Starting phenix.real_space_refine on Fri Mar 6 19:29:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tqt_26071/03_2026/7tqt_26071.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tqt_26071/03_2026/7tqt_26071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tqt_26071/03_2026/7tqt_26071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tqt_26071/03_2026/7tqt_26071.map" model { file = "/net/cci-nas-00/data/ceres_data/7tqt_26071/03_2026/7tqt_26071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tqt_26071/03_2026/7tqt_26071.cif" } resolution = 4.1 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= 0.000 sd= 0.002 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 210 5.16 5 C 21454 2.51 5 N 5744 2.21 5 O 6469 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 179 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: 33877 Number of models: 1 Model: "" Number of chains: 27 Chain: "L" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 490 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'TRANS': 97} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 98 Planarities with less than four sites: {'UNK:plan-1': 98} Unresolved non-hydrogen planarities: 98 Chain: "H" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 540 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'TRANS': 107} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 108 Planarities with less than four sites: {'UNK:plan-1': 108} Unresolved non-hydrogen planarities: 108 Chain: "a" Number of atoms: 2213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2213 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 260} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHE%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2053 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 247} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "c" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1848 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 20, 'TRANS': 218} Chain: "d" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "e" Number of atoms: 2219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2219 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 20, 'TRANS': 261} Chain: "f" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2008 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 16, 'TRANS': 241} Chain breaks: 1 Chain: "g" Number of atoms: 1810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1810 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 20, 'TRANS': 213} Chain: "h" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "i" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2226 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 20, 'TRANS': 262} Chain: "j" Number of atoms: 2003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2003 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 16, 'TRANS': 240} Chain breaks: 2 Chain: "k" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1801 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 20, 'TRANS': 212} Chain: "l" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 64} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 2176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2176 Classifications: {'peptide': 276} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 256} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHE%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "n" Number of atoms: 2029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2029 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 16, 'TRANS': 244} Chain breaks: 1 Chain: "o" Number of atoms: 1810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1810 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 20, 'TRANS': 213} Chain: "p" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 504 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "q" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2226 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 20, 'TRANS': 262} Chain: "r" Number of atoms: 1975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1975 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 16, 'TRANS': 236} Chain breaks: 2 Chain: "s" Number of atoms: 1818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1818 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 20, 'TRANS': 214} Chain: "t" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "a" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.51, per 1000 atoms: 0.25 Number of scatterers: 33877 At special positions: 0 Unit cell: (125.4, 179.74, 158.84, 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 210 16.00 O 6469 8.00 N 5744 7.00 C 21454 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: 3.30 Conformation dependent library (CDL) restraints added in 1.4 seconds 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8326 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 69 sheets defined 15.2% alpha, 35.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'a' and resid 41 through 45 Processing helix chain 'a' and resid 51 through 56 Processing helix chain 'a' and resid 67 through 70 Processing helix chain 'a' and resid 71 through 76 Processing helix chain 'a' and resid 95 through 98 Processing helix chain 'a' and resid 110 through 118 Processing helix chain 'a' and resid 167 through 172 Processing helix chain 'a' and resid 225 through 230 Processing helix chain 'a' and resid 282 through 286 removed outlier: 4.089A pdb=" N ILE a 286 " --> pdb=" O SER a 283 " (cutoff:3.500A) Processing helix chain 'b' and resid 35 through 37 No H-bonds generated for 'chain 'b' and resid 35 through 37' Processing helix chain 'b' and resid 43 through 47 Processing helix chain 'b' and resid 56 through 60 Processing helix chain 'b' and resid 82 through 86 Processing helix chain 'b' and resid 89 through 98 Processing helix chain 'b' and resid 144 through 149 Processing helix chain 'b' and resid 150 through 154 removed outlier: 4.067A pdb=" N ARG b 153 " --> pdb=" O PRO b 150 " (cutoff:3.500A) Processing helix chain 'b' and resid 167 through 171 removed outlier: 3.634A pdb=" N GLU b 170 " --> pdb=" O ASP b 167 " (cutoff:3.500A) Processing helix chain 'b' and resid 186 through 193 removed outlier: 4.436A pdb=" N PHE b 191 " --> pdb=" O GLY b 188 " (cutoff:3.500A) Processing helix chain 'c' and resid 43 through 48 Processing helix chain 'c' and resid 64 through 69 Processing helix chain 'c' and resid 97 through 104 Processing helix chain 'c' and resid 143 through 148 Processing helix chain 'd' and resid 35 through 39 Processing helix chain 'd' and resid 50 through 55 Processing helix chain 'e' and resid 51 through 56 Processing helix chain 'e' and resid 71 through 76 Processing helix chain 'e' and resid 92 through 98 removed outlier: 5.193A pdb=" N LYS e 97 " --> pdb=" O GLY e 94 " (cutoff:3.500A) Processing helix chain 'e' and resid 110 through 118 removed outlier: 3.856A pdb=" N LYS e 116 " --> pdb=" O GLN e 112 " (cutoff:3.500A) Processing helix chain 'e' and resid 167 through 172 Processing helix chain 'e' and resid 225 through 230 Processing helix chain 'f' and resid 35 through 37 No H-bonds generated for 'chain 'f' and resid 35 through 37' Processing helix chain 'f' and resid 43 through 47 Processing helix chain 'f' and resid 56 through 60 Processing helix chain 'f' and resid 82 through 86 Processing helix chain 'f' and resid 89 through 96 Processing helix chain 'f' and resid 144 through 149 Processing helix chain 'f' and resid 186 through 193 removed outlier: 4.539A pdb=" N PHE f 191 " --> pdb=" O GLY f 188 " (cutoff:3.500A) Processing helix chain 'g' and resid 43 through 48 Processing helix chain 'g' and resid 64 through 69 Processing helix chain 'g' and resid 97 through 104 Processing helix chain 'g' and resid 143 through 150 Processing helix chain 'g' and resid 181 through 185 removed outlier: 3.831A pdb=" N GLU g 185 " --> pdb=" O ASP g 182 " (cutoff:3.500A) Processing helix chain 'h' and resid 35 through 39 Processing helix chain 'h' and resid 50 through 55 Processing helix chain 'i' and resid 41 through 45 Processing helix chain 'i' and resid 51 through 55 Processing helix chain 'i' and resid 67 through 70 Processing helix chain 'i' and resid 71 through 76 Processing helix chain 'i' and resid 95 through 98 Processing helix chain 'i' and resid 110 through 118 Processing helix chain 'i' and resid 168 through 172 Processing helix chain 'i' and resid 225 through 229 Processing helix chain 'i' and resid 282 through 286 removed outlier: 4.080A pdb=" N ILE i 286 " --> pdb=" O SER i 283 " (cutoff:3.500A) Processing helix chain 'j' and resid 35 through 37 No H-bonds generated for 'chain 'j' and resid 35 through 37' Processing helix chain 'j' and resid 56 through 61 Processing helix chain 'j' and resid 82 through 86 Processing helix chain 'j' and resid 89 through 98 Processing helix chain 'j' and resid 150 through 154 removed outlier: 4.098A pdb=" N ARG j 153 " --> pdb=" O PRO j 150 " (cutoff:3.500A) Processing helix chain 'j' and