Starting phenix.real_space_refine on Sat Mar 7 06:26:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z5s_39780/03_2026/8z5s_39780.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z5s_39780/03_2026/8z5s_39780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8z5s_39780/03_2026/8z5s_39780.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z5s_39780/03_2026/8z5s_39780.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z5s_39780/03_2026/8z5s_39780.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z5s_39780/03_2026/8z5s_39780.map" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.103 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 297 5.16 5 C 24262 2.51 5 N 6453 2.21 5 O 7324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38336 Number of models: 1 Model: "" Number of chains: 48 Chain: "1" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1599 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 10, 'TRANS': 196} Chain: "2" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1608 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 10, 'TRANS': 197} Chain: "3" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1608 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 10, 'TRANS': 197} Chain: "4" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 722 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 4, 'TRANS': 84} Chain: "5" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 722 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 4, 'TRANS': 84} Chain: "6" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 722 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 4, 'TRANS': 84} Chain: "7" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 722 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 4, 'TRANS': 84} Chain: "8" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1896 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 8, 'TRANS': 233} Chain breaks: 1 Chain: "AA" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 135 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 3, 'TRANS': 15} Chain: "AB" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 135 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 3, 'TRANS': 15} Chain: "AC" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 139 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 3, 'TRANS': 16} Chain: "AD" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 135 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 3, 'TRANS': 15} Chain: "AE" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 135 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 3, 'TRANS': 15} Chain: "AF" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 158 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 4, 'TRANS': 18} Chain: "AG" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 73 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 3, 'TRANS': 7} Chain: "AH" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 73 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 3, 'TRANS': 7} Chain: "AI" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 73 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 3, 'TRANS': 7} Chain: "AJ" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 163 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 4, 'TRANS': 19} Chain: "AK" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 169 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 4, 'TRANS': 20} Chain: "AL" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 220 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 4, 'TRANS': 27} Chain: "AM" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 224 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 4, 'TRANS': 28} Chain: "AN" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 224 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 4, 'TRANS': 28} Chain: "AO" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 220 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 4, 'TRANS': 27} Chain: "b" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 845 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain breaks: 1 Chain: "c" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 835 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain breaks: 1 Chain: "d" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 845 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain breaks: 1 Chain: "e" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 837 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain breaks: 1 Chain: "f" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 837 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain breaks: 1 Chain: "g" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 983 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain breaks: 1 Chain: "h" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 983 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain breaks: 1 Chain: "i" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 983 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain breaks: 1 Chain: "j" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 983 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain breaks: 1 Chain: "k" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 983 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain breaks: 1 Chain: "l" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 983 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain breaks: 1 Chain: "m" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1879 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 10, 'TRANS': 237} Chain: "n" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1879 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 10, 'TRANS': 237} Chain: "o" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1879 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 10, 'TRANS': 237} Chain: "p" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1879 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 10, 'TRANS': 237} Chain: "q" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1879 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 10, 'TRANS': 237} Chain: "r" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 560 Classifications: {'peptide': 72} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "s" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 605 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "t" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 605 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "u" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 560 Classifications: {'peptide': 72} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "v" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 560 Classifications: {'peptide': 72} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "w" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 311 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "x" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 552 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "y" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1608 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 10, 'TRANS': 197} Chain: "z" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1608 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 10, 'TRANS': 197} Time building chain proxies: 8.29, per 1000 atoms: 0.22 Number of scatterers: 38336 At special positions: 0 Unit cell: (135.6, 135.6, 253.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 297 16.00 O 7324 8.00 N 6453 7.00 C 24262 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 1.5 seconds 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9434 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 58 sheets defined 61.1% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain '1' and resid 84 through 97 removed outlier: 3.857A pdb=" N GLY 1 97 " --> pdb=" O MET 1 93 " (cutoff:3.500A) Processing helix chain '1' and resid 98 through 107 Processing helix chain '1' and resid 108 through 123 removed outlier: 3.744A pdb=" N ILE 1 112 " --> pdb=" O SER 1 108 " (cutoff:3.500A) Processing helix chain '1' and resid 130 through 146 removed outlier: 3.506A pdb=" N MET 1 146 " --> pdb=" O THR 1 142 " (cutoff:3.500A) Processing helix chain '1' and resid 146 through 157 Processing helix chain '1' and resid 157 through 163 Processing helix chain '1' and resid 167 through 186 Proline residue: 1 178 - end of helix Processing helix chain '1' and resid 188 through 200 Processing helix chain '1' and resid 205 through 209 removed outlier: 3.526A pdb=" N VAL 1 209 " --> pdb=" O PRO 1 206 " (cutoff:3.500A) Processing helix chain '1' and resid 210 through 251 Proline residue: 1 216 - end of helix Proline residue: 1 236 - end of helix removed outlier: 3.599A pdb=" N MET 1 251 " --> pdb=" O VAL 1 247 " (cutoff:3.500A) Processing helix chain '1' and resid 257 through 273 removed outlier: 3.803A pdb=" N VAL 1 261 " --> pdb=" O SER 1 257 " (cutoff:3.500A) Proline residue: 1 264 - end of helix Processing helix chain '1' and resid 274 through 287 removed outlier: 4.228A pdb=" N LEU 1 280 " --> pdb=" O TRP 1 276 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE 1 287 " --> pdb=" O LEU 1 283 " (cutoff:3.500A) Processing helix chain '2' and resid 84 through 98 removed outlier: 3.569A pdb=" N MET 2 95 " --> pdb=" O ALA 2 91 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU 2 96 " --> pdb=" O LEU 2 92 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY 2 97 " --> pdb=" O MET 2 93 " (cutoff:3.500A) Processing helix chain '2' and resid 98 through 107 removed outlier: 3.851A pdb=" N THR 2 107 " --> pdb=" O VAL 2 103 " (cutoff:3.500A) Processing helix chain '2' and resid 108 through 123 Processing helix chain '2' and resid 130 through 146 Processing helix chain '2' and resid 146 through 157 Processing helix chain '2' and resid 157 through 163 Processing helix chain '2' and resid 167 through 186 Proline residue: 2 178 - end of helix Processing helix chain '2' and resid 188 through 200 Processing helix chain '2' and resid 205 through 209 removed outlier: 3.623A pdb=" N ASP 2 208 " --> pdb=" O ASN 2 205 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL 2 209 " --> pdb=" O PRO 2 206 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 205 through 209' Processing helix chain '2' and resid 210 through 252 Proline residue: 2 216 - end of helix Proline residue: 2 236 - end of helix Processing helix chain '2' and resid 257 through 273 removed outlier: 3.542A pdb=" N VAL 2 261 " --> pdb=" O SER 2 257 " (cutoff:3.500A) Proline residue: 2 264 - end of helix Processing helix chain '2' and resid 274 through 287 removed outlier: 3.550A pdb=" N LEU 2 278 " --> pdb=" O ASP 2 274 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU 2 280 " --> pdb=" O TRP 2 276 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE 2 287 " --> pdb=" O LEU 2 283 " (cutoff:3.500A) Processing helix chain '3' and resid 84 through 98 Processing helix chain '3' and resid 98 through 106 Processing helix chain '3' and resid 108 through 123 Processing helix chain '3' and resid 130 through 146 removed outlier: 3.878A pdb=" N ILE 3 134 " --> pdb=" O SER 3 130 " (cutoff:3.500A) Processing helix chain '3' and resid 146 through 157 Processing helix chain '3' and resid 157 through 163 Processing helix chain '3' and resid 167 through 186 Proline residue: 3 178 - end of helix Processing helix chain '3' and resid 188 through 200 Processing helix chain '3' and resid 205 through 209 removed outlier: 3.517A pdb=" N ASP 3 208 " --> pdb=" O ASN 3 205 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL 3 209 " --> pdb=" O PRO 3 206 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 205 through 209' Processing helix chain '3' and resid 210 through 251 Proline residue: 3 216 - end of helix Proline residue: 3 236 - end of helix Processing helix chain '3' and resid 257 through 273 removed outlier: 4.217A pdb=" N VAL 3 261 " --> pdb=" O SER 3 257 " (cutoff:3.500A) Proline residue: 3 264 - end of helix removed outlier: 3.808A pdb=" N VAL 3 273 " --> pdb=" O LEU 3 269 " (cutoff:3.500A) Processing helix chain '3' and resid 274 through 285 Processing helix chain '4' and resid 2 through 43 removed outlier: 4.372A pdb=" N ILE 4 24 " --> pdb=" O MET 4 20 " (cutoff:3.500A) Proline residue: 4 27 - end of helix Processing helix chain '4' and resid 50 through 89 removed outlier: 5.263A pdb=" N HIS 4 67 " --> pdb=" O MET 4 63 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N TRP 4 68 " --> pdb=" O LEU 4 64 " (cutoff:3.500A) Proline residue: 4 85 - end of helix Processing helix chain '5' and resid 2 through 42 Proline residue: 5 27 - end of helix Processing helix chain '5' and resid 51 through 65 Processing helix chain '5' and resid 65 through 88 Proline residue: 5 85 - end of helix Processing helix chain '6' and resid 2 through 43 Proline residue: 6 27 - end of helix Processing helix chain '6' and resid 51 through 65 Processing helix chain '6' and resid 65 through 83 Processing helix chain '6' and resid 83 through 89 removed outlier: 3.836A pdb=" N VAL 6 87 " --> pdb=" O ARG 6 83 " (cutoff:3.500A) Processing helix chain '7' and resid 2 through 43 Proline residue: 7 27 - end of helix Processing helix chain '7' and resid 47 through 50 removed outlier: 3.780A pdb=" N SER 7 50 " --> pdb=" O GLN 7 47 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 47 through 50' Processing helix chain '7' and resid 51 through 65 Processing helix chain '7' and resid 65 through 88 Proline residue: 7 85 - end of helix Processing helix chain '8' and resid 3 through 29 removed outlier: 4.261A pdb=" N VAL 8 7 " --> pdb=" O TYR 8 3 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TRP 8 17 " --> pdb=" O ALA 8 13 " (cutoff:3.500A) Proline residue: 8 18 - end of helix removed outlier: 3.567A pdb=" N ARG 8 21 " --> pdb=" O TRP 8 17 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL 8 28 " --> pdb=" O SER 8 24 " (cutoff:3.500A) Processing helix chain '8' and resid 38 through 53 Processing helix chain '8' and resid 54 through 57 Processing helix chain '8' and resid 68 through 107 Processing helix chain '8' and resid 126 through 141 Processing helix chain '8' and resid 142 through 158 removed outlier: 3.604A pdb=" N LYS 8 156 " --> pdb=" O VAL 8 152 " (cutoff:3.500A) Processing helix chain '8' and resid 166 through 175 Processing helix chain '8' and resid 175 through 206 removed outlier: 3.732A pdb=" N ILE 8 179 " --> pdb=" O GLY 8 175 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N SER 8 190 " --> pdb=" O SER 8 186 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLY 8 191 " --> pdb=" O MET 8 187 " (cutoff:3.500A) Processing helix chain '8' and resid 214 through 236 removed outlier: 3.597A pdb=" N GLY 8 236 " --> pdb=" O TYR 8 232 " (cutoff:3.500A) Processing helix chain '8' and resid 236 through 256 removed outlier: 4.167A pdb=" N HIS 8 240 " --> pdb=" O GLY 8 236 " (cutoff:3.500A) Processing helix chain 'AF' and resid 349 through 355 removed outlier: 3.866A pdb=" N VALAF 353 " --> pdb=" O ILEAF 349 " (cutoff:3.500A) Processing helix chain 'AK' and resid 343 through 347 Processing helix chain 'AL' and resid 350 through 357 removed outlier: 3.569A pdb=" N LYSAL 357 " --> pdb=" O VALAL 353 " (cutoff:3.500A) Processing helix chain 'AM' and resid 343 through 347 Processing helix chain 'AM' and resid 350 through 359 removed outlier: 4.121A pdb=" N ASPAM 358 " --> pdb=" O ALAAM 354 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLYAM 359 " --> pdb=" O GLNAM 355 " (cutoff:3.500A) Processing helix chain 'AN' and resid 337 through 342 removed outlier: 3.513A pdb=" N ASNAN 341 " --> pdb=" O GLYAN 337 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLNAN 342 " --> pdb=" O ALAAN 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'AN' and resid 337 through 342' Processing helix chain 'AN' and resid 343 through 347 Processing helix chain 'AN' and resid 350 through 355 Processing helix chain 'AN' and resid 356 through 358 No H-bonds generated for 'chain 'AN' and resid 356 through 358' Processing helix chain 'AO' and resid 350 through 357 removed outlier: 3.574A pdb=" N METAO 356 " --> pdb=" O ASPAO 352 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYSAO 357 " --> pdb=" O VALAO 353 " (cutoff:3.500A) Processing helix chain 'b' and resid 4 through 10 Processing helix chain 'b' and resid 11 through 32 removed outlier: 3.810A pdb=" N VAL b 16 " --> pdb=" O HIS b 12 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY b 17 " --> pdb=" O GLN b 13 " (cutoff:3.500A) Processing helix chain 'b' and resid 44 through 54 Processing helix chain 'b' and resid 95 through 130 removed outlier: 3.540A pdb=" N ASN b 101 " --> pdb=" O ASP b 97 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE b 121 " --> pdb=" O LEU b 117 " (cutoff:3.500A) Processing helix chain 'c' and resid 4 through 10 Processing helix chain 'c' and resid 11 through 32 removed outlier: 3.911A pdb=" N VAL c 16 " --> pdb=" O HIS c 12 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLY c 17 " --> pdb=" O GLN c 13 " (cutoff:3.500A) Processing helix chain 'c' and resid 44 through 53 removed outlier: 3.641A pdb=" N GLU c 48 " --> pdb=" O ASP c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 95 through 130 removed outlier: 3.504A pdb=" N ASN c 101 " --> pdb=" O ASP c 97 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE c 121 " --> pdb=" O LEU c 117 " (cutoff:3.500A) Processing helix chain 'd' and resid 4 through 10 Processing helix chain 'd' and resid 11 through 32 removed outlier: 3.788A pdb=" N VAL d 16 " --> pdb=" O HIS d 12 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N GLY d 17 " --> pdb=" O GLN d 13 " (cutoff:3.500A) Processing helix chain 'd' and resid 44 through 54 Processing helix chain 'd' and resid 95 through 130 removed outlier: 3.821A pdb=" N ASN d 101 " --> pdb=" O ASP d 97 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE d 121 " --> pdb=" O LEU d 117 " (cutoff:3.500A) Processing helix chain 'e' and resid 4 through 9 Processing helix chain 'e' and resid 11 through 32 removed outlier: 3.591A pdb=" N VAL e 16 " --> pdb=" O HIS e 12 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLY e 17 " --> pdb=" O GLN e 13 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 54 Processing helix chain 'e' and resid 95 through 130 removed outlier: 3.561A pdb=" N PHE e 121 " --> pdb=" O LEU e 117 " (cutoff:3.500A) Processing helix chain 'f' and resid 4 through 10 Processing helix chain 'f' and resid 11 through 32 removed outlier: 3.783A pdb=" N VAL f 16 " --> pdb=" O HIS f 12 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLY f 17 " --> pdb=" O GLN f 13 " (cutoff:3.500A) Processing helix chain 'f' and resid 44 through 54 Processing helix chain 'f' and resid 95 through 130 removed outlier: 3.521A pdb=" N PHE f 121 " --> pdb=" O LEU f 117 " (cutoff:3.500A) Processing helix chain 'g' and resid 4 through 30 Processing helix chain 'g' and resid 100 through 134 removed outlier: 3.509A pdb=" N GLN g 127 " --> pdb=" O ASP g 123 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN g 134 " --> pdb=" O LEU g 130 " (cutoff:3.500A) Processing helix chain 'h' and resid 3 through 30 removed outlier: 3.517A pdb=" N PHE h 7 " --> pdb=" O LEU h 3 " (cutoff:3.500A) Processing helix chain 'h' and resid 100 through 134 removed outlier: 3.526A pdb=" N ASN h 118 " --> pdb=" O ALA h 114 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL h 119 " --> pdb=" O TYR h 115 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN h 134 " --> pdb=" O LEU h 130 " (cutoff:3.500A) Processing helix chain 'i' and resid 3 through 29 removed outlier: 3.834A pdb=" N PHE i 7 " --> pdb=" O LEU i 3 " (cutoff:3.500A) Processing helix chain 'i' and resid 100 through 135 removed outlier: 3.506A pdb=" N VAL i 119 " --> pdb=" O TYR i 115 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL i 121 " --> pdb=" O THR i 117 " (cutoff:3.500A) Processing helix chain 'j' and resid 3 through 30 removed outlier: 3.666A pdb=" N PHE j 7 " --> pdb=" O LEU j 3 " (cutoff:3.500A) Processing helix chain 'j' and resid 100 through 134 removed outlier: 3.573A pdb=" N VAL j 119 " --> pdb=" O TYR j 115 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL j 121 " --> pdb=" O THR j 117 " (cutoff:3.500A) Processing helix chain 'k' and resid 4 through 30 removed outlier: 3.672A pdb=" N ASN k 8 " --> pdb=" O PHE k 4 " (cutoff:3.500A) Processing helix chain 'k' and resid 100 through 134 removed outlier: 3.538A pdb=" N ALA k 106 " --> pdb=" O MET k 102 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL k 119 " --> pdb=" O TYR k 115 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 30 Processing helix chain 'l' and resid 100 through 134 Processing helix chain 'm' and resid 3 through 28 removed outlier: 3.527A pdb=" N ASN m 25 " --> pdb=" O LEU m 21 " (cutoff:3.500A) Processing helix chain 'm' and resid 154 through 158 removed outlier: 4.080A pdb=" N PHE m 158 " --> pdb=" O ALA m 155 " (cutoff:3.500A) Processing helix chain 'm' and resid 170 through 172 No H-bonds generated for 'chain 'm' and resid 170 through 172' Processing helix chain 'm' and resid 210 through 243 removed outlier: 3.854A pdb=" N ARG m 223 " --> pdb=" O ILE m 219 " (cutoff:3.500A) Processing helix chain 'm' and resid 244 through 247 Processing helix chain 'n' and resid 3 through 28 removed outlier: 3.538A pdb=" N GLY n 11 " --> pdb=" O LEU n 7 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN n 14 " --> pdb=" O SER n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 170 through 172 No H-bonds generated for 'chain 'n' and resid 170 through 172' Processing helix chain 'n' and resid 210 through 242 removed outlier: 3.888A pdb=" N ASP n 220 " --> pdb=" O THR n 216 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG n 223 " --> pdb=" O ILE n 219 " (cutoff:3.500A) Processing helix chain 'n' and resid 243 through 246 removed outlier: 4.000A pdb=" N LEU n 246 " --> pdb=" O ASP n 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 243 through 246' Processing helix chain 'o' and resid 3 through 28 removed outlier: 3.747A pdb=" N GLY o 11 " --> pdb=" O LEU o 7 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN o 25 " --> pdb=" O LEU o 21 " (cutoff:3.500A) Processing helix chain 'o' and resid 170 through 172 No H-bonds generated for 'chain 'o' and resid 170 through 172' Processing helix chain 'o' and resid 210 through 243 removed outlier: 3.752A pdb=" N ASP o 220 " --> pdb=" O THR o 216 " (cutoff:3.500A) Processing helix chain 'p' and resid 3 through 28 removed