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain d residue 68 THR Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain h residue 149 MET Chi-restraints excluded: chain h residue 167 VAL Chi-restraints excluded: chain h residue 332 GLU Chi-restraints excluded: chain j residue 156 VAL Chi-restraints excluded: chain j residue 176 SER Chi-restraints excluded: chain j residue 184 LEU Chi-restraints excluded: chain j residue 189 ASP Chi-restraints excluded: chain j residue 223 THR Chi-restraints excluded: chain j residue 236 VAL Chi-restraints excluded: chain l residue 22 VAL Chi-restraints excluded: chain l residue 27 GLU Chi-restraints excluded: chain l residue 71 THR Chi-restraints excluded: chain l residue 237 ARG Chi-restraints excluded: chain l residue 316 MET Chi-restraints excluded: chain n residue 37 VAL Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 58 PHE Chi-restraints excluded: chain n residue 314 MET Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 86 ASP Chi-restraints excluded: chain p residue 93 ILE Chi-restraints excluded: chain p residue 118 LEU Chi-restraints excluded: chain p residue 148 THR Chi-restraints excluded: chain p residue 201 LEU Chi-restraints excluded: chain r residue 100 ILE Chi-restraints excluded: chain r residue 132 VAL Chi-restraints excluded: chain r residue 237 ASN Chi-restraints excluded: chain t residue 62 ASP Chi-restraints excluded: chain v residue 77 LEU Chi-restraints excluded: chain v residue 91 GLU Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 201 MET Chi-restraints excluded: chain N residue 332 GLU Chi-restraints excluded: chain N residue 335 LEU Chi-restraints excluded: chain N residue 343 VAL Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain O residue 184 LEU Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain O residue 272 THR Chi-restraints excluded: chain O residue 342 LEU Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 237 ARG Chi-restraints excluded: chain P residue 316 MET Chi-restraints excluded: chain P residue 321 ASP Chi-restraints excluded: chain Q residue 14 VAL Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 64 MET Chi-restraints excluded: chain Q residue 271 MET Chi-restraints excluded: chain R residue 138 ASP Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 288 GLU Chi-restraints excluded: chain S residue 310 LYS Chi-restraints excluded: chain T residue 31 LYS Chi-restraints excluded: chain T residue 62 ASP Chi-restraints excluded: chain V residue 77 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 479 optimal weight: 6.9990 chunk 309 optimal weight: 10.0000 chunk 462 optimal weight: 1.9990 chunk 233 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 chunk 150 optimal weight: 9.9990 chunk 492 optimal weight: 2.9990 chunk 527 optimal weight: 4.9990 chunk 383 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 609 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 ASN k 310 ASN o 267 GLN o 310 ASN u 39 GLN d 57 ASN p 310 ASN v 39 GLN L 64 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 67560 Z= 0.255 Angle : 0.578 23.965 91212 Z= 0.305 Chirality : 0.044 0.328 10356 Planarity : 0.004 0.042 11940 Dihedral : 4.263 30.194 9325 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.59 % Favored : 96.40 % Rotamer: Outliers : 2.80 % Allowed : 17.73 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.50 (0.09), residues: 8184 helix: 2.20 (0.08), residues: 4332 sheet: 0.33 (0.13), residues: 1548 loop : -0.86 (0.12), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 92 HIS 0.003 0.001 HIS G 238 PHE 0.025 0.001 PHE U 238 TYR 0.019 0.001 TYR X 34 ARG 0.007 0.000 ARG M 65 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16368 Ramachandran restraints generated. 8184 Oldfield, 0 Emsley, 8184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16368 Ramachandran restraints generated. 8184 Oldfield, 0 Emsley, 8184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 997 residues out of total 7224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 795 time to evaluate : 5.818 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: A 34 TYR cc_start: 0.5959 (t80) cc_final: 0.5661 (t80) REVERT: B 43 ASN cc_start: 0.6903 (t0) cc_final: 0.6338 (t0) REVERT: B 45 GLN cc_start: 0.7371 (mt0) cc_final: 0.7123 (mt0) REVERT: D 30 ARG cc_start: 0.5572 (ttm170) cc_final: 0.5328 (ptt180) REVERT: D 41 VAL cc_start: 0.7417 (t) cc_final: 0.7125 (p) REVERT: D 70 ILE cc_start: 0.5663 (mm) cc_final: 0.5196 (mm) REVERT: E 131 GLU cc_start: 0.7233 (tp30) cc_final: 0.6896 (tp30) REVERT: E 179 SER cc_start: 0.8282 (t) cc_final: 0.7904 (p) REVERT: E 242 ARG cc_start: 0.7589 (mmm-85) cc_final: 0.7125 (ptp-110) REVERT: F 131 GLU cc_start: 0.6780 (tp30) cc_final: 0.6239 (mp0) REVERT: G 75 GLN cc_start: 0.8224 (mm-40) cc_final: 0.7936 (mp10) REVERT: G 241 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7698 (tm-30) REVERT: G 311 GLN cc_start: 0.8157 (mp10) cc_final: 