resid 186 through 193 removed outlier: 4.432A pdb=" N PHE j 191 " --> pdb=" O GLY j 188 " (cutoff:3.500A) Processing helix chain 'k' and resid 43 through 48 Processing helix chain 'k' and resid 64 through 69 Processing helix chain 'k' and resid 97 through 104 Processing helix chain 'k' and resid 143 through 150 Processing helix chain 'l' and resid 35 through 39 Processing helix chain 'l' and resid 50 through 55 Processing helix chain 'm' and resid 41 through 45 Processing helix chain 'm' and resid 51 through 56 Processing helix chain 'm' and resid 71 through 76 Processing helix chain 'm' and resid 92 through 98 removed outlier: 4.900A pdb=" N LYS m 97 " --> pdb=" O GLY m 94 " (cutoff:3.500A) Processing helix chain 'm' and resid 110 through 118 Processing helix chain 'm' and resid 167 through 172 Processing helix chain 'm' and resid 225 through 230 Processing helix chain 'n' and resid 35 through 37 No H-bonds generated for 'chain 'n' and resid 35 through 37' Processing helix chain 'n' and resid 56 through 60 Processing helix chain 'n' and resid 82 through 86 removed outlier: 3.972A pdb=" N LEU n 86 " --> pdb=" O LEU n 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 82 through 86' Processing helix chain 'n' and resid 89 through 98 Processing helix chain 'n' and resid 144 through 149 Processing helix chain 'n' and resid 186 through 193 removed outlier: 4.317A pdb=" N PHE n 191 " --> pdb=" O GLY n 188 " (cutoff:3.500A) Processing helix chain 'o' and resid 43 through 48 Processing helix chain 'o' and resid 64 through 69 Processing helix chain 'o' and resid 93 through 96 removed outlier: 3.906A pdb=" N HIS o 96 " --> pdb=" O ARG o 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 93 through 96' Processing helix chain 'o' and resid 97 through 104 Processing helix chain 'o' and resid 143 through 148 Processing helix chain 'p' and resid 35 through 39 Processing helix chain 'p' and resid 50 through 55 Processing helix chain 'q' and resid 51 through 56 removed outlier: 3.786A pdb=" N VAL q 55 " --> pdb=" O ILE q 51 " (cutoff:3.500A) Processing helix chain 'q' and resid 71 through 76 Processing helix chain 'q' and resid 92 through 98 removed outlier: 4.867A pdb=" N LYS q 97 " --> pdb=" O GLY q 94 " (cutoff:3.500A) Processing helix chain 'q' and resid 110 through 118 removed outlier: 3.604A pdb=" N LYS q 116 " --> pdb=" O GLN q 112 " (cutoff:3.500A) Processing helix chain 'q' and resid 168 through 172 Processing helix chain 'q' and resid 225 through 230 Processing helix chain 'q' and resid 282 through 286 removed outlier: 4.197A pdb=" N ILE q 286 " --> pdb=" O SER q 283 " (cutoff:3.500A) Processing helix chain 'r' and resid 35 through 37 No H-bonds generated for 'chain 'r' and resid 35 through 37' Processing helix chain 'r' and resid 43 through 47 Processing helix chain 'r' and resid 56 through 60 Processing helix chain 'r' and resid 82 through 86 Processing helix chain 'r' and resid 89 through 99 removed outlier: 3.681A pdb=" N TYR r 97 " --> pdb=" O GLY r 93 " (cutoff:3.500A) Processing helix chain 'r' and resid 150 through 154 removed outlier: 4.363A pdb=" N ARG r 153 " --> pdb=" O PRO r 150 " (cutoff:3.500A) Processing helix chain 'r' and resid 186 through 193 removed outlier: 4.346A pdb=" N PHE r 191 " --> pdb=" O GLY r 188 " (cutoff:3.500A) Processing helix chain 's' and resid 43 through 48 Processing helix chain 's' and resid 64 through 69 Processing helix chain 's' and resid 91 through 96 removed outlier: 3.924A pdb=" N HIS s 96 " --> pdb=" O LYS s 92 " (cutoff:3.500A) Processing helix chain 's' and resid 97 through 104 Processing helix chain 's' and resid 145 through 149 Processing helix chain 't' and resid 35 through 39 Processing helix chain 't' and resid 50 through 55 Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AA3, first strand: chain 'L' and resid 34 through 37 removed outlier: 4.323A pdb=" N UNK L 80 " --> pdb=" O UNK L 37 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 7 through 8 Processing sheet with id=AA5, first strand: chain 'H' and resid 19 through 22 removed outlier: 4.156A pdb=" N UNK H 73 " --> pdb=" O UNK H 19 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 19 through 22 removed outlier: 4.156A pdb=" N UNK H 73 " --> pdb=" O UNK H 19 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N UNK H 70 " --> pdb=" O UNK H 66 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 42 through 43 Processing sheet with id=AA8, first strand: chain 'H' and resid 46 through 48 Processing sheet with id=AA9, first strand: chain 'a' and resid 39 through 40 Processing sheet with id=AB1, first strand: chain 'a' and resid 39 through 40 Processing sheet with id=AB2, first strand: chain 'a' and resid 80 through 89 removed outlier: 6.724A pdb=" N VAL a 254 " --> pdb=" O VAL a 82 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE a 84 " --> pdb=" O VAL a 252 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL a 252 " --> pdb=" O ILE a 84 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N SER a 86 " --> pdb=" O THR a 250 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR a 250 " --> pdb=" O SER a 86 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR a 88 " --> pdb=" O ILE a 248 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE a 248 " --> pdb=" O THR a 88 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE a 261 " --> pdb=" O ARG a 124 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ARG a 124 " --> pdb=" O ILE a 261 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N CYS a 263 " --> pdb=" O TYR a 122 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N TYR a 122 " --> pdb=" O CYS a 263 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N CYS a 265 " --> pdb=" O PHE a 120 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N PHE a 120 " --> pdb=" O CYS a 265 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 188 through 191 removed outlier: 5.260A pdb=" N PHE a 120 " --> pdb=" O CYS a 265 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N CYS a 265 " --> pdb=" O PHE a 120 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N TYR a 122 " --> pdb=" O CYS a 263 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N CYS a 263 " --> pdb=" O TYR a 122 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ARG a 124 " --> pdb=" O ILE a 261 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE a 261 " --> pdb=" O ARG a 124 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N CYS a 263 " --> pdb=" O VAL c 40 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'a' and resid 100 through 104 Processing sheet with id=AB5, first strand: chain 'b' and resid 14 through 18 Processing sheet with id=AB6, first strand: chain 'b' and resid 32 through 33 removed outlier: 6.514A pdb=" N ILE b 32 " --> pdb=" O VAL b 209 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N HIS b 99 " --> pdb=" O GLY b 262 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLY b 262 " --> pdb=" O HIS b 99 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU b 101 " --> pdb=" O PHE b 260 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N PHE b 260 " --> pdb=" O LEU b 101 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ARG b 103 " --> pdb=" O THR b 258 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR b 258 " --> pdb=" O ARG b 103 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'b' and resid 32 through 33 removed outlier: 6.514A pdb=" N ILE b 32 " --> pdb=" O VAL b 209 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N HIS b 99 " --> pdb=" O GLY b 262 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLY b 262 " --> pdb=" O HIS b 99 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU b 101 " --> pdb=" O PHE b 260 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N PHE b 260 " --> pdb=" O LEU b 101 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ARG b 103 " --> pdb=" O THR b 258 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR b 258 " --> pdb=" O ARG b 103 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'b' and resid 155 through 156 removed outlier: 6.218A pdb=" N ALA b 121 " --> pdb=" O LEU b 234 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N GLN b 119 " --> pdb=" O PRO b 236 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'c' and resid 2 through 6 removed outlier: 7.685A pdb=" N THR g 4 " --> pdb=" O PRO c 3 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N MET c 5 " --> pdb=" O THR g 4 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ASN g 6 " --> pdb=" O MET c 5 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N THR k 4 " --> pdb=" O PRO g 3 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N MET g 5 " --> pdb=" O THR k 4 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ASN k 6 " --> pdb=" O MET g 5 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N THR o 4 " --> pdb=" O PRO k 3 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N MET k 5 " --> pdb=" O THR o 4 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ASN o 6 " --> pdb=" O MET k 5 