outlier: 3.581A pdb=" N GLY p 11 " --> pdb=" O LEU p 7 " (cutoff:3.500A) Processing helix chain 'p' and resid 154 through 158 removed outlier: 4.118A pdb=" N PHE p 158 " --> pdb=" O ALA p 155 " (cutoff:3.500A) Processing helix chain 'p' and resid 170 through 172 No H-bonds generated for 'chain 'p' and resid 170 through 172' Processing helix chain 'p' and resid 210 through 244 removed outlier: 3.589A pdb=" N SER p 241 " --> pdb=" O GLU p 237 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER p 244 " --> pdb=" O LYS p 240 " (cutoff:3.500A) Processing helix chain 'p' and resid 245 through 248 removed outlier: 4.184A pdb=" N MET p 248 " --> pdb=" O LEU p 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 245 through 248' Processing helix chain 'q' and resid 3 through 28 removed outlier: 3.506A pdb=" N GLY q 11 " --> pdb=" O LEU q 7 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN q 25 " --> pdb=" O LEU q 21 " (cutoff:3.500A) Processing helix chain 'q' and resid 170 through 172 No H-bonds generated for 'chain 'q' and resid 170 through 172' Processing helix chain 'q' and resid 210 through 242 Processing helix chain 'q' and resid 243 through 247 removed outlier: 3.777A pdb=" N LEU q 246 " --> pdb=" O ASP q 243 " (cutoff:3.500A) Processing helix chain 'r' and resid 33 through 60 Processing helix chain 'r' and resid 66 through 100 Processing helix chain 's' and resid 25 through 61 removed outlier: 3.873A pdb=" N VAL s 29 " --> pdb=" O SER s 25 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY s 61 " --> pdb=" O ARG s 57 " (cutoff:3.500A) Processing helix chain 's' and resid 66 through 100 removed outlier: 3.552A pdb=" N ASN s 100 " --> pdb=" O LYS s 96 " (cutoff:3.500A) Processing helix chain 't' and resid 25 through 61 Processing helix chain 't' and resid 66 through 100 Processing helix chain 'u' and resid 33 through 61 Processing helix chain 'u' and resid 66 through 100 Processing helix chain 'v' and resid 33 through 60 removed outlier: 4.245A pdb=" N LEU v 37 " --> pdb=" O PHE v 33 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR v 38 " --> pdb=" O ASN v 34 " (cutoff:3.500A) Processing helix chain 'v' and resid 66 through 100 Processing helix chain 'w' and resid 66 through 100 Processing helix chain 'x' and resid 37 through 66 removed outlier: 3.880A pdb=" N TRP x 48 " --> pdb=" O ILE x 44 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU x 51 " --> pdb=" O MET x 47 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA x 52 " --> pdb=" O TRP x 48 " (cutoff:3.500A) Processing helix chain 'x' and resid 68 through 73 Processing helix chain 'x' and resid 74 through 106 removed outlier: 3.651A pdb=" N PHE x 91 " --> pdb=" O THR x 87 " (cutoff:3.500A) Proline residue: x 92 - end of helix removed outlier: 3.573A pdb=" N ALA x 103 " --> pdb=" O THR x 99 " (cutoff:3.500A) Processing helix chain 'y' and resid 84 through 98 Processing helix chain 'y' and resid 98 through 107 removed outlier: 3.743A pdb=" N THR y 107 " --> pdb=" O VAL y 103 " (cutoff:3.500A) Processing helix chain 'y' and resid 108 through 123 Processing helix chain 'y' and resid 130 through 146 Processing helix chain 'y' and resid 146 through 158 Processing helix chain 'y' and resid 158 through 163 Processing helix chain 'y' and resid 167 through 186 Proline residue: y 178 - end of helix removed outlier: 3.574A pdb=" N GLN y 186 " --> pdb=" O PHE y 182 " (cutoff:3.500A) Processing helix chain 'y' and resid 188 through 200 Processing helix chain 'y' and resid 210 through 251 Proline residue: y 216 - end of helix Proline residue: y 236 - end of helix Processing helix chain 'y' and resid 257 through 273 removed outlier: 4.088A pdb=" N VAL y 261 " --> pdb=" O SER y 257 " (cutoff:3.500A) Proline residue: y 264 - end of helix Processing helix chain 'y' and resid 274 through 287 removed outlier: 3.866A pdb=" N PHE y 287 " --> pdb=" O LEU y 283 " (cutoff:3.500A) Processing helix chain 'z' and resid 84 through 98 removed outlier: 3.619A pdb=" N GLY z 97 " --> pdb=" O MET z 93 " (cutoff:3.500A) Processing helix chain 'z' and resid 98 through 107 removed outlier: 3.704A pdb=" N THR z 107 " --> pdb=" O VAL z 103 " (cutoff:3.500A) Processing helix chain 'z' and resid 108 through 123 Processing helix chain 'z' and resid 130 through 146 Processing helix chain 'z' and resid 146 through 157 Processing helix chain 'z' and resid 157 through 163 Processing helix chain 'z' and resid 167 through 186 Proline residue: z 178 - end of helix Processing helix chain 'z' and resid 188 through 200 Processing helix chain 'z' and resid 205 through 209 Processing helix chain 'z' and resid 210 through 251 Proline residue: z 216 - end of helix Proline residue: z 236 - end of helix Processing helix chain 'z' and resid 257 through 273 removed outlier: 3.842A pdb=" N VAL z 261 " --> pdb=" O SER z 257 " (cutoff:3.500A) Proline residue: z 264 - end of helix Processing helix chain 'z' and resid 274 through 286 removed outlier: 4.213A pdb=" N LEU z 280 " --> pdb=" O TRP z 276 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'AA' and resid 339 through 340 removed outlier: 4.245A pdb=" N LEU b 79 " --> pdb=" O GLY b 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'AB' and resid 339 through 340 Processing sheet with id=AA3, first strand: chain 'AC' and resid 339 through 340 Processing sheet with id=AA4, first strand: chain 'AD' and resid 339 through 340 Processing sheet with id=AA5, first strand: chain 'AE' and resid 339 through 340 Processing sheet with id=AA6, first strand: chain 'AK' and resid 331 through 334 removed outlier: 3.522A pdb=" N ALA g 51 " --> pdb=" O VALAK 332 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLY g 69 " --> pdb=" O VAL g 48 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLY g 50 " --> pdb=" O VAL g 67 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N VAL g 67 " --> pdb=" O GLY g 50 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLU g 52 " --> pdb=" O VAL g 65 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N VAL g 65 " --> pdb=" O GLU g 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'AL' and resid 332 through 334 removed outlier: 4.145A pdb=" N GLY h 69 " --> pdb=" O VAL h 48 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY h 50 " --> pdb=" O VAL h 67 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL h 67 " --> pdb=" O GLY h 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'AM' and resid 332 through 334 removed outlier: 4.426A pdb=" N GLY l 69 " --> pdb=" O VAL l 48 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY l 50 " --> pdb=" O VAL l 67 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N VAL l 67 " --> pdb=" O GLY l 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'AN' and resid 332 through 334 removed outlier: 4.435A pdb=" N GLY j 69 " --> pdb=" O VAL j 48 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLY j 50 " --> pdb=" O VAL j 67 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL j 67 " --> pdb=" O GLY j 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'AO' and resid 331 through 334 removed outlier: 4.356A pdb=" N GLY k 69 " --> pdb=" O VAL k 48 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLY k 50 " --> pdb=" O VAL k 67 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N VAL k 67 " --> pdb=" O GLY k 50 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N GLU k 52 " --> pdb=" O VAL k 65 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N VAL k 65 " --> pdb=" O GLU k 52 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'g' and resid 78 through 81 Processing sheet with id=AB3, first strand: chain 'h' and resid 35 through 36 removed outlier: 7.220A pdb=" N SER h 35 " --> pdb=" O SER o 43 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N GLN o 45 " --> pdb=" O SER h 35 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'h' and resid 78 through 81 Processing sheet with id=AB5, first strand: chain 'i' and resid 35 through 36 removed outlier: 7.528A pdb=" N SER i 35 " --> pdb=" O SER n 43 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N GLN n 45 " --> pdb=" O SER i 35 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'i' and resid 45 through 51 removed outlier: 3.830A pdb=" N VAL i 48 " --> pdb=" O GLY i 69 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLY i 69 " --> pdb=" O VAL i 48 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLY i 50 " --> pdb=" O VAL i 67 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N VAL i 67 " --> pdb=" O GLY i 50 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'i' and resid 78 through 81 Processing sheet with id=AB8, first strand: chain 'j' and resid 33 through 36 removed outlier: 6.346A pdb=" N ALA m 41 " --> pdb=" O SER j 33 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'j' and resid 78 through 81 Processing sheet with id=AC1, first strand: chain 'k' and resid 35 through 36 removed outlier: 7.239A pdb=" N SER k 35 " --> pdb=" O SER p 43 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N GLN p 45 " --> pdb=" O SER k 35 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'k' and resid 78 through 81 Processing sheet with id=AC3, first strand: chain 'l' and resid 35 through 36 removed outlier: 3.673A pdb=" N SER q 43 " --> pdb=" O SER l 35 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'l' and resid 78 through 81 Processing sheet with id=AC5, first strand: chain 'm' and resid 71 through 73 Processing sheet with id=AC6, first strand: chain 'm' and resid 80 through 83 removed outlier: 4.666A pdb=" N SER m 198 " --> pdb=" O GLU m 83 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'm' and resid 97 through 100 Processing sheet with id=AC8, first strand: chain 'm' and resid 97 through 100 Processing sheet with id=AC9, first strand: chain 'm' and resid 105 through 107 Processing sheet with id=AD1, first strand: chain 'm' and resid 135 through 140 removed outlier: 3.908A pdb=" N LYS m 137 " --> pdb=" O LEU m 149 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP m 162 " --> pdb=" O ILE m 146 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL m 148 " --> pdb=" O ALA m 160 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ALA m 160 " --> pdb=" O VAL m 148 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'm' and resid 174 through 176 Processing sheet with id=AD3, first strand: chain 'n' and resid 36 through 37 removed outlier: 3.726A pdb=" N ALA n 36 " --> pdb=" O ASN n 65 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'n' and resid 71 through 73 Processing sheet with id=AD5, first strand: chain 'n' and resid 80 through 83 removed outlier: 4.613A pdb=" N SER n 198 " --> pdb=" O GLU n 83 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'n' and resid 97 through 100 Processing sheet with id=AD7, first strand: chain 'n' and resid 97 through 100 Processing sheet with id=AD8, first strand: chain 'n' and resid 106 through 107 Processing sheet with id=AD9, first strand: chain 'n' and resid 135 through 140 removed outlier: 3.746A pdb=" N LYS n 137 " --> pdb=" O LEU n 149 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP n 162 " --> pdb=" O ILE n 146 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL n 148 " --> pdb=" O ALA n 160 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ALA n 160 " --> pdb=" O VAL n 148 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'n' and resid 174 through 176 Processing sheet with id=AE2, first strand: chain 'o' and resid 71 through 73 Processing sheet with id=AE3, first strand: chain 'o' and resid 82 through 83 removed outlier: 4.773A pdb=" N SER o 198 " --> pdb=" O GLU o 83 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'o' and resid 97 through 100 Processing sheet with id=AE5, first strand: chain 'o' and resid 97 through 100 Processing sheet with id=AE6, first strand: chain 'o' and resid 105 through 107 Processing sheet with id=AE7, first strand: chain 'o' and resid 135 through 140 removed outlier: 3.801A pdb=" N LYS o 137 " --> pdb=" O LEU o 149 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP o 162 " --> pdb=" O ILE o 146 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL o 148 " --> pdb=" O ALA o 160 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ALA o 160 " --> pdb=" O VAL o 148 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'o' and resid 174 through 176 Processing sheet with id=AE9, first strand: chain 'p' and resid 71 through 73 Processing sheet with id=AF1, first strand: chain 'p' and resid 80 through 83 removed outlier: 4.821A pdb=" N SER p 198 " --> pdb=" O GLU p 83 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'p' and resid 97 through 100 Processing sheet with id=AF3, first strand: chain 'p' and resid 97 through 100 Processing sheet with id=AF4, first strand: chain 'p' and resid 106 through 107 Processing sheet with id=AF5, first strand: chain 'p' and resid 135 through 140 removed outlier: 6.309A pdb=" N LEU p 149 " --> pdb=" O SER p 136 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE p 138 " --> pdb=" O SER p 147 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N SER p 147 " --> pdb=" O ILE p 138 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILE p 140 " --> pdb=" O THR p 145 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N THR p 145 " --> pdb=" O ILE p 140 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP p 162 " --> pdb=" O ILE p 146 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL p 148 " --> pdb=" O ALA p 160 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ALA p 160 " --> pdb=" O VAL p 148 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'p' and resid 174 through 176 Processing sheet with id=AF7, first strand: chain 'q' and resid 71 through 73 Processing sheet with id=AF8, first strand: chain 'q' and resid 80 through 83 removed outlier: 3.565A pdb=" N THR q 81 " --> pdb=" O GLN q 200 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER q 198 " --> pdb=" O GLU q 83 " (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 97 through 100 Processing sheet with id=AG2, first strand: chain 'q' and resid 105 through 107 Processing sheet with id=AG3, first strand: chain 'q' and resid 135 through 140 removed outlier: 3.795A pdb=" N LYS q 137 " --> pdb=" O LEU q 149 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP q 162 " --> pdb=" O ILE q 146 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL q 148 " --> pdb=" O ALA q 160 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ALA q 160 " --> pdb=" O VAL q 148 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'q' and resid 174 through 176 2477 hydrogen bonds defined for protein. 7296 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: 7.17 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6572 1.31 - 1.44: 9243 1.44 - 1.56: 22523 1.56 - 1.69: 0 1.69 - 1.81: 588 Bond restraints: 38926 Sorted by residual: bond pdb=" C PRO 6 85 " pdb=" O PRO 6 85 " ideal model delta sigma weight residual 1.238 1.185 0.053 1.33e-02 5.65e+03 1.62e+01 bond pdb=" C PHE b 5 " pdb=" O PHE b 5 " ideal model delta sigma weight residual 1.237 1.197 0.039 1.19e-02 7.06e+03 1.09e+01 bond pdb=" C PROAI 343 " pdb=" O PROAI 343 " ideal model delta sigma weight residual 1.240 1.206 0.035 1.12e-02 7.97e+03 9.51e+00 bond pdb=" N ASPAL 358 " pdb=" CA ASPAL 358 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.43e+00 bond pdb=" C PHE r 33 " pdb=" O PHE r 33 " ideal model delta sigma weight residual 1.237 1.270 -0.034 1.17e-02 7.31e+03 8.30e+00 ... (remaining 38921 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 51692 1.61 - 3.22: 818 3.22 - 4.83: 139 4.83 - 6.43: 41 6.43 - 8.04: 5 Bond angle restraints: 52695 Sorted by residual: angle pdb=" CA SER i 37 " pdb=" C SER i 37 " pdb=" O SER i 37 " ideal model delta sigma weight residual 121.56 116.28 5.28 1.09e+00 8.42e-01 2.34e+01 angle pdb=" C GLNAF 351 " pdb=" N ASPAF 352 " pdb=" CA ASPAF 352 " ideal model delta sigma weight residual 120.58 112.54 8.04 1.71e+00 3.42e-01 2.21e+01 angle pdb=" N GLN 6 86 " pdb=" CA GLN 6 86 " pdb=" C GLN 6 86 " ideal model delta sigma weight residual 111.28 106.15 5.13 1.09e+00 8.42e-01 2.21e+01 angle pdb=" C ASPAF 352 " pdb=" N VALAF 353 " pdb=" CA VALAF 353 " ideal model delta sigma weight residual 120.62 113.73 6.89 1.64e+00 3.72e-01 1.77e+01 angle pdb=" N GLU 2 193 " pdb=" CA GLU 2 193 " pdb=" C GLU 2 193 " ideal model delta sigma weight residual 111.36 106.78 4.58 1.09e+00 8.42e-01 1.76e+01 ... (remaining 52690 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 22490 17.98 - 35.97: 1031 35.97 - 53.95: 238 53.95 - 71.93: 62 71.93 - 89.92: 10 Dihedral angle restraints: 23831 sinusoidal: 9356 harmonic: 14475 Sorted by residual: dihedral pdb=" C PROAF 343 " pdb=" N PROAF 343 " pdb=" CA PROAF 343 " pdb=" CB PROAF 343 " ideal model delta harmonic sigma weight residual -120.70 -112.57 -8.13 0 2.50e+00 1.60e-01 1.06e+01 dihedral pdb=" CA LYS j 126 " pdb=" CB LYS j 126 " pdb=" CG LYS j 126 " pdb=" CD LYS j 126 " ideal model delta sinusoidal sigma weight residual -60.00 -119.51 59.51 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N GLNAH 342 " pdb=" CA GLNAH 342 " pdb=" CB GLNAH 342 " pdb=" CG GLNAH 342 " ideal model delta sinusoidal sigma weight residual -60.00 -119.39 59.39 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 23828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4980 0.045 - 0.090: 956 0.090 - 0.135: 256 0.135 - 0.180: 16 0.180 - 0.225: 11 Chirality restraints: 6219 Sorted by residual: chirality pdb=" CA VALAK 332 " pdb=" N VALAK 332 " pdb=" C VALAK 332 " pdb=" CB VALAK 332 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA GLU i 52 " pdb=" N GLU i 52 " pdb=" C GLU i 52 " pdb=" CB GLU i 52 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA GLN 6 71 " pdb=" N GLN 6 71 " pdb=" C GLN 6 71 " pdb=" CB GLN 6 71 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 6216 not shown) Planarity restraints: 6827 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL 5 87 " 0.027 2.00e-02 2.50e+03 5.31e-02 2.82e+01 pdb=" C VAL 5 87 " -0.092 2.00e-02 2.50e+03 pdb=" O VAL 5 87 " 0.034 2.00e-02 2.50e+03 pdb=" N LEU 5 88 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG 2 188 " -0.376 9.50e-02 1.11e+02 1.69e-01 1.74e+01 pdb=" NE ARG 2 188 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG 2 188 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG 2 188 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG 2 188 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYSAL 357 " 0.021 2.00e-02 2.50e+03 4.13e-02 1.70e+01 pdb=" C LYSAL 357 " -0.071 2.00e-02 2.50e+03 pdb=" O LYSAL 357 " 0.026 2.00e-02 2.50e+03 pdb=" N ASPAL 358 " 0.024 2.00e-02 2.50e+03 ... (remaining 6824 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 849 2.69 - 3.25: 39043 3.25 - 3.80: 60329 3.80 - 4.35: 81376 4.35 - 4.90: 135912 Nonbonded interactions: 317509 Sorted by model distance: nonbonded pdb=" OE1 GLN y 88 " pdb=" OH TYR y 161 " model vdw 2.143 3.040 nonbonded pdb=" O ILEAO 335 " pdb=" OG SERAO 340 " model vdw 2.144 3.040 nonbonded pdb=" O VAL y 103 " pdb=" OG1 THR y 107 " model vdw 2.151 3.040 nonbonded pdb=" O GLU i 52 " pdb=" CG GLU i 52 " model vdw 2.154 3.440 nonbonded pdb=" O VAL z 103 " pdb=" OG1 THR z 107 " model vdw 2.169 3.040 ... (remaining 317504 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 '1' selection = (chain '2' and resid 82 through 288) selection = (chain '3' and resid 82 through 288) selection = (chain 'y' and resid 82 through 288) selection = (chain 'z' and resid 82 through 288) } ncs_group { reference = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' } ncs_group { reference = chain 'AA' selection = chain 'AB' selection = (chain 'AC' and resid 338 through 356) selection = chain 'AD' selection = chain 'AE' } ncs_group { reference = (chain 'AF' and resid 334 through 354) selection = (chain 'AJ' and resid 334 through 354) selection = (chain 'AK' and resid 334 through 354) } ncs_group { reference = chain 'AG' selection = chain 'AH' selection = chain 'AI' } ncs_group { reference = chain 'AL' selection = (chain 'AM' and resid 330 through 361) selection = (chain 'AN' and resid 330 through 361) selection = chain 'AO' } ncs_group { reference = (chain 'b' and (resid 2 through 53 or resid 78 through 131)) selection = (chain 'c' and (resid 2 through 53 or resid 78 through 131)) selection = (chain 'd' and (resid 2 through 53 or resid 78 through 131)) selection = (chain 'e' and (resid 2 through 53 or resid 78 through 131)) selection = (chain 'f' and (resid 2 through 53 or resid 78 through 131)) } ncs_group { reference = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } ncs_group { reference = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' } ncs_group { reference = chain 'r' selection = (chain 's' and resid 32 through 103) selection = (chain 't' and resid 32 through 103) selection = chain 'u' selection = chain 'v' } 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: 18.