0.7911 (mp10) REVERT: H 58 PHE cc_start: 0.6452 (OUTLIER) cc_final: 0.6118 (t80) REVERT: H 321 ASP cc_start: 0.7551 (t0) cc_final: 0.7261 (t70) REVERT: I 84 LYS cc_start: 0.7995 (mtmt) cc_final: 0.7644 (mppt) REVERT: I 117 VAL cc_start: 0.7657 (t) cc_final: 0.7449 (m) REVERT: U 149 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.6997 (mtt) REVERT: e 76 LYS cc_start: 0.6792 (pttp) cc_final: 0.6539 (tmtt) REVERT: e 79 ASP cc_start: 0.7914 (m-30) cc_final: 0.6982 (t70) REVERT: f 76 LYS cc_start: 0.8685 (mmmt) cc_final: 0.7529 (ptmm) REVERT: W 55 GLU cc_start: 0.6512 (tp30) cc_final: 0.5462 (tp30) REVERT: Y 43 ASN cc_start: 0.7248 (t0) cc_final: 0.6623 (t0) REVERT: Y 87 LYS cc_start: 0.7123 (OUTLIER) cc_final: 0.6700 (mtpt) REVERT: c 34 TYR cc_start: 0.4764 (t80) cc_final: 0.4407 (t80) REVERT: c 47 ARG cc_start: 0.6361 (tmm-80) cc_final: 0.6078 (tmm160) REVERT: c 84 LYS cc_start: 0.6472 (mtpp) cc_final: 0.6191 (mmmt) REVERT: g 149 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7375 (mtt) REVERT: g 331 MET cc_start: 0.8242 (mmm) cc_final: 0.8006 (mmm) REVERT: k 48 TYR cc_start: 0.5658 (OUTLIER) cc_final: 0.5068 (m-10) REVERT: k 241 GLN cc_start: 0.8041 (tm-30) cc_final: 0.7806 (tm-30) REVERT: k 310 ASN cc_start: 0.6556 (OUTLIER) cc_final: 0.6311 (t0) REVERT: k 314 MET cc_start: 0.8381 (ttt) cc_final: 0.8025 (ttm) REVERT: m 120 LYS cc_start: 0.8273 (ttmm) cc_final: 0.7951 (mttm) REVERT: o 290 ASP cc_start: 0.7934 (t0) cc_final: 0.7582 (t70) REVERT: q 217 GLN cc_start: 0.7391 (OUTLIER) cc_final: 0.6788 (tp40) REVERT: q 238 PHE cc_start: 0.8253 (t80) cc_final: 0.7933 (t80) REVERT: q 267 GLU cc_start: 0.7618 (tp30) cc_final: 0.7398 (tp30) REVERT: u 76 LYS cc_start: 0.8702 (mmmt) cc_final: 0.7867 (ptmt) REVERT: X 55 GLU cc_start: 0.5000 (tp30) cc_final: 0.4644 (tp30) REVERT: Z 43 ASN cc_start: 0.7793 (t0) cc_final: 0.6936 (t0) REVERT: d 34 TYR cc_start: 0.6272 (t80) cc_final: 0.5956 (t80) REVERT: d 47 ARG cc_start: 0.6736 (tmm160) cc_final: 0.6482 (ttp-110) REVERT: d 70 ILE cc_start: 0.5752 (mp) cc_final: 0.5352 (mm) REVERT: d 76 LYS cc_start: 0.6155 (ptmt) cc_final: 0.5409 (pttm) REVERT: d 89 VAL cc_start: 0.5993 (t) cc_final: 0.5695 (p) REVERT: h 149 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.7282 (mmm) REVERT: j 161 MET cc_start: 0.7459 (mtm) cc_final: 0.7195 (mtt) REVERT: l 74 ASN cc_start: 0.7892 (m-40) cc_final: 0.7582 (m110) REVERT: l 237 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7385 (ttm170) REVERT: l 312 ASP cc_start: 0.8562 (p0) cc_final: 0.8258 (p0) REVERT: l 314 MET cc_start: 0.8579 (ttt) cc_final: 0.8236 (ttm) REVERT: p 84 LYS cc_start: 0.7839 (mtmt) cc_final: 0.7394 (mppt) REVERT: r 160 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7581 (mp0) REVERT: r 201 MET cc_start: 0.8552 (ttt) cc_final: 0.8320 (ttp) REVERT: t 38 LEU cc_start: 0.8217 (mt) cc_final: 0.7981 (tt) REVERT: t 48 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8095 (tm-30) REVERT: t 79 ASP cc_start: 0.7720 (m-30) cc_final: 0.7075 (t70) REVERT: v 64 ASN cc_start: 0.7724 (m110) cc_final: 0.7258 (m-40) REVERT: v 76 LYS cc_start: 0.8879 (mmmt) cc_final: 0.7967 (ptmm) REVERT: J 55 GLU cc_start: 0.5595 (tp30) cc_final: 0.4859 (tp30) REVERT: K 43 ASN cc_start: 0.7385 (t0) cc_final: 0.6553 (t0) REVERT: K 87 LYS cc_start: 0.7647 (mmtt) cc_final: 0.7423 (tptt) REVERT: L 81 LEU cc_start: 0.7140 (mp) cc_final: 0.6768 (tt) REVERT: L 82 LEU cc_start: 0.5858 (mt) cc_final: 0.5631 (mp) REVERT: M 70 ILE cc_start: 0.6087 (mp) cc_final: 0.5519 (mm) REVERT: M 84 LYS cc_start: 0.6885 (mttp) cc_final: 0.6463 (mttm) REVERT: M 91 GLU cc_start: 0.5603 (mt-10) cc_final: 0.5394 (mt-10) REVERT: N 335 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8291 (mp) REVERT: P 38 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8486 (mm) REVERT: P 212 GLN cc_start: 0.8021 (pt0) cc_final: 0.7486 (pt0) REVERT: P 241 GLN cc_start: 0.8049 (tm-30) cc_final: 0.7572 (tm-30) REVERT: Q 70 GLN cc_start: 0.8349 (mt0) cc_final: 0.7926 (mp10) REVERT: Q 100 PHE cc_start: 0.7566 (m-80) cc_final: 0.7122 (m-80) REVERT: R 18 MET cc_start: 0.6064 (tpt) cc_final: 0.5711 (tpp) REVERT: R 38 LEU cc_start: 0.7549 (pp) cc_final: 0.7099 (tp) REVERT: R 144 ARG cc_start: 0.7210 (tpt170) cc_final: 0.6944 (tpt90) REVERT: V 33 ASP cc_start: 0.7465 (p0) cc_final: 0.7171 (p0) REVERT: V 64 ASN cc_start: 0.7757 (m110) cc_final: 0.7482 (m-40) REVERT: V 76 LYS cc_start: 0.9002 (mmmt) cc_final: 0.8190 (pttt) outliers start: 202 outliers final: 160 residues processed: 928 average time/residue: 0.6040 time to fit residues: 957.6154 Evaluate side-chains 942 residues out of total 7224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 771 time to evaluate : 5.