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N THR s 4 " --> pdb=" O PRO o 3 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N MET o 5 " --> pdb=" O THR s 4 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ASN s 6 " --> pdb=" O MET o 5 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'c' and resid 13 through 14 Processing sheet with id=AC2, first strand: chain 'c' and resid 82 through 85 removed outlier: 3.593A pdb=" N PHE c 82 " --> pdb=" O CYS c 191 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS c 128 " --> pdb=" O GLN c 194 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG c 196 " --> pdb=" O THR c 126 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR c 126 " --> pdb=" O ARG c 196 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'c' and resid 176 through 177 Processing sheet with id=AC4, first strand: chain 'd' and resid 4 through 7 Processing sheet with id=AC5, first strand: chain 'e' and resid 39 through 40 Processing sheet with id=AC6, first strand: chain 'e' and resid 39 through 40 Processing sheet with id=AC7, first strand: chain 'e' and resid 80 through 89 removed outlier: 6.628A pdb=" N VAL e 254 " --> pdb=" O VAL e 82 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE e 84 " --> pdb=" O VAL e 252 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL e 252 " --> pdb=" O ILE e 84 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N SER e 86 " --> pdb=" O THR e 250 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR e 250 " --> pdb=" O SER e 86 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR e 88 " --> pdb=" O ILE e 248 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE e 248 " --> pdb=" O THR e 88 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE e 261 " --> pdb=" O ARG e 124 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG e 124 " --> pdb=" O ILE e 261 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N CYS e 263 " --> pdb=" O TYR e 122 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N TYR e 122 " --> pdb=" O CYS e 263 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N CYS e 265 " --> pdb=" O PHE e 120 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N PHE e 120 " --> pdb=" O CYS e 265 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'e' and resid 188 through 191 removed outlier: 5.032A pdb=" N PHE e 120 " --> pdb=" O CYS e 265 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N CYS e 265 " --> pdb=" O PHE e 120 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N TYR e 122 " --> pdb=" O CYS e 263 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N CYS e 263 " --> pdb=" O TYR e 122 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG e 124 " --> pdb=" O ILE e 261 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE e 261 " --> pdb=" O ARG e 124 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N CYS e 263 " --> pdb=" O VAL g 40 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'e' and resid 100 through 104 Processing sheet with id=AD1, first strand: chain 'f' and resid 14 through 18 Processing sheet with id=AD2, first strand: chain 'f' and resid 32 through 33 removed outlier: 6.568A pdb=" N ILE f 32 " --> pdb=" O VAL f 209 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N HIS f 99 " --> pdb=" O GLY f 262 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLY f 262 " --> pdb=" O HIS f 99 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU f 101 " --> pdb=" O PHE f 260 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE f 260 " --> pdb=" O LEU f 101 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ARG f 103 " --> pdb=" O THR f 258 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR f 258 " --> pdb=" O ARG f 103 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'f' and resid 32 through 33 removed outlier: 6.568A pdb=" N ILE f 32 " --> pdb=" O VAL f 209 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N HIS f 99 " --> pdb=" O GLY f 262 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLY f 262 " --> pdb=" O HIS f 99 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU f 101 " --> pdb=" O PHE f 260 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE f 260 " --> pdb=" O LEU f 101 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ARG f 103 " --> pdb=" O THR f 258 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR f 258 " --> pdb=" O ARG f 103 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'f' and resid 155 through 156 removed outlier: 6.141A pdb=" N ALA f 121 " --> pdb=" O LEU f 234 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N GLN f 119 " --> pdb=" O PRO f 236 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'g' and resid 83 through 84 Processing sheet with id=AD6, first strand: chain 'g' and resid 176 through 177 Processing sheet with id=AD7, first strand: chain 'h' and resid 4 through 6 Processing sheet with id=AD8, first strand: chain 'i' and resid 39 through 40 Processing sheet with id=AD9, first strand: chain 'i' and resid 39 through 40 Processing sheet with id=AE1, first strand: chain 'i' and resid 80 through 89 removed outlier: 6.787A pdb=" N VAL i 254 " --> pdb=" O VAL i 82 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE i 84 " --> pdb=" O VAL i 252 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL i 252 " --> pdb=" O ILE i 84 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N SER i 86 " --> pdb=" O THR i 250 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N THR i 250 " --> pdb=" O SER i 86 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N THR i 88 " --> pdb=" O ILE i 248 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE i 248 " --> pdb=" O THR i 88 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE i 261 " --> pdb=" O ARG i 124 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG i 124 " --> pdb=" O ILE i 261 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N CYS i 263 " --> pdb=" O TYR i 122 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TYR i 122 " --> pdb=" O CYS i 263 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N CYS i 265 " --> pdb=" O PHE i 120 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N PHE i 120 " --> pdb=" O CYS i 265 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'i' and resid 188 through 191 removed outlier: 4.842A pdb=" N PHE i 120 " --> pdb=" O CYS i 265 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N CYS i 265 " --> pdb=" O PHE i 120 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TYR i 122 " --> pdb=" O CYS i 263 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N CYS i 263 " --> pdb=" O TYR i 122 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG i 124 " --> pdb=" O ILE i 261 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE i 261 " --> pdb=" O ARG i 124 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N CYS i 263 " --> pdb=" O VAL k 40 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'i' and resid 100 through 104 Processing sheet with id=AE4, first strand: chain 'j' and resid 14 through 18 Processing sheet with id=AE5, first strand: chain 'j' and resid 32 through 33 removed outlier: 6.921A pdb=" N ILE j 32 " --> pdb=" O VAL j 209 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N HIS j 99 " --> pdb=" O GLY j 262 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY j 262 " --> pdb=" O HIS j 99 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU j 101 " --> pdb=" O PHE j 260 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE j 260 " --> pdb=" O LEU j 101 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ARG j 103 " --> pdb=" O THR j 258 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR j 258 " --> pdb=" O ARG j 103 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'j' and resid 32 through 33 removed outlier: 6.921A pdb=" N ILE j 32 " --> pdb=" O VAL j 209 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N HIS j 99 " --> pdb=" O GLY j 262 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY j 262 " --> pdb=" O HIS j 99 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU j 101 " --> pdb=" O PHE j 260 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE j 260 " --> pdb=" O LEU j 101 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ARG j 103 " --> pdb=" O THR j 258 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR j 258 " --> pdb=" O ARG j 103 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'j' and resid 155 through 156 removed outlier: 6.230A pdb=" N ALA j 121 " --> pdb=" O LEU j 234 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N GLN j 119 " --> pdb=" O PRO j 236 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'k' and resid 82 through 85 removed outlier: 3.672A pdb=" N PHE k 82 " --> pdb=" O CYS k 191 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LYS k 128 " --> pdb=" O GLN k 194 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ARG k 196 " --> pdb=" O THR k 126 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N THR k 126 " --> pdb=" O ARG k 196 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'k' and resid 