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 31.760 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.130 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: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 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 0.053 38926 Z= 0.171 Angle : 0.522 8.043 52695 Z= 0.309 Chirality : 0.039 0.225 6219 Planarity : 0.004 0.169 6827 Dihedral : 11.419 89.917 14397 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.00 % Favored : 97.94 % Rotamer: Outliers : 3.53 % Allowed : 6.91 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.12), residues: 4896 helix: 1.52 (0.09), residues: 2901 sheet: -1.01 (0.25), residues: 397 loop : 0.00 (0.15), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG m 42 TYR 0.010 0.001 TYR 8 3 PHE 0.011 0.001 PHE 8 215 TRP 0.008 0.001 TRP x 48 HIS 0.002 0.000 HIS 8 144 Details of bonding type rmsd covalent geometry : bond 0.00281 (38926) covalent geometry : angle 0.52157 (52695) hydrogen bonds : bond 0.21721 ( 2457) hydrogen bonds : angle 6.43770 ( 7296) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1329 residues out of total 4223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 1180 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 83 TYR cc_start: 0.7196 (m-10) cc_final: 0.6889 (m-10) REVERT: 1 172 PHE cc_start: 0.6223 (t80) cc_final: 0.5858 (t80) REVERT: 1 180 LYS cc_start: 0.7813 (ttpp) cc_final: 0.7556 (tttm) REVERT: 1 249 MET cc_start: 0.8283 (tpt) cc_final: 0.8075 (tpp) REVERT: 1 255 MET cc_start: 0.7685 (tpp) cc_final: 0.7112 (mmt) REVERT: 2 156 LYS cc_start: 0.8589 (mptp) cc_final: 0.8321 (mtpp) REVERT: 2 163 ASN cc_start: 0.7917 (m-40) cc_final: 0.7366 (m110) REVERT: 2 173 ASP cc_start: 0.8330 (m-30) cc_final: 0.8118 (m-30) REVERT: 2 186 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7387 (mp10) REVERT: 2 287 PHE cc_start: 0.7336 (m-80) cc_final: 0.7078 (m-80) REVERT: 3 86 THR cc_start: 0.9088 (m) cc_final: 0.8676 (p) REVERT: 3 102 MET cc_start: 0.8534 (mtp) cc_final: 0.8288 (mtt) REVERT: 3 179 MET cc_start: 0.6315 (mmt) cc_final: 0.5964 (mtt) REVERT: 3 186 GLN cc_start: 0.8390 (mm110) cc_final: 0.7845 (mp10) REVERT: 3 187 THR cc_start: 0.8638 (t) cc_final: 0.8390 (m) REVERT: 4 63 MET cc_start: 0.6223 (tmm) cc_final: 0.6019 (mmm) REVERT: 5 76 TYR cc_start: 0.8082 (t80) cc_final: 0.7859 (t80) REVERT: 5 89 TYR cc_start: 0.4523 (OUTLIER) cc_final: 0.4255 (p90) REVERT: 7 15 TRP cc_start: 0.6733 (t-100) cc_final: 0.6348 (t-100) REVERT: 7 49 LEU cc_start: 0.8219 (tp) cc_final: 0.7980 (tp) REVERT: 8 70 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.7259 (ttp-110) REVERT: 8 105 MET cc_start: 0.6832 (tpp) cc_final: 0.6575 (mmt) REVERT: 8 246 THR cc_start: 0.7946 (m) cc_final: 0.7643 (p) REVERT: AB 356 MET cc_start: 0.7867 (tpt) cc_final: 0.7612 (mmt) REVERT: AF 346 ASP cc_start: 0.4493 (OUTLIER) cc_final: 0.3869 (m-30) REVERT: AF 352 ASP cc_start: 0.4379 (OUTLIER) cc_final: 0.4112 (m-30) REVERT: AJ 342 GLN cc_start: 0.7506 (mm110) cc_final: 0.7239 (mm-40) REVERT: AM 331 MET cc_start: 0.7662 (ttp) cc_final: 0.7445 (ttm) REVERT: AN 339 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8546 (mp) REVERT: AO 330 ASN cc_start: 0.8272 (OUTLIER) cc_final: 0.7554 (p0) REVERT: AO 356 MET cc_start: 0.8855 (mtm) cc_final: 0.8539 (mtp) REVERT: b 90 ASP cc_start: 0.7224 (p0) cc_final: 0.7006 (p0) REVERT: b 129 LYS cc_start: 0.8338 (mtpt) cc_final: 0.8126 (mtpp) REVERT: c 21 ARG cc_start: 0.7584 (mtp180) cc_final: 0.7301 (mtp85) REVERT: d 4 SER cc_start: 0.8293 (OUTLIER) cc_final: 0.8025 (p) REVERT: d 6 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7999 (m-30) REVERT: d 7 ASN cc_start: 0.8446 (OUTLIER) cc_final: 0.8157 (m110) REVERT: d 84 THR cc_start: 0.9137 (t) cc_final: 0.8904 (m) REVERT: d 90 ASP cc_start: 0.8527 (p0) cc_final: 0.8316 (p0) REVERT: d 101 ASN cc_start: 0.8514 (t0) cc_final: 0.8270 (t0) REVERT: d 115 ASP cc_start: 0.8677 (m-30) cc_final: 0.8473 (m-30) REVERT: d 119 SER cc_start: 0.8606 (t) cc_final: 0.8316 (m) REVERT: e 7 ASN cc_start: 0.8196 (OUTLIER) cc_final: 0.7914 (m110) REVERT: e 27 SER cc_start: 0.8643 (t) cc_final: 0.8237 (p) REVERT: e 87 ASP cc_start: 0.8402 (p0) cc_final: 0.8170 (p0) REVERT: e 126 LYS cc_start: 0.7802 (ttpt) cc_final: 0.7383 (tttp) REVERT: f 47 LYS cc_start: 0.7529 (ttmm) cc_final: 0.7083 (ttpp) REVERT: g 39 LYS cc_start: 0.6162 (OUTLIER) cc_final: 0.5788 (ptpt) REVERT: g 78 SER cc_start: 0.8579 (t) cc_final: 0.8054 (m) REVERT: g 134 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7475 (mt0) REVERT: g 135 MET cc_start: 0.8341 (ttm) cc_final: 0.7896 (ttm) REVERT: h 14 MET cc_start: 0.8989 (mtm) cc_final: 0.8771 (mtm) REVERT: h 17 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7505 (mm-30) REVERT: i 42 TYR cc_start: 0.7709 (t80) cc_final: 0.7375 (t80) REVERT: i 66 LYS cc_start: 0.7777 (pttt) cc_final: 0.7482 (pttm) REVERT: i 105 MET cc_start: 0.8510 (mmm) cc_final: 0.8281 (mmm) REVERT: i 110 SER cc_start: 0.8546 (t) cc_final: 0.8320 (m) REVERT: i 123 ASP cc_start: 0.8202 (t70) cc_final: 0.7821 (t0) REVERT: i 131 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.8124 (mmm160) REVERT: j 80 GLU cc_start: 0.7712 (mt-10) cc_final: 0.6675 (tp30) REVERT: j 95 TYR cc_start: 0.8827 (m-80) cc_final: 0.8582 (m-80) REVERT: k 101 VAL cc_start: 0.8424 (t) cc_final: 0.8209 (m) REVERT: k 113 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7717 (mmp-170) REVERT: k 123 ASP cc_start: 0.8711 (t70) cc_final: 0.8396 (t0) REVERT: l 14 MET cc_start: 0.9103 (mtp) cc_final: 0.8772 (mtm) REVERT: l 91 GLU cc_start: 0.7306 (mm-30) cc_final: 0.6868 (mt-10) REVERT: l 108 MET cc_start: 0.8875 (ttm) cc_final: 0.8611 (ttp) REVERT: m 58 MET cc_start: 0.8983 (mtp) cc_final: 0.8678 (mtm) REVERT: m 60 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.6466 (pp20) REVERT: m 72 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7902 (mm) REVERT: m 226 GLU cc_start: 0.8424 (mt-10) cc_final: 0.7094 (mm-30) REVERT: m 238 MET cc_start: 0.8657 (mtm) cc_final: 0.8176 (mtp) REVERT: n 40 GLN cc_start: 0.8444 (pt0) cc_final: 0.8241 (pt0) REVERT: n 60 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.6794 (mt-10) REVERT: n 204 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8448 (tp) REVERT: o 158 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.7434 (m-80) REVERT: o 188 ASN cc_start: 0.8692 (m110) cc_final: 0.8471 (m-40) REVERT: o 201 THR cc_start: 0.8404 (t) cc_final: 0.8186 (m) REVERT: o 215 MET cc_start: 0.8435 (mmm) cc_final: 0.7847 (mtm) REVERT: o 222 GLN cc_start: 0.8445 (mt0) cc_final: 0.8129 (mt0) REVERT: o 232 MET cc_start: 0.8786 (mtp) cc_final: 0.8547 (mtm) REVERT: o 240 LYS cc_start: 0.8173 (mttt) cc_final: 0.7705 (mtpp) REVERT: p 96 LYS cc_start: 0.7779 (ttmm) cc_final: 0.7408 (tttm) REVERT: p 135 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8536 (pp) REVERT: p 157 GLU cc_start: 0.6790 (mt-10) cc_final: 0.6246 (tm-30) REVERT: p 163 ARG cc_start: 0.8440 (ttt-90) cc_final: 0.8211 (tpt-90) REVERT: p 172 GLN cc_start: 0.7966 (mm-40) cc_final: 0.7633 (mp10) REVERT: p 215 MET cc_start: 0.8039 (mmt) cc_final: 0.7761 (mtt) REVERT: r 34 ASN cc_start: 0.4162 (OUTLIER) cc_final: 0.3217 (t0) REVERT: r 39 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7148 (tttm) REVERT: r 99 MET cc_start: 0.8677 (mmm) cc_final: 0.8393 (mmm) REVERT: r 101 MET cc_start: 0.7318 (mtm) cc_final: 0.6929 (mtt) REVERT: s 87 ILE cc_start: 0.7533 (mt) cc_final: 0.7029 (pt) REVERT: s 96 LYS cc_start: 0.7483 (mttt) cc_final: 0.7226 (mttp) REVERT: s 99 MET cc_start: 0.7135 (ppp) cc_final: 0.6355 (ppp) REVERT: s 101 MET cc_start: 0.7131 (ptm) cc_final: 0.6831 (ptp) REVERT: t 67 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8344 (tp) REVERT: t 71 MET cc_start: 0.9047 (mmt) cc_final: 0.8720 (mmm) REVERT: u 78 SER cc_start: 0.8394 (t) cc_final: 0.7841 (m) REVERT: v 99 MET cc_start: 0.9234 (mmt) cc_final: 0.8872 (mmt) REVERT: v 101 MET cc_start: 0.8646 (mtm) cc_final: 0.8369 (mtt) REVERT: y 83 TYR cc_start: 0.8420 (m-80) cc_final: 0.8217 (m-80) REVERT: y 104 ILE cc_start: 0.8830 (tt) cc_final: 0.8538 (pt) REVERT: y 143 PHE cc_start: 0.8050 (t80) cc_final: 0.7822 (t80) REVERT: y 180 LYS cc_start: 0.8169 (ttmt) cc_final: 0.7896 (tttt) REVERT: y 255 MET cc_start: 0.6346 (mmm) cc_final: 0.5734 (mmm) REVERT: y 265 PHE cc_start: 0.8407 (m-80) cc_final: 0.7804 (m-80) REVERT: z 172 PHE cc_start: 0.8315 (t80) cc_final: 0.8094 (t80) REVERT: z 179 MET cc_start: 0.8048 (tpp) cc_final: 0.7689 (tpp) REVERT: z 232 MET cc_start: 0.7338 (mmt) cc_final: 0.7107 (mmm) REVERT: z 277 ASN cc_start: 0.7535 (m-40) cc_final: 0.7090 (m-40) outliers start: 149 outliers final: 40 residues processed: 1280 average time/residue: 0.2267 time to fit residues: 477.7312 Evaluate side-chains 951 residues out of total 4223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 888 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 127 GLN Chi-restraints excluded: chain 1 residue 208 ASP Chi-restraints excluded: chain 2 residue 149 VAL Chi-restraints excluded: chain 2 residue 272 LEU Chi-restraints excluded: chain 3 residue 133 VAL Chi-restraints excluded: chain 3 residue 149 VAL Chi-restraints excluded: chain 5 residue 45 ASN Chi-restraints excluded: chain 5 residue 89 TYR Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 8 residue 70 ARG Chi-restraints excluded: chain 8 residue 125 LEU Chi-restraints excluded: chain 8 residue 192 ILE Chi-restraints excluded: chain 8 residue 212 LEU Chi-restraints excluded: chain 8 residue 214 ILE Chi-restraints excluded: chain AD residue 349 ILE Chi-restraints excluded: chain AF residue 346 ASP Chi-restraints excluded: chain AF residue 352 ASP Chi-restraints excluded: chain AN residue 339 LEU Chi-restraints excluded: chain AN residue 352 ASP Chi-restraints excluded: chain AO residue 330 ASN Chi-restraints excluded: chain c residue 6 ASP Chi-restraints excluded: chain c residue 87 ASP Chi-restraints excluded: chain d residue 4 SER Chi-restraints excluded: chain d residue 6 ASP Chi-restraints excluded: chain d residue 7 ASN Chi-restraints excluded: chain e residue 7 ASN Chi-restraints excluded: chain e residue 88 THR Chi-restraints excluded: chain g residue 39 LYS Chi-restraints excluded: chain g residue 53 LEU Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain g residue 134 GLN Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain h residue 34 VAL Chi-restraints excluded: chain h residue 65 VAL Chi-restraints excluded: chain i residue 36 SER Chi-restraints excluded: chain i residue 131 ARG Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain k residue 40 ASP Chi-restraints excluded: chain k residue 53 LEU Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain k residue 113 ARG Chi-restraints excluded: chain l residue 40 ASP Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 65 VAL Chi-restraints excluded: chain m residue 7 LEU Chi-restraints excluded: chain m residue 60 GLU Chi-restraints excluded: chain m residue 72 ILE Chi-restraints excluded: chain n residue 60 GLU Chi-restraints excluded: chain n residue 158 PHE Chi-restraints excluded: chain n residue 204 ILE Chi-restraints excluded: chain o residue 158 PHE Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain r residue 34 ASN Chi-restraints excluded: chain r residue 39 LYS Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain x residue 48 TRP Chi-restraints excluded: chain y residue 86 THR Chi-restraints excluded: chain z residue 86 THR Chi-restraints excluded: chain z residue 113 VAL Chi-restraints excluded: chain z residue 128 THR Chi-restraints excluded: chain z residue 184 LEU Chi-restraints excluded: chain z residue 272 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 7.9990 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.0370 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 4.9990 chunk 470 optimal weight: 0.9990 overall best weight: 2.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 88 GLN 1 127 GLN 1 228 GLN 3 186 GLN 4 47 GLN 6 39 GLN 6 47 GLN 7 39 GLN 7 86 GLN 8 90 GLN 8 94 GLN 8 182 GLN 8 211 GLN AB 355 GLN AJ 342 GLN AL 341 ASN AM 355 GLN AN 342 GLN AO 342 GLN b 105 GLN b 123 ASN c 32 GLN c 106 ASN c 111 GLN c 123 ASN d 105 GLN d 107 GLN e 101 ASN e 105 GLN e 107 GLN f 34 ASN f 105 GLN g 30 ASN g 46 HIS g 100 ASN g 118 ASN ** h 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 100 ASN i 116 GLN j 22 ASN j 100 ASN j 118 ASN j 127 GLN k 22 ASN k 100 ASN k 118 ASN l 22 ASN l 100 ASN l 118 ASN m 110 ASN m 179 ASN ** n 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 125 ASN p 28 ASN p 119 HIS q 20 GLN ** r 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 48 GLN r 86 GLN s 45 ASN s 86 GLN t 45 ASN t 75 ASN u 86 GLN v 55 GLN y 163 ASN y 228 GLN z 126 GLN z 127 GLN z 176 GLN Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.143892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.118615 restraints weight = 47222.865| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.45 r_work: 0.3220 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 38926 Z= 0.187 Angle : 0.608 10.143 52695 Z= 0.311 Chirality : 0.043 0.240 6219 Planarity : 0.004 0.042 6827 Dihedral : 6.139 61.887 5364 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.00 % Favored : 97.98 % Rotamer: Outliers : 3.88 % Allowed : 11.30 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.12), residues: 4896 helix: 2.42 (0.09), residues: 2890 sheet: -0.95 (0.25), residues: 403 loop : 0.08 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG h 20 TYR 0.017 0.002 TYR 4 76 PHE 0.021 0.002 PHE 8 221 TRP 0.013 0.001 TRP x 48 HIS 0.005 0.001 HIS p 51 Details of bonding type rmsd covalent geometry : bond 0.00428 (38926) covalent geometry : angle 0.60816 (52695) hydrogen bonds : bond 0.06116 ( 2457) hydrogen bonds : angle 4.26796 ( 7296) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1057 residues out of total 4223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 893 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 106 MET cc_start: 0.7608 (mtt) cc_final: 0.7368 (mtm) REVERT: 1 249 MET cc_start: 0.8185 (tpt) cc_final: 0.7775 (tpp) REVERT: 1 255 MET cc_start: 0.8134 (tpp) cc_final: 0.7260 (mmt) REVERT: 2 156 LYS cc_start: 0.8681 (mptp) cc_final: 0.8311 (mtpp) REVERT: 2 173 ASP cc_start: 0.8466 (m-30) cc_final: 0.8251 (m-30) REVERT: 2 180 LYS cc_start: 0.7486 (mtpp) cc_final: 0.7123 (mtpt) REVERT: 2 185 LYS cc_start: 0.7584 (tppp) cc_final: 0.7292 (tptp) REVERT: 2 190 LYS cc_start: 0.7463 (mmtm) cc_final: 0.7121 (mppt) REVERT: 2 255 MET cc_start: 0.8698 (mmp) cc_final: 0.8446 (mmm) REVERT: 3 86 THR cc_start: 0.9061 (m) cc_final: 0.8760 (p) REVERT: 3 179 MET cc_start: 0.6910 (mmt) cc_final: 0.6336 (mtt) REVERT: 3 185 LYS cc_start: 0.7837 (mptt) cc_final: 0.7542 (mttt) REVERT: 3 253 MET cc_start: 0.7329 (ptm) cc_final: 0.6726 (ptm) REVERT: 4 63 MET cc_start: 0.6708 (tmm) cc_final: 0.5682 (mmm) REVERT: 5 26 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8495 (mp) REVERT: 5 84 LEU cc_start: 0.7740 (tp) cc_final: 0.7491 (tp) REVERT: 6 5 MET cc_start: 0.7419 (ttt) cc_final: 0.7082 (mtt) REVERT: 7 4 GLU cc_start: 0.8658 (mp0) cc_final: 0.8439 (mp0) REVERT: 7 15 TRP cc_start: 0.7135 (t-100) cc_final: 0.6424 (t-100) REVERT: 8 70 ARG cc_start: 0.7104 (OUTLIER) cc_final: 0.6686 (ttp-170) REVERT: AD 352 ASP cc_start: 0.8369 (m-30) cc_final: 0.8104 (m-30) REVERT: AK 339 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8272 (mp) REVERT: AM 331 MET cc_start: 0.8238 (ttp) cc_final: 0.8027 (ttm) REVERT: AN 339 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8810 (mp) REVERT: AO 330 ASN cc_start: 0.8456 (p0) cc_final: 0.7808 (p0) REVERT: AO 356 MET cc_start: 0.9255 (mtm) cc_final: 0.9008 (mtp) REVERT: c 90 ASP cc_start: 0.7459 (m-30) cc_final: 0.6920 (m-30) REVERT: d 84 THR cc_start: 0.9305 (t) cc_final: 0.9023 (m) REVERT: d 90 ASP cc_start: 0.8864 (p0) cc_final: 0.8555 (p0) REVERT: e 7 ASN cc_start: 0.8772 (OUTLIER) cc_final: 0.8500 (m110) REVERT: e 126 LYS cc_start: 0.8689 (ttpt) cc_final: 0.8457 (tttp) REVERT: f 47 LYS cc_start: 0.8256 (ttmm) cc_final: 0.7897 (ttpp) REVERT: g 39 LYS cc_start: 0.5823 (OUTLIER) cc_final: 0.5429 (ptpt) REVERT: g 43 LYS cc_start: 0.8763 (mttp) cc_final: 0.8442 (mttm) REVERT: g 78 SER cc_start: 0.8661 (t) cc_final: 0.8136 (m) REVERT: g 134 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7929 (mt0) REVERT: g 135 MET cc_start: 0.8803 (ttm) cc_final: 0.8229 (ttm) REVERT: i 42 TYR cc_start: 0.8165 (t80) cc_final: 0.7875 (t80) REVERT: i 66 LYS cc_start: 0.7872 (pttt) cc_final: 0.7523 (pttp) REVERT: i 102 MET cc_start: 0.7620 (mmp) cc_final: 0.6839 (mpp) REVERT: i 131 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8331 (mmm160) REVERT: j 80 GLU cc_start: 0.8405 (mt-10) cc_final: 0.7440 (tp30) REVERT: l 14 MET cc_start: 0.9090 (mtp) cc_final: 0.8801 (mtm) REVERT: l 91 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7925 (mt-10) REVERT: l 108 MET cc_start: 0.8978 (ttm) cc_final: 0.8721 (ttp) REVERT: l 113 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.8717 (mmp-170) REVERT: m 58 MET cc_start: 0.8817 (mtp) cc_final: 0.8573 (mtm) REVERT: m 60 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8466 (pm20) REVERT: m 72 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8320 (mm) REVERT: m 238 MET cc_start: 0.8777 (mtm) cc_final: 0.8442 (mtp) REVERT: n 60 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.6765 (mt-10) REVERT: n 157 GLU cc_start: 0.5938 (OUTLIER) cc_final: 0.5724 (mt-10) REVERT: n 215 MET cc_start: 0.8554 (mmm) cc_final: 0.8279 (mtm) REVERT: o 158 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7606 (m-80) REVERT: o 201 THR cc_start: 0.8625 (t) cc_final: 0.8412 (m) REVERT: o 215 MET cc_start: 0.8415 (mmm) cc_final: 0.7879 (mtt) REVERT: o 222 GLN cc_start: 0.8450 (mt0) cc_final: 0.8208 (mt0) REVERT: p 96 LYS cc_start: 0.8092 (ttmm) cc_final: 0.7871 (tttm) REVERT: p 135 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8710 (pp) REVERT: p 157 GLU cc_start: 0.7465 (mt-10) cc_final: 0.6457 (tm-30) REVERT: q 162 ASP cc_start: 0.8369 (t70) cc_final: 0.7932 (t70) REVERT: q 238 MET cc_start: 0.9011 (mtp) cc_final: 0.8777 (mtp) REVERT: r 34 ASN cc_start: 0.4364 (OUTLIER) cc_final: 0.3494 (t0) REVERT: r 101 MET cc_start: 0.7787 (mtm) cc_final: 0.7436 (mtt) REVERT: s 96 LYS cc_start: 0.7598 (mttt) cc_final: 0.7301 (mttp) REVERT: t 62 ASP cc_start: 0.8230 (m-30) cc_final: 0.7647 (m-30) REVERT: t 67 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8090 (tt) REVERT: u 69 ASP cc_start: 0.7697 (m-30) cc_final: 0.7371 (m-30) REVERT: u 78 SER cc_start: 0.8701 (t) cc_final: 0.8083 (m) REVERT: y 83 TYR cc_start: 0.8829 (m-80) cc_final: 0.8555 (m-80) REVERT: y 104 ILE cc_start: 0.8848 (tt) cc_final: 0.8523 (pt) REVERT: y 180 LYS cc_start: 0.8445 (ttmt) cc_final: 0.8104 (tttt) REVERT: y 255 MET cc_start: 0.7212 (mmm) cc_final: 0.6280 (mmm) REVERT: y 265 PHE cc_start: 0.8594 (m-80) cc_final: 0.7986 (m-80) REVERT: z 183 MET cc_start: 0.8858 (mtm) cc_final: 0.8576 (mtp) REVERT: z 222 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7713 (mm-30) REVERT: z 232 MET cc_start: 0.7786 (mmt) cc_final: 0.7214 (mmt) REVERT: z 255 MET cc_start: 0.8615 (mmm) cc_final: 0.7584 (mmm) outliers start: 164 outliers final: 89 residues processed: 1002 average time/residue: 0.2187 time to fit residues: 363.9962 Evaluate side-chains 929 residues out of total 4223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 822 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 128 THR Chi-restraints excluded: chain 1 residue 208 ASP Chi-restraints excluded: chain 2 residue 149 VAL Chi-restraints excluded: chain 3 residue 110 THR Chi-restraints excluded: chain 3 residue 133 VAL Chi-restraints excluded: chain 3 residue 145 VAL Chi-restraints excluded: chain 3 residue 149 VAL Chi-restraints excluded: chain 4 residue 12 GLU Chi-restraints excluded: chain 5 residue 26 ILE Chi-restraints excluded: chain 5 residue 45 ASN Chi-restraints excluded: chain 6 residue 17 VAL Chi-restraints excluded: chain 6 residue 31 ILE Chi-restraints excluded: chain 6 residue 87 VAL Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 70 ARG Chi-restraints excluded: chain 8 residue 125 LEU Chi-restraints excluded: chain 8 residue 131 MET Chi-restraints excluded: chain 8 residue 192 ILE Chi-restraints excluded: chain 8 residue 212 LEU Chi-restraints excluded: chain 8 residue 214 ILE Chi-restraints excluded: chain AC residue 353 VAL Chi-restraints excluded: chain AE residue 348 SER Chi-restraints excluded: chain AJ residue 356 MET Chi-restraints excluded: chain AK residue 339 LEU Chi-restraints excluded: chain AN residue 331 MET Chi-restraints excluded: chain AN residue 339 LEU Chi-restraints excluded: chain AN residue 342 GLN Chi-restraints excluded: chain AO residue 339 LEU Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain c residue 6 ASP Chi-restraints excluded: chain c residue 97 ASP Chi-restraints excluded: chain c residue 98 LEU Chi-restraints excluded: chain e residue 7 ASN Chi-restraints excluded: chain e residue 88 THR Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain g residue 39 LYS Chi-restraints excluded: chain g residue 53 LEU Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain g residue 134 GLN Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain h residue 34 VAL Chi-restraints excluded: chain h residue 65 VAL Chi-restraints excluded: chain h residue 68 MET Chi-restraints excluded: chain h residue 71 VAL Chi-restraints excluded: chain h residue 112 SER Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 73 SER Chi-restraints excluded: chain i residue 78 SER Chi-restraints excluded: chain i residue 124 SER Chi-restraints excluded: chain i residue 131 ARG Chi-restraints excluded: chain j residue 3 LEU Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 101 VAL Chi-restraints excluded: chain k residue 40 ASP Chi-restraints excluded: chain k residue 53 LEU Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain l residue 3 LEU Chi-restraints excluded: chain l residue 40 ASP Chi-restraints excluded: chain l residue 65 VAL Chi-restraints excluded: chain l residue 87 LEU Chi-restraints excluded: chain l residue 113 ARG Chi-restraints excluded: chain m residue 60 GLU Chi-restraints excluded: chain m residue 72 ILE Chi-restraints excluded: chain m residue 94 THR Chi-restraints excluded: chain n residue 10 SER Chi-restraints excluded: chain n residue 60 GLU Chi-restraints excluded: chain n residue 85 SER Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain n residue 107 VAL Chi-restraints excluded: chain n residue 157 GLU Chi-restraints excluded: chain n residue 158 PHE Chi-restraints excluded: chain o residue 43 SER Chi-restraints excluded: chain o residue 81 THR Chi-restraints excluded: chain o residue 94 THR Chi-restraints excluded: chain o residue 158 PHE Chi-restraints excluded: chain o residue 233 SER Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain p residue 196 THR Chi-restraints excluded: chain p residue 212 VAL Chi-restraints excluded: chain q residue 16 MET Chi-restraints excluded: chain q residue 81 THR Chi-restraints excluded: chain q residue 204 ILE Chi-restraints excluded: chain q residue 212 VAL Chi-restraints excluded: chain q residue 241 SER Chi-restraints excluded: chain r residue 34 ASN Chi-restraints excluded: chain s residue 46 THR Chi-restraints excluded: chain s residue 51 SER Chi-restraints excluded: chain s residue 98 LEU Chi-restraints excluded: chain t residue 37 LEU Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain v residue 38 THR Chi-restraints excluded: chain v residue 51 SER Chi-restraints excluded: chain v residue 103 VAL Chi-restraints excluded: chain w residue 66 SER Chi-restraints excluded: chain x residue 48 TRP Chi-restraints excluded: chain y residue 141 LEU Chi-restraints excluded: chain y residue 147 SER Chi-restraints excluded: chain y residue 167 THR Chi-restraints excluded: chain y residue 198 MET Chi-restraints excluded: chain y residue 271 VAL Chi-restraints excluded: chain z residue 86 THR Chi-restraints excluded: chain z residue 113 VAL Chi-restraints excluded: chain z residue 128 THR Chi-restraints excluded: chain z residue 184 LEU Chi-restraints excluded: chain z residue 222 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 408 optimal weight: 1.9990 chunk 182 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 