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain F residue 181 ASP Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 58 PHE Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain I residue 258 THR Chi-restraints excluded: chain I residue 274 GLU Chi-restraints excluded: chain U residue 90 ILE Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain U residue 135 VAL Chi-restraints excluded: chain U residue 143 LEU Chi-restraints excluded: chain U residue 149 MET Chi-restraints excluded: chain U residue 190 SER Chi-restraints excluded: chain U residue 217 GLN Chi-restraints excluded: chain U residue 342 LEU Chi-restraints excluded: chain e residue 36 THR Chi-restraints excluded: chain e residue 39 GLN Chi-restraints excluded: chain f residue 33 ASP Chi-restraints excluded: chain W residue 80 ASN Chi-restraints excluded: chain Y residue 58 VAL Chi-restraints excluded: chain Y residue 77 LEU Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain a residue 56 ILE Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 70 ILE Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain g residue 143 LEU Chi-restraints excluded: chain g residue 149 MET Chi-restraints excluded: chain g residue 167 VAL Chi-restraints excluded: chain g residue 343 VAL Chi-restraints excluded: chain i residue 114 PHE Chi-restraints excluded: chain i residue 184 LEU Chi-restraints excluded: chain i residue 196 ILE Chi-restraints excluded: chain i residue 220 LEU Chi-restraints excluded: chain i residue 275 VAL Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 48 TYR Chi-restraints excluded: chain k residue 72 MET Chi-restraints excluded: chain k residue 310 ASN Chi-restraints excluded: chain k residue 316 MET Chi-restraints excluded: chain k residue 321 ASP Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain m residue 241 GLN Chi-restraints excluded: chain o residue 22 VAL Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain o residue 131 ILE Chi-restraints excluded: chain o residue 192 VAL Chi-restraints excluded: chain o residue 217 THR Chi-restraints excluded: chain o residue 265 GLU Chi-restraints excluded: chain o residue 285 ASP Chi-restraints excluded: chain q residue 100 ILE Chi-restraints excluded: chain q residue 132 VAL Chi-restraints excluded: chain q residue 217 GLN Chi-restraints excluded: chain s residue 62 ASP Chi-restraints excluded: chain u residue 33 ASP Chi-restraints excluded: chain u residue 68 THR Chi-restraints excluded: chain u residue 70 ILE Chi-restraints excluded: chain u residue 72 VAL Chi-restraints excluded: chain u residue 77 LEU Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain Z residue 32 VAL Chi-restraints excluded: chain Z residue 58 VAL Chi-restraints excluded: chain Z residue 77 LEU Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain b residue 70 ILE Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain d residue 68 THR Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain h residue 149 MET Chi-restraints excluded: chain h residue 167 VAL Chi-restraints excluded: chain h residue 332 GLU Chi-restraints excluded: chain j residue 114 PHE Chi-restraints excluded: chain j residue 156 VAL Chi-restraints excluded: chain j residue 176 SER Chi-restraints excluded: chain j residue 184 LEU Chi-restraints excluded: chain j residue 189 ASP Chi-restraints excluded: chain j residue 223 THR Chi-restraints excluded: chain j residue 275 VAL Chi-restraints excluded: chain l residue 22 VAL Chi-restraints excluded: chain l residue 27 GLU Chi-restraints excluded: chain l residue 71 THR Chi-restraints excluded: chain l residue 237 ARG Chi-restraints excluded: chain l residue 316 MET Chi-restraints excluded: chain n residue 37 VAL Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 58 PHE Chi-restraints excluded: chain n residue 314 MET Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 86 ASP Chi-restraints excluded: chain p residue 93 ILE Chi-restraints excluded: chain p residue 118 LEU Chi-restraints excluded: chain p residue 148 THR Chi-restraints excluded: chain p residue 201 LEU Chi-restraints excluded: chain p residue 217 THR Chi-restraints excluded: chain r residue 100 ILE Chi-restraints excluded: chain r residue 132 VAL Chi-restraints excluded: chain r residue 210 THR Chi-restraints excluded: chain r residue 237 ASN Chi-restraints excluded: chain t residue 62 ASP Chi-restraints excluded: chain v residue 77 LEU Chi-restraints excluded: chain v residue 91 GLU Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 201 MET Chi-restraints excluded: chain N residue 332 GLU Chi-restraints excluded: chain N residue 335 LEU Chi-restraints excluded: chain N residue 343 VAL Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 142 GLU Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain O residue 184 LEU Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain O residue 272 THR Chi-restraints excluded: chain O residue 342 LEU Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 321 ASP Chi-restraints excluded: chain Q residue 14 VAL Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 64 MET Chi-restraints excluded: chain Q residue 271 MET Chi-restraints excluded: chain Q residue 314 