176 through 177 Processing sheet with id=AF1, first strand: chain 'l' and resid 4 through 6 Processing sheet with id=AF2, first strand: chain 'm' and resid 39 through 40 Processing sheet with id=AF3, first strand: chain 'm' and resid 39 through 40 Processing sheet with id=AF4, first strand: chain 'm' and resid 80 through 89 removed outlier: 6.656A pdb=" N VAL m 254 " --> pdb=" O VAL m 82 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE m 84 " --> pdb=" O VAL m 252 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL m 252 " --> pdb=" O ILE m 84 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N SER m 86 " --> pdb=" O THR m 250 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR m 250 " --> pdb=" O SER m 86 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N THR m 88 " --> pdb=" O ILE m 248 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE m 248 " --> pdb=" O THR m 88 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE m 261 " --> pdb=" O ARG m 124 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG m 124 " --> pdb=" O ILE m 261 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N CYS m 263 " --> pdb=" O TYR m 122 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N TYR m 122 " --> pdb=" O CYS m 263 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'm' and resid 80 through 89 removed outlier: 6.656A pdb=" N VAL m 254 " --> pdb=" O VAL m 82 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE m 84 " --> pdb=" O VAL m 252 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL m 252 " --> pdb=" O ILE m 84 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N SER m 86 " --> pdb=" O THR m 250 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR m 250 " --> pdb=" O SER m 86 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N THR m 88 " --> pdb=" O ILE m 248 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE m 248 " --> pdb=" O THR m 88 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE m 261 " --> pdb=" O ARG m 124 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG m 124 " --> pdb=" O ILE m 261 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N CYS m 263 " --> pdb=" O TYR m 122 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N TYR m 122 " --> pdb=" O CYS m 263 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'm' and resid 100 through 104 Processing sheet with id=AF7, first strand: chain 'n' and resid 14 through 18 Processing sheet with id=AF8, first strand: chain 'n' and resid 32 through 33 removed outlier: 6.910A pdb=" N ILE n 32 " --> pdb=" O VAL n 209 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N HIS n 99 " --> pdb=" O GLY n 262 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLY n 262 " --> pdb=" O HIS n 99 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU n 101 " --> pdb=" O PHE n 260 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N PHE n 260 " --> pdb=" O LEU n 101 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ARG n 103 " --> pdb=" O THR n 258 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N THR n 258 " --> pdb=" O ARG n 103 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'n' and resid 32 through 33 removed outlier: 6.910A pdb=" N ILE n 32 " --> pdb=" O VAL n 209 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N HIS n 99 " --> pdb=" O GLY n 262 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLY n 262 " --> pdb=" O HIS n 99 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU n 101 " --> pdb=" O PHE n 260 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N PHE n 260 " --> pdb=" O LEU n 101 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ARG n 103 " --> pdb=" O THR n 258 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N THR n 258 " --> pdb=" O ARG n 103 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'n' and resid 155 through 156 removed outlier: 6.278A pdb=" N ALA n 121 " --> pdb=" O LEU n 234 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLN n 119 " --> pdb=" O PRO n 236 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'o' and resid 82 through 85 removed outlier: 3.561A pdb=" N PHE o 82 " --> pdb=" O CYS o 191 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'o' and resid 176 through 177 Processing sheet with id=AG4, first strand: chain 'p' and resid 4 through 7 Processing sheet with id=AG5, first strand: chain 'q' and resid 80 through 89 removed outlier: 6.688A pdb=" N VAL q 254 " --> pdb=" O VAL q 82 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE q 84 " --> pdb=" O VAL q 252 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N VAL q 252 " --> pdb=" O ILE q 84 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER q 86 " --> pdb=" O THR q 250 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR q 250 " --> pdb=" O SER q 86 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N THR q 88 " --> pdb=" O ILE q 248 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE q 248 " --> pdb=" O THR q 88 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE q 261 " --> pdb=" O ARG q 124 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ARG q 124 " --> pdb=" O ILE q 261 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N CYS q 263 " --> pdb=" O TYR q 122 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N TYR q 122 " --> pdb=" O CYS q 263 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N CYS q 265 " --> pdb=" O PHE q 120 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N PHE q 120 " --> pdb=" O CYS q 265 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'q' and resid 188 through 191 removed outlier: 4.979A pdb=" N PHE q 120 " --> pdb=" O CYS q 265 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N CYS q 265 " --> pdb=" O PHE q 120 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N TYR q 122 " --> pdb=" O CYS q 263 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N CYS q 263 " --> pdb=" O TYR q 122 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ARG q 124 " --> pdb=" O ILE q 261 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE q 261 " --> pdb=" O ARG q 124 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N CYS q 263 " --> pdb=" O VAL s 40 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'r' and resid 14 through 18 Processing sheet with id=AG8, first strand: chain 'r' and resid 32 through 33 removed outlier: 6.418A pdb=" N ILE r 32 " --> pdb=" O VAL r 209 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU r 101 " --> pdb=" O PHE r 260 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N PHE r 260 " --> pdb=" O LEU r 101 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ARG r 103 " --> pdb=" O THR r 258 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR r 258 " --> pdb=" O ARG r 103 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'r' and resid 32 through 33 removed outlier: 6.418A pdb=" N ILE r 32 " --> pdb=" O VAL r 209 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU r 101 " --> pdb=" O PHE r 260 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N PHE r 260 " --> pdb=" O LEU r 101 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ARG r 103 " --> pdb=" O THR r 258 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR r 258 " --> pdb=" O ARG r 103 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'r' and resid 155 through 156 removed outlier: 6.288A pdb=" N ALA r 121 " --> pdb=" O LEU r 234 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLN r 119 " --> pdb=" O PRO r 236 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 's' and resid 51 through 52 Processing sheet with id=AH3, first strand: chain 's' and resid 51 through 52 removed outlier: 3.972A pdb=" N PHE s 208 " --> pdb=" O CYS s 120 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 's' and resid 80 through 85 removed outlier: 6.958A pdb=" N CYS s 191 " --> pdb=" O ILE s 81 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N CYS s 83 " --> pdb=" O ILE s 189 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE s 189 " --> pdb=" O CYS s 83 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS s 128 " --> pdb=" O GLN s 194 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ARG s 196 " --> pdb=" O THR s 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N THR s 126 " --> pdb=" O ARG s 196 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 's' and resid 176 through 177 Processing sheet with id=AH6, first strand: chain 't' and resid 4 through 7 1094 hydrogen bonds defined for protein. 2583 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: 7.19 Time building geometry restraints manager: 4.