chunk 469 optimal weight: 4.9990 chunk 268 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 282 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 176 GLN 2 228 GLN 8 106 GLN 8 149 GLN 8 251 GLN AB 355 GLN AD 351 GLN AJ 355 GLN AN 342 GLN c 123 ASN d 34 ASN ** h 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 46 HIS h 127 GLN ** i 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 134 GLN n 15 ASN n 51 HIS ** n 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 125 ASN p 20 GLN ** r 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 163 ASN z 176 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.144267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.119292 restraints weight = 46919.239| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.46 r_work: 0.3228 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 38926 Z= 0.135 Angle : 0.527 8.208 52695 Z= 0.266 Chirality : 0.040 0.190 6219 Planarity : 0.004 0.033 6827 Dihedral : 5.451 60.939 5317 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.92 % Favored : 98.06 % Rotamer: Outliers : 3.79 % Allowed : 12.48 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.12), residues: 4896 helix: 2.73 (0.09), residues: 2888 sheet: -1.00 (0.24), residues: 403 loop : 0.19 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG n 54 TYR 0.011 0.001 TYR 4 76 PHE 0.019 0.001 PHE 1 182 TRP 0.015 0.001 TRP 8 245 HIS 0.003 0.001 HIS p 51 Details of bonding type rmsd covalent geometry : bond 0.00297 (38926) covalent geometry : angle 0.52696 (52695) hydrogen bonds : bond 0.05117 ( 2457) hydrogen bonds : angle 3.91678 ( 7296) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1045 residues out of total 4223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 885 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 156 LYS cc_start: 0.6808 (mmmt) cc_final: 0.6559 (mtpp) REVERT: 1 249 MET cc_start: 0.8127 (tpt) cc_final: 0.7839 (tpp) REVERT: 2 156 LYS cc_start: 0.8652 (mptp) cc_final: 0.8277 (mtpp) REVERT: 2 173 ASP cc_start: 0.8490 (m-30) cc_final: 0.8257 (m-30) REVERT: 2 180 LYS cc_start: 0.7421 (mtpp) cc_final: 0.6996 (mttt) REVERT: 2 255 MET cc_start: 0.8673 (mmp) cc_final: 0.8346 (mmm) REVERT: 3 86 THR cc_start: 0.9052 (OUTLIER) cc_final: 0.8694 (p) REVERT: 3 121 GLN cc_start: 0.8362 (tp40) cc_final: 0.7853 (tt0) REVERT: 3 179 MET cc_start: 0.6915 (mmt) cc_final: 0.6334 (mtt) REVERT: 3 185 LYS cc_start: 0.7911 (mptt) cc_final: 0.7634 (mttt) REVERT: 3 255 MET cc_start: 0.7332 (tpt) cc_final: 0.7087 (tpp) REVERT: 4 63 MET cc_start: 0.6702 (tmm) cc_final: 0.5630 (mmm) REVERT: 7 15 TRP cc_start: 0.7152 (t-100) cc_final: 0.6454 (t-100) REVERT: 8 70 ARG cc_start: 0.7014 (OUTLIER) cc_final: 0.6136 (ttt-90) REVERT: 8 105 MET cc_start: 0.7542 (tpp) cc_final: 0.7335 (mmt) REVERT: 8 173 MET cc_start: 0.7206 (mmm) cc_final: 0.6568 (mmm) REVERT: AD 352 ASP cc_start: 0.8453 (m-30) cc_final: 0.8140 (m-30) REVERT: AJ 342 GLN cc_start: 0.7335 (mm-40) cc_final: 0.6699 (mt0) REVERT: AJ 356 MET cc_start: 0.4187 (OUTLIER) cc_final: 0.3970 (tpt) REVERT: AK 331 MET cc_start: 0.7826 (ttm) cc_final: 0.7338 (ttm) REVERT: AK 339 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8318 (mp) REVERT: AO 330 ASN cc_start: 0.8423 (p0) cc_final: 0.7831 (p0) REVERT: AO 356 MET cc_start: 0.9248 (mtm) cc_final: 0.8980 (mtp) REVERT: c 90 ASP cc_start: 0.7474 (m-30) cc_final: 0.6862 (m-30) REVERT: c 100 ARG cc_start: 0.8908 (mtt90) cc_final: 0.8676 (mtt180) REVERT: d 84 THR cc_start: 0.9331 (t) cc_final: 0.9071 (m) REVERT: d 90 ASP cc_start: 0.8851 (p0) cc_final: 0.8432 (p0) REVERT: e 7 ASN cc_start: 0.8786 (OUTLIER) cc_final: 0.8541 (m110) REVERT: e 115 ASP cc_start: 0.8181 (m-30) cc_final: 0.7860 (m-30) REVERT: f 47 LYS cc_start: 0.8173 (ttmm) cc_final: 0.7826 (ttpp) REVERT: g 39 LYS cc_start: 0.5845 (OUTLIER) cc_final: 0.5422 (ptpt) REVERT: g 78 SER cc_start: 0.8665 (t) cc_final: 0.8115 (m) REVERT: g 80 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7318 (tp30) REVERT: g 134 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7867 (mt0) REVERT: g 135 MET cc_start: 0.8773 (ttm) cc_final: 0.8199 (ttm) REVERT: i 42 TYR cc_start: 0.8392 (t80) cc_final: 0.8165 (t80) REVERT: i 66 LYS cc_start: 0.7830 (pttt) cc_final: 0.7485 (pttp) REVERT: i 102 MET cc_start: 0.7441 (mmp) cc_final: 0.6771 (mpp) REVERT: i 127 GLN cc_start: 0.8168 (mt0) cc_final: 0.7932 (mm-40) REVERT: i 131 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8363 (mmm160) REVERT: j 80 GLU cc_start: 0.8410 (mt-10) cc_final: 0.7477 (tp30) REVERT: k 132 THR cc_start: 0.9132 (m) cc_final: 0.8919 (m) REVERT: l 14 MET cc_start: 0.9078 (mtp) cc_final: 0.8860 (mtm) REVERT: l 53 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9000 (pp) REVERT: l 91 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7852 (mt-10) REVERT: l 108 MET cc_start: 0.8938 (ttm) cc_final: 0.8624 (ttp) REVERT: l 113 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8621 (mmp-170) REVERT: m 60 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8409 (pm20) REVERT: m 172 GLN cc_start: 0.8462 (mm-40) cc_final: 0.8068 (mm-40) REVERT: m 238 MET cc_start: 0.8699 (mtm) cc_final: 0.8482 (mtp) REVERT: n 59 THR cc_start: 0.8949 (t) cc_final: 0.8662 (m) REVERT: n 60 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7289 (mt-10) REVERT: o 158 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7484 (m-80) REVERT: o 201 THR cc_start: 0.8620 (t) cc_final: 0.8404 (m) REVERT: o 222 GLN cc_start: 0.8408 (mt0) cc_final: 0.8119 (tt0) REVERT: p 44 MET cc_start: 0.8953 (mtp) cc_final: 0.8736 (mtp) REVERT: p 135 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8704 (pp) REVERT: p 157 GLU cc_start: 0.7353 (mt-10) cc_final: 0.6405 (tm-30) REVERT: q 215 MET cc_start: 0.8498 (mmm) cc_final: 0.8192 (mtp) REVERT: r 34 ASN cc_start: 0.4288 (OUTLIER) cc_final: 0.3528 (t0) REVERT: r 101 MET cc_start: 0.7746 (mtm) cc_final: 0.7417 (mtt) REVERT: s 96 LYS cc_start: 0.7522 (mttt) cc_final: 0.7305 (mttp) REVERT: s 99 MET cc_start: 0.6724 (ppp) cc_final: 0.5948 (ppp) REVERT: t 57 ARG cc_start: 0.8394 (mtm-85) cc_final: 0.7942 (mtp180) REVERT: t 71 MET cc_start: 0.9119 (mmm) cc_final: 0.8915 (mmm) REVERT: u 69 ASP cc_start: 0.7619 (m-30) cc_final: 0.7289 (m-30) REVERT: u 78 SER cc_start: 0.8651 (t) cc_final: 0.7455 (m) REVERT: u 82 ASP cc_start: 0.8115 (m-30) cc_final: 0.7723 (m-30) REVERT: v 92 VAL cc_start: 0.9098 (t) cc_final: 0.8886 (t) REVERT: x 47 MET cc_start: 0.6525 (ttp) cc_final: 0.6304 (tmm) REVERT: y 104 ILE cc_start: 0.8870 (tt) cc_final: 0.8572 (pt) REVERT: y 143 PHE cc_start: 0.8319 (t80) cc_final: 0.7915 (t80) REVERT: y 180 LYS cc_start: 0.8455 (ttmt) cc_final: 0.8130 (tttt) REVERT: y 191 ASP cc_start: 0.7986 (m-30) cc_final: 0.7686 (m-30) REVERT: y 255 MET cc_start: 0.7193 (mmm) cc_final: 0.6225 (mmm) REVERT: y 265 PHE cc_start: 0.8573 (m-80) cc_final: 0.7990 (m-10) REVERT: z 183 MET cc_start: 0.8990 (mtm) cc_final: 0.8719 (mtp) REVERT: z 222 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7815 (mm-30) REVERT: z 232 MET cc_start: 0.7766 (mmt) cc_final: 0.7523 (mmm) REVERT: z 239 ILE cc_start: 0.8480 (mm) cc_final: 0.8024 (mt) REVERT: z 255 MET cc_start: 0.8406 (mmm) cc_final: 0.7321 (mmm) REVERT: z 277 ASN cc_start: 0.7583 (m110) cc_final: 0.7197 (m110) outliers start: 160 outliers final: 105 residues processed: 996 average time/residue: 0.2252 time to fit residues: 372.1649 Evaluate side-chains 960 residues out of total 4223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 839 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 128 THR Chi-restraints excluded: chain 1 residue 208 ASP Chi-restraints excluded: chain 2 residue 149 VAL Chi-restraints excluded: chain 2 residue 273 VAL Chi-restraints excluded: chain 3 residue 86 THR Chi-restraints excluded: chain 3 residue 133 VAL Chi-restraints excluded: chain 3 residue 149 VAL Chi-restraints excluded: chain 3 residue 155 ASP Chi-restraints excluded: chain 3 residue 273 VAL Chi-restraints excluded: chain 4 residue 12 GLU Chi-restraints excluded: chain 5 residue 45 ASN Chi-restraints excluded: chain 5 residue 75 GLU Chi-restraints excluded: chain 6 residue 17 VAL Chi-restraints excluded: chain 6 residue 28 SER Chi-restraints excluded: chain 6 residue 31 ILE Chi-restraints excluded: chain 8 residue 24 SER Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 66 LEU Chi-restraints excluded: chain 8 residue 70 ARG Chi-restraints excluded: chain 8 residue 125 LEU Chi-restraints excluded: chain 8 residue 131 MET Chi-restraints excluded: chain 8 residue 192 ILE Chi-restraints excluded: chain 8 residue 214 ILE Chi-restraints excluded: chain AD residue 349 ILE Chi-restraints excluded: chain AE residue 348 SER Chi-restraints excluded: chain AJ residue 356 MET Chi-restraints excluded: chain AK residue 339 LEU Chi-restraints excluded: chain AK residue 352 ASP Chi-restraints excluded: chain c residue 6 ASP Chi-restraints excluded: chain c residue 88 THR Chi-restraints excluded: chain c residue 97 ASP Chi-restraints excluded: chain c residue 98 LEU Chi-restraints excluded: chain d residue 129 LYS Chi-restraints excluded: chain e residue 7 ASN Chi-restraints excluded: chain e residue 88 THR Chi-restraints excluded: chain f residue 128 ILE Chi-restraints excluded: chain g residue 39 LYS Chi-restraints excluded: chain g residue 53 LEU Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain g residue 85 HIS Chi-restraints excluded: chain g residue 134 GLN Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain h residue 34 VAL Chi-restraints excluded: chain h residue 40 ASP Chi-restraints excluded: chain h residue 53 LEU Chi-restraints excluded: chain h residue 65 VAL Chi-restraints excluded: chain h residue 68 MET Chi-restraints excluded: chain h residue 71 VAL Chi-restraints excluded: chain h residue 112 SER Chi-restraints excluded: chain i residue 3 LEU Chi-restraints excluded: chain i residue 18 SER Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 78 SER Chi-restraints excluded: chain i residue 101 VAL Chi-restraints excluded: chain i residue 124 SER Chi-restraints excluded: chain i residue 131 ARG Chi-restraints excluded: chain j residue 3 LEU Chi-restraints excluded: chain j residue 40 ASP Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 101 VAL Chi-restraints excluded: chain k residue 40 ASP Chi-restraints excluded: chain k residue 53 LEU Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain l residue 53 LEU Chi-restraints excluded: chain l residue 65 VAL Chi-restraints excluded: chain l residue 78 SER Chi-restraints excluded: chain l residue 87 LEU Chi-restraints excluded: chain l residue 113 ARG Chi-restraints excluded: chain m residue 60 GLU Chi-restraints excluded: chain m residue 81 THR Chi-restraints excluded: chain m residue 94 THR Chi-restraints excluded: chain m residue 196 THR Chi-restraints excluded: chain n residue 10 SER Chi-restraints excluded: chain n residue 60 GLU Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain n residue 107 VAL Chi-restraints excluded: chain n residue 114 THR Chi-restraints excluded: chain n residue 158 PHE Chi-restraints excluded: chain n residue 196 THR Chi-restraints excluded: chain n residue 242 SER Chi-restraints excluded: chain o residue 19 LEU Chi-restraints excluded: chain o residue 43 SER Chi-restraints excluded: chain o residue 81 THR Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain o residue 94 THR Chi-restraints excluded: chain o residue 126 ASP Chi-restraints excluded: chain o residue 158 PHE Chi-restraints excluded: chain o residue 162 ASP Chi-restraints excluded: chain o residue 204 ILE Chi-restraints excluded: chain o residue 233 SER Chi-restraints excluded: chain o residue 242 SER Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain p residue 196 THR Chi-restraints excluded: chain p residue 212 VAL Chi-restraints excluded: chain p residue 245 LEU Chi-restraints excluded: chain q residue 72 ILE Chi-restraints excluded: chain q residue 147 SER Chi-restraints excluded: chain q residue 204 ILE Chi-restraints excluded: chain q residue 241 SER Chi-restraints excluded: chain q residue 243 ASP Chi-restraints excluded: chain r residue 34 ASN Chi-restraints excluded: chain s residue 46 THR Chi-restraints excluded: chain s residue 51 SER Chi-restraints excluded: chain t residue 32 ASP Chi-restraints excluded: chain t residue 37 LEU Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain u residue 53 ASP Chi-restraints excluded: chain v residue 38 THR Chi-restraints excluded: chain v residue 51 SER Chi-restraints excluded: chain v residue 103 VAL Chi-restraints excluded: chain w residue 66 SER Chi-restraints excluded: chain x residue 48 TRP Chi-restraints excluded: chain y residue 86 THR Chi-restraints excluded: chain y residue 167 THR Chi-restraints excluded: chain y residue 185 LYS Chi-restraints excluded: chain z residue 86 THR Chi-restraints excluded: chain z residue 113 VAL Chi-restraints excluded: chain z residue 184 LEU Chi-restraints excluded: chain z residue 222 GLU Chi-restraints excluded: chain z residue 253 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 311 optimal weight: 8.9990 chunk 352 optimal weight: 4.9990 chunk 291 optimal weight: 4.9990 chunk 231 optimal weight: 0.6980 chunk 451 optimal weight: 8.9990 chunk 211 optimal weight: 1.9990 chunk 383 optimal weight: 9.9990 chunk 241 optimal weight: 0.7980 chunk 169 optimal weight: 0.0020 chunk 329 optimal weight: 8.9990 chunk 283 optimal weight: 1.9990 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 228 GLN 6 67 HIS AN 342 GLN h 22 ASN h 120 GLN ** i 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 134 GLN n 15 ASN n 20 GLN ** n 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 125 ASN n 170 ASN ** r 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 163 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.144900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.120049 restraints weight = 46707.874| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.44 r_work: 0.3221 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 38926 Z= 0.127 Angle : 0.512 8.223 52695 Z= 0.257 Chirality : 0.040 0.203 6219 Planarity : 0.003 0.032 6827 Dihedral : 5.256 59.375 5308 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.96 % Favored : 98.00 % Rotamer: Outliers : 3.84 % Allowed : 13.73 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.56 (0.12), residues: 4896 helix: 2.86 (0.09), residues: 2888 sheet: -1.05 (0.25), residues: 373 loop : 0.27 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG m 247 TYR 0.011 0.001 TYR 8 3 PHE 0.016 0.001 PHE 1 182 TRP 0.014 0.001 TRP x 48 HIS 0.003 0.001 HIS p 51 Details of bonding type rmsd covalent geometry : bond 0.00280 (38926) covalent geometry : angle 0.51164 (52695) hydrogen bonds : bond 0.04580 ( 2457) hydrogen bonds : angle 3.77145 ( 7296) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1033 residues out of total 4223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 871 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 156 LYS cc_start: 0.6732 (mmmt) cc_final: 0.6496 (mtpp) REVERT: 1 223 LEU cc_start: 0.7943 (mp) cc_final: 0.7503 (mm) REVERT: 1 249 MET cc_start: 0.8076 (tpt) cc_final: 0.7793 (tpp) REVERT: 2 123 MET cc_start: 0.8086 (mtm) cc_final: 0.7533 (mtm) REVERT: 2 156 LYS cc_start: 0.8689 (mptp) cc_final: 0.8232 (mtpp) REVERT: 2 173 ASP cc_start: 0.8461 (m-30) cc_final: 0.8222 (m-30) REVERT: 2 180 LYS cc_start: 0.7340 (mtpp) cc_final: 0.6923 (mttt) REVERT: 2 211 MET cc_start: 0.7151 (mmt) cc_final: 0.6761 (tpp) REVERT: 2 255 MET cc_start: 0.8671 (mmp) cc_final: 0.8299 (mmm) REVERT: 3 86 THR cc_start: 0.9019 (OUTLIER) cc_final: 0.8654 (p) REVERT: 3 121 GLN cc_start: 0.8190 (tp40) cc_final: 0.7715 (tt0) REVERT: 3 179 MET cc_start: 0.6875 (mmt) cc_final: 0.6197 (mtt) REVERT: 3 185 LYS cc_start: 0.7749 (mptt) cc_final: 0.7518 (mttt) REVERT: 3 255 MET cc_start: 0.7169 (tpt) cc_final: 0.6933 (tpp) REVERT: 4 63 MET cc_start: 0.6650 (tmm) cc_final: 0.5592 (mmm) REVERT: 5 26 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8305 (mp) REVERT: 7 15 TRP cc_start: 0.7390 (t-100) cc_final: 0.7099 (t-100) REVERT: 7 16 MET cc_start: 0.8296 (tpp) cc_final: 0.7921 (tpt) REVERT: 8 70 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.5917 (ttt-90) REVERT: AI 340 SER cc_start: 0.8820 (p) cc_final: 0.8610 (m) REVERT: AJ 342 GLN cc_start: 0.7368 (mm-40) cc_final: 0.6685 (mt0) REVERT: AJ 356 MET cc_start: 0.4093 (OUTLIER) cc_final: 0.3865 (tpt) REVERT: AK 331 MET cc_start: 0.7822 (ttm) cc_final: 0.7371 (ttm) REVERT: AK 339 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8358 (mp) REVERT: AN 339 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8862 (mp) REVERT: AO 330 ASN cc_start: 0.8346 (p0) cc_final: 0.7788 (p0) REVERT: AO 356 MET cc_start: 0.9242 (mtm) cc_final: 0.8974 (mtp) REVERT: c 24 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8146 (mt-10) REVERT: c 90 ASP cc_start: 0.7468 (m-30) cc_final: 0.6850 (m-30) REVERT: c 100 ARG cc_start: 0.8870 (mtt90) cc_final: 0.8666 (mtt180) REVERT: d 47 LYS cc_start: 0.8612 (tptt) cc_final: 0.7630 (ttpt) REVERT: d 84 THR cc_start: 0.9318 (t) cc_final: 0.9047 (m) REVERT: d 90 ASP cc_start: 0.8864 (p0) cc_final: 0.8425 (p0) REVERT: d 126 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8458 (tttp) REVERT: e 115 ASP cc_start: 0.8246 (m-30) cc_final: 0.7892 (m-30) REVERT: f 47 LYS cc_start: 0.8167 (ttmm) cc_final: 0.7800 (ttpp) REVERT: g 39 LYS cc_start: 0.5936 (OUTLIER) cc_final: 0.5476 (ptpt) REVERT: g 78 SER cc_start: 0.8618 (t) cc_final: 0.8018 (m) REVERT: g 80 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7372 (tp30) REVERT: g 95 TYR cc_start: 0.8687 (m-80) cc_final: 0.8303 (m-80) REVERT: g 134 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7765 (mt0) REVERT: g 135 MET cc_start: 0.8666 (ttm) cc_final: 0.8040 (ttm) REVERT: i 42 TYR cc_start: 0.8451 (t80) cc_final: 0.8218 (t80) REVERT: i 66 LYS cc_start: 0.7737 (pttt) cc_final: 0.7397 (pttp) REVERT: i 102 MET cc_start: 0.7505 (mmp) cc_final: 0.6844 (mpp) REVERT: i 131 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8234 (mmm160) REVERT: j 80 GLU cc_start: 0.8413 (mt-10) cc_final: 0.7428 (tp30) REVERT: k 132 THR cc_start: 0.9089 (m) cc_final: 0.8869 (m) REVERT: l 14 MET cc_start: 0.9088 (mtp) cc_final: 0.8849 (mtm) REVERT: l 91 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7820 (mt-10) REVERT: l 108 MET cc_start: 0.8843 (ttm) cc_final: 0.8502 (ttp) REVERT: l 113 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8670 (mmp-170) REVERT: m 238 MET cc_start: 0.8691 (mtm) cc_final: 0.8317 (mtp) REVERT: o 58 MET cc_start: 0.8634 (mtp) cc_final: 0.8331 (mtt) REVERT: o 158 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7472 (m-80) REVERT: o 201 THR cc_start: 0.8621 (t) cc_final: 0.8398 (m) REVERT: o 222 GLN cc_start: 0.8384 (mt0) cc_final: 0.8094 (tt0) REVERT: p 135 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8736 (pp) REVERT: p 157 GLU cc_start: 0.7380 (mt-10) cc_final: 0.6367 (tm-30) REVERT: q 91 LEU cc_start: 0.8409 (pt) cc_final: 0.8095 (pt) REVERT: q 215 MET cc_start: 0.8382 (mmm) cc_final: 0.7991 (mtt) REVERT: q 238 MET cc_start: 0.8998 (mtp) cc_final: 0.8656 (mtp) REVERT: r 34 ASN cc_start: 0.4038 (OUTLIER) cc_final: 0.3504 (t0) REVERT: r 101 MET cc_start: 0.7718 (mtm) cc_final: 0.7387 (mtt) REVERT: s 35 ASP cc_start: 0.6765 (OUTLIER) cc_final: 0.6414 (m-30) REVERT: s 96 LYS cc_start: 0.7416 (mttt) cc_final: 0.7193 (mttp) REVERT: t 57 ARG cc_start: 0.8345 (mtm-85) cc_final: 0.7908 (mtp180) REVERT: t 71 MET cc_start: 0.9128 (mmm) cc_final: 0.8843 (mmm) REVERT: u 78 SER cc_start: 0.8639 (t) cc_final: 0.7964 (m) REVERT: u 82 ASP cc_start: 0.8120 (m-30) cc_final: 0.7872 (m-30) REVERT: v 92 VAL cc_start: 0.9064 (t) cc_final: 0.8862 (t) REVERT: y 104 ILE cc_start: 0.8827 (tt) cc_final: 0.8497 (pt) REVERT: y 180 LYS cc_start: 0.8265 (ttmt) cc_final: 0.7967 (tttt) REVERT: y 191 ASP cc_start: 0.7741 (m-30) cc_final: 0.7390 (m-30) REVERT: y 265 PHE cc_start: 0.8533 (m-80) cc_final: 0.7997 (m-10) REVERT: z 185 LYS cc_start: 0.8219 (tttm) cc_final: 0.7995 (tmtt) REVERT: z 222 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7498 (mm-30) REVERT: z 232 MET cc_start: 0.7864 (mmt) cc_final: 0.7583 (mmm) REVERT: z 239 ILE cc_start: 0.8424 (mm) cc_final: 0.7994 (mt) REVERT: z 255 MET cc_start: 0.8259 (mmm) cc_final: 0.7153 (mmm) outliers start: 162 outliers final: 116 residues processed: 980 average time/residue: 0.2345 time to fit residues: 379.7922 Evaluate side-chains 970 residues out of total 4223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 838 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 123 MET Chi-restraints excluded: chain 1 residue 127 GLN Chi-restraints excluded: chain 1 residue 128 THR Chi-restraints excluded: chain 1 residue 208 ASP Chi-restraints excluded: chain 1 residue 242 LEU Chi-restraints excluded: chain 2 residue 128 THR Chi-restraints excluded: chain 2 residue 149 VAL Chi-restraints excluded: chain 2 residue 179 MET Chi-restraints excluded: chain 2 residue 253 MET Chi-restraints excluded: chain 2 residue 273 VAL Chi-restraints excluded: chain 3 residue 86 THR Chi-restraints excluded: chain 3 residue 149 VAL Chi-restraints excluded: chain 3 residue 155 ASP Chi-restraints excluded: chain 3 residue 239 ILE Chi-restraints excluded: chain 3 residue 273 VAL Chi-restraints excluded: chain 4 residue 12 GLU Chi-restraints excluded: chain 5 residue 26 ILE Chi-restraints excluded: chain 5 residue 45 ASN Chi-restraints excluded: chain 5 residue 75 GLU Chi-restraints excluded: chain 6 residue 17 VAL Chi-restraints excluded: chain 6 residue 28 SER Chi-restraints excluded: chain 6 residue 31 ILE Chi-restraints excluded: chain 7 residue 19 ILE Chi-restraints excluded: chain 7 residue 84 LEU Chi-restraints excluded: chain 8 residue 70 ARG Chi-restraints excluded: chain 8 residue 125 LEU Chi-restraints excluded: chain 8 residue 131 MET Chi-restraints excluded: chain 8 residue 192 ILE Chi-restraints excluded: chain 8 residue 214 ILE Chi-restraints excluded: chain 8 residue 258 LEU Chi-restraints excluded: chain AA residue 353 VAL Chi-restraints excluded: chain AC residue 353 VAL Chi-restraints excluded: chain AD residue 349 ILE Chi-restraints excluded: chain AE residue 348 SER Chi-restraints excluded: chain AJ residue 356 MET Chi-restraints excluded: chain AK residue 339 LEU Chi-restraints excluded: chain AN residue 339 LEU Chi-restraints excluded: chain AO residue 339 LEU Chi-restraints excluded: chain b residue 28 THR Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain c residue 6 ASP Chi-restraints excluded: chain c residue 97 ASP Chi-restraints