MET Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 86 ASP Chi-restraints excluded: chain R residue 138 ASP Chi-restraints excluded: chain R residue 285 ASP Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 288 GLU Chi-restraints excluded: chain S residue 310 LYS Chi-restraints excluded: chain S residue 342 LEU Chi-restraints excluded: chain T residue 31 LYS Chi-restraints excluded: chain T residue 62 ASP Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 91 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 704 optimal weight: 0.9980 chunk 742 optimal weight: 2.9990 chunk 677 optimal weight: 0.6980 chunk 722 optimal weight: 0.0870 chunk 434 optimal weight: 2.9990 chunk 314 optimal weight: 2.9990 chunk 567 optimal weight: 0.9990 chunk 221 optimal weight: 9.9990 chunk 652 optimal weight: 1.9990 chunk 682 optimal weight: 0.7980 chunk 719 optimal weight: 10.0000 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 ASN e 85 ASN c 57 ASN g 239 GLN ** k 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 310 ASN o 156 ASN u 39 GLN p 310 ASN v 39 GLN L 64 ASN M 85 ASN R 310 ASN V 39 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 67560 Z= 0.163 Angle : 0.537 18.234 91212 Z= 0.284 Chirality : 0.043 0.201 10356 Planarity : 0.003 0.041 11940 Dihedral : 4.089 31.281 9325 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.36 % Favored : 96.63 % Rotamer: Outliers : 2.34 % Allowed : 18.37 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.73 (0.09), residues: 8184 helix: 2.39 (0.08), residues: 4328 sheet: 0.45 (0.13), residues: 1528 loop : -0.77 (0.12), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 92 HIS 0.003 0.001 HIS i 116 PHE 0.021 0.001 PHE S 238 TYR 0.020 0.001 TYR X 34 ARG 0.007 0.000 ARG p 146 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16368 Ramachandran restraints generated. 8184 Oldfield, 0 Emsley, 8184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16368 Ramachandran restraints generated. 8184 Oldfield, 0 Emsley, 8184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1000 residues out of total 7224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 831 time to evaluate : 5.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 ASN cc_start: 0.6866 (t0) cc_final: 0.6353 (t0) REVERT: B 45 GLN cc_start: 0.7325 (mt0) cc_final: 0.7082 (mt0) REVERT: B 87 LYS cc_start: 0.7405 (mmtt) cc_final: 0.7124 (tppt) REVERT: D 30 ARG cc_start: 0.5622 (ttm170) cc_final: 0.5420 (ptt180) REVERT: D 41 VAL cc_start: 0.7291 (t) cc_final: 0.6989 (p) REVERT: E 131 GLU cc_start: 0.7221 (tp30) cc_final: 0.6859 (tp30) REVERT: E 179 SER cc_start: 0.8055 (t) cc_final: 0.7684 (p) REVERT: E 242 ARG cc_start: 0.7578 (mmm-85) cc_final: 0.7104 (ptp-110) REVERT: F 131 GLU cc_start: 0.6714 (tp30) cc_final: 0.6222 (mp0) REVERT: F 343 VAL cc_start: 0.9633 (m) cc_final: 0.9356 (t) REVERT: G 75 GLN cc_start: 0.8179 (mm-40) cc_final: 0.7886 (mp10) REVERT: G 241 GLN cc_start: 0.7974 (tm-30) cc_final: 0.7635 (tm-30) REVERT: G 311 GLN cc_start: 0.8067 (mp10) cc_final: 0.7840 (mp10) REVERT: I 84 LYS cc_start: 0.7892 (mtmt) cc_final: 0.7635 (mppt) REVERT: I 290 ASP cc_start: 0.8138 (t0) cc_final: 0.7811 (t0) REVERT: U 149 MET cc_start: 0.7289 (OUTLIER) cc_final: 0.7010 (mtt) REVERT: e 48 GLU cc_start: 0.8429 (tm-30) cc_final: 0.7969 (tm-30) REVERT: e 76 LYS cc_start: 0.6787 (pttp) cc_final: 0.6553 (tmtt) REVERT: f 76 LYS cc_start: 0.8688 (mmmt) cc_final: 0.7501 (ptmm) REVERT: W 55 GLU cc_start: 0.6560 (tp30) cc_final: 0.5454 (tp30) REVERT: Y 43 ASN cc_start: 0.7199 (t0) cc_final: 0.6593 (t0) REVERT: Y 87 LYS cc_start: 0.7045 (OUTLIER) cc_final: 0.6625 (mtpt) REVERT: c 47 ARG cc_start: 0.6423 (tmm-80) cc_final: 0.6138 (tmm160) REVERT: c 84 LYS cc_start: 0.6703 (mtpp) cc_final: 0.6244 (mmmt) REVERT: c 91 GLU cc_start: 0.5896 (mm-30) cc_final: 0.5583 (mt-10) REVERT: g 149 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7531 (mtt) REVERT: g 331 MET cc_start: 0.8199 (mmm) cc_final: 0.7968 (mmm) REVERT: k 48 TYR cc_start: 0.5720 (OUTLIER) cc_final: 0.5004 (m-10) REVERT: k 77 ASP cc_start: 0.8055 (p0) cc_final: 0.7104 (t0) REVERT: k 314 MET cc_start: 0.8377 (ttt) cc_final: 0.8071 (ttm) REVERT: m 120 LYS cc_start: 0.8258 (ttmm) cc_final: 0.7903 (mttt) REVERT: q 217 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.6680 (tp40) REVERT: q 228 ASP cc_start: 0.7815 (t0) cc_final: 0.7461 (t0) REVERT: q 238 PHE cc_start: 0.8192 (t80) cc_final: 0.7849 (t80) REVERT: q 252 ASP cc_start: 0.7539 (p0) cc_final: 0.7327 (p0) REVERT: q 267 GLU cc_start: 0.7621 (tp30) cc_final: 0.7412 (tp30) REVERT: u 76 LYS cc_start: 0.8722 (mmmt) cc_final: 0.7986 (pttt) REVERT: X 55 GLU cc_start: 0.5156 (tp30) cc_final: 0.4613 (tp30) REVERT: Z 43 ASN cc_start: 0.7613 (t0) cc_final: 0.6814 (t0) REVERT: Z 62 ASP cc_start: 0.6854 (p0) cc_final: 0.6647 (p0) REVERT: d 34 TYR cc_start: 0.6182 (t80) cc_final: 0.5825 (t80) REVERT: d 47 ARG cc_start: 0.6696 (tmm160) cc_final: 0.6474 (ttp-110) REVERT: d 70 