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 6064 1.31 - 1.44: 10258 1.44 - 1.57: 18001 1.57 - 1.71: 73 1.71 - 1.84: 338 Bond restraints: 34734 Sorted by residual: bond pdb=" CB HIS b 224 " pdb=" CG HIS b 224 " ideal model delta sigma weight residual 1.497 1.342 0.155 1.40e-02 5.10e+03 1.22e+02 bond pdb=" CD ARG b 103 " pdb=" NE ARG b 103 " ideal model delta sigma weight residual 1.458 1.367 0.091 1.40e-02 5.10e+03 4.20e+01 bond pdb=" CD ARG q 238 " pdb=" NE ARG q 238 " ideal model delta sigma weight residual 1.458 1.370 0.088 1.40e-02 5.10e+03 3.98e+01 bond pdb=" CB HIS e 246 " pdb=" CG HIS e 246 " ideal model delta sigma weight residual 1.497 1.409 0.088 1.40e-02 5.10e+03 3.92e+01 bond pdb=" CB HIS r 224 " pdb=" CG HIS r 224 " ideal model delta sigma weight residual 1.497 1.410 0.087 1.40e-02 5.10e+03 3.85e+01 ... (remaining 34729 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 40429 2.48 - 4.97: 5908 4.97 - 7.45: 917 7.45 - 9.94: 104 9.94 - 12.42: 21 Bond angle restraints: 47379 Sorted by residual: angle pdb=" C PRO g 135 " pdb=" N PRO g 136 " pdb=" CA PRO g 136 " ideal model delta sigma weight residual 120.21 129.18 -8.97 9.60e-01 1.09e+00 8.73e+01 angle pdb=" C PRO o 135 " pdb=" N PRO o 136 " pdb=" CA PRO o 136 " ideal model delta sigma weight residual 120.03 129.14 -9.11 9.90e-01 1.02e+00 8.46e+01 angle pdb=" C PRO s 135 " pdb=" N PRO s 136 " pdb=" CA PRO s 136 " ideal model delta sigma weight residual 120.21 128.95 -8.74 9.60e-01 1.09e+00 8.29e+01 angle pdb=" C PRO k 135 " pdb=" N PRO k 136 " pdb=" CA PRO k 136 " ideal model delta sigma weight residual 119.92 129.66 -9.74 1.07e+00 8.73e-01 8.28e+01 angle pdb=" CA ASP o 17 " pdb=" CB ASP o 17 " pdb=" CG ASP o 17 " ideal model delta sigma weight residual 112.60 121.56 -8.96 1.00e+00 1.00e+00 8.02e+01 ... (remaining 47374 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 20025 17.74 - 35.48: 513 35.48 - 53.22: 114 53.22 - 70.96: 46 70.96 - 88.70: 18 Dihedral angle restraints: 20716 sinusoidal: 7815 harmonic: 12901 Sorted by residual: dihedral pdb=" C TYR i 274 " pdb=" N TYR i 274 " pdb=" CA TYR i 274 " pdb=" CB TYR i 274 " ideal model delta harmonic sigma weight residual -122.60 -107.83 -14.77 0 2.50e+00 1.60e-01 3.49e+01 dihedral pdb=" CA ARG c 222 " pdb=" C ARG c 222 " pdb=" N LEU c 223 " pdb=" CA LEU c 223 " ideal model delta harmonic sigma weight residual -180.00 -152.55 -27.45 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" C ARG c 222 " pdb=" N ARG c 222 " pdb=" CA ARG c 222 " pdb=" CB ARG c 222 " ideal model delta harmonic sigma weight residual -122.60 -111.28 -11.32 0 2.50e+00 1.60e-01 2.05e+01 ... (remaining 20713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 3902 0.104 - 0.208: 1240 0.208 - 0.312: 156 0.312 - 0.416: 20 0.416 - 0.519: 4 Chirality restraints: 5322 Sorted by residual: chirality pdb=" CG LEU s 235 " pdb=" CB LEU s 235 " pdb=" CD1 LEU s 235 " pdb=" CD2 LEU s 235 " both_signs ideal model delta sigma weight residual False -2.59 -3.11 0.52 2.00e-01 2.50e+01 6.74e+00 chirality pdb=" CB VAL q 16 " pdb=" CA VAL q 16 " pdb=" CG1 VAL q 16 " pdb=" CG2 VAL q 16 " both_signs ideal model delta sigma weight residual False -2.63 -3.11 0.49 2.00e-01 2.50e+01 5.89e+00 chirality pdb=" CA TRP m 264 " pdb=" N TRP m 264 " pdb=" C TRP m 264 " pdb=" CB TRP m 264 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.52e+00 ... (remaining 5319 not shown) Planarity restraints: 6150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP r 79 " 0.064 2.00e-02 2.50e+03 3.18e-02 2.53e+01 pdb=" CG TRP r 79 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP r 79 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP r 79 " -0.025 2.00e-02 2.50e+03 pdb=" NE1 TRP r 79 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP r 79 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP r 79 " -0.044 2.00e-02 2.50e+03 pdb=" CZ2 TRP r 79 " 0.035 2.00e-02 2.50e+03 pdb=" CZ3 TRP r 79 " -0.016 2.00e-02 2.50e+03 pdb=" CH2 TRP r 79 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR m 150 " 0.059 2.00e-02 2.50e+03 3.14e-02 1.97e+01 pdb=" CG TYR m 150 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR m 150 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR m 150 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR m 150 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR m 150 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR m 150 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR m 150 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR r 98 " 0.060 2.00e-02 2.50e+03 3.14e-02 1.97e+01 pdb=" CG TYR r 98 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR r 98 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR r 98 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR r 98 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR r 98 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR r 98 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR r 98 " 0.043 2.00e-02 2.50e+03 ... (remaining 6147 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 10358 2.82 - 3.34: 32301 3.34 - 3.86: 59940 3.86 - 4.38: 74489 4.38 - 4.90: 118218 Nonbonded interactions: 295306 Sorted by model distance: nonbonded pdb=" N ASP f 11 " pdb=" OD1 ASP f 11 " model vdw 2.300 3.120 nonbonded pdb=" NH2 ARG q 115 " pdb=" OE1 GLU s 101 " model vdw 2.366 3.120 nonbonded pdb=" N ASP m 221 " pdb=" OD1 ASP m 221 " model vdw 2.374 3.120 nonbonded pdb=" NZ LYS h 34 " pdb=" OD2 ASP k 18 " model vdw 2.377 3.120 nonbonded pdb=" ND2 ASN e 241 " pdb=" OG1 THR i 134 " model vdw 2.393 3.120 ... (remaining 295301 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 'H' and resid 12 through 109) selection = chain 'L' } ncs_group { reference = (chain 'a' and (resid 19 through 213 or resid 218 through 300)) selection = (chain 'e' and (resid 19 through 213 or resid 218 through 300)) selection = (chain 'i' and (resid 19 through 213 or resid 218 through 300)) selection = chain 'm' selection = (chain 'q' and (resid 19 through 213 or resid 218 through 300)) } ncs_group { reference = (chain 'b' and (resid 10 through 164 or resid 170 through 239 or resid 245 throu \ gh 271)) selection = (chain 'f' and (resid 10 through 164 or resid 170 through 239 or resid 245 throu \ gh 271)) selection = (chain 'j' and (resid 10 through 164 or resid 170 through 239 or resid 245 throu \ gh 271)) selection = (chain 'n' and (resid 10 through 164 or resid 170 through 239 or resid 245 throu \ gh 271)) selection = (chain 'r' and (resid 10 through 239 or resid 245 through 271)) } ncs_group { reference = (chain 'c' and resid 1 through 233) selection = (chain 'g' and resid 1 through 233) selection = chain 'k' selection = (chain 'o' and resid 1 through 233) selection = (chain 's' and resid 1 through 233) } ncs_group { reference = (chain 'd' and resid 2 through 68) selection = (chain 'h' and resid 2 through 68) selection = (chain 'l' and resid 2 through 68) selection = chain 'p' selection = (chain 't' and resid 2 through 68) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 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: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 33.350 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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 : 0.021 0.160 34734 Z= 1.118 Angle : 1.842 12.421 47379 Z= 1.247 Chirality : 0.097 0.519 5322 Planarity : 0.009 0.065 6150 Dihedral : 9.913 88.698 12390 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.07 % 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: 0.55 (0.12), residues: 4158 helix: -2.98 (0.18), residues: 418 sheet: 1.54 (0.15), residues: 1016 loop : 0.58 (0.11), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG q 114 TYR 0.060 0.009 TYR r 98 PHE 0.041 0.006 PHE q 120 TRP 0.064 0.009 TRP r 79 HIS 0.017 0.003 HIS i 99 Details of bonding type rmsd covalent geometry : bond 0.02059 (34734) covalent geometry : angle 1.84245 (47379) hydrogen bonds : bond 0.15905 ( 900) hydrogen bonds : angle 8.97206 ( 2583) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1898 residues out of total 3659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1898 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN b 272 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE m 298 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 40 THR cc_start: 0.8637 (t) cc_final: 0.8327 (t) REVERT: a 49 GLN cc_start: 0.9088 (mm-40) cc_final: 0.8727 (mm110) REVERT: a 66 THR cc_start: 0.9064 (t) cc_final: 0.8829 (p) REVERT: a 69 GLU cc_start: 0.8119 (mp0) cc_final: 0.7917 (mp0) REVERT: a 107 TYR cc_start: 0.9131 (p90) cc_final: 0.8824 (p90) REVERT: a 118 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8181 (mt-10) REVERT: a 127 LEU cc_start: 0.8896 (tp) cc_final: 0.8399 (tt) REVERT: a 132 VAL cc_start: 0.9563 (t) cc_final: 0.9335 (p) REVERT: a 150 TYR cc_start: 0.8734 (m-80) cc_final: 0.8530 (m-80) REVERT: a 151 GLN cc_start: 0.8865 (tt0) cc_final: 0.8563 (tt0) REVERT: a 165 TRP cc_start: 0.8187 (p-90) cc_final: 0.7806 (p-90) REVERT: a 171 GLN cc_start: 0.8595 (mt0) cc_final: 0.8330 (mt0) REVERT: a 178 ILE cc_start: 0.9536 (mt) cc_final: 0.9239 (mm) REVERT: a 182 TYR cc_start: 0.8398 (t80) cc_final: 0.8037 (t80) REVERT: a 194 VAL cc_start: 0.9216 (m) cc_final: 0.8908 (p) REVERT: a 287 LEU cc_start: 0.9065 (mt) cc_final: 0.8815 (pt) REVERT: a 291 LYS cc_start: 0.8844 (ptmt) cc_final: 0.8273 (ptpt) REVERT: b 42 ILE cc_start: 0.8934 (mt) cc_final: 0.8632 (mt) REVERT: b 99 HIS cc_start: 0.8694 (m90) cc_final: 0.8125 (m170) REVERT: b 112 