excluded: chain c residue 98 LEU Chi-restraints excluded: chain d residue 119 SER Chi-restraints excluded: chain d residue 126 LYS Chi-restraints excluded: chain d residue 129 LYS Chi-restraints excluded: chain e residue 88 THR Chi-restraints excluded: chain f residue 88 THR Chi-restraints excluded: chain f residue 128 ILE Chi-restraints excluded: chain g residue 39 LYS Chi-restraints excluded: chain g residue 53 LEU Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain g residue 85 HIS Chi-restraints excluded: chain g residue 134 GLN Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain h residue 34 VAL Chi-restraints excluded: chain h residue 40 ASP Chi-restraints excluded: chain h residue 53 LEU Chi-restraints excluded: chain h residue 65 VAL Chi-restraints excluded: chain h residue 68 MET Chi-restraints excluded: chain h residue 71 VAL Chi-restraints excluded: chain h residue 112 SER Chi-restraints excluded: chain i residue 3 LEU Chi-restraints excluded: chain i residue 18 SER Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 78 SER Chi-restraints excluded: chain i residue 124 SER Chi-restraints excluded: chain i residue 131 ARG Chi-restraints excluded: chain j residue 3 LEU Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 101 VAL Chi-restraints excluded: chain k residue 40 ASP Chi-restraints excluded: chain k residue 53 LEU Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain l residue 37 SER Chi-restraints excluded: chain l residue 65 VAL Chi-restraints excluded: chain l residue 78 SER Chi-restraints excluded: chain l residue 87 LEU Chi-restraints excluded: chain l residue 113 ARG Chi-restraints excluded: chain m residue 60 GLU Chi-restraints excluded: chain m residue 162 ASP Chi-restraints excluded: chain m residue 196 THR Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 10 SER Chi-restraints excluded: chain n residue 19 LEU Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain n residue 107 VAL Chi-restraints excluded: chain n residue 114 THR Chi-restraints excluded: chain n residue 138 ILE Chi-restraints excluded: chain n residue 158 PHE Chi-restraints excluded: chain o residue 19 LEU Chi-restraints excluded: chain o residue 43 SER Chi-restraints excluded: chain o residue 81 THR Chi-restraints excluded: chain o residue 94 THR Chi-restraints excluded: chain o residue 126 ASP Chi-restraints excluded: chain o residue 158 PHE Chi-restraints excluded: chain o residue 162 ASP Chi-restraints excluded: chain o residue 233 SER Chi-restraints excluded: chain o residue 234 THR Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain p residue 196 THR Chi-restraints excluded: chain p residue 212 VAL Chi-restraints excluded: chain q residue 81 THR Chi-restraints excluded: chain q residue 147 SER Chi-restraints excluded: chain q residue 241 SER Chi-restraints excluded: chain q residue 243 ASP Chi-restraints excluded: chain r residue 34 ASN Chi-restraints excluded: chain s residue 35 ASP Chi-restraints excluded: chain s residue 46 THR Chi-restraints excluded: chain s residue 51 SER Chi-restraints excluded: chain t residue 32 ASP Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain v residue 38 THR Chi-restraints excluded: chain v residue 51 SER Chi-restraints excluded: chain v residue 103 VAL Chi-restraints excluded: chain w residue 66 SER Chi-restraints excluded: chain x residue 48 TRP Chi-restraints excluded: chain y residue 84 SER Chi-restraints excluded: chain y residue 125 LEU Chi-restraints excluded: chain y residue 147 SER Chi-restraints excluded: chain y residue 167 THR Chi-restraints excluded: chain y residue 185 LYS Chi-restraints excluded: chain y residue 198 MET Chi-restraints excluded: chain y residue 253 MET Chi-restraints excluded: chain z residue 86 THR Chi-restraints excluded: chain z residue 113 VAL Chi-restraints excluded: chain z residue 123 MET Chi-restraints excluded: chain z residue 128 THR Chi-restraints excluded: chain z residue 184 LEU Chi-restraints excluded: chain z residue 222 GLU Chi-restraints excluded: chain z residue 253 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 296 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 347 optimal weight: 4.9990 chunk 424 optimal weight: 0.1980 chunk 11 optimal weight: 0.8980 chunk 422 optimal weight: 0.9990 chunk 391 optimal weight: 5.9990 chunk 393 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 188 optimal weight: 6.9990 chunk 233 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 277 ASN 7 86 GLN b 123 ASN h 22 ASN ** h 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 134 GLN ** n 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 125 ASN ** r 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 121 GLN y 163 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.144966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.120153 restraints weight = 46719.606| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.44 r_work: 0.3246 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 38926 Z= 0.121 Angle : 0.503 9.563 52695 Z= 0.252 Chirality : 0.039 0.234 6219 Planarity : 0.003 0.032 6827 Dihedral : 5.102 59.683 5302 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.90 % Favored : 98.06 % Rotamer: Outliers : 4.05 % Allowed : 14.47 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.69 (0.12), residues: 4896 helix: 2.96 (0.09), residues: 2886 sheet: -1.11 (0.27), residues: 338 loop : 0.33 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG m 247 TYR 0.011 0.001 TYR k 115 PHE 0.026 0.001 PHE y 231 TRP 0.014 0.001 TRP x 48 HIS 0.002 0.001 HIS p 51 Details of bonding type rmsd covalent geometry : bond 0.00267 (38926) covalent geometry : angle 0.50349 (52695) hydrogen bonds : bond 0.04350 ( 2457) hydrogen bonds : angle 3.68839 ( 7296) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1034 residues out of total 4223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 863 time to evaluate : 1.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 156 LYS cc_start: 0.6824 (mmmt) cc_final: 0.6588 (mtpp) REVERT: 1 223 LEU cc_start: 0.7988 (mp) cc_final: 0.7547 (mm) REVERT: 1 249 MET cc_start: 0.7964 (tpt) cc_final: 0.7698 (tpp) REVERT: 1 277 ASN cc_start: 0.7939 (m110) cc_final: 0.7664 (m-40) REVERT: 2 123 MET cc_start: 0.8047 (mtm) cc_final: 0.7577 (mtm) REVERT: 2 156 LYS cc_start: 0.8674 (mptp) cc_final: 0.8232 (mtpp) REVERT: 2 173 ASP cc_start: 0.8500 (m-30) cc_final: 0.8260 (m-30) REVERT: 2 180 LYS cc_start: 0.7484 (mtpp) cc_final: 0.7058 (mttt) REVERT: 2 211 MET cc_start: 0.7105 (mmt) cc_final: 0.6643 (tpp) REVERT: 2 255 MET cc_start: 0.8683 (mmp) cc_final: 0.8334 (mmm) REVERT: 3 86 THR cc_start: 0.9021 (OUTLIER) cc_final: 0.8669 (p) REVERT: 3 121 GLN cc_start: 0.8208 (tp40) cc_final: 0.7769 (tt0) REVERT: 3 132 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7792 (mm-40) REVERT: 3 179 MET cc_start: 0.6945 (mmt) cc_final: 0.6282 (mtt) REVERT: 3 185 LYS cc_start: 0.7880 (mptt) cc_final: 0.7629 (mttt) REVERT: 4 55 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6851 (tp) REVERT: 4 63 MET cc_start: 0.6728 (tmm) cc_final: 0.5657 (mmm) REVERT: 5 26 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8360 (mp) REVERT: 5 74 MET cc_start: 0.8232 (mtp) cc_final: 0.7893 (mtp) REVERT: 6 69 MET cc_start: 0.8049 (mtm) cc_final: 0.7844 (mtm) REVERT: 7 15 TRP cc_start: 0.7196 (t-100) cc_final: 0.6928 (t-100) REVERT: 7 16 MET cc_start: 0.8307 (tpp) cc_final: 0.7917 (tpt) REVERT: 8 70 ARG cc_start: 0.6889 (OUTLIER) cc_final: 0.5883 (ttt-90) REVERT: 8 173 MET cc_start: 0.6913 (mmm) cc_final: 0.6590 (mmp) REVERT: 8 231 TRP cc_start: 0.7124 (t60) cc_final: 0.6679 (t60) REVERT: AJ 342 GLN cc_start: 0.7420 (mm-40) cc_final: 0.6693 (mt0) REVERT: AJ 356 MET cc_start: 0.4250 (mmt) cc_final: 0.3962 (tpt) REVERT: AK 331 MET cc_start: 0.7900 (ttm) cc_final: 0.7547 (ttm) REVERT: AK 339 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8410 (mp) REVERT: AN 339 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8753 (mp) REVERT: AO 330 ASN cc_start: 0.8375 (p0) cc_final: 0.7825 (p0) REVERT: AO 331 MET cc_start: 0.8242 (mmm) cc_final: 0.7869 (mmm) REVERT: AO 356 MET cc_start: 0.9229 (mtm) cc_final: 0.8971 (mtp) REVERT: c 24 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8270 (mt-10) REVERT: c 90 ASP cc_start: 0.7581 (m-30) cc_final: 0.6929 (m-30) REVERT: d 47 LYS cc_start: 0.8601 (tptt) cc_final: 0.7708 (ttpt) REVERT: d 84 THR cc_start: 0.9341 (t) cc_final: 0.9077 (m) REVERT: d 90 ASP cc_start: 0.8868 (p0) cc_final: 0.8403 (p0) REVERT: d 126 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8465 (tttp) REVERT: e 115 ASP cc_start: 0.8274 (m-30) cc_final: 0.7926 (m-30) REVERT: f 47 LYS cc_start: 0.8151 (ttmm) cc_final: 0.7779 (ttpp) REVERT: g 39 LYS cc_start: 0.6004 (OUTLIER) cc_final: 0.5542 (ptpt) REVERT: g 80 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7507 (tp30) REVERT: g 95 TYR cc_start: 0.8691 (m-80) cc_final: 0.8316 (m-80) REVERT: g 134 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7773 (mt0) REVERT: g 135 MET cc_start: 0.8679 (ttm) cc_final: 0.8092 (ttm) REVERT: i 66 LYS cc_start: 0.7818 (pttt) cc_final: 0.7486 (pttp) REVERT: i 131 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8337 (tpt170) REVERT: j 68 MET cc_start: 0.8779 (mtm) cc_final: 0.8560 (mtp) REVERT: j 80 GLU cc_start: 0.8507 (mt-10) cc_final: 0.7553 (tp30) REVERT: k 132 THR cc_start: 0.9018 (m) cc_final: 0.8803 (m) REVERT: l 14 MET cc_start: 0.9095 (mtp) cc_final: 0.8884 (mtm) REVERT: l 36 SER cc_start: 0.8962 (p) cc_final: 0.8590 (t) REVERT: l 91 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7898 (mt-10) REVERT: l 108 MET cc_start: 0.8797 (ttm) cc_final: 0.8453 (ttp) REVERT: l 113 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8677 (mmp-170) REVERT: m 172 GLN cc_start: 0.8413 (mm-40) cc_final: 0.7989 (mm-40) REVERT: m 238 MET cc_start: 0.8695 (mtm) cc_final: 0.8329 (mtp) REVERT: o 58 MET cc_start: 0.8617 (mtp) cc_final: 0.8376 (mtt) REVERT: o 158 PHE cc_start: 0.8090 (OUTLIER) cc_final: 0.7472 (m-80) REVERT: o 201 THR cc_start: 0.8626 (t) cc_final: 0.8405 (m) REVERT: o 222 GLN cc_start: 0.8313 (mt0) cc_final: 0.8043 (tt0) REVERT: p 112 MET cc_start: 0.8082 (mtm) cc_final: 0.7826 (tpp) REVERT: p 135 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8641 (pp) REVERT: p 157 GLU cc_start: 0.7380 (mt-10) cc_final: 0.6436 (tm-30) REVERT: q 91 LEU cc_start: 0.8418 (pt) cc_final: 0.8119 (pt) REVERT: q 215 MET cc_start: 0.8346 (mmm) cc_final: 0.7990 (mtt) REVERT: r 34 ASN cc_start: 0.3787 (OUTLIER) cc_final: 0.3312 (t0) REVERT: r 101 MET cc_start: 0.7759 (mtm) cc_final: 0.7386 (mtt) REVERT: s 35 ASP cc_start: 0.6748 (OUTLIER) cc_final: 0.6445 (m-30) REVERT: s 96 LYS cc_start: 0.7440 (mttt) cc_final: 0.7194 (mttp) REVERT: s 99 MET cc_start: 0.6715 (ppp) cc_final: 0.5975 (ppp) REVERT: t 57 ARG cc_start: 0.8396 (mtm-85) cc_final: 0.7977 (mtp180) REVERT: t 71 MET cc_start: 0.9121 (mmm) cc_final: 0.8857 (mmm) REVERT: u 69 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.7422 (m-30) REVERT: u 78 SER cc_start: 0.8668 (t) cc_final: 0.8007 (m) REVERT: u 82 ASP cc_start: 0.8140 (m-30) cc_final: 0.7889 (m-30) REVERT: v 92 VAL cc_start: 0.9069 (t) cc_final: 0.8859 (t) REVERT: y 104 ILE cc_start: 0.8799 (tt) cc_final: 0.8530 (pt) REVERT: y 180 LYS cc_start: 0.8320 (ttmt) cc_final: 0.8042 (tttt) REVERT: y 191 ASP cc_start: 0.7740 (m-30) cc_final: 0.7361 (m-30) REVERT: y 251 MET cc_start: 0.7964 (mmt) cc_final: 0.7706 (mmt) REVERT: y 265 PHE cc_start: 0.8550 (m-80) cc_final: 0.8151 (m-10) REVERT: z 185 LYS cc_start: 0.8267 (tttm) cc_final: 0.8043 (tmtt) REVERT: z 188 ARG cc_start: 0.8207 (mtt90) cc_final: 0.7870 (mtt90) REVERT: z 222 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7472 (mm-30) REVERT: z 255 MET cc_start: 0.8197 (mmm) cc_final: 0.7183 (mmm) outliers start: 171 outliers final: 129 residues processed: 973 average time/residue: 0.2310 time to fit residues: 372.5912 Evaluate side-chains 980 residues out of total 4223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 833 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 123 MET Chi-restraints excluded: chain 1 residue 127 GLN Chi-restraints excluded: chain 1 residue 128 THR Chi-restraints excluded: chain 1 residue 185 LYS Chi-restraints excluded: chain 1 residue 208 ASP Chi-restraints excluded: chain 2 residue 128 THR Chi-restraints excluded: chain 2 residue 149 VAL Chi-restraints excluded: chain 2 residue 179 MET Chi-restraints excluded: chain 2 residue 253 MET Chi-restraints excluded: chain 2 residue 273 VAL Chi-restraints excluded: chain 3 residue 86 THR Chi-restraints excluded: chain 3 residue 132 GLN Chi-restraints excluded: chain 3 residue 149 VAL Chi-restraints excluded: chain 3 residue 155 ASP Chi-restraints excluded: chain 3 residue 239 ILE Chi-restraints excluded: chain 3 residue 273 VAL Chi-restraints excluded: chain 4 residue 12 GLU Chi-restraints excluded: chain 4 residue 55 LEU Chi-restraints excluded: chain 5 residue 26 ILE Chi-restraints excluded: chain 5 residue 45 ASN Chi-restraints excluded: chain 5 residue 75 GLU Chi-restraints excluded: chain 6 residue 17 VAL Chi-restraints excluded: chain 6 residue 28 SER Chi-restraints excluded: chain 6 residue 31 ILE Chi-restraints excluded: chain 7 residue 19 ILE Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 66 LEU Chi-restraints excluded: chain 8 residue 70 ARG Chi-restraints excluded: chain 8 residue 125 LEU Chi-restraints excluded: chain 8 residue 131 MET Chi-restraints excluded: chain 8 residue 152 VAL Chi-restraints excluded: chain 8 residue 192 ILE Chi-restraints excluded: chain 8 residue 214 ILE Chi-restraints excluded: chain 8 residue 258 LEU Chi-restraints excluded: chain AB residue 341 ASN Chi-restraints excluded: chain AC residue 353 VAL Chi-restraints excluded: chain AD residue 349 ILE Chi-restraints excluded: chain AE residue 348 SER Chi-restraints excluded: chain AK residue 339 LEU Chi-restraints excluded: chain AK residue 342 GLN Chi-restraints excluded: chain AK residue 352 ASP Chi-restraints excluded: chain AM residue 331 MET Chi-restraints excluded: chain AN residue 339 LEU Chi-restraints excluded: chain AO residue 339 LEU Chi-restraints excluded: chain b residue 28 THR Chi-restraints excluded: chain c residue 6 ASP Chi-restraints excluded: chain c residue 97 ASP Chi-restraints excluded: chain c residue 98 LEU Chi-restraints excluded: chain d residue 88 THR Chi-restraints excluded: chain d residue 97 ASP Chi-restraints excluded: chain d residue 119 SER Chi-restraints excluded: chain d residue 126 LYS Chi-restraints excluded: chain d residue 129 LYS Chi-restraints excluded: chain e residue 88 THR Chi-restraints excluded: chain f residue 88 THR Chi-restraints excluded: chain f residue 128 ILE Chi-restraints excluded: chain g residue 39 LYS Chi-restraints excluded: chain g residue 53 LEU Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain g residue 102 MET Chi-restraints excluded: chain g residue 134 GLN Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain h residue 34 VAL Chi-restraints excluded: chain h residue 40 ASP Chi-restraints excluded: chain h residue 53 LEU Chi-restraints excluded: chain h residue 65 VAL Chi-restraints excluded: chain h residue 68 MET Chi-restraints excluded: chain h residue 71 VAL Chi-restraints excluded: chain h residue 112 SER Chi-restraints excluded: chain i residue 3 LEU Chi-restraints excluded: chain i residue 18 SER Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 78 SER Chi-restraints excluded: chain i residue 101 VAL Chi-restraints excluded: chain i residue 124 SER Chi-restraints excluded: chain i residue 131 ARG Chi-restraints excluded: chain j residue 3 LEU Chi-restraints excluded: chain j residue 40 ASP Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 101 VAL Chi-restraints excluded: chain k residue 40 ASP Chi-restraints excluded: chain k residue 53 LEU Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain l residue 3 LEU Chi-restraints excluded: chain l residue 37 SER Chi-restraints excluded: chain l residue 61 ASP Chi-restraints excluded: chain l residue 65 VAL Chi-restraints excluded: chain l residue 78 SER Chi-restraints excluded: chain l residue 87 LEU Chi-restraints excluded: chain l residue 113 ARG Chi-restraints excluded: chain m residue 60 GLU Chi-restraints excluded: chain m residue 81 THR Chi-restraints excluded: chain m residue 94 THR Chi-restraints excluded: chain m residue 162 ASP Chi-restraints excluded: chain m residue 196 THR Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 10 SER Chi-restraints excluded: chain n residue 19 LEU Chi-restraints excluded: chain n residue 85 SER Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain n residue 107 VAL Chi-restraints excluded: chain n residue 114 THR Chi-restraints excluded: chain n residue 158 PHE Chi-restraints excluded: chain n residue 233 SER Chi-restraints excluded: chain o residue 9 MET Chi-restraints excluded: chain o residue 43 SER Chi-restraints excluded: chain o residue 81 THR Chi-restraints excluded: chain o residue 94 THR Chi-restraints excluded: chain o residue 126 ASP Chi-restraints excluded: chain o residue 158 PHE Chi-restraints excluded: chain o residue 162 ASP Chi-restraints excluded: chain o residue 233 SER Chi-restraints excluded: chain o residue 234 THR Chi-restraints excluded: chain o residue 248 MET Chi-restraints excluded: chain p residue 58 MET Chi-restraints excluded: chain p residue 81 THR Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain p residue 196 THR Chi-restraints excluded: chain p residue 212 VAL Chi-restraints excluded: chain q residue 81 THR Chi-restraints excluded: chain q residue 147 SER Chi-restraints excluded: chain q residue 241 SER Chi-restraints excluded: chain r residue 34 ASN Chi-restraints excluded: chain s residue 35 ASP Chi-restraints excluded: chain s residue 46 THR Chi-restraints excluded: chain s residue 51 SER Chi-restraints excluded: chain s residue 98 LEU Chi-restraints excluded: chain t residue 32 ASP Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain u residue 53 ASP Chi-restraints excluded: chain u residue 69 ASP Chi-restraints excluded: chain v residue 38 THR Chi-restraints excluded: chain v residue 51 SER Chi-restraints excluded: chain w residue 66 SER Chi-restraints excluded: chain x residue 48 TRP Chi-restraints excluded: chain y residue 84 SER Chi-restraints excluded: chain y residue 125 LEU Chi-restraints excluded: chain y residue 141 LEU Chi-restraints excluded: chain y residue 147 SER Chi-restraints excluded: chain y residue 167 THR Chi-restraints excluded: chain y residue 198 MET Chi-restraints excluded: chain z residue 113 VAL Chi-restraints excluded: chain z residue 128 THR Chi-restraints excluded: chain z residue 184 LEU Chi-restraints excluded: chain z residue 222 GLU Chi-restraints excluded: chain z residue 253 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 318 optimal weight: 7.9990 chunk 178 optimal weight: 7.9990 chunk 168 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 405 optimal weight: 0.9980 chunk 114 optimal weight: 9.9990 chunk 149 optimal weight: 7.9990 chunk 172 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 367 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 50 GLN f 34 ASN ** h 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 134 GLN m 15 ASN ** n 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 119 HIS n 125 ASN ** r 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 75 ASN y 121 GLN y 163 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.141193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.116206 restraints weight = 46937.509| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.44 r_work: 0.3211 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 38926 Z= 0.187 Angle : 0.574 9.992 52695 Z= 0.288 Chirality : 0.042 0.234 6219 Planarity : 0.004 0.062 6827 Dihedral : 5.354 62.728 5301 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.17 % Favored : 97.77 % Rotamer: Outliers : 4.45 % Allowed : 14.52 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.12), residues: 4896 helix: 2.77 (0.09), residues: 2887 sheet: -1.33 (0.26), residues: 348 loop : 0.26 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG m 247 TYR 0.014 0.002 TYR h 115 PHE 0.025 0.002 PHE y 231 TRP 0.013 0.001 TRP x 48 HIS 0.005 0.001 HIS p 51 Details of bonding type rmsd covalent geometry : bond 0.00448 (38926) covalent geometry : angle 0.57407 (52695) hydrogen bonds : bond 0.05022 ( 2457) hydrogen bonds : angle 3.86756 ( 7296) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1046 residues out of total 4223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 858 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 156 LYS cc_start: 0.6851 (mmmt) cc_final: 0.6588 (mtpp) REVERT: 1 249 MET cc_start: 0.8109 (tpt) cc_final: 0.7748 (tpp) REVERT: 1 255 MET cc_start: 0.8230 (tpp) cc_final: 0.7708 (mmp) REVERT: 2 123 MET cc_start: 0.8271 (mtm) cc_final: 0.7795 (mtm) REVERT: 2 156 LYS cc_start: 0.8651 (mptp) cc_final: 0.8138 (mtpp) REVERT: 2 180 LYS cc_start: 0.7625 (mtpp) cc_final: 0.6810 (mmtt) REVERT: 3 86 THR cc_start: 0.9086 (OUTLIER) cc_final: 0.8770 (p) REVERT: 3 121 GLN cc_start: 0.8282 (tp40) cc_final: 0.7853 (tt0) REVERT: 3 132 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7883 (mm110) REVERT: 3 179 MET cc_start: 0.7008 (mmt) cc_final: 0.6343 (mtt) REVERT: 3 185 LYS cc_start: 0.7958 (mptt) cc_final: 0.7677 (mttt) REVERT: 4 22 CYS cc_start: 0.8240 (t) cc_final: 0.7849 (m) REVERT: 4 63 MET cc_start: 0.6708 (tmm) cc_final: 0.5670 (mmm) REVERT: 5 26 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8414 (mp) REVERT: 5 74 MET cc_start: 0.8298 (mtp) cc_final: 0.8004 (mtp) REVERT: 7 16 MET cc_start: 0.8422 (tpp) cc_final: 0.8090 (tpt) REVERT: 8 29 MET cc_start: 0.7094 (ttt) cc_final: 0.6870 (ttt) REVERT: 8 70 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.6068 (ttt-90) REVERT: 8 231 TRP cc_start: 0.7146 (t60) cc_final: 0.6669 (t60) REVERT: AJ 342 GLN cc_start: 0.7502 (mm-40) cc_final: 0.6767 (mt0) REVERT: AK 331 MET cc_start: 0.8006 (ttm) cc_final: 0.7741 (ttm) REVERT: AK 339 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8475 (mp) REVERT: AN 339 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8828 (mp) REVERT: AO 330 ASN cc_start: 0.8273 (p0) cc_final: 0.7767 (p0) REVERT: AO 331 MET cc_start: 0.8330 (mmm) cc_final: 0.8056 (mmm) REVERT: AO 356 MET cc_start: 0.9244 (mtm) cc_final: 0.9008 (mtp) REVERT: c 21 ARG cc_start: 0.8334 (mtp180) cc_final: 0.8074 (mtp85) REVERT: c 24 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8348 (mt-10) REVERT: d 47 LYS cc_start: 0.8591 (tptt) cc_final: 0.7734 (ttpt) REVERT: d 84 THR cc_start: 0.9358 (OUTLIER) cc_final: 0.9075 (m) REVERT: d 90 ASP cc_start: 0.8847 (p0) cc_final: 0.8409 (p0) REVERT: d 126 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8532 (tttp) REVERT: e 115 ASP cc_start: 0.8277 (m-30) cc_final: 0.7952 (m-30) REVERT: f 47 LYS cc_start: 0.8185 (ttmm) cc_final: 0.7819 (ttpp) REVERT: g 39 LYS cc_start: 0.6015 (OUTLIER) cc_final: 0.5498 (ptpt) REVERT: g 78 SER cc_start: 0.8667 (t) cc_final: 0.8108 (m) REVERT: g 95 TYR cc_start: 0.8714 (m-80) cc_final: 0.8251 (m-80) REVERT: g 134 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7880 (mt0) REVERT: g 135 MET cc_start: 0.8696 (ttm) cc_final: 0.8124 (ttm) REVERT: i 66 LYS cc_start: 0.7885 (pttt) cc_final: 0.7596 (pttm) REVERT: i 102 MET cc_start: 0.7551 (mmp) cc_final: 0.6852 (mpp) REVERT: i 123 ASP cc_start: 0.8451 (t70) cc_final: 0.8043 (t0) REVERT: i 131 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8490 (tpt170) REVERT: j 80 GLU cc_start: 0.8655 (mt-10) cc_final: 0.7670 (tp30) REVERT: l 14 MET cc_start: 0.9110 (mtp) cc_final: 0.8853 (mtm) REVERT: l 36 SER cc_start: 0.9092 (p) cc_final: 0.8789 (t) REVERT: l 108 MET cc_start: 0.8895 (ttm) cc_final: 0.8590 (ttp) REVERT: l 113 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.8675 (mmp-170) REVERT: l 131 ARG cc_start: 0.7958 (mmm-85) cc_final: 0.7699 (mmt-90) REVERT: m 172 GLN cc_start: 0.8346 (mm-40) cc_final: 0.7935 (mm-40) REVERT: o 58 MET cc_start: 0.8693 (mtp) cc_final: 0.8141 (ttt) REVERT: o 158 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7768 (m-80) REVERT: o 222 GLN cc_start: 0.8357 (mt0) cc_final: 0.8108 (tt0) REVERT: o 231 MET cc_start: 0.9022 (tpp) cc_final: 0.8634 (tpp) REVERT: p 112 MET cc_start: 0.8242 (mtm) cc_final: 0.7944 (tpp) REVERT: p 135 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8613 (pp) REVERT: p 157 GLU cc_start: 0.7483 (mt-10) cc_final: 0.6482 (tm-30) REVERT: q 83 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7581 (mm-30) REVERT: q 91 LEU cc_start: 0.8534 (pt) cc_final: 0.8325 (pt) REVERT: q 215 MET cc_start: 0.8528 (mmm) cc_final: 0.8190 (mtt) REVERT: r 34 ASN cc_start: 0.3871 (OUTLIER) cc_final: 0.3382 (t0) REVERT: r 101 MET cc_start: 0.7723 (mtm) cc_final: 0.7405 (mtt) REVERT: t 57 ARG cc_start: 0.8417 (mtm-85) cc_final: 0.8042 (mtp180) REVERT: t 71 MET cc_start: 0.9173 (mmm) cc_final: 0.8868 (mmm) REVERT: u 69 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7510 (m-30) REVERT: u 78 SER cc_start: 0.8691 (t) cc_final: 0.7977 (m) REVERT: u 82 ASP cc_start: 0.8213 (m-30) cc_final: 0.7969 (m-30) REVERT: v 82 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7828 (t0) REVERT: v 92 VAL cc_start: 0.9129 (t) cc_final: 0.8916 (t) REVERT: y 104 ILE cc_start: 0.8885 (tt) cc_final: 0.8632 (pt) REVERT: y 180 LYS cc_start: 0.8396 (ttmt) cc_final: 0.8022 (tttt) REVERT: y 191 ASP cc_start: 0.7723 (m-30) cc_final: 0.7426 (m-30) REVERT: y 251 MET cc_start: 0.8096 (mmt) cc_final: 0.7856 (mmt) REVERT: y 255 MET cc_start: 0.7197 (mmp) cc_final: 0.6921 (mmp) REVERT: y 265 PHE cc_start: 0.8597 (m-80) cc_final: 0.8072 (m-10) REVERT: z 222 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7800 (mm-30) REVERT: z 232 MET cc_start: 0.8085 (mmt) cc_final: 0.7526 (mmt) REVERT: z 255 MET cc_start: 0.8239 (mmm) cc_final: 0.7392 (mmm) outliers start: 188 outliers final: 138 residues processed: 985 average time/residue: 0.2253 time to fit residues: 370.2975 Evaluate side-chains 991 residues out of total 4223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 835 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 123 MET Chi-restraints excluded: chain 1 residue 127 GLN Chi-restraints excluded: chain 1 residue 128 THR Chi-restraints excluded: chain 1 residue 185 LYS Chi-restraints excluded: chain 1 residue 208 ASP Chi-restraints excluded: chain 2 residue 128 THR Chi-restraints excluded: chain 2 residue 149 VAL Chi-restraints excluded: chain 2 residue 179 MET Chi-restraints excluded: chain 2 residue 273 VAL Chi-restraints excluded: chain 3 residue 86 THR Chi-restraints excluded: chain 3 residue 132 GLN Chi-restraints excluded: chain 3 residue 149 VAL Chi-restraints excluded: chain 3 residue 155 ASP Chi-restraints excluded: chain 3 residue 203 VAL Chi-restraints excluded: chain 3 residue 273 VAL Chi-restraints excluded: chain 4 residue 12 GLU Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 4 residue 28 SER Chi-restraints excluded: chain 5 residue 26 ILE Chi-restraints excluded: chain 5 residue 45 ASN Chi-restraints excluded: chain 5 residue 75 GLU Chi-restraints excluded: chain 6 residue 17 VAL Chi-restraints excluded: chain 6 residue 28 SER Chi-restraints excluded: chain 6 residue 31 ILE Chi-restraints excluded: chain 7 residue 84 LEU Chi-restraints excluded: chain 8 residue 24 SER Chi-restraints excluded: chain 8 residue 27 MET Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 66 LEU Chi-restraints excluded: chain 8 residue 70 ARG Chi-restraints excluded: chain 8 residue 125 LEU Chi-restraints excluded: chain 8 residue 131 MET Chi-restraints excluded: chain 8 residue 152 VAL Chi-restraints excluded: chain 8 residue 190 SER Chi-restraints excluded: chain 8 residue 192 ILE Chi-restraints excluded: chain 8 residue 200 LEU Chi-restraints excluded: chain 8 residue 229 LEU Chi-restraints excluded: chain 8 residue 258 LEU Chi-restraints excluded: chain AA residue 353 VAL Chi-restraints excluded: chain AB residue 341 ASN Chi-restraints excluded: chain AC residue 353 VAL Chi-restraints excluded: chain AE residue 348 SER Chi-restraints excluded: chain AE residue 349 ILE Chi-restraints excluded: chain AK residue 339 LEU Chi-restraints excluded: chain AK residue 342 GLN Chi-restraints excluded: chain AK residue 352 ASP Chi-restraints excluded: chain AN residue 339 LEU Chi-restraints excluded: chain AO residue 339 LEU Chi-restraints excluded: chain b residue 28 THR Chi-restraints excluded: chain b residue 88 THR Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain c residue 6 ASP Chi-restraints excluded: chain c residue 87 ASP Chi-restraints excluded: chain c residue 97 ASP Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 88 THR Chi-restraints excluded: chain d residue 97 ASP Chi-restraints excluded: chain d residue 119 SER Chi-restraints excluded: chain d residue 126 LYS Chi-restraints excluded: chain d residue 129 LYS Chi-restraints excluded: chain e residue 88 THR Chi-restraints excluded: chain f residue 88 THR Chi-restraints excluded: chain f residue 128 ILE Chi-restraints excluded: chain g residue 39 LYS Chi-restraints excluded: chain g residue 53 LEU Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain g residue 134 GLN Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain h residue 34 VAL Chi-restraints excluded: chain h residue 40 ASP Chi-restraints excluded: chain h residue 53 LEU Chi-restraints excluded: chain h residue 65 VAL Chi-restraints excluded: chain h residue 68 MET Chi-restraints excluded: chain h residue 71 VAL Chi-restraints excluded: chain h residue 87 LEU Chi-restraints excluded: chain h residue 112 SER Chi-restraints excluded: chain i residue 3 LEU Chi-restraints excluded: chain i residue 18 SER Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 78 SER Chi-restraints excluded: chain i residue 101 VAL Chi-restraints excluded: chain i residue 124 SER Chi-restraints excluded: chain i residue 131 ARG Chi-restraints excluded: chain j residue 3 LEU Chi-restraints excluded: chain j residue 23 THR Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 101 VAL Chi-restraints excluded: chain k residue 40 ASP Chi-restraints excluded: chain k residue 53 LEU Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain l residue 3 LEU Chi-restraints excluded: chain l residue 37 SER Chi-restraints excluded: chain l residue 61 ASP Chi-restraints excluded: chain l residue 65 VAL Chi-restraints excluded: chain l residue 78 SER Chi-restraints excluded: chain l residue 87 LEU Chi-restraints excluded: chain l residue 113 ARG Chi-restraints excluded: chain m residue 81 THR Chi-restraints excluded: chain m residue 94 THR Chi-restraints excluded: chain m residue 196 THR Chi-restraints excluded: chain m residue 248 MET Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 10 SER Chi-restraints excluded: chain n residue 19 LEU Chi-restraints excluded: chain n residue 85 SER Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain n residue 107 VAL Chi-restraints excluded: chain n residue 114 THR Chi-restraints excluded: chain n residue 158 PHE Chi-restraints excluded: chain n residue 233 SER Chi-restraints excluded: chain o residue 81 THR Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain o residue 94 THR Chi-restraints excluded: chain o residue 158 PHE Chi-restraints excluded: chain o residue 233 SER Chi-restraints excluded: chain o residue 234 THR Chi-restraints excluded: chain o residue 248 MET Chi-restraints excluded: chain p residue 81 THR Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain p residue 196 THR Chi-restraints excluded: chain p residue 212 VAL Chi-restraints excluded: chain p residue 243 ASP Chi-restraints excluded: chain q residue 81 THR Chi-restraints excluded: chain q residue 147 SER Chi-restraints excluded: chain q residue 212 VAL Chi-restraints excluded: chain q residue 241 SER Chi-restraints excluded: chain q residue 243 ASP Chi-restraints excluded: chain r residue 34 ASN Chi-restraints excluded: chain s residue 46 THR Chi-restraints excluded: chain s residue 51 SER Chi-restraints excluded: chain t residue 32 ASP Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain u residue 53 ASP Chi-restraints excluded: chain u residue 69 ASP Chi-restraints excluded: chain v residue 38 THR Chi-restraints excluded: chain v residue 49 LYS Chi-restraints excluded: chain v residue 51 SER Chi-restraints excluded: chain v residue 82 ASP Chi-restraints excluded: chain v residue 103 VAL Chi-restraints excluded: chain w residue 66 SER Chi-restraints excluded: chain x residue 48 TRP Chi-restraints excluded: chain y residue 84 SER Chi-restraints excluded: chain y residue 117 SER Chi-restraints excluded: chain y residue 125 LEU Chi-restraints excluded: chain y residue 141 LEU Chi-restraints excluded: chain y residue 147 SER Chi-restraints excluded: chain y residue 167 THR Chi-restraints excluded: chain y residue 198 MET Chi-restraints excluded: chain y residue 210 SER Chi-restraints excluded: chain z residue 113 VAL Chi-restraints excluded: chain z residue 123 MET Chi-restraints excluded: chain z residue 128 THR Chi-restraints excluded: chain z residue 184 LEU Chi-restraints excluded: chain z residue 222 GLU Chi-restraints excluded: chain z residue 253 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 41 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 222 optimal weight: 8.9990 chunk 379 optimal weight: 0.7980 chunk 295 optimal weight: 0.7980 chunk 411 optimal weight: 0.8980 chunk 175 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 329 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 277 ASN 2 205 ASN AM 355 GLN AO 341 ASN f 34 ASN ** h 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 134 GLN ** n 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 125 ASN ** r 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 75 ASN y 121 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.144541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.119731 restraints weight = 46859.253| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.44 r_work: 0.3218 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 38926 Z= 0.124 Angle : 0.516 9.957 52695 Z= 0.258 Chirality : 0.040 0.225 6219 Planarity : 0.003 0.050 6827 Dihedral : 5.104 61.557 5296 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.86 % Favored : 98.10 % Rotamer: Outliers : 3.88 % Allowed : 15.34 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.65 (0.12), residues: 4896 helix: 2.94 (0.09), residues: 2887 sheet: -1.18 (0.27), residues: 338 loop : 0.29 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG m 247 TYR 0.017 0.001 TYR k 115 PHE 0.019 0.001 PHE y 231 TRP 0.013 0.001 TRP x 48 HIS 0.002 0.001 HIS p 51 Details of bonding type rmsd covalent geometry : bond 0.00276 (38926) covalent geometry : angle 0.51616 (52695) hydrogen bonds : bond 0.04404 ( 2457) hydrogen bonds : angle 3.70812 ( 7296) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1019 residues out of total 4223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 855 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 123 MET cc_start: 0.6034 (OUTLIER) cc_final: 0.5619 (mpp) REVERT: 1 156 LYS cc_start: 0.6850 (mmmt) cc_final: 0.6594 (mtpp) REVERT: 1 223 LEU cc_start: 0.7968 (mp) cc_final: 0.7521 (mm) REVERT: 1 249 MET cc_start: 0.8029 (tpt) cc_final: 0.7770 (tpp) REVERT: 1 255 MET cc_start: 0.8202 (tpp) cc_final: 0.7656 (mmp) REVERT: 2 123 MET cc_start: 0.8111 (mtm) cc_final: 0.7679 (mtm) REVERT: 2 156 LYS cc_start: 0.8627 (mptp) cc_final: 0.8101 (mtpp) REVERT: 2 249 MET cc_start: 0.8528 (mmm) cc_final: 0.8043 (tpt) REVERT: 2 272 LEU cc_start: 0.8134 (pp) cc_final: 0.6934 (mt) REVERT: 3 86 THR cc_start: 0.9019 (OUTLIER) cc_final: 0.8693 (p) REVERT: 3 121 GLN cc_start: 0.8202 (tp40) cc_final: 0.7789 (tt0) REVERT: 3 132 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7794 (mm-40) REVERT: 3 179 MET cc_start: 0.6976 (mmt) cc_final: 0.6287 (mtt) REVERT: 3 185 LYS cc_start: 0.7887 (mptt) cc_final: 0.7642 (mttt) REVERT: 3 251 MET cc_start: 0.7264 (OUTLIER) cc_final: 0.6936 (ttt) REVERT: 4 63 MET cc_start: 0.6880 (tmm) cc_final: 0.5804 (mmm) REVERT: 5 26 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8302 (mp) REVERT: 5 74 MET cc_start: 0.8212 (mtp) cc_final: 0.7908 (mtp) REVERT: 5 75 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7415 (mp0) REVERT: 7 15 TRP cc_start: 0.7077 (t-100) cc_final: 0.6435 (t-100) REVERT: 7 16 MET cc_start: 0.8341 (tpp) cc_final: 0.8011 (tpt) REVERT: 8 70 ARG cc_start: 0.7022 (OUTLIER) cc_final: 0.6031 (ttt-90) REVERT: 8 231 TRP cc_start: 0.7197 (t60) cc_final: 0.6682 (t60) REVERT: AC 355 GLN cc_start: 0.8003 (mp10) cc_final: 0.7769 (mp10) REVERT: AJ 356 MET cc_start: 0.2772 (tpt) cc_final: 0.2392 (tpt) REVERT: AK 331 MET cc_start: 0.8038 (ttm) cc_final: 0.7700 (ttm) REVERT: AK 339 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8523 (mp) REVERT: AN 339 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8663 (mp) REVERT: AO 330 ASN cc_start: 0.8247 (p0) cc_final: 0.7697 (p0) REVERT: AO 331 MET cc_start: 0.8301 (mmm) cc_final: 0.8066 (mmm) REVERT: AO 356 MET cc_start: 0.9210 (mtm) cc_final: 0.8965 (mtp) REVERT: c 24 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8305 (mt-10) REVERT: d 47 LYS cc_start: 0.8584 (tptt) cc_final: 0.7744 (ttpt) REVERT: d 84 THR cc_start: 0.9348 (t) cc_final: 0.9073 (m) REVERT: d 90 ASP cc_start: 0.8792 (p0) cc_final: 0.8339 (p0) REVERT: d 126 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8546 (tttp) REVERT: e 115 ASP cc_start: 0.8245 (m-30) cc_final: 0.7910 (m-30) REVERT: f 41 ARG cc_start: 0.8234 (tpp80) cc_final: 0.8017 (tpp80) REVERT: f 47 LYS cc_start: 0.8134 (ttmm) cc_final: 0.7761 (ttpp) REVERT: g 39 LYS cc_start: 0.5982 (OUTLIER) cc_final: 0.5480 (ptpt) REVERT: g 78 SER cc_start: 0.8646 (t) cc_final: 0.8120 (m) REVERT: g 80 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7521 (tp30) REVERT: g 95 TYR cc_start: 0.8639 (m-80) cc_final: 0.8175 (m-80) REVERT: g 134 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7856 (mt0) REVERT: g 135 MET cc_start: 0.8659 (ttm) cc_final: 0.8089 (ttm) REVERT: i 66 LYS cc_start: 0.7820 (pttt) cc_final: 0.7536 (pttm) REVERT: i 102 MET cc_start: 0.7466 (mmp) cc_final: 0.6740 (mpp) REVERT: i 131 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8471 (tpt170) REVERT: j 80 GLU cc_start: 0.8553 (mt-10) cc_final: 0.7598 (tp30) REVERT: l 14 MET cc_start: 0.9086 (mtp) cc_final: 0.8872 (mtm) REVERT: l 36 SER cc_start: 0.9017 (p) cc_final: 0.8721 (t) REVERT: l 91 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7889 (mt-10) REVERT: l 108 MET cc_start: 0.8776 (ttm) cc_final: 0.8462 (ttp) REVERT: l 113 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8654 (mmp-170) REVERT: l 131 ARG cc_start: 0.7915 (mmm-85) cc_final: 0.7671 (mmt-90) REVERT: m 172 GLN cc_start: 0.8342 (mm-40) cc_final: 0.7875 (mm-40) REVERT: o 58 MET cc_start: 0.8586 (mtp) cc_final: 0.8058 (ttt) REVERT: o 158 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7566 (m-80) REVERT: o 222 GLN cc_start: 0.8267 (mt0) cc_final: 0.8048 (tt0) REVERT: o 231 MET cc_start: 0.9019 (tpp) cc_final: 0.8634 (tpp) REVERT: p 112 MET cc_start: 0.8204 (mtm) cc_final: 0.7902 (tpp) REVERT: p 135 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8608 (pp) REVERT: p 157 GLU cc_start: 0.7445 (mt-10) cc_final: 0.6457 (tm-30) REVERT: q 91 LEU cc_start: 0.8459 (pt) cc_final: 0.8227 (pt) REVERT: q 196 THR cc_start: 0.9075 (p) cc_final: 0.8871 (p) REVERT: q 215 MET cc_start: 0.8384 (mmm) cc_final: 0.8048 (mtt) REVERT: q 240 LYS cc_start: 0.8756 (ttmm) cc_final: 0.8377 (ttpp) REVERT: r 34 ASN cc_start: 0.3697 (OUTLIER) cc_final: 0.3236 (t0) REVERT: r 101 MET cc_start: 0.7586 (mtm) cc_final: 0.7289 (mtt) REVERT: s 96 LYS cc_start: 0.7614 (mttm) cc_final: 0.7404 (mttp) REVERT: s 99 MET cc_start: 0.6707 (ppp) cc_final: 0.5780 (ppp) REVERT: t 57 ARG cc_start: 0.8392 (mtm-85) cc_final: 0.7993 (mtp180) REVERT: t 71 MET cc_start: 0.9127 (mmm) cc_final: 0.8865 (mmm) REVERT: u 69 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7470 (m-30) REVERT: u 78 SER cc_start: 0.8703 (t) cc_final: 0.7965 (m) REVERT: u 82 ASP cc_start: 0.8171 (m-30) cc_final: 0.7917 (m-30) REVERT: v 82 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7788 (t0) REVERT: v 92 VAL cc_start: 0.9075 (t) cc_final: 0.8864 (t) REVERT: y 180 LYS cc_start: 0.8287 (ttmt) cc_final: 0.7991 (tttt) REVERT: y 191 ASP cc_start: 0.7760 (m-30) cc_final: 0.7451 (m-30) REVERT: y 265 PHE cc_start: 0.8560 (m-80) cc_final: 0.8066 (m-10) REVERT: z 222 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7469 (mm-30) REVERT: z 232 MET cc_start: 0.7886 (mmt) cc_final: 0.7415 (mmt) REVERT: z 255 MET cc_start: 0.8170 (mmm) cc_final: 0.7323 (mmm) outliers start: 164 outliers final: 121 residues processed: 967 average time/residue: 0.2219 time to fit residues: 357.2779 Evaluate side-chains 984 residues out of total 4223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 843 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 123 MET Chi-restraints excluded: chain 1 residue 127 GLN Chi-restraints excluded: chain 1 residue 128 THR Chi-restraints excluded: chain 1 residue 185 LYS Chi-restraints excluded: chain 2 residue 128 THR Chi-restraints excluded: chain 2 residue 147 SER Chi-restraints excluded: chain 2 residue 149 VAL Chi-restraints excluded: chain 2 residue 273 VAL Chi-restraints excluded: chain 3 residue 86 THR Chi-restraints excluded: chain 3 residue 110 THR Chi-restraints excluded: chain 3 residue 132 GLN Chi-restraints excluded: chain 3 residue 149 VAL Chi-restraints excluded: chain 3 residue 155 ASP Chi-restraints excluded: chain 3 residue 176 GLN Chi-restraints excluded: chain 3 residue 203 VAL Chi-restraints excluded: chain 3 residue 239 ILE Chi-restraints excluded: chain 3 residue 251 MET Chi-restraints excluded: chain 3 residue 273 VAL Chi-restraints excluded: chain 4 residue 12 GLU Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 4 residue 28 SER Chi-restraints excluded: chain 4 residue 55 LEU Chi-restraints excluded: chain 5 residue 26 ILE Chi-restraints excluded: chain 5 residue 75 GLU Chi-restraints excluded: chain 6 residue 17 VAL Chi-restraints excluded: chain 6 residue 28 SER Chi-restraints excluded: chain 6 residue 31 ILE Chi-restraints excluded: chain 7 residue 19 ILE Chi-restraints excluded: chain 8 residue 66 LEU Chi-restraints excluded: chain 8 residue 70 ARG Chi-restraints excluded: chain 8 residue 125 LEU Chi-restraints excluded: chain 8 residue 131 MET Chi-restraints excluded: chain 8 residue 152 VAL Chi-restraints excluded: chain 8 residue 190 SER Chi-restraints excluded: chain 8 residue 192 ILE Chi-restraints excluded: chain 8 residue 200 LEU Chi-restraints excluded: chain 8 residue 258 LEU Chi-restraints excluded: chain AC residue 353 VAL Chi-restraints excluded: chain AE residue 348 SER Chi-restraints excluded: chain AK residue 339 LEU Chi-restraints excluded: chain AK residue 342 GLN Chi-restraints excluded: chain AK residue 352 ASP Chi-restraints excluded: chain AL residue 356 MET Chi-restraints excluded: chain AN residue 339 LEU Chi-restraints excluded: chain AO residue 339 LEU Chi-restraints excluded: chain b residue 28 THR Chi-restraints excluded: chain b residue 88 THR Chi-restraints excluded: chain c residue 6 ASP Chi-restraints excluded: chain c residue 97 ASP Chi-restraints excluded: chain d residue 88 THR Chi-restraints excluded: chain d residue 126 LYS Chi-restraints excluded: chain d residue 129 LYS Chi-restraints excluded: chain e residue 88 THR Chi-restraints excluded: chain f residue 88 THR Chi-restraints excluded: chain f residue 128 ILE Chi-restraints excluded: chain g residue 39 LYS Chi-restraints excluded: chain g residue 53 LEU Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain g residue 134 GLN Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain h residue 34 VAL Chi-restraints excluded: chain h residue 40 ASP Chi-restraints excluded: chain h residue 53 LEU Chi-restraints excluded: chain h residue 65 VAL Chi-restraints excluded: chain h residue 68 MET Chi-restraints excluded: chain h residue 71 VAL Chi-restraints excluded: chain h residue 112 SER Chi-restraints excluded: chain i residue 3 LEU Chi-restraints excluded: chain i residue 18 SER Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 78 SER Chi-restraints excluded: chain i residue 124 SER Chi-restraints excluded: chain i residue 131 ARG Chi-restraints excluded: chain j residue 3 LEU Chi-restraints excluded: chain j residue 23 THR Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 101 VAL Chi-restraints excluded: chain k residue 40 ASP Chi-restraints excluded: chain k residue 53 LEU Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain l residue 3 LEU Chi-restraints excluded: chain l residue 37 SER Chi-restraints excluded: chain l residue 40 ASP Chi-restraints excluded: chain l residue 61 ASP Chi-restraints excluded: chain l residue 65 VAL Chi-restraints excluded: chain l residue 78 SER Chi-restraints excluded: chain l residue 87 LEU Chi-restraints excluded: chain l residue 113 ARG Chi-restraints excluded: chain m residue 94 THR Chi-restraints excluded: chain m residue 196 THR Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 10 SER Chi-restraints excluded: chain n residue 19 LEU Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain n residue 107 VAL Chi-restraints excluded: chain n residue 114 THR Chi-restraints excluded: chain n residue 149 LEU Chi-restraints excluded: chain n residue 158 PHE Chi-restraints excluded: chain n residue 233 SER Chi-restraints excluded: chain o residue 43 SER Chi-restraints excluded: chain o residue 94 THR Chi-restraints excluded: chain o residue 158 PHE Chi-restraints excluded: chain o residue 233 SER Chi-restraints excluded: chain o residue 234 THR Chi-restraints excluded: chain o residue 248 MET Chi-restraints excluded: chain p residue 81 THR Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain p residue 196 THR Chi-restraints excluded: chain p residue 212 VAL Chi-restraints excluded: chain p residue 243 ASP Chi-restraints excluded: chain q residue 81 THR Chi-restraints excluded: chain q residue 147 SER Chi-restraints excluded: chain q residue 241 SER Chi-restraints excluded: chain q residue 243 ASP Chi-restraints excluded: chain r residue 34 ASN Chi-restraints excluded: chain s residue 46 THR Chi-restraints excluded: chain s residue 51 SER Chi-restraints excluded: chain s residue 98 LEU Chi-restraints excluded: chain t residue 32 ASP Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 103 VAL Chi-restraints excluded: chain u residue 53 ASP Chi-restraints excluded: chain u residue 69 ASP Chi-restraints excluded: chain v residue 51 SER Chi-restraints excluded: chain v residue 82 ASP Chi-restraints excluded: chain v residue 103 VAL Chi-restraints excluded: chain x residue 48 TRP Chi-restraints excluded: chain y residue 84 SER Chi-restraints excluded: chain y residue 117 SER Chi-restraints excluded: chain y residue 125 LEU Chi-restraints excluded: chain y residue 141 LEU Chi-restraints excluded: chain y residue 147 SER Chi-restraints excluded: chain y residue 167 THR Chi-restraints excluded: chain y residue 198 MET Chi-restraints excluded: chain y residue 210 SER Chi-restraints excluded: chain z residue 113 VAL Chi-restraints excluded: chain z residue 128 THR Chi-restraints excluded: chain z residue 184 LEU Chi-restraints excluded: chain z residue 222 GLU Chi-restraints excluded: chain z residue 253 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 241 optimal weight: 0.9990 chunk 318 optimal weight: 8.9990 chunk 112 optimal weight: 0.9990 chunk 296 optimal weight: 2.9990 chunk 127 optimal weight: 0.0980 chunk 276 optimal weight: 1.9990 chunk 438 optimal weight: 9.9990 chunk 162 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 219 optimal weight: 0.9990 chunk 206 optimal weight: 2.