ILE cc_start: 0.5909 (mp) cc_final: 0.5477 (mm) REVERT: d 89 VAL cc_start: 0.6080 (t) cc_final: 0.5848 (p) REVERT: h 149 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7343 (mmm) REVERT: j 161 MET cc_start: 0.7408 (mtm) cc_final: 0.7138 (mtt) REVERT: j 238 PHE cc_start: 0.8251 (t80) cc_final: 0.8009 (t80) REVERT: l 74 ASN cc_start: 0.7924 (m-40) cc_final: 0.7658 (m110) REVERT: l 237 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7446 (ttm170) REVERT: l 312 ASP cc_start: 0.8499 (p0) cc_final: 0.8191 (p0) REVERT: l 314 MET cc_start: 0.8538 (ttt) cc_final: 0.8267 (ttm) REVERT: p 84 LYS cc_start: 0.7846 (mtmt) cc_final: 0.7439 (mppt) REVERT: p 290 ASP cc_start: 0.7980 (t0) cc_final: 0.7697 (t0) REVERT: r 160 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7367 (mp0) REVERT: r 161 MET cc_start: 0.7710 (mmt) cc_final: 0.7331 (mmm) REVERT: t 38 LEU cc_start: 0.8157 (mt) cc_final: 0.7827 (tt) REVERT: t 48 GLU cc_start: 0.8370 (tm-30) cc_final: 0.8130 (tm-30) REVERT: t 79 ASP cc_start: 0.7661 (m-30) cc_final: 0.7072 (t70) REVERT: v 76 LYS cc_start: 0.8826 (mmmt) cc_final: 0.8062 (ptmm) REVERT: J 55 GLU cc_start: 0.5667 (tp30) cc_final: 0.4828 (tp30) REVERT: K 43 ASN cc_start: 0.7456 (t0) cc_final: 0.6646 (t0) REVERT: K 87 LYS cc_start: 0.7608 (mmtt) cc_final: 0.7169 (tppt) REVERT: M 70 ILE cc_start: 0.5991 (mp) cc_final: 0.5596 (mm) REVERT: M 84 LYS cc_start: 0.6852 (mttp) cc_final: 0.6363 (mtpt) REVERT: P 212 GLN cc_start: 0.8008 (pt0) cc_final: 0.7463 (pt0) REVERT: P 241 GLN cc_start: 0.7981 (tm-30) cc_final: 0.7546 (tm-30) REVERT: Q 70 GLN cc_start: 0.8214 (mt0) cc_final: 0.7839 (mp10) REVERT: Q 100 PHE cc_start: 0.7523 (m-80) cc_final: 0.7135 (m-80) REVERT: R 18 MET cc_start: 0.6053 (tpt) cc_final: 0.5686 (tpp) REVERT: R 72 MET cc_start: 0.7652 (ptm) cc_final: 0.7444 (ptm) REVERT: R 144 ARG cc_start: 0.7142 (tpt170) cc_final: 0.6895 (tpt90) REVERT: T 48 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8239 (tm-30) REVERT: V 33 ASP cc_start: 0.7485 (p0) cc_final: 0.7203 (p0) REVERT: V 76 LYS cc_start: 0.8930 (mmmt) cc_final: 0.8131 (pttt) outliers start: 169 outliers final: 126 residues processed: 939 average time/residue: 0.6091 time to fit residues: 978.3766 Evaluate side-chains 897 residues out of total 7224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 764 time to evaluate : 5.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain I residue 274 GLU Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain U residue 135 VAL Chi-restraints excluded: chain U residue 143 LEU Chi-restraints excluded: chain U residue 149 MET Chi-restraints excluded: chain U residue 217 GLN Chi-restraints excluded: chain e residue 39 GLN Chi-restraints excluded: chain e residue 85 ASN Chi-restraints excluded: chain f residue 33 ASP Chi-restraints excluded: chain W residue 72 VAL Chi-restraints excluded: chain W residue 80 ASN Chi-restraints excluded: chain Y residue 58 VAL Chi-restraints excluded: chain Y residue 77 LEU Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain a residue 56 ILE Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 70 ILE Chi-restraints excluded: chain g residue 143 LEU Chi-restraints excluded: chain g residue 149 MET Chi-restraints excluded: chain g residue 167 VAL Chi-restraints excluded: chain g residue 343 VAL Chi-restraints excluded: chain i residue 114 PHE Chi-restraints excluded: chain i residue 184 LEU Chi-restraints excluded: chain i residue 196 ILE Chi-restraints excluded: chain i residue 220 LEU Chi-restraints excluded: chain i residue 275 VAL Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 48 TYR Chi-restraints excluded: chain k residue 72 MET Chi-restraints excluded: chain k residue 316 MET Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain o residue 22 VAL Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain o residue 131 ILE Chi-restraints excluded: chain o residue 192 VAL Chi-restraints excluded: chain o residue 217 THR Chi-restraints excluded: chain o residue 265 GLU Chi-restraints excluded: chain q residue 100 ILE Chi-restraints excluded: chain q residue 132 VAL Chi-restraints excluded: chain q residue 217 GLN Chi-restraints excluded: chain s residue 62 ASP Chi-restraints excluded: chain u residue 33 ASP Chi-restraints excluded: chain u residue 68 THR Chi-restraints excluded: chain u residue 72 VAL Chi-restraints excluded: chain u residue 77 LEU Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain Z residue 32 VAL Chi-restraints excluded: chain Z residue 58 VAL Chi-restraints excluded: chain Z residue 77 LEU Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain b residue 70 ILE Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain d residue 68 THR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain h residue 149 MET Chi-restraints excluded: chain h residue 167 VAL Chi-restraints excluded: chain j residue 184 LEU Chi-restraints excluded: chain j residue 189 ASP Chi-restraints excluded: chain l residue 22 VAL Chi-restraints excluded: chain l residue 27 GLU Chi-restraints excluded: chain l residue 71 THR Chi-restraints excluded: chain l residue 72 MET Chi-restraints excluded: chain l residue 237 ARG Chi-restraints excluded: chain n residue 37 VAL Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 314 MET Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 93 ILE Chi-restraints excluded: chain p residue 118 LEU Chi-restraints excluded: chain p residue 148 THR Chi-restraints excluded: chain p residue 201 LEU Chi-restraints excluded: chain p residue 217 THR Chi-restraints excluded: chain p residue 310 ASN Chi-restraints excluded: chain r residue 100 ILE Chi-restraints excluded: chain r residue 132 VAL Chi-restraints excluded: chain r residue 237 ASN Chi-restraints excluded: chain t residue 62 ASP Chi-restraints excluded: chain v residue 91 GLU Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 332 GLU Chi-restraints excluded: chain N residue 343 VAL Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 142 GLU Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain O residue 184 LEU Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain O residue 272 THR Chi-restraints excluded: chain O residue 342 LEU Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 321 ASP Chi-restraints excluded: chain Q residue 14 VAL Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 64 MET Chi-restraints excluded: chain Q residue 271 MET Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 342 LEU Chi-restraints excluded: chain T residue 31 LYS Chi-restraints excluded: chain T residue 62 ASP Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 91 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 474 optimal weight: 1.9990 chunk 763 optimal weight: 0.9990 chunk 466 optimal weight: 0.6980 chunk 362 optimal weight: 0.8980 chunk 530 optimal weight: 2.9990 chunk 800 optimal weight: 4.9990 chunk 737 optimal weight: 50.0000 chunk 637 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 492 optimal weight: 9.9990 chunk 391 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 ASN e 85 ASN ** k 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 310 ASN o 267 GLN o 310 ASN u 39 GLN d 52 ASN p 310 ASN v 39 GLN v 64 ASN L 64 ASN Q 74 ASN V 39 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 67560 Z= 0.175 Angle : 0.570 30.830 91212 Z= 0.295 Chirality : 0.043 0.259 10356 Planarity : 0.004 0.043 11940 Dihedral : 4.079 28.820 9325 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.42 % Favored : 96.57 % Rotamer: Outliers : 2.16 % Allowed : 18.81 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.09), residues: 8184 helix: 2.42 (0.08), residues: 4328 sheet: 0.56 (0.13), residues: 1496 loop : -0.74 (0.12), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 92 HIS 0.002 0.001 HIS r 116 PHE 0.036 0.001 PHE d 37 TYR 0.033 0.001 TYR M 34 ARG 0.009 0.000 ARG M 65 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16368 Ramachandran restraints generated. 8184 Oldfield, 0 Emsley, 8184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16368 Ramachandran restraints generated. 8184 Oldfield, 0 Emsley, 8184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 945 residues out of total 7224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 789 time to evaluate : 5.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 ASN cc_start: 0.6921 (t0) cc_final: 0.6404 (t0) REVERT: B 45 GLN cc_start: 0.7346 (mt0) cc_final: 0.7125 (mt0) REVERT: B 87 LYS cc_start: 0.7370 (mmtt) cc_final: 0.7071 (tppt) REVERT: D 41 VAL cc_start: 0.7285 (t) cc_final: 0.6983 (p) REVERT: E 131 GLU cc_start: 0.7214 (tp30) cc_final: 0.6856 (tp30) REVERT: E 179 SER cc_start: 0.8026 (t) cc_final: 0.7656 (p) REVERT: E 242 ARG cc_start: 0.7577 (mmm-85) cc_final: 0.7128 (ptp-110) REVERT: F 131 GLU cc_start: 0.6749 (tp30) cc_final: 0.6216 (mp0) REVERT: F 343 VAL cc_start: 0.9642 (m) cc_final: 0.9374 (t) REVERT: G 75 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7885 (mp10) REVERT: G 241 GLN cc_start: 0.7956 (tm-30) cc_final: 0.7622 (tm-30) REVERT: G 311 GLN cc_start: 0.8069 (mp10) cc_final: 0.7845 (mp10) REVERT: H 58 PHE cc_start: 0.6426 (OUTLIER) cc_final: 0.6146 (t80) REVERT: I 84 LYS cc_start: 0.8008 (mtmt) cc_final: 0.7659 (mppt) REVERT: I 290 ASP cc_start: 0.8107 (t0) cc_final: 0.7810 (t0) REVERT: U 149 MET cc_start: 0.7293 (OUTLIER) cc_final: 0.7007 (mtt) REVERT: e 48 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8008 (tm-30) REVERT: e 76 LYS cc_start: 0.6707 (pttp) cc_final: 0.6432 (tmtt) REVERT: e 79 ASP cc_start: 0.7932 (m-30) cc_final: 0.7017 (t70) REVERT: f 76 LYS cc_start: 0.8694 (mmmt) cc_final: 0.7632 (pttp) REVERT: W 55 GLU cc_start: 0.6574 (tp30) cc_final: 0.5466 (tp30) REVERT: Y 43 ASN cc_start: 0.7205 (t0) cc_final: 0.6598 (t0) REVERT: Y 87 LYS cc_start: 0.7032 (OUTLIER) cc_final: 0.6622 (mtpt) REVERT: c 47 ARG cc_start: 0.6425 (tmm-80) cc_final: 0.6149 (tmm160) REVERT: c 