CYS cc_start: 0.8716 (t) cc_final: 0.8364 (t) REVERT: b 223 LYS cc_start: 0.8781 (mtmt) cc_final: 0.8398 (mttm) REVERT: b 249 ILE cc_start: 0.9169 (mt) cc_final: 0.8750 (mm) REVERT: c 55 MET cc_start: 0.8728 (ttm) cc_final: 0.8273 (ttm) REVERT: c 70 ILE cc_start: 0.9061 (mt) cc_final: 0.8472 (mt) REVERT: c 159 LEU cc_start: 0.8816 (mt) cc_final: 0.8439 (mt) REVERT: c 160 GLN cc_start: 0.8470 (mm-40) cc_final: 0.8255 (mm110) REVERT: c 193 TYR cc_start: 0.8753 (m-80) cc_final: 0.8513 (m-80) REVERT: c 209 MET cc_start: 0.7897 (ttp) cc_final: 0.7668 (ttp) REVERT: c 219 PHE cc_start: 0.8512 (t80) cc_final: 0.8284 (t80) REVERT: c 224 LEU cc_start: 0.8497 (mt) cc_final: 0.8214 (mt) REVERT: e 32 ASN cc_start: 0.8021 (m-40) cc_final: 0.7803 (m-40) REVERT: e 51 ILE cc_start: 0.9285 (pt) cc_final: 0.9004 (pt) REVERT: e 57 GLU cc_start: 0.5486 (mp0) cc_final: 0.4835 (mp0) REVERT: e 88 THR cc_start: 0.8208 (m) cc_final: 0.7684 (m) REVERT: e 101 ASN cc_start: 0.8812 (t0) cc_final: 0.8406 (t0) REVERT: e 111 VAL cc_start: 0.9167 (m) cc_final: 0.8809 (p) REVERT: e 128 GLU cc_start: 0.7577 (tt0) cc_final: 0.6837 (tt0) REVERT: e 171 GLN cc_start: 0.9061 (mt0) cc_final: 0.8686 (mt0) REVERT: e 188 ARG cc_start: 0.8566 (ttm170) cc_final: 0.8283 (ttt180) REVERT: e 194 VAL cc_start: 0.9156 (m) cc_final: 0.8858 (p) REVERT: e 241 ASN cc_start: 0.8165 (m110) cc_final: 0.7533 (m110) REVERT: e 255 TYR cc_start: 0.9127 (m-80) cc_final: 0.8851 (m-10) REVERT: e 267 ARG cc_start: 0.9363 (mtp85) cc_final: 0.9143 (mtt-85) REVERT: e 280 ASP cc_start: 0.8185 (m-30) cc_final: 0.7303 (t0) REVERT: e 295 ILE cc_start: 0.8456 (mt) cc_final: 0.8167 (mt) REVERT: f 80 TRP cc_start: 0.9121 (m-90) cc_final: 0.8762 (m-90) REVERT: f 100 TYR cc_start: 0.8171 (t80) cc_final: 0.7666 (t80) REVERT: f 149 ASN cc_start: 0.8713 (m-40) cc_final: 0.8417 (m-40) REVERT: f 199 ASN cc_start: 0.8707 (t0) cc_final: 0.7792 (p0) REVERT: f 218 ILE cc_start: 0.9564 (tt) cc_final: 0.9345 (mt) REVERT: f 252 THR cc_start: 0.9370 (m) cc_final: 0.9148 (p) REVERT: g 41 LYS cc_start: 0.8867 (mttm) cc_final: 0.8595 (mmmm) REVERT: g 44 MET cc_start: 0.9189 (mmp) cc_final: 0.8934 (mmm) REVERT: g 55 MET cc_start: 0.7998 (tpt) cc_final: 0.7697 (tpt) REVERT: g 85 SER cc_start: 0.9049 (m) cc_final: 0.8410 (p) REVERT: g 91 ASP cc_start: 0.8302 (t0) cc_final: 0.7428 (t0) REVERT: g 112 SER cc_start: 0.8581 (m) cc_final: 0.8147 (p) REVERT: g 118 LEU cc_start: 0.8919 (tp) cc_final: 0.8461 (tt) REVERT: g 148 MET cc_start: 0.7738 (ttm) cc_final: 0.7357 (ttt) REVERT: g 155 TRP cc_start: 0.9220 (t60) cc_final: 0.8994 (t60) REVERT: g 169 TRP cc_start: 0.9085 (t-100) cc_final: 0.8453 (t-100) REVERT: g 207 MET cc_start: 0.8109 (pmm) cc_final: 0.7629 (pmm) REVERT: g 216 CYS cc_start: 0.8414 (m) cc_final: 0.8027 (m) REVERT: g 225 ARG cc_start: 0.8761 (ptt90) cc_final: 0.8250 (ptt-90) REVERT: g 230 ILE cc_start: 0.9249 (tt) cc_final: 0.8798 (tt) REVERT: i 54 ASP cc_start: 0.8084 (m-30) cc_final: 0.7851 (m-30) REVERT: i 75 PHE cc_start: 0.9232 (t80) cc_final: 0.9018 (t80) REVERT: i 83 THR cc_start: 0.9234 (t) cc_final: 0.8998 (m) REVERT: i 131 PHE cc_start: 0.8929 (m-80) cc_final: 0.8707 (m-80) REVERT: i 169 THR cc_start: 0.9043 (p) cc_final: 0.8671 (t) REVERT: i 298 PHE cc_start: 0.8329 (m-80) cc_final: 0.7635 (m-80) REVERT: j 99 HIS cc_start: 0.8433 (m90) cc_final: 0.8014 (m90) REVERT: j 147 ASN cc_start: 0.7684 (m-40) cc_final: 0.7278 (t0) REVERT: j 149 ASN cc_start: 0.8670 (m-40) cc_final: 0.8345 (m-40) REVERT: j 213 VAL cc_start: 0.9031 (t) cc_final: 0.8685 (m) REVERT: j 252 THR cc_start: 0.9120 (m) cc_final: 0.8899 (m) REVERT: k 11 ASN cc_start: 0.9167 (m-40) cc_final: 0.8939 (m-40) REVERT: k 43 MET cc_start: 0.8843 (mmm) cc_final: 0.8277 (mmm) REVERT: k 51 THR cc_start: 0.8967 (p) cc_final: 0.8657 (p) REVERT: k 112 SER cc_start: 0.8736 (m) cc_final: 0.8238 (p) REVERT: k 116 THR cc_start: 0.9197 (m) cc_final: 0.8922 (t) REVERT: k 118 LEU cc_start: 0.8516 (tp) cc_final: 0.8179 (tt) REVERT: k 130 LEU cc_start: 0.8875 (tp) cc_final: 0.8463 (tt) REVERT: k 154 ILE cc_start: 0.8556 (mm) cc_final: 0.8242 (mt) REVERT: k 216 CYS cc_start: 0.8601 (m) cc_final: 0.7516 (m) REVERT: k 218 ASP cc_start: 0.8440 (p0) cc_final: 0.8169 (p0) REVERT: l 25 ILE cc_start: 0.8479 (mm) cc_final: 0.8132 (mm) REVERT: l 64 THR cc_start: 0.9005 (p) cc_final: 0.7579 (p) REVERT: m 49 GLN cc_start: 0.8625 (mm-40) cc_final: 0.7699 (mm110) REVERT: m 57 GLU cc_start: 0.6906 (mp0) cc_final: 0.6664 (mp0) REVERT: m 70 SER cc_start: 0.9180 (p) cc_final: 0.8505 (t) REVERT: m 71 CYS cc_start: 0.8709 (m) cc_final: 0.8167 (t) REVERT: m 105 ILE cc_start: 0.9123 (mm) cc_final: 0.8890 (mm) REVERT: m 128 GLU cc_start: 0.7892 (tt0) cc_final: 0.7326 (tt0) REVERT: m 151 GLN cc_start: 0.8845 (tt0) cc_final: 0.7752 (tt0) REVERT: m 170 TRP cc_start: 0.8821 (m100) cc_final: 0.8287 (m100) REVERT: m 180 TYR cc_start: 0.9343 (t80) cc_final: 0.9029 (t80) REVERT: m 203 PHE cc_start: 0.8883 (m-80) cc_final: 0.8467 (m-10) REVERT: m 223 PHE cc_start: 0.7189 (m-80) cc_final: 0.6961 (m-10) REVERT: m 281 MET cc_start: 0.8158 (mtm) cc_final: 0.7302 (mtm) REVERT: n 50 VAL cc_start: 0.9251 (m) cc_final: 0.8976 (t) REVERT: n 61 ASN cc_start: 0.9017 (m-40) cc_final: 0.8422 (m110) REVERT: n 74 THR cc_start: 0.8076 (p) cc_final: 0.7776 (t) REVERT: n 84 ASP cc_start: 0.7467 (t70) cc_final: 0.6913 (t0) REVERT: n 87 LYS cc_start: 0.8684 (pttt) cc_final: 0.8330 (ptmt) REVERT: n 113 ASN cc_start: 0.8425 (m-40) cc_final: 0.8097 (t0) REVERT: n 129 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7644 (mm-30) REVERT: n 130 PHE cc_start: 0.8804 (t80) cc_final: 0.8529 (t80) REVERT: n 149 ASN cc_start: 0.8833 (m-40) cc_final: 0.8152 (m110) REVERT: n 178 ASP cc_start: 0.7955 (p0) cc_final: 0.7578 (p0) REVERT: n 212 TYR cc_start: 0.9216 (t80) cc_final: 0.8783 (t80) REVERT: n 219 ASP cc_start: 0.8569 (t0) cc_final: 0.8341 (t0) REVERT: n 258 THR cc_start: 0.8156 (m) cc_final: 0.7955 (t) REVERT: o 10 SER cc_start: 0.9286 (m) cc_final: 0.8817 (p) REVERT: o 36 ILE cc_start: 0.9597 (mt) cc_final: 0.9295 (mt) REVERT: o 41 LYS cc_start: 0.8930 (mmtt) cc_final: 0.8388 (mmtp) REVERT: o 43 MET cc_start: 0.9015 (mmm) cc_final: 0.8731 (mmm) REVERT: o 44 MET cc_start: 0.9136 (mmp) cc_final: 0.8793 (mmm) REVERT: o 53 ILE cc_start: 0.9140 (mt) cc_final: 0.8821 (mt) REVERT: o 70 ILE cc_start: 0.9364 (mt) cc_final: 0.8989 (mt) REVERT: o 74 ASP cc_start: 0.7951 (p0) cc_final: 0.7557 (p0) REVERT: o 93 ARG cc_start: 0.8833 (mtm-85) cc_final: 0.8373 (mtm-85) REVERT: o 94 LEU cc_start: 0.9407 (mt) cc_final: 0.9155 (mm) REVERT: o 104 ASN cc_start: 0.8063 (m-40) cc_final: 0.7250 (m-40) REVERT: o 120 CYS cc_start: 0.7712 (m) cc_final: 0.7292 (m) REVERT: o 146 ASP cc_start: 0.8642 (m-30) cc_final: 0.8439 (m-30) REVERT: o 156 ASP cc_start: 0.5333 (m-30) cc_final: 0.5052 (m-30) REVERT: o 169 TRP cc_start: 0.8538 (t-100) cc_final: 0.7933 (t-100) REVERT: o 182 ASP cc_start: 0.7917 (m-30) cc_final: 0.7540 (m-30) REVERT: o 208 PHE cc_start: 0.8024 (m-80) cc_final: 0.7802 (m-80) REVERT: o 216 CYS cc_start: 0.7618 (m) cc_final: 0.7010 (m) REVERT: o 218 ASP cc_start: 0.8786 (p0) cc_final: 0.8533 (p0) REVERT: o 234 LYS cc_start: 0.7791 (tttm) cc_final: 0.7555 (ttpt) REVERT: p 7 THR cc_start: 0.9190 (m) cc_final: 0.8885 (p) REVERT: p 33 TYR cc_start: 0.9030 (m-80) cc_final: 0.8821 (m-10) REVERT: p 54 THR cc_start: 0.9227 (p) cc_final: 0.8093 (m) REVERT: q 54 ASP cc_start: 0.8220 (m-30) cc_final: 0.7880 (m-30) REVERT: q 55 VAL cc_start: 0.9128 (m) cc_final: 0.8798 (t) REVERT: q 189 MET cc_start: 0.8536 (ptt) cc_final: 0.8297 (ptm) REVERT: q 203 PHE cc_start: 0.9131 (m-80) cc_final: 0.8557 (m-80) REVERT: q 226 LEU cc_start: 0.9257 (tp) cc_final: 0.8985 (tp) REVERT: q 257 LYS cc_start: 0.9104 (ttpt) cc_final: 0.8588 (ptmt) REVERT: q 279 VAL cc_start: 0.9308 (m) cc_final: 0.8971 (p) REVERT: r 89 MET cc_start: 0.8897 (mmt) cc_final: 0.8677 (mmm) REVERT: r 122 LEU cc_start: 0.9321 (mt) cc_final: 0.9083 (mt) REVERT: s 18 ASP cc_start: 0.7376 (t0) cc_final: 0.6964 (t0) REVERT: s 27 ASN cc_start: 0.8945 (m-40) cc_final: 0.8660 (t0) REVERT: s 73 ASN cc_start: 0.9000 (p0) cc_final: 0.8572 (m-40) REVERT: s 75 ASN cc_start: 0.8103 (t0) cc_final: 0.7549 (p0) REVERT: s 166 VAL cc_start: 0.9697 (t) cc_final: 0.9474 (m) REVERT: s 173 THR cc_start: 0.9070 (p) cc_final: 0.8799 (p) REVERT: s 216 CYS cc_start: 0.8401 (m) cc_final: 0.8076 (m) REVERT: s 218 ASP cc_start: 0.8706 (p0) cc_final: 0.8354 (p0) REVERT: s 223 LEU cc_start: 0.8753 (tp) cc_final: 0.8023 (tp) REVERT: s 226 ASP cc_start: 0.7117 (m-30) cc_final: 0.6426 (m-30) REVERT: t 42 THR cc_start: 0.8529 (p) cc_final: 0.8318 (t) REVERT: t 44 GLN cc_start: 0.8759 (pt0) cc_final: 0.8415 (pt0) REVERT: t 54 THR cc_start: 0.9246 (p) cc_final: 0.9015 (t) outliers start: 0 outliers final: 0 residues processed: 1898 average time/residue: 0.2232 time to fit residues: 682.0457 Evaluate side-chains 1313 residues out of total 3659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1313 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 5.9990 chunk 424 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 18 GLN ** a 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 35 HIS ** c 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 194 GLN ** c 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 60 HIS ** e 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 43 ASN f 226 ASN f 246 GLN g 27 ASN ** g 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 160 GLN ** g 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 232 GLN ** h 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 26 ASN i 198 ASN ** j 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 196 GLN j 271 HIS ** k 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 75 ASN k 96 HIS k 108 HIS l 44 GLN m 32 ASN n 15 GLN n 118 HIS ** n 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 27 ASN o 96 HIS o 229 HIS p 4 GLN p 17 ASN q 101 ASN q 184 ASN q 198 ASN q 202 HIS ** r 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 118 HIS ** r 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 162 ASN r 224 HIS ** s 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.117393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.105658 restraints weight = 76385.