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 205 ASN 2 228 GLN AJ 342 GLN f 34 ASN ** i 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 134 GLN ** n 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 125 ASN ** r 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 75 ASN y 121 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.144920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.119885 restraints weight = 46678.105| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.41 r_work: 0.3267 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 38926 Z= 0.122 Angle : 0.519 11.829 52695 Z= 0.257 Chirality : 0.039 0.237 6219 Planarity : 0.003 0.044 6827 Dihedral : 5.014 60.080 5292 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.94 % Favored : 98.02 % Rotamer: Outliers : 3.98 % Allowed : 15.61 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.12), residues: 4896 helix: 2.98 (0.09), residues: 2888 sheet: -1.03 (0.24), residues: 403 loop : 0.39 (0.16), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG m 247 TYR 0.012 0.001 TYR u 95 PHE 0.030 0.001 PHE 2 231 TRP 0.012 0.001 TRP x 48 HIS 0.002 0.001 HIS p 51 Details of bonding type rmsd covalent geometry : bond 0.00271 (38926) covalent geometry : angle 0.51938 (52695) hydrogen bonds : bond 0.04266 ( 2457) hydrogen bonds : angle 3.65024 ( 7296) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1025 residues out of total 4223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 857 time to evaluate : 1.538 Fit side-chains revert: symmetry clash REVERT: 1 123 MET cc_start: 0.5931 (OUTLIER) cc_final: 0.5559 (mpp) REVERT: 1 156 LYS cc_start: 0.6891 (mmmt) cc_final: 0.6670 (mtpp) REVERT: 1 223 LEU cc_start: 0.7974 (mp) cc_final: 0.7518 (mm) REVERT: 1 249 MET cc_start: 0.8023 (tpt) cc_final: 0.7787 (tpp) REVERT: 2 156 LYS cc_start: 0.8602 (mptp) cc_final: 0.8072 (mtpp) REVERT: 2 180 LYS cc_start: 0.7504 (mtpp) cc_final: 0.7157 (mttt) REVERT: 2 249 MET cc_start: 0.8440 (mmm) cc_final: 0.8211 (tpp) REVERT: 3 86 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8675 (p) REVERT: 3 121 GLN cc_start: 0.8222 (tp40) cc_final: 0.7823 (tt0) REVERT: 3 132 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7870 (mm110) REVERT: 3 179 MET cc_start: 0.6959 (mmt) cc_final: 0.6274 (mtt) REVERT: 3 185 LYS cc_start: 0.7879 (mptt) cc_final: 0.7644 (mttt) REVERT: 3 251 MET cc_start: 0.7287 (OUTLIER) cc_final: 0.6835 (ttt) REVERT: 4 63 MET cc_start: 0.6852 (tmm) cc_final: 0.5776 (mmm) REVERT: 5 26 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8367 (mp) REVERT: 5 74 MET cc_start: 0.8171 (mtp) cc_final: 0.7853 (mtp) REVERT: 5 75 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7450 (mp0) REVERT: 7 15 TRP cc_start: 0.6992 (t-100) cc_final: 0.6347 (t-100) REVERT: 7 16 MET cc_start: 0.8346 (tpp) cc_final: 0.7998 (tpt) REVERT: 8 70 ARG cc_start: 0.6940 (OUTLIER) cc_final: 0.5958 (ttt-90) REVERT: 8 231 TRP cc_start: 0.7181 (t60) cc_final: 0.6630 (t60) REVERT: AC 355 GLN cc_start: 0.8003 (mp10) cc_final: 0.7786 (mp10) REVERT: AJ 356 MET cc_start: 0.2596 (tpt) cc_final: 0.2292 (tpt) REVERT: AK 339 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8566 (mp) REVERT: AN 339 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8697 (mp) REVERT: AO 330 ASN cc_start: 0.8262 (p0) cc_final: 0.7717 (p0) REVERT: AO 356 MET cc_start: 0.9218 (mtm) cc_final: 0.9000 (mtp) REVERT: c 24 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8352 (mt-10) REVERT: d 47 LYS cc_start: 0.8656 (tptt) cc_final: 0.7847 (ttpt) REVERT: d 84 THR cc_start: 0.9363 (t) cc_final: 0.9074 (m) REVERT: d 126 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8545 (tttp) REVERT: e 115 ASP cc_start: 0.8175 (m-30) cc_final: 0.7851 (m-30) REVERT: f 47 LYS cc_start: 0.8153 (ttmm) cc_final: 0.7773 (ttpp) REVERT: g 39 LYS cc_start: 0.5999 (OUTLIER) cc_final: 0.5511 (ptpt) REVERT: g 68 MET cc_start: 0.8534 (mmm) cc_final: 0.8095 (mmm) REVERT: g 80 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7521 (tp30) REVERT: g 95 TYR cc_start: 0.8645 (m-80) cc_final: 0.8207 (m-80) REVERT: g 134 GLN cc_start: 0.8112 (tp40) cc_final: 0.7908 (mt0) REVERT: g 135 MET cc_start: 0.8648 (ttm) cc_final: 0.8036 (ttm) REVERT: i 66 LYS cc_start: 0.7822 (pttt) cc_final: 0.7552 (pttm) REVERT: i 102 MET cc_start: 0.7485 (mmp) cc_final: 0.6775 (mpp) REVERT: i 131 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8500 (tpt170) REVERT: j 80 GLU cc_start: 0.8548 (mt-10) cc_final: 0.7619 (tp30) REVERT: l 36 SER cc_start: 0.9005 (p) cc_final: 0.8726 (t) REVERT: l 91 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7948 (mt-10) REVERT: l 108 MET cc_start: 0.8719 (ttm) cc_final: 0.8386 (ttp) REVERT: l 113 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8648 (mmp-170) REVERT: l 131 ARG cc_start: 0.7927 (mmm-85) cc_final: 0.7660 (mmt-90) REVERT: m 172 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7807 (mm-40) REVERT: o 58 MET cc_start: 0.8620 (mtp) cc_final: 0.8105 (ttt) REVERT: o 93 HIS cc_start: 0.7137 (OUTLIER) cc_final: 0.6936 (m-70) REVERT: o 158 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7550 (m-80) REVERT: o 222 GLN cc_start: 0.8198 (mt0) cc_final: 0.7989 (tt0) REVERT: p 112 MET cc_start: 0.8191 (mtm) cc_final: 0.7898 (tpp) REVERT: p 135 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8608 (pp) REVERT: p 157 GLU cc_start: 0.7511 (mt-10) cc_final: 0.6520 (tm-30) REVERT: q 215 MET cc_start: 0.8364 (mmm) cc_final: 0.8035 (mtt) REVERT: q 240 LYS cc_start: 0.8688 (ttmm) cc_final: 0.8293 (ttpp) REVERT: r 34 ASN cc_start: 0.3685 (OUTLIER) cc_final: 0.3263 (t0) REVERT: r 101 MET cc_start: 0.7622 (mtm) cc_final: 0.7313 (mtt) REVERT: t 57 ARG cc_start: 0.8461 (mtm-85) cc_final: 0.8052 (mtp180) REVERT: t 71 MET cc_start: 0.9148 (mmm) cc_final: 0.8930 (mmm) REVERT: u 69 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7476 (m-30) REVERT: u 78 SER cc_start: 0.8717 (t) cc_final: 0.7988 (m) REVERT: u 82 ASP cc_start: 0.8231 (m-30) cc_final: 0.7992 (m-30) REVERT: v 82 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7830 (t0) REVERT: v 92 VAL cc_start: 0.9079 (t) cc_final: 0.8877 (t) REVERT: y 180 LYS cc_start: 0.8310 (ttmt) cc_final: 0.8009 (tttt) REVERT: y 191 ASP cc_start: 0.7745 (m-30) cc_final: 0.7428 (m-30) REVERT: y 265 PHE cc_start: 0.8553 (m-80) cc_final: 0.8056 (m-10) REVERT: z 222 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7490 (mm-30) REVERT: z 255 MET cc_start: 0.8203 (mmm) cc_final: 0.7368 (mmm) outliers start: 168 outliers final: 131 residues processed: 971 average time/residue: 0.2282 time to fit residues: 369.4154 Evaluate side-chains 990 residues out of total 4223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 839 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 123 MET Chi-restraints excluded: chain 1 residue 127 GLN Chi-restraints excluded: chain 1 residue 128 THR Chi-restraints excluded: chain 1 residue 185 LYS Chi-restraints excluded: chain 2 residue 128 THR Chi-restraints excluded: chain 2 residue 147 SER Chi-restraints excluded: chain 2 residue 149 VAL Chi-restraints excluded: chain 2 residue 179 MET Chi-restraints excluded: chain 2 residue 273 VAL Chi-restraints excluded: chain 3 residue 86 THR Chi-restraints excluded: chain 3 residue 132 GLN Chi-restraints excluded: chain 3 residue 149 VAL Chi-restraints excluded: chain 3 residue 155 ASP Chi-restraints excluded: chain 3 residue 176 GLN Chi-restraints excluded: chain 3 residue 203 VAL Chi-restraints excluded: chain 3 residue 239 ILE Chi-restraints excluded: chain 3 residue 251 MET Chi-restraints excluded: chain 3 residue 273 VAL Chi-restraints excluded: chain 4 residue 12 GLU Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 4 residue 28 SER Chi-restraints excluded: chain 4 residue 55 LEU Chi-restraints excluded: chain 5 residue 26 ILE Chi-restraints excluded: chain 5 residue 45 ASN Chi-restraints excluded: chain 5 residue 75 GLU Chi-restraints excluded: chain 6 residue 17 VAL Chi-restraints excluded: chain 6 residue 28 SER Chi-restraints excluded: chain 6 residue 31 ILE Chi-restraints excluded: chain 7 residue 19 ILE Chi-restraints excluded: chain 8 residue 24 SER Chi-restraints excluded: chain 8 residue 27 MET Chi-restraints excluded: chain 8 residue 66 LEU Chi-restraints excluded: chain 8 residue 70 ARG Chi-restraints excluded: chain 8 residue 125 LEU Chi-restraints excluded: chain 8 residue 131 MET Chi-restraints excluded: chain 8 residue 190 SER Chi-restraints excluded: chain 8 residue 192 ILE Chi-restraints excluded: chain 8 residue 200 LEU Chi-restraints excluded: chain 8 residue 258 LEU Chi-restraints excluded: chain AC residue 353 VAL Chi-restraints excluded: chain AD residue 349 ILE Chi-restraints excluded: chain AE residue 348 SER Chi-restraints excluded: chain AE residue 349 ILE Chi-restraints excluded: chain AK residue 339 LEU Chi-restraints excluded: chain AK residue 342 GLN Chi-restraints excluded: chain AK residue 352 ASP Chi-restraints excluded: chain AL residue 356 MET Chi-restraints excluded: chain AN residue 339 LEU Chi-restraints excluded: chain AO residue 339 LEU Chi-restraints excluded: chain b residue 28 THR Chi-restraints excluded: chain b residue 88 THR Chi-restraints excluded: chain c residue 88 THR Chi-restraints excluded: chain c residue 97 ASP Chi-restraints excluded: chain c residue 98 LEU Chi-restraints excluded: chain d residue 88 THR Chi-restraints excluded: chain d residue 126 LYS Chi-restraints excluded: chain d residue 129 LYS Chi-restraints excluded: chain e residue 88 THR Chi-restraints excluded: chain f residue 88 THR Chi-restraints excluded: chain f residue 128 ILE Chi-restraints excluded: chain g residue 39 LYS Chi-restraints excluded: chain g residue 53 LEU Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain h residue 34 VAL Chi-restraints excluded: chain h residue 40 ASP Chi-restraints excluded: chain h residue 53 LEU Chi-restraints excluded: chain h residue 65 VAL Chi-restraints excluded: chain h residue 68 MET Chi-restraints excluded: chain h residue 71 VAL Chi-restraints excluded: chain h residue 87 LEU Chi-restraints excluded: chain h residue 112 SER Chi-restraints excluded: chain i residue 3 LEU Chi-restraints excluded: chain i residue 18 SER Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 78 SER Chi-restraints excluded: chain i residue 101 VAL Chi-restraints excluded: chain i residue 124 SER Chi-restraints excluded: chain i residue 131 ARG Chi-restraints excluded: chain j residue 3 LEU Chi-restraints excluded: chain j residue 23 THR Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 101 VAL Chi-restraints excluded: chain k residue 40 ASP Chi-restraints excluded: chain k residue 53 LEU Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain l residue 3 LEU Chi-restraints excluded: chain l residue 37 SER Chi-restraints excluded: chain l residue 40 ASP Chi-restraints excluded: chain l residue 61 ASP Chi-restraints excluded: chain l residue 65 VAL Chi-restraints excluded: chain l residue 78 SER Chi-restraints excluded: chain l residue 87 LEU Chi-restraints excluded: chain l residue 113 ARG Chi-restraints excluded: chain m residue 94 THR Chi-restraints excluded: chain m residue 162 ASP Chi-restraints excluded: chain m residue 196 THR Chi-restraints excluded: chain m residue 248 MET Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 10 SER Chi-restraints excluded: chain n residue 19 LEU Chi-restraints excluded: chain n residue 85 SER Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain n residue 107 VAL Chi-restraints excluded: chain n residue 114 THR Chi-restraints excluded: chain n residue 149 LEU Chi-restraints excluded: chain n residue 158 PHE Chi-restraints excluded: chain n residue 233 SER Chi-restraints excluded: chain o residue 43 SER Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain o residue 93 HIS Chi-restraints excluded: chain o residue 94 THR Chi-restraints excluded: chain o residue 158 PHE Chi-restraints excluded: chain o residue 233 SER Chi-restraints excluded: chain o residue 234 THR Chi-restraints excluded: chain o residue 248 MET Chi-restraints excluded: chain p residue 81 THR Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain p residue 196 THR Chi-restraints excluded: chain p residue 212 VAL Chi-restraints excluded: chain p residue 243 ASP Chi-restraints excluded: chain q residue 81 THR Chi-restraints excluded: chain q residue 147 SER Chi-restraints excluded: chain q residue 241 SER Chi-restraints excluded: chain q residue 243 ASP Chi-restraints excluded: chain r residue 34 ASN Chi-restraints excluded: chain s residue 46 THR Chi-restraints excluded: chain s residue 51 SER Chi-restraints excluded: chain s residue 98 LEU Chi-restraints excluded: chain t residue 32 ASP Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 103 VAL Chi-restraints excluded: chain u residue 53 ASP Chi-restraints excluded: chain u residue 69 ASP Chi-restraints excluded: chain v residue 51 SER Chi-restraints excluded: chain v residue 82 ASP Chi-restraints excluded: chain v residue 103 VAL Chi-restraints excluded: chain x residue 48 TRP Chi-restraints excluded: chain y residue 84 SER Chi-restraints excluded: chain y residue 117 SER Chi-restraints excluded: chain y residue 125 LEU Chi-restraints excluded: chain y residue 141 LEU Chi-restraints excluded: chain y residue 147 SER Chi-restraints excluded: chain y residue 167 THR Chi-restraints excluded: chain y residue 185 LYS Chi-restraints excluded: chain y residue 198 MET Chi-restraints excluded: chain z residue 113 VAL Chi-restraints excluded: chain z residue 184 LEU Chi-restraints excluded: chain z residue 196 VAL Chi-restraints excluded: chain z residue 222 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 131 optimal weight: 0.9980 chunk 450 optimal weight: 2.9990 chunk 325 optimal weight: 5.9990 chunk 307 optimal weight: 0.0980 chunk 442 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 353 optimal weight: 8.9990 chunk 250 optimal weight: 0.9990 chunk 418 optimal weight: 0.8980 chunk 179 optimal weight: 0.9980 chunk 156 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 205 ASN 2 228 GLN ** c 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 34 ASN ** i 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 134 GLN ** n 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 125 ASN o 102 ASN ** r 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 121 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.145062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.119968 restraints weight = 47203.811| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.43 r_work: 0.3233 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 38926 Z= 0.114 Angle : 0.517 14.641 52695 Z= 0.254 Chirality : 0.039 0.297 6219 Planarity : 0.003 0.042 6827 Dihedral : 4.820 59.753 5287 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.92 % Favored : 98.04 % Rotamer: Outliers : 3.41 % Allowed : 16.05 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.83 (0.12), residues: 4896 helix: 3.08 (0.09), residues: 2868 sheet: -0.99 (0.24), residues: 403 loop : 0.46 (0.16), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG m 247 TYR 0.016 0.001 TYR u 95 PHE 0.025 0.001 PHE 2 231 TRP 0.013 0.001 TRP x 48 HIS 0.002 0.000 HIS 7 67 Details of bonding type rmsd covalent geometry : bond 0.00247 (38926) covalent geometry : angle 0.51720 (52695) hydrogen bonds : bond 0.04062 ( 2457) hydrogen bonds : angle 3.60661 ( 7296) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1000 residues out of total 4223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 856 time to evaluate : 1.272 Fit side-chains revert: symmetry clash REVERT: 1 123 MET cc_start: 0.5768 (OUTLIER) cc_final: 0.5431 (mpp) REVERT: 1 156 LYS cc_start: 0.6878 (mmmt) cc_final: 0.6653 (mtpp) REVERT: 1 249 MET cc_start: 0.8111 (tpt) cc_final: 0.7880 (tpp) REVERT: 2 123 MET cc_start: 0.7977 (mtm) cc_final: 0.7543 (mtm) REVERT: 2 156 LYS cc_start: 0.8596 (mptp) cc_final: 0.8050 (mtpp) REVERT: 2 180 LYS cc_start: 0.7338 (mtpp) cc_final: 0.6807 (mttt) REVERT: 2 249 MET cc_start: 0.8409 (mmm) cc_final: 0.8190 (tpp) REVERT: 2 272 LEU cc_start: 0.8112 (pp) cc_final: 0.6889 (mt) REVERT: 3 86 THR cc_start: 0.8997 (OUTLIER) cc_final: 0.8660 (p) REVERT: 3 121 GLN cc_start: 0.8189 (tp40) cc_final: 0.7783 (tt0) REVERT: 3 132 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7856 (mm110) REVERT: 3 179 MET cc_start: 0.6889 (mmt) cc_final: 0.6101 (mtt) REVERT: 3 185 LYS cc_start: 0.7927 (mptt) cc_final: 0.7649 (mttt) REVERT: 3 251 MET cc_start: 0.7454 (OUTLIER) cc_final: 0.6919 (ttt) REVERT: 4 22 CYS cc_start: 0.8287 (t) cc_final: 0.7691 (m) REVERT: 4 63 MET cc_start: 0.6826 (tmm) cc_final: 0.5795 (mmm) REVERT: 5 26 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8347 (mp) REVERT: 5 74 MET cc_start: 0.8128 (mtp) cc_final: 0.7815 (mtp) REVERT: 5 75 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7501 (mp0) REVERT: 7 15 TRP cc_start: 0.7101 (t-100) cc_final: 0.6489 (t-100) REVERT: 7 16 MET cc_start: 0.8323 (tpp) cc_final: 0.7972 (tpt) REVERT: 8 29 MET cc_start: 0.7429 (tpp) cc_final: 0.6971 (ttm) REVERT: 8 70 ARG cc_start: 0.6825 (OUTLIER) cc_final: 0.5847 (ttt-90) REVERT: 8 231 TRP cc_start: 0.7186 (t60) cc_final: 0.6636 (t60) REVERT: AJ 356 MET cc_start: 0.2419 (tpt) cc_final: 0.2165 (tpt) REVERT: AK 339 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8522 (mp) REVERT: AN 339 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8689 (mp) REVERT: AO 330 ASN cc_start: 0.8076 (p0) cc_final: 0.7706 (p0) REVERT: c 24 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8344 (mt-10) REVERT: d 47 LYS cc_start: 0.8630 (tptt) cc_final: 0.7818 (ttpt) REVERT: d 84 THR cc_start: 0.9360 (t) cc_final: 0.9088 (m) REVERT: d 126 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8543 (tttp) REVERT: e 115 ASP cc_start: 0.8254 (m-30) cc_final: 0.7910 (m-30) REVERT: f 47 LYS cc_start: 0.8129 (ttmm) cc_final: 0.7744 (ttpp) REVERT: g 39 LYS cc_start: 0.5988 (OUTLIER) cc_final: 0.5512 (ptpt) REVERT: g 80 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7504 (tp30) REVERT: g 95 TYR cc_start: 0.8643 (m-80) cc_final: 0.8138 (m-10) REVERT: g 134 GLN cc_start: 0.8080 (tp40) cc_final: 0.7829 (mt0) REVERT: g 135 MET cc_start: 0.8626 (ttm) cc_final: 0.8013 (ttm) REVERT: i 66 LYS cc_start: 0.7793 (pttt) cc_final: 0.7516 (pttm) REVERT: i 102 MET cc_start: 0.7301 (mmp) cc_final: 0.6825 (mpp) REVERT: i 123 ASP cc_start: 0.8358 (t70) cc_final: 0.8036 (t0) REVERT: i 131 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8515 (tpt170) REVERT: i 135 MET cc_start: 0.8045 (ttm) cc_final: 0.7811 (ttt) REVERT: j 80 GLU cc_start: 0.8539 (mt-10) cc_final: 0.7596 (tp30) REVERT: l 36 SER cc_start: 0.8985 (p) cc_final: 0.8706 (t) REVERT: l 91 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7969 (mt-10) REVERT: l 108 MET cc_start: 0.8703 (ttm) cc_final: 0.8367 (ttp) REVERT: l 113 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8716 (mmp-170) REVERT: l 120 GLN cc_start: 0.8686 (mm-40) cc_final: 0.8398 (mt0) REVERT: l 131 ARG cc_start: 0.7977 (mmm-85) cc_final: 0.7690 (mmt-90) REVERT: m 172 GLN cc_start: 0.8272 (mm-40) cc_final: 0.7820 (mm-40) REVERT: o 58 MET cc_start: 0.8590 (mtp) cc_final: 0.8091 (ttt) REVERT: o 158 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7513 (m-80) REVERT: o 222 GLN cc_start: 0.8171 (mt0) cc_final: 0.7941 (tt0) REVERT: p 112 MET cc_start: 0.8199 (mtm) cc_final: 0.7901 (tpp) REVERT: p 135 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8585 (pp) REVERT: p 157 GLU cc_start: 0.7489 (mt-10) cc_final: 0.6491 (tm-30) REVERT: q 215 MET cc_start: 0.8307 (mmm) cc_final: 0.7983 (mtt) REVERT: q 240 LYS cc_start: 0.8751 (ttmm) cc_final: 0.8310 (ttpp) REVERT: r 34 ASN cc_start: 0.3734 (OUTLIER) cc_final: 0.3331 (t0) REVERT: r 101 MET cc_start: 0.7549 (mtm) cc_final: 0.7114 (mtt) REVERT: t 57 ARG cc_start: 0.8447 (mtm-85) cc_final: 0.8027 (mtp180) REVERT: t 71 MET cc_start: 0.9132 (mmm) cc_final: 0.8884 (mmm) REVERT: u 69 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7466 (m-30) REVERT: u 78 SER cc_start: 0.8714 (t) cc_final: 0.7997 (m) REVERT: u 82 ASP cc_start: 0.8220 (m-30) cc_final: 0.7982 (m-30) REVERT: v 82 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7826 (t0) REVERT: y 180 LYS cc_start: 0.8292 (ttmt) cc_final: 0.7991 (tttt) REVERT: y 191 ASP cc_start: 0.7758 (m-30) cc_final: 0.7456 (m-30) REVERT: y 251 MET cc_start: 0.7480 (mmm) cc_final: 0.7172 (mmt) REVERT: y 265 PHE cc_start: 0.8528 (m-80) cc_final: 0.8048 (m-10) REVERT: z 222 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7494 (mm-30) REVERT: z 255 MET cc_start: 0.8189 (mmm) cc_final: 0.7371 (mmm) outliers start: 144 outliers final: 116 residues processed: 953 average time/residue: 0.2193 time to fit residues: 346.8287 Evaluate side-chains 979 residues out of total 4223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 844 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 123 MET Chi-restraints excluded: chain 1 residue 127 GLN Chi-restraints excluded: chain 1 residue 128 THR Chi-restraints excluded: chain 1 residue 185 LYS Chi-restraints excluded: chain 2 residue 128 THR Chi-restraints excluded: chain 2 residue 147 SER Chi-restraints excluded: chain 2 residue 149 VAL Chi-restraints excluded: chain 2 residue 273 VAL Chi-restraints excluded: chain 3 residue 86 THR Chi-restraints excluded: chain 3 residue 132 GLN Chi-restraints excluded: chain 3 residue 149 VAL Chi-restraints excluded: chain 3 residue 155 ASP Chi-restraints excluded: chain 3 residue 176 GLN Chi-restraints excluded: chain 3 residue 203 VAL Chi-restraints excluded: chain 3 residue 239 ILE Chi-restraints excluded: chain 3 residue 251 MET Chi-restraints excluded: chain 3 residue 273 VAL Chi-restraints excluded: chain 4 residue 12 GLU Chi-restraints excluded: chain 4 residue 55 LEU Chi-restraints excluded: chain 5 residue 26 ILE Chi-restraints excluded: chain 5 residue 45 ASN Chi-restraints excluded: chain 5 residue 75 GLU Chi-restraints excluded: chain 6 residue 28 SER Chi-restraints excluded: chain 6 residue 31 ILE Chi-restraints excluded: chain 7 residue 19 ILE Chi-restraints excluded: chain 8 residue 66 LEU Chi-restraints excluded: chain 8 residue 70 ARG Chi-restraints excluded: chain 8 residue 89 THR Chi-restraints excluded: chain 8 residue 125 LEU Chi-restraints excluded: chain 8 residue 131 MET Chi-restraints excluded: chain 8 residue 190 SER Chi-restraints excluded: chain 8 residue 192 ILE Chi-restraints excluded: chain 8 residue 200 LEU Chi-restraints excluded: chain 8 residue 258 LEU Chi-restraints excluded: chain AD residue 349 ILE Chi-restraints excluded: chain AE residue 348 SER Chi-restraints excluded: chain AE residue 349 ILE Chi-restraints excluded: chain AK residue 339 LEU Chi-restraints excluded: chain AK residue 342 GLN Chi-restraints excluded: chain AK residue 352 ASP Chi-restraints excluded: chain AL residue 356 MET Chi-restraints excluded: chain AN residue 339 LEU Chi-restraints excluded: chain AO residue 339 LEU Chi-restraints excluded: chain b residue 28 THR Chi-restraints excluded: chain b residue 88 THR Chi-restraints excluded: chain c residue 97 ASP Chi-restraints excluded: chain c residue 98 LEU Chi-restraints excluded: chain d residue 88 THR Chi-restraints excluded: chain d residue 119 SER Chi-restraints excluded: chain d residue 126 LYS Chi-restraints excluded: chain d residue 129 LYS Chi-restraints excluded: chain e residue 88 THR Chi-restraints excluded: chain f residue 88 THR Chi-restraints excluded: chain f residue 128 ILE Chi-restraints excluded: chain g residue 39 LYS Chi-restraints excluded: chain g residue 53 LEU Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain h residue 34 VAL Chi-restraints excluded: chain h residue 40 ASP Chi-restraints excluded: chain h residue 53 LEU Chi-restraints excluded: chain h residue 65 VAL Chi-restraints excluded: chain h residue 68 MET Chi-restraints excluded: chain h residue 71 VAL Chi-restraints excluded: chain h residue 112 SER Chi-restraints excluded: chain i residue 3 LEU Chi-restraints excluded: chain i residue 18 SER Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 78 SER Chi-restraints excluded: chain i residue 101 VAL Chi-restraints excluded: chain i residue 124 SER Chi-restraints excluded: chain i residue 131 ARG Chi-restraints excluded: chain j residue 3 LEU Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain k residue 40 ASP Chi-restraints excluded: chain k residue 53 LEU Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain l residue 3 LEU Chi-restraints excluded: chain l residue 37 SER Chi-restraints excluded: chain l residue 40 ASP Chi-restraints excluded: chain l residue 61 ASP Chi-restraints excluded: chain l residue 65 VAL Chi-restraints excluded: chain l residue 78 SER Chi-restraints excluded: chain l residue 87 LEU Chi-restraints excluded: chain l residue 113 ARG Chi-restraints excluded: chain m residue 94 THR Chi-restraints excluded: chain m residue 162 ASP Chi-restraints excluded: chain m residue 196 THR Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 10 SER Chi-restraints excluded: chain n residue 19 LEU Chi-restraints excluded: chain n residue 85 SER Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain n residue 107 VAL Chi-restraints excluded: chain n residue 114 THR Chi-restraints excluded: chain n residue 149 LEU Chi-restraints excluded: chain n residue 158 PHE Chi-restraints excluded: chain n residue 233 SER Chi-restraints excluded: chain o residue 9 MET Chi-restraints excluded: chain o residue 43 SER Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain o residue 94 THR Chi-restraints excluded: chain o residue 158 PHE Chi-restraints excluded: chain o residue 234 THR Chi-restraints excluded: chain o residue 248 MET Chi-restraints excluded: chain p residue 81 THR Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain p residue 196 THR Chi-restraints excluded: chain p residue 212 VAL Chi-restraints excluded: chain p residue 243 ASP Chi-restraints excluded: chain q residue 81 THR Chi-restraints excluded: chain q residue 147 SER Chi-restraints excluded: chain q residue 241 SER Chi-restraints excluded: chain q residue 243 ASP Chi-restraints excluded: chain r residue 34 ASN Chi-restraints excluded: chain s residue 51 SER Chi-restraints excluded: chain s residue 98 LEU Chi-restraints excluded: chain t residue 32 ASP Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 103 VAL Chi-restraints excluded: chain u residue 53 ASP Chi-restraints excluded: chain u residue 69 ASP Chi-restraints excluded: chain v residue 51 SER Chi-restraints excluded: chain v residue 82 ASP Chi-restraints excluded: chain v residue 103 VAL Chi-restraints excluded: chain x residue 48 TRP Chi-restraints excluded: chain y residue 125 LEU Chi-restraints excluded: chain y residue 147 SER Chi-restraints excluded: chain y residue 198 MET Chi-restraints excluded: chain z residue 113 VAL Chi-restraints excluded: chain z residue 128 THR Chi-restraints excluded: chain z residue 184 LEU Chi-restraints excluded: chain z residue 196 VAL Chi-restraints excluded: chain z residue 203 VAL Chi-restraints excluded: chain z residue 222 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 286 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 327 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 70 optimal weight: 0.0870 chunk 409 optimal weight: 0.7980 chunk 255 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 108 optimal weight: 0.9980 chunk 349 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 overall best weight: 1.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 121 GLN 2 205 ASN 6 67 HIS f 34 ASN ** i 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 134 GLN ** n 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 125 ASN ** r 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 121 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.150180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.125229 restraints weight = 46285.854| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.44 r_work: 0.3251 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 38926 Z= 0.127 Angle : 0.532 14.401 52695 Z= 0.261 Chirality : 0.040 0.251 6219 Planarity : 0.003 0.042 6827 Dihedral : 4.833 59.956 5285 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.02 % Favored : 97.94 % Rotamer: Outliers : 3.43 % Allowed : 16.01 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.79 (0.12), residues: 4896 helix: 3.04 (0.09), residues: 2868 sheet: -0.96 (0.24), residues: 403 loop : 0.46 (0.16), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG f 41 TYR 0.019 0.001 TYR u 95 PHE 0.023 0.001 PHE 2 231 TRP 0.012 0.001 TRP x 48 HIS 0.003 0.001 HIS 6 67 Details of bonding type rmsd covalent geometry : bond 0.00288 (38926) covalent geometry : angle 0.53170 (52695) hydrogen bonds : bond 0.04176 ( 2457) hydrogen bonds : angle 3.62167 ( 7296) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 982 residues out of total 4223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 837 time to evaluate : 1.397 Fit side-chains revert: symmetry clash REVERT: 1 123 MET cc_start: 0.5994 (OUTLIER) cc_final: 0.5625 (mpp) REVERT: 1 156 LYS cc_start: 0.6880 (mmmt) cc_final: 0.6659 (mtpp) REVERT: 1 249 MET cc_start: 0.8030 (tpt) cc_final: 0.7790 (tpp) REVERT: 2 123 MET cc_start: 0.8015 (mtm) cc_final: 0.7590 (mtm) REVERT: 2 156 LYS cc_start: 0.8612 (mptp) cc_final: 0.8088 (mtpp) REVERT: 2 180 LYS cc_start: 0.7319 (mtpp) cc_final: 0.6956 (mttt) REVERT: 2 249 MET cc_start: 0.8427 (mmm) cc_final: 0.8210 (tpp) REVERT: 2 272 LEU cc_start: 0.8104 (pp) cc_final: 0.6958 (mt) REVERT: 3 86 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8678 (p) REVERT: 3 121 GLN cc_start: 0.8225 (tp40) cc_final: 0.7824 (tt0) REVERT: 3 132 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7875 (mm110) REVERT: 3 179 MET cc_start: 0.6866 (mmt) cc_final: 0.6099 (mtt) REVERT: 3 185 LYS cc_start: 0.7898 (mptt) cc_final: 0.7626 (mttt) REVERT: 3 251 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.6765 (ttt) REVERT: 4 22 CYS cc_start: 0.8336 (t) cc_final: 0.7734 (m) REVERT: 4 63 MET cc_start: 0.6820 (tmm) cc_final: 0.5809 (mmm) REVERT: 5 26 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8345 (mp) REVERT: 5 74 MET cc_start: 0.8073 (mtp) cc_final: 0.7748 (mtp) REVERT: 5 75 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7523 (mp0) REVERT: 7 15 TRP cc_start: 0.7135 (t-100) cc_final: 0.6519 (t-100) REVERT: 7 16 MET cc_start: 0.8350 (tpp) cc_final: 0.7966 (tpt) REVERT: 8 70 ARG cc_start: 0.6839 (OUTLIER) cc_final: 0.5884 (ttt-90) REVERT: 8 231 TRP cc_start: 0.7221 (t60) cc_final: 0.6655 (t60) REVERT: AC 355 GLN cc_start: 0.8041 (mp10) cc_final: 0.7458 (pm20) REVERT: AJ 356 MET cc_start: 0.2420 (tpt) cc_final: 0.2199 (tpt) REVERT: AK 339 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8466 (mp) REVERT: AN 339 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8694 (mp) REVERT: AO 330 ASN cc_start: 0.7921 (p0) cc_final: 0.7694 (p0) REVERT: c 24 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8378 (mt-10) REVERT: d 47 LYS cc_start: 0.8643 (tptt) cc_final: 0.7843 (ttpt) REVERT: d 84 THR cc_start: 0.9366 (t) cc_final: 0.9101 (m) REVERT: e 115 ASP cc_start: 0.8168 (m-30) cc_final: 0.7841 (m-30) REVERT: f 47 LYS cc_start: 0.8133 (ttmm) cc_final: 0.7755 (ttpp) REVERT: g 39 LYS cc_start: 0.6017 (OUTLIER) cc_final: 0.5541 (ptpt) REVERT: g 80 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7533 (tp30) REVERT: g 95 TYR cc_start: 0.8602 (m-80) cc_final: 0.8336 (m-10) REVERT: g 135 MET cc_start: 0.8641 (ttm) cc_final: 0.8037 (ttm) REVERT: i 66 LYS cc_start: 0.7760 (pttt) cc_final: 0.7487 (pttm) REVERT: i 102 MET cc_start: 0.7290 (mmp) cc_final: 0.6779 (mpp) REVERT: i 123 ASP cc_start: 0.8390 (t70) cc_final: 0.7962 (t0) REVERT: i 131 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8582 (tpt170) REVERT: i 135 MET cc_start: 0.8058 (ttm) cc_final: 0.7819 (ttt) REVERT: j 80 GLU cc_start: 0.8550 (mt-10) cc_final: 0.7614 (tp30) REVERT: l 36 SER cc_start: 0.8999 (p) cc_final: 0.8733 (t) REVERT: l 91 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7991 (mt-10) REVERT: l 108 MET cc_start: 0.8709 (ttm) cc_final: 0.8371 (ttp) REVERT: l 113 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8723 (mmp-170) REVERT: l 120 GLN cc_start: 0.8692 (mm-40) cc_final: 0.8406 (mt0) REVERT: l 131 ARG cc_start: 0.7968 (mmm-85) cc_final: 0.7679 (mmt-90) REVERT: m 172 GLN cc_start: 0.8269 (mm-40) cc_final: 0.7824 (mm-40) REVERT: o 58 MET cc_start: 0.8611 (mtp) cc_final: 0.8114 (ttt) REVERT: o 158 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7594 (m-80) REVERT: o 222 GLN cc_start: 0.8174 (mt0) cc_final: 0.7944 (tt0) REVERT: p 112 MET cc_start: 0.8179 (mtm) cc_final: 0.7902 (tpp) REVERT: p 135 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8591 (pp) REVERT: p 157 GLU cc_start: 0.7510 (mt-10) cc_final: 0.6504 (tm-30) REVERT: q 215 MET cc_start: 0.8343 (mmm) cc_final: 0.8023 (mtt) REVERT: q 240 LYS cc_start: 0.8788 (ttmm) cc_final: 0.8339 (ttpp) REVERT: r 34 ASN cc_start: 0.3606 (OUTLIER) cc_final: 0.3239 (t0) REVERT: r 101 MET cc_start: 0.7597 (mtm) cc_final: 0.7117 (mtt) REVERT: t 57 ARG cc_start: 0.8455 (mtm-85) cc_final: 0.8044 (mtp180) REVERT: t 71 MET cc_start: 0.9142 (mmm) cc_final: 0.8922 (mmm) REVERT: u 69 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7458 (m-30) REVERT: u 78 SER cc_start: 0.8716 (t) cc_final: 0.8004 (m) REVERT: u 82 ASP cc_start: 0.8265 (m-30) cc_final: 0.8031 (m-30) REVERT: u 101 MET cc_start: 0.8436 (ptp) cc_final: 0.8205 (ptp) REVERT: v 82 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7860 (t0) REVERT: y 180 LYS cc_start: 0.8328 (ttmt) cc_final: 0.8026 (tttt) REVERT: y 191 ASP cc_start: 0.7755 (m-30) cc_final: 0.7459 (m-30) REVERT: y 265 PHE cc_start: 0.8532 (m-80) cc_final: 0.8051 (m-10) REVERT: z 222 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7504 (mm-30) REVERT: z 255 MET cc_start: 0.8169 (mmm) cc_final: 0.7459 (mmm) outliers start: 145 outliers final: 126 residues processed: 934 average time/residue: 0.2200 time to fit residues: 342.3568 Evaluate side-chains 978 residues out of total 4223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 834 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 123 MET Chi-restraints excluded: chain 1 residue 127 GLN Chi-restraints excluded: chain 1 residue 128 THR Chi-restraints excluded: chain 1 residue 185 LYS Chi-restraints excluded: chain 2 residue 128 THR Chi-restraints excluded: chain 2 residue 147 SER Chi-restraints excluded: chain 2 residue 149 VAL Chi-restraints excluded: chain 2 residue 273 VAL Chi-restraints excluded: chain 3 residue 86 THR Chi-restraints excluded: chain 3 residue 110 THR Chi-restraints excluded: chain 3 residue 132 GLN Chi-restraints excluded: chain 3 residue 149 VAL Chi-restraints excluded: chain 3 residue 155 ASP Chi-restraints excluded: chain 3 residue 176 GLN Chi-restraints excluded: chain 3 residue 203 VAL Chi-restraints excluded: chain 3 residue 239 ILE Chi-restraints excluded: chain 3 residue 251 MET Chi-restraints excluded: chain 3 residue 273 VAL Chi-restraints excluded: chain 4 residue 12 GLU Chi-restraints excluded: chain 4 residue 55 LEU Chi-restraints excluded: chain 4 residue 87 VAL Chi-restraints excluded: chain 5 residue 26 ILE Chi-restraints excluded: chain 5 residue 45 ASN Chi-restraints excluded: chain 5 residue 75 GLU Chi-restraints excluded: chain 6 residue 28 SER Chi-restraints excluded: chain 6 residue 31 ILE Chi-restraints excluded: chain 7 residue 19 ILE Chi-restraints excluded: chain 8 residue 66 LEU Chi-restraints excluded: chain 8 residue 70 ARG Chi-restraints excluded: chain 8 residue 89 THR Chi-restraints excluded: chain 8 residue 125 LEU Chi-restraints excluded: chain 8 residue 131 MET Chi-restraints excluded: chain 8 residue 190 SER Chi-restraints excluded: chain 8 residue 192 ILE Chi-restraints excluded: chain 8 residue 200 LEU Chi-restraints excluded: chain 8 residue 258 LEU Chi-restraints excluded: chain AD residue 349 ILE Chi-restraints excluded: chain AE residue 348 SER Chi-restraints excluded: chain AE residue 349 ILE Chi-restraints excluded: chain AK residue 339 LEU Chi-restraints excluded: chain AK residue 342 GLN Chi-restraints excluded: chain AK residue 352 ASP Chi-restraints excluded: chain AL residue 356 MET Chi-restraints excluded: chain AN residue 339 LEU Chi-restraints excluded: chain AO residue 339 LEU Chi-restraints excluded: chain b residue 28 THR Chi-restraints excluded: chain b residue 88 THR Chi-restraints excluded: chain c residue 97 ASP Chi-restraints excluded: chain c residue 98 LEU Chi-restraints excluded: chain d residue 88 THR Chi-restraints excluded: chain d residue 119 SER Chi-restraints excluded: chain d residue 126 LYS Chi-restraints excluded: chain d residue 129 LYS Chi-restraints excluded: chain e residue 88 THR Chi-restraints excluded: chain f residue 88 THR Chi-restraints excluded: chain f residue 128 ILE Chi-restraints excluded: chain g residue 39 LYS Chi-restraints excluded: chain g residue 53 LEU Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain h residue 34 VAL Chi-restraints excluded: chain h residue 40 ASP Chi-restraints excluded: chain h residue 53 LEU Chi-restraints excluded: chain h residue 65 VAL Chi-restraints excluded: chain h residue 68 MET Chi-restraints excluded: chain h residue 71 VAL Chi-restraints excluded: chain h residue 112 SER Chi-restraints excluded: chain i residue 3 LEU Chi-restraints excluded: chain i residue 18 SER Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 78 SER Chi-restraints excluded: chain i residue 101 VAL Chi-restraints excluded: chain i residue 124 SER Chi-restraints excluded: chain i residue 131 ARG Chi-restraints excluded: chain j residue 3 LEU Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain k residue 40 ASP Chi-restraints excluded: chain k residue 53 LEU Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain l residue 32 ASP Chi-restraints excluded: chain l residue 37 SER Chi-restraints excluded: chain l residue 40 ASP Chi-restraints excluded: chain l residue 53 LEU Chi-restraints excluded: chain l residue 61 ASP Chi-restraints excluded: chain l residue 65 VAL Chi-restraints excluded: chain l residue 78 SER Chi-restraints excluded: chain l residue 87 LEU Chi-restraints excluded: chain l residue 113 ARG Chi-restraints excluded: chain m residue 94 THR Chi-restraints excluded: chain m residue 99 LEU Chi-restraints excluded: chain m residue 162 ASP Chi-restraints excluded: chain m residue 196 THR Chi-restraints excluded: chain m residue 248 MET Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 10 SER Chi-restraints excluded: chain n residue 19 LEU Chi-restraints excluded: chain n residue 85 SER Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain n residue 107 VAL Chi-restraints excluded: chain n residue 114 THR Chi-restraints excluded: chain n residue 149 LEU Chi-restraints excluded: chain n residue 158 PHE Chi-restraints excluded: chain n residue 233 SER Chi-restraints excluded: chain o residue 9 MET Chi-restraints excluded: chain o residue 43 SER Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain o residue 94 THR Chi-restraints excluded: chain o residue 158 PHE Chi-restraints excluded: chain o residue 234 THR Chi-restraints excluded: chain o residue 248 MET Chi-restraints excluded: chain p residue 81 THR Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain p residue 196 THR Chi-restraints excluded: chain p residue 212 VAL Chi-restraints excluded: chain p residue 243 ASP Chi-restraints excluded: chain q residue 81 THR Chi-restraints excluded: chain q residue 147 SER Chi-restraints excluded: chain q residue 241 SER Chi-restraints excluded: chain q residue 243 ASP Chi-restraints excluded: chain r residue 34 ASN Chi-restraints excluded: chain s residue 51 SER Chi-restraints excluded: chain s residue 98 LEU Chi-restraints excluded: chain t residue 32 ASP Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 103 VAL Chi-restraints excluded: chain u residue 53 ASP Chi-restraints excluded: chain u residue 69 ASP Chi-restraints excluded: chain v residue 51 SER Chi-restraints excluded: chain v residue 82 ASP Chi-restraints excluded: chain v residue 103 VAL Chi-restraints excluded: chain x residue 48 TRP Chi-restraints excluded: chain y residue 117 SER Chi-restraints excluded: chain y residue 125 LEU Chi-restraints excluded: chain y residue 141 LEU Chi-restraints excluded: chain y residue 147 SER Chi-restraints excluded: chain y residue 185 LYS Chi-restraints excluded: chain y residue 198 MET Chi-restraints excluded: chain y residue 210 SER Chi-restraints excluded: chain z residue 113 VAL Chi-restraints excluded: chain z residue 128 THR Chi-restraints excluded: chain z residue 184 LEU Chi-restraints excluded: chain z residue 196 VAL Chi-restraints excluded: chain z residue 203 VAL Chi-restraints excluded: chain z residue 222 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 320 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 430 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 chunk 289 optimal weight: 3.9990 chunk 434 optimal weight: 7.9990 chunk 301 optimal weight: 5.9990 chunk 326 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 205 ASN 6 67 HIS c 111 GLN f 34 ASN ** i 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 125 ASN ** r 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 121 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.143704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.118612 restraints weight = 47021.789| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.42 r_work: 0.3195 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 38926 Z= 0.143 Angle : 0.549 14.505 52695 Z= 0.270 Chirality : 0.040 0.286 6219 Planarity : 0.004 0.041 6827 Dihedral : 4.909 59.763 5285 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.06 % Favored : 97.90 % Rotamer: Outliers : 3.81 % Allowed : 15.82 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.72 (0.12), residues: 4896 helix: 2.98 (0.09), residues: 2868 sheet: -0.99 (0.24), residues: 403 loop : 0.43 (0.16), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG f 41 TYR 0.020 0.001 TYR u 95 PHE 0.021 0.001 PHE z 231 TRP 0.012 0.001 TRP x 48 HIS 0.003 0.001 HIS p 51 Details of bonding type rmsd covalent geometry : bond 0.00334 (38926) covalent geometry : angle 0.54860 (52695) hydrogen bonds : bond 0.04373 ( 2457) hydrogen bonds : angle 3.68200 ( 7296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12388.96 seconds wall clock time: 211 minutes 49.10 seconds (12709.10 seconds total)