91 GLU cc_start: 0.5910 (mm-30) cc_final: 0.5613 (mt-10) REVERT: g 149 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7507 (mtt) REVERT: g 331 MET cc_start: 0.8218 (mmm) cc_final: 0.7981 (mmm) REVERT: k 48 TYR cc_start: 0.5698 (OUTLIER) cc_final: 0.4992 (m-10) REVERT: k 77 ASP cc_start: 0.8055 (p0) cc_final: 0.7094 (t0) REVERT: k 314 MET cc_start: 0.8403 (ttt) cc_final: 0.8095 (ttm) REVERT: m 120 LYS cc_start: 0.8256 (ttmm) cc_final: 0.7902 (mttt) REVERT: o 117 VAL cc_start: 0.7308 (t) cc_final: 0.7077 (m) REVERT: q 149 MET cc_start: 0.7079 (ttm) cc_final: 0.6526 (mtp) REVERT: q 217 GLN cc_start: 0.7275 (OUTLIER) cc_final: 0.6584 (mm-40) REVERT: q 238 PHE cc_start: 0.8198 (t80) cc_final: 0.7786 (t80) REVERT: q 267 GLU cc_start: 0.7629 (tp30) cc_final: 0.7421 (tp30) REVERT: u 76 LYS cc_start: 0.8655 (mmmt) cc_final: 0.7958 (ptmt) REVERT: X 55 GLU cc_start: 0.5267 (tp30) cc_final: 0.4729 (tp30) REVERT: Z 30 ARG cc_start: 0.4419 (ptm160) cc_final: 0.4173 (ptt180) REVERT: Z 43 ASN cc_start: 0.7572 (t0) cc_final: 0.6798 (t0) REVERT: d 34 TYR cc_start: 0.6143 (t80) cc_final: 0.5877 (t80) REVERT: d 70 ILE cc_start: 0.5808 (mp) cc_final: 0.5420 (mm) REVERT: d 89 VAL cc_start: 0.5866 (t) cc_final: 0.5534 (p) REVERT: h 149 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7307 (mmm) REVERT: j 149 MET cc_start: 0.8291 (mpp) cc_final: 0.7739 (mtt) REVERT: j 161 MET cc_start: 0.7424 (mtm) cc_final: 0.7138 (mtt) REVERT: j 238 PHE cc_start: 0.8267 (t80) cc_final: 0.8031 (t80) REVERT: l 74 ASN cc_start: 0.7926 (m-40) cc_final: 0.7666 (m110) REVERT: l 237 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7395 (ttm170) REVERT: l 312 ASP cc_start: 0.8473 (p0) cc_final: 0.8173 (p0) REVERT: l 314 MET cc_start: 0.8531 (ttt) cc_final: 0.8252 (ttm) REVERT: p 84 LYS cc_start: 0.7846 (mtmt) cc_final: 0.7439 (mppt) REVERT: p 290 ASP cc_start: 0.7979 (t0) cc_final: 0.7645 (t0) REVERT: r 160 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7413 (mp0) REVERT: r 161 MET cc_start: 0.7640 (mmt) cc_final: 0.7306 (mmm) REVERT: r 201 MET cc_start: 0.8530 (ttt) cc_final: 0.8295 (ttp) REVERT: t 38 LEU cc_start: 0.8169 (mt) cc_final: 0.7834 (tt) REVERT: t 79 ASP cc_start: 0.7720 (m-30) cc_final: 0.6921 (t70) REVERT: v 76 LYS cc_start: 0.8821 (mmmt) cc_final: 0.8043 (ptmm) REVERT: J 55 GLU cc_start: 0.5674 (tp30) cc_final: 0.4798 (tp30) REVERT: K 43 ASN cc_start: 0.7484 (t0) cc_final: 0.6677 (t0) REVERT: K 87 LYS cc_start: 0.7606 (mmtt) cc_final: 0.7154 (tppt) REVERT: L 81 LEU cc_start: 0.7065 (mt) cc_final: 0.6303 (tt) REVERT: M 70 ILE cc_start: 0.6114 (mp) cc_final: 0.5575 (mm) REVERT: M 76 LYS cc_start: 0.6155 (pttm) cc_final: 0.5950 (tptt) REVERT: M 84 LYS cc_start: 0.6887 (mttp) cc_final: 0.6383 (mtpt) REVERT: N 331 MET cc_start: 0.8351 (mmm) cc_final: 0.8115 (mmm) REVERT: P 38 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8503 (mm) REVERT: P 212 GLN cc_start: 0.8007 (pt0) cc_final: 0.7446 (pt0) REVERT: P 241 GLN cc_start: 0.7977 (tm-30) cc_final: 0.7542 (tm-30) REVERT: Q 70 GLN cc_start: 0.8279 (mt0) cc_final: 0.7935 (mp10) REVERT: Q 100 PHE cc_start: 0.7586 (m-80) cc_final: 0.7182 (m-80) REVERT: R 18 MET cc_start: 0.6059 (tpt) cc_final: 0.5689 (tpp) REVERT: R 144 ARG cc_start: 0.7140 (tpt170) cc_final: 0.6887 (tpt90) REVERT: T 54 ARG cc_start: 0.6677 (tpt-90) cc_final: 0.6115 (tmm160) REVERT: V 33 ASP cc_start: 0.7482 (p0) cc_final: 0.7204 (p0) REVERT: V 76 LYS cc_start: 0.8919 (mmmt) cc_final: 0.8112 (pttt) outliers start: 156 outliers final: 136 residues processed: 886 average time/residue: 0.6026 time to fit residues: 911.7116 Evaluate side-chains 905 residues out of total 7224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 760 time to evaluate : 5.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 58 PHE Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain I residue 274 GLU Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain U residue 135 VAL Chi-restraints excluded: chain U residue 143 LEU Chi-restraints excluded: chain U residue 149 MET Chi-restraints excluded: chain U residue 190 SER Chi-restraints excluded: chain U residue 217 GLN Chi-restraints excluded: chain U residue 342 LEU Chi-restraints excluded: chain e residue 39 GLN Chi-restraints excluded: chain e residue 77 LEU Chi-restraints excluded: chain e residue 85 ASN Chi-restraints excluded: chain f residue 33 ASP Chi-restraints excluded: chain W residue 72 VAL Chi-restraints excluded: chain W residue 80 ASN Chi-restraints excluded: chain Y residue 58 VAL Chi-restraints excluded: chain Y residue 77 LEU Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain a residue 56 ILE Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 70 ILE Chi-restraints excluded: chain g residue 143 LEU Chi-restraints excluded: chain g residue 149 MET Chi-restraints excluded: chain g residue 167 VAL Chi-restraints excluded: chain g residue 343 VAL Chi-restraints excluded: chain i residue 114 PHE Chi-restraints excluded: chain i residue 184 LEU Chi-restraints excluded: chain i residue 196 ILE Chi-restraints excluded: chain i residue 220 LEU Chi-restraints excluded: chain i residue 275 VAL Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 48 TYR Chi-restraints excluded: chain k residue 72 MET Chi-restraints excluded: chain k residue 316 MET Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain o residue 22 VAL Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain o residue 131 ILE Chi-restraints excluded: chain o residue 192 VAL Chi-restraints excluded: chain o residue 217 THR Chi-restraints excluded: chain o residue 265 GLU Chi-restraints excluded: chain q residue 100 ILE Chi-restraints excluded: chain q residue 132 VAL Chi-restraints excluded: chain q residue 217 GLN Chi-restraints excluded: chain s residue 62 ASP Chi-restraints excluded: chain u residue 33 ASP Chi-restraints excluded: chain u residue 68 THR Chi-restraints excluded: chain u residue 72 VAL Chi-restraints excluded: chain u residue 77 LEU Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain Z residue 32 VAL Chi-restraints excluded: chain Z residue 58 VAL Chi-restraints excluded: chain Z residue 77 LEU Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain b residue 70 ILE Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain d residue 52 ASN Chi-restraints excluded: chain d residue 68 THR Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain h residue 149 MET Chi-restraints excluded: chain h residue 167 VAL Chi-restraints excluded: chain j residue 184 LEU Chi-restraints excluded: chain j residue 189 ASP Chi-restraints excluded: chain l residue 22 VAL Chi-restraints excluded: chain l residue 27 GLU Chi-restraints excluded: chain l residue 71 THR Chi-restraints excluded: chain l residue 72 MET Chi-restraints excluded: chain l residue 237 ARG Chi-restraints excluded: chain n residue 37 VAL Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 58 PHE Chi-restraints excluded: chain n residue 271 MET Chi-restraints excluded: chain n residue 314 MET Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 93 ILE Chi-restraints excluded: chain p residue 118 LEU Chi-restraints excluded: chain p residue 148 THR Chi-restraints excluded: chain p residue 201 LEU Chi-restraints excluded: chain p residue 217 THR Chi-restraints excluded: chain r residue 100 ILE Chi-restraints excluded: chain r residue 132 VAL Chi-restraints excluded: chain r residue 237 ASN Chi-restraints excluded: chain t residue 62 ASP Chi-restraints excluded: chain v residue 91 GLU Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 332 GLU Chi-restraints excluded: chain N residue 343 VAL Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain O residue 184 LEU Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain O residue 272 THR Chi-restraints excluded: chain O residue 342 LEU Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 321 ASP Chi-restraints excluded: chain Q residue 14 VAL Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 64 MET Chi-restraints excluded: chain Q residue 271 MET Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 342 LEU Chi-restraints excluded: chain T residue 31 LYS Chi-restraints excluded: chain T residue 62 ASP Chi-restraints excluded: chain V residue 40 GLU Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 91 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 506 optimal weight: 5.9990 chunk 679 optimal weight: 10.0000 chunk 195 optimal weight: 6.9990 chunk 588 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 177 optimal weight: 0.1980 chunk 638 optimal weight: 0.9980 chunk 267 optimal weight: 1.9990 chunk 655 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 ASN e 85 ASN ** c 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 310 ASN u 39 GLN d 52 ASN p 310 ASN v 39 GLN L 64 ASN V 39 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.148433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 114)---------------| | r_work = 0.3598 r_free = 0.3598 target = 0.108711 restraints weight = 131384.358| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.95 r_work: 0.3418 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.125 67560 Z= 0.180 Angle : 0.563 27.395 91212 Z= 0.293 Chirality : 0.043 0.209 10356 Planarity : 0.004 0.042 11940 Dihedral : 4.053 29.489 9325 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.40 % Favored : 96.59 % Rotamer: Outliers : 2.24 % Allowed : 18.77 % Favored : 78.99 % Cbeta Deviations : 0.01 % 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: 1.83 (0.09), residues: 8184 helix: 2.45 (0.08), residues: 4328 sheet: 0.58 (0.13), residues: 1496 loop : -0.73 (0.12), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 92 HIS 0.003 0.001 HIS r 116 PHE 0.020 0.001 PHE S 238 TYR 0.034 0.001 TYR M 34 ARG 0.010 0.000 ARG f 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17855.58 seconds wall clock time: 310 minutes 48.76 seconds (18648.76 seconds total)