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.108783 restraints weight = 37393.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.110870 restraints weight = 21608.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.112197 restraints weight = 13915.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.113153 restraints weight = 9725.515| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 34734 Z= 0.238 Angle : 0.745 11.716 47379 Z= 0.400 Chirality : 0.047 0.218 5322 Planarity : 0.006 0.118 6150 Dihedral : 6.181 65.827 4820 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.08 % Allowed : 3.31 % Favored : 96.61 % 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: 0.16 (0.12), residues: 4158 helix: -2.49 (0.21), residues: 418 sheet: 1.27 (0.15), residues: 1039 loop : 0.14 (0.11), residues: 2701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG r 264 TYR 0.029 0.002 TYR c 175 PHE 0.040 0.002 PHE j 174 TRP 0.021 0.002 TRP r 80 HIS 0.014 0.002 HIS c 229 Details of bonding type rmsd covalent geometry : bond 0.00512 (34734) covalent geometry : angle 0.74521 (47379) hydrogen bonds : bond 0.04936 ( 900) hydrogen bonds : angle 6.95258 ( 2583) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1584 residues out of total 3659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1581 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE a 298 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN b 272 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASN l 69 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PHE m 298 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 63 ASN cc_start: 0.8249 (t0) cc_final: 0.8024 (t0) REVERT: a 66 THR cc_start: 0.9128 (t) cc_final: 0.8899 (m) REVERT: a 98 LYS cc_start: 0.8973 (mmmt) cc_final: 0.8467 (tppt) REVERT: a 127 LEU cc_start: 0.9242 (tp) cc_final: 0.8617 (tt) REVERT: a 128 GLU cc_start: 0.8145 (mp0) cc_final: 0.7922 (mp0) REVERT: a 132 VAL cc_start: 0.9638 (t) cc_final: 0.9376 (p) REVERT: a 151 GLN cc_start: 0.9123 (tt0) cc_final: 0.8443 (tt0) REVERT: a 170 TRP cc_start: 0.9159 (m100) cc_final: 0.8793 (m100) REVERT: a 171 GLN cc_start: 0.8844 (mt0) cc_final: 0.8461 (mt0) REVERT: a 264 TRP cc_start: 0.9255 (m-90) cc_final: 0.8837 (m-90) REVERT: a 274 TYR cc_start: 0.7035 (m-80) cc_final: 0.6807 (m-10) REVERT: a 291 LYS cc_start: 0.9202 (ptmt) cc_final: 0.8276 (ptpt) REVERT: a 295 ILE cc_start: 0.9330 (mp) cc_final: 0.8746 (mt) REVERT: b 50 VAL cc_start: 0.8856 (m) cc_final: 0.8372 (p) REVERT: b 112 CYS cc_start: 0.8518 (t) cc_final: 0.7994 (t) REVERT: b 214 ASN cc_start: 0.8817 (t0) cc_final: 0.8291 (t0) REVERT: b 216 LEU cc_start: 0.8808 (mt) cc_final: 0.8398 (mt) REVERT: b 223 LYS cc_start: 0.9019 (mtmt) cc_final: 0.8381 (mttm) REVERT: b 249 ILE cc_start: 0.9211 (mt) cc_final: 0.8710 (mm) REVERT: c 43 MET cc_start: 0.9359 (mmm) cc_final: 0.9125 (mmm) REVERT: c 61 LYS cc_start: 0.8727 (mmtm) cc_final: 0.8516 (mmmt) REVERT: c 67 MET cc_start: 0.8729 (ptp) cc_final: 0.8411 (ptp) REVERT: c 69 GLN cc_start: 0.8609 (mt0) cc_final: 0.8177 (mp10) REVERT: c 104 ASN cc_start: 0.7996 (t0) cc_final: 0.7492 (t0) REVERT: c 118 LEU cc_start: 0.8984 (tp) cc_final: 0.8525 (tt) REVERT: c 157 LEU cc_start: 0.9251 (mt) cc_final: 0.8966 (mt) REVERT: c 163 CYS cc_start: 0.7956 (p) cc_final: 0.7609 (p) REVERT: c 164 SER cc_start: 0.9646 (p) cc_final: 0.9329 (m) REVERT: c 209 MET cc_start: 0.7451 (ttp) cc_final: 0.7224 (ttp) REVERT: c 222 ARG cc_start: 0.7978 (mmm-85) cc_final: 0.7566 (mtp85) REVERT: c 227 THR cc_start: 0.8468 (p) cc_final: 0.8178 (p) REVERT: d 61 MET cc_start: 0.8125 (ptp) cc_final: 0.7902 (ptp) REVERT: e 33 SER cc_start: 0.8696 (t) cc_final: 0.8443 (t) REVERT: e 57 GLU cc_start: 0.4966 (mp0) cc_final: 0.3891 (mp0) REVERT: e 69 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7652 (mt-10) REVERT: e 179 PHE cc_start: 0.8595 (m-80) cc_final: 0.7963 (m-80) REVERT: e 200 TYR cc_start: 0.8767 (m-10) cc_final: 0.8547 (m-10) REVERT: e 231 ASP cc_start: 0.7332 (t0) cc_final: 0.7066 (t0) REVERT: e 241 ASN cc_start: 0.8159 (m110) cc_final: 0.7546 (m110) REVERT: e 267 ARG cc_start: 0.9300 (mtp85) cc_final: 0.8972 (ttm110) REVERT: e 275 ARG cc_start: 0.6560 (ttt-90) cc_final: 0.5589 (ttm-80) REVERT: e 280 ASP cc_start: 0.7766 (m-30) cc_final: 0.7288 (t0) REVERT: e 295 ILE cc_start: 0.8694 (mt) cc_final: 0.8484 (mt) REVERT: f 101 LEU cc_start: 0.9618 (mt) cc_final: 0.9385 (mp) REVERT: f 126 LEU cc_start: 0.9557 (mt) cc_final: 0.9145 (mt) REVERT: f 127 ILE cc_start: 0.9126 (mp) cc_final: 0.8761 (mt) REVERT: f 142 TYR cc_start: 0.7147 (t80) cc_final: 0.6935 (t80) REVERT: f 149 ASN cc_start: 0.8398 (m-40) cc_final: 0.8087 (m110) REVERT: f 161 TYR cc_start: 0.8016 (t80) cc_final: 0.7777 (t80) REVERT: f 162 ASN cc_start: 0.8428 (m-40) cc_final: 0.7803 (p0) REVERT: f 196 GLN cc_start: 0.8835 (mt0) cc_final: 0.8470 (mt0) REVERT: f 199 ASN cc_start: 0.8535 (t0) cc_final: 0.8214 (t0) REVERT: f 221 MET cc_start: 0.8873 (mmm) cc_final: 0.8583 (mmm) REVERT: g 41 LYS cc_start: 0.9272 (mttm) cc_final: 0.9066 (mttp) REVERT: g 85 SER cc_start: 0.8981 (m) cc_final: 0.8519 (p) REVERT: g 91 ASP cc_start: 0.8555 (t0) cc_final: 0.8136 (t0) REVERT: g 101 GLU cc_start: 0.8368 (tp30) cc_final: 0.7813 (mm-30) REVERT: g 112 SER cc_start: 0.8773 (m) cc_final: 0.7833 (p) REVERT: g 128 LYS cc_start: 0.8005 (mppt) cc_final: 0.7185 (mmtt) REVERT: g 148 MET cc_start: 0.7035 (ttm) cc_final: 0.6572 (ttt) REVERT: g 153 ILE cc_start: 0.9011 (pt) cc_final: 0.8765 (tp) REVERT: g 156 ASP cc_start: 0.8149 (t0) cc_final: 0.7875 (t0) REVERT: g 162 SER cc_start: 0.9038 (m) cc_final: 0.8692 (p) REVERT: g 163 CYS cc_start: 0.8805 (p) cc_final: 0.8212 (p) REVERT: g 169 TRP cc_start: 0.8788 (t-100) cc_final: 0.8582 (t-100) REVERT: g 216 CYS cc_start: 0.8397 (m) cc_final: 0.7813 (m) REVERT: g 224 LEU cc_start: 0.9089 (tp) cc_final: 0.8877 (tp) REVERT: g 225 ARG cc_start: 0.8681 (ptt90) cc_final: 0.8003 (ptt-90) REVERT: h 8 GLN cc_start: 0.7931 (mt0) cc_final: 0.7449 (mt0) REVERT: i 72 LEU cc_start: 0.9400 (mt) cc_final: 0.9180 (mt) REVERT: i 166 ASP cc_start: 0.8265 (p0) cc_final: 0.7689 (p0) REVERT: i 169 THR cc_start: 0.9140 (p) cc_final: 0.8691 (t) REVERT: i 182 TYR cc_start: 0.8927 (t80) cc_final: 0.8688 (t80) REVERT: i 250 THR cc_start: 0.7987 (m) cc_final: 0.7288 (t) REVERT: i 274 TYR cc_start: 0.8426 (m-80) cc_final: 0.7738 (m-80) REVERT: j 32 ILE cc_start: 0.9190 (mm) cc_final: 0.8917 (tp) REVERT: j 37 GLU cc_start: 0.7585 (tt0) cc_final: 0.7385 (tt0) REVERT: j 100 TYR cc_start: 0.8221 (t80) cc_final: 0.8010 (t80) REVERT: j 109 HIS cc_start: 0.8553 (t70) cc_final: 0.8253 (t70) REVERT: j 132 MET cc_start: 0.8069 (mtt) cc_final: 0.7509 (mmt) REVERT: j 147 ASN cc_start: 0.7497 (m-40) cc_final: 0.7224 (t0) REVERT: j 198 ILE cc_start: 0.9267 (mt) cc_final: 0.9037 (tt) REVERT: j 213 VAL cc_start: 0.9099 (t) cc_final: 0.8843 (m) REVERT: k 2 LEU cc_start: 0.9502 (tp) cc_final: 0.9175 (tp) REVERT: k 27 ASN cc_start: 0.9051 (m110) cc_final: 0.8516 (m110) REVERT: k 29 ASP cc_start: 0.9373 (t0) cc_final: 0.8782 (t0) REVERT: k 43 MET cc_start: 0.9131 (mmm) cc_final: 0.8336 (mmm) REVERT: k 56 ASN cc_start: 0.8734 (t0) cc_final: 0.8044 (t0) REVERT: k 110 THR cc_start: 0.9152 (t) cc_final: 0.8590 (t) REVERT: k 116 THR cc_start: 0.9139 (m) cc_final: 0.8821 (t) REVERT: k 119 PHE cc_start: 0.8417 (t80) cc_final: 0.8046 (t80) REVERT: k 169 TRP cc_start: 0.8356 (t-100) cc_final: 0.7653 (t-100) REVERT: k 176 ARG cc_start: 0.8760 (mtp85) cc_final: 0.8210 (mtt-85) REVERT: k 216 CYS cc_start: 0.8482 (m) cc_final: 0.7454 (m) REVERT: k 218 ASP cc_start: 0.8880 (p0) cc_final: 0.8598 (p0) REVERT: k 226 ASP cc_start: 0.7683 (m-30) cc_final: 0.7454 (m-30) REVERT: l 38 SER cc_start: 0.9566 (m) cc_final: 0.9273 (t) REVERT: l 42 THR cc_start: 0.8628 (p) cc_final: 0.8306 (t) REVERT: l 64 THR cc_start: 0.9044 (p) cc_final: 0.7916 (p) REVERT: m 49 GLN cc_start: 0.8242 (mm-40) cc_final: 0.7828 (mm110) REVERT: m 70 SER cc_start: 0.9159 (p) cc_final: 0.8388 (t) REVERT: m 105 ILE cc_start: 0.8942 (mm) cc_final: 0.8682 (tp) REVERT: m 110 THR cc_start: 0.7963 (p) cc_final: 0.7673 (p) REVERT: m 170 TRP cc_start: 0.8453 (m100) cc_final: 0.7870 (m100) REVERT: n 61 ASN cc_start: 0.9135 (m-40) cc_final: 0.8831 (m-40) REVERT: n 74 THR cc_start: 0.8295 (p) cc_final: 0.8022 (t) REVERT: n 84 ASP cc_start: 0.8028 (t70) cc_final: 0.7526 (t0) REVERT: n 106 TYR cc_start: 0.8635 (m-80) cc_final: 0.8220 (m-80) REVERT: n 113 ASN cc_start: 0.7725 (m-40) cc_final: 0.7383 (t0) REVERT: n 183 SER cc_start: 0.8973 (p) cc_final: 0.8483 (t) REVERT: n 193 TYR cc_start: 0.8583 (m-80) cc_final: 0.8271 (m-80) REVERT: n 199 ASN cc_start: 0.8808 (t0) cc_final: 0.8522 (t0) REVERT: n 212 TYR cc_start: 0.9190 (t80) cc_final: 0.8886 (t80) REVERT: n 219 ASP cc_start: 0.9192 (t0) cc_final: 0.8009 (t0) REVERT: n 257 CYS cc_start: 0.8545 (m) cc_final: 0.8259 (m) REVERT: o 10 SER cc_start: 0.9105 (m) cc_final: 0.8814 (p) REVERT: o 25 LEU cc_start: 0.9068 (mt) cc_final: 0.8807 (mt) REVERT: o 39 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8097 (tm-30) REVERT: o 41 LYS cc_start: 0.8353 (mmtt) cc_final: 0.7917 (mmtp) REVERT: o 43 MET cc_start: 0.8985 (mmm) cc_final: 0.8631 (mmm) REVERT: o 44 MET cc_start: 0.9351 (mmp) cc_final: 0.9015 (mmm) REVERT: o 73 ASN cc_start: 0.8890 (m110) cc_final: 0.8622 (m-40) REVERT: o 95 SER cc_start: 0.8644 (p) cc_final: 0.7885 (t) REVERT: o 101 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8101 (mm-30) REVERT: o 104 ASN cc_start: 0.7947 (m-40) cc_final: 0.6806 (m110) REVERT: o 151 THR cc_start: 0.8990 (m) cc_final: 0.8513 (t) REVERT: o 163 CYS cc_start: 0.8288 (p) cc_final: 0.7996 (p) REVERT: o 181 ASP cc_start: 0.8271 (m-30) cc_final: 0.8048 (m-30) REVERT: o 191 CYS cc_start: 0.8502 (m) cc_final: 0.8296 (m) REVERT: o 216 CYS cc_start: 0.7796 (m) cc_final: 0.7019 (m) REVERT: q 69 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8782 (tt0) REVERT: q 89 ASN cc_start: 0.8929 (t0) cc_final: 0.8630 (t0) REVERT: q 101 ASN cc_start: 0.7622 (m110) cc_final: 0.7370 (m110) REVERT: q 112 GLN cc_start: 0.7408 (tt0) cc_final: 0.6740 (tt0) REVERT: q 122 TYR cc_start: 0.9101 (m-80) cc_final: 0.8825 (m-10) REVERT: q 126 ASP cc_start: 0.8789 (m-30) cc_final: 0.8542 (m-30) REVERT: q 164 SER cc_start: 0.8825 (t) cc_final: 0.8427 (p) REVERT: q 262 ARG cc_start: 0.8070 (mtm-85) cc_final: 0.7794 (mtm-85) REVERT: q 279 VAL cc_start: 0.9102 (m) cc_final: 0.8734 (p) REVERT: r 20 ASN cc_start: 0.8996 (p0) cc_final: 0.8727 (p0) REVERT: r 87 LYS cc_start: 0.8313 (mtmm) cc_final: 0.8026 (mtmt) REVERT: r 89 MET cc_start: 0.9231 (mmt) cc_final: 0.8866 (mmm) REVERT: r 122 LEU cc_start: 0.9412 (mt) cc_final: 0.9142 (mt) REVERT: r 127 ILE cc_start: 0.9066 (mt) cc_final: 0.8844 (mt) REVERT: r 200 LEU cc_start: 0.9491 (mt) cc_final: 0.9274 (mt) REVERT: s 18 ASP cc_start: 0.7633 (t0) cc_final: 0.7202 (t0) REVERT: s 34 ILE cc_start: 0.9159 (pt) cc_final: 0.8784 (pt) REVERT: s 44 MET cc_start: 0.8857 (mmm) cc_final: 0.8484 (mmm) REVERT: s 73 ASN cc_start: 0.9009 (p0) cc_final: 0.8769 (p0) REVERT: s 84 LEU cc_start: 0.9389 (mt) cc_final: 0.9169 (mt) REVERT: s 91 ASP cc_start: 0.8406 (t0) cc_final: 0.8161 (t0) REVERT: s 107 THR cc_start: 0.9116 (p) cc_final: 0.8559 (t) REVERT: s 123 MET cc_start: 0.8572 (tpp) cc_final: 0.8318 (tpp) REVERT: s 128 LYS cc_start: 0.7729 (mmtp) cc_final: 0.7436 (mmtm) REVERT: s 216 CYS cc_start: 0.8504 (m) cc_final: 0.8244 (m) REVERT: s 218 ASP cc_start: 0.8765 (p0) cc_final: 0.8495 (p0) REVERT: s 219 PHE cc_start: 0.8970 (t80) cc_final: 0.8605 (t80) REVERT: t 44 GLN cc_start: 0.8652 (pt0) cc_final: 0.8391 (pt0) outliers start: 3 outliers final: 1 residues processed: 1582 average time/residue: 0.2122 time to fit residues: 551.7919 Evaluate side-chains 1290 residues out of total 3659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1289 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 380 optimal weight: 8.9990 chunk 415 optimal weight: 7.9990 chunk 326 optimal weight: 3.9990 chunk 100 optimal weight: 20.0000 chunk 7 optimal weight: 50.0000 chunk 253 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 229 optimal weight: 8.9990 chunk 120 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 397 optimal weight: 0.7980 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 147 ASN ** a 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 232 GLN ** e 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 30 ASN f 43 ASN ** g 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 27 ASN ** g 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 4 GLN i 112 GLN i 151 GLN ** i 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 149 ASN ** j 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 196 GLN j 226 ASN ** k 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 175 ASN n 147 ASN ** n 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 27 ASN ** o 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 229 HIS p 4 GLN q 49 GLN ** q 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 108 HIS s 232 GLN t 39 ASN t 44 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.115921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.104609 restraints weight = 77604.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.107598 restraints weight = 38382.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.109622 restraints weight = 22502.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.110896 restraints weight = 14691.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.111816 restraints weight = 10455.953| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 34734 Z= 0.234 Angle : 0.693 9.574 47379 Z= 0.366 Chirality : 0.047 0.197 5322 Planarity : 0.006 0.113 6150 Dihedral : 6.026 56.823 4820 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.08 % Allowed : 3.33 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.25 (0.12), residues: 4158 helix: -2.73 (0.20), residues: 455 sheet: 0.98 (0.15), residues: 1044 loop : -0.11 (0.12), residues: 2659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG r 264 TYR 0.029 0.002 TYR i 274 PHE 0.033 0.002 PHE q 120 TRP 0.020 0.002 TRP m 103 HIS 0.018 0.002 HIS r 109 Details of bonding type rmsd covalent geometry : bond 0.00527 (34734) covalent geometry : angle 0.69340 (47379) hydrogen bonds : bond 0.04439 ( 900) hydrogen bonds : angle 6.43212 ( 2583) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1535 residues out of total 3659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1532 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN b 272 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASN l 69 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PHE m 298 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 98 LYS cc_start: 0.8928 (mmmt) cc_final: 0.8540 (mmtt) REVERT: a 118 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7826 (mt-10) REVERT: a 122 TYR cc_start: 0.9325 (m-10) cc_final: 0.9066 (m-10) REVERT: a 126 ASP cc_start: 0.8702 (m-30) cc_final: 0.8483 (m-30) REVERT: a 127 LEU cc_start: 0.9163 (tp) cc_final: 0.8835 (tt) REVERT: a 132 VAL cc_start: 0.9595 (t) cc_final: 0.9290 (p) REVERT: a 171 GLN cc_start: 0.8783 (mt0) cc_final: 0.8434 (mt0) REVERT: a 264 TRP cc_start: 0.9169 (m-90) cc_final: 0.8611 (m-90) REVERT: a 274 TYR cc_start: 0.7434 (m-80) cc_final: 0.7230 (m-10) REVERT: b 12 ARG cc_start: 0.8186 (mmt90) cc_final: 0.7887 (mmt90) REVERT: b 18 LEU cc_start: 0.9345 (mt) cc_final: 0.9113 (mt) REVERT: b 64 TYR cc_start: 0.9088 (m-80) cc_final: 0.8875 (m-10) REVERT: b 80 TRP cc_start: 0.9205 (m-90) cc_final: 0.8566 (m-90) REVERT: b 214 ASN cc_start: 0.8877 (t0) cc_final: 0.8300 (t0) REVERT: b 216 LEU cc_start: 0.8985 (mt) cc_final: 0.8500 (mt) REVERT: b 223 LYS cc_start: 0.8970 (mtmt) cc_final: 0.8424 (mttm) REVERT: b 260 PHE cc_start: 0.8841 (m-10) cc_final: 0.8597 (m-10) REVERT: c 44 MET cc_start: 0.9334 (mmm) cc_final: 0.9099 (mmm) REVERT: c 59 ASP cc_start: 0.8562 (m-30) cc_final: 0.8174 (m-30) REVERT: c 61 LYS cc_start: 0.8761 (mmtm) cc_final: 0.8470 (mmmt) REVERT: c 67 MET cc_start: 0.8861 (ptp) cc_final: 0.8545 (ptp) REVERT: c 69 GLN cc_start: 0.8507 (mt0) cc_final: 0.8173 (mp10) REVERT: c 209 MET cc_start: 0.7491 (ttp) cc_final: 0.7157 (ttp) REVERT: d 49 ASP cc_start: 0.8985 (t0) cc_final: 0.8692 (t0) REVERT: e 57 GLU cc_start: 0.5048 (mp0) cc_final: 0.4000 (mp0) REVERT: e 66 THR cc_start: 0.8780 (m) cc_final: 0.8396 (p) REVERT: e 91 SER cc_start: 0.8661 (p) cc_final: 0.8383 (m) REVERT: e 171 GLN cc_start: 0.9013 (mt0) cc_final: 0.8725 (mt0) REVERT: e 180 TYR cc_start: 0.8749 (t80) cc_final: 0.8233 (t80) REVERT: e 232 PHE cc_start: 0.7570 (m-80) cc_final: 0.7344 (m-80) REVERT: e 255 TYR cc_start: 0.9215 (m-80) cc_final: 0.8894 (m-10) REVERT: e 267 ARG cc_start: 0.9305 (mtp85) cc_final: 0.8959 (ttm110) REVERT: f 15 GLN cc_start: 0.7495 (tt0) cc_final: 0.7016 (mt0) REVERT: f 21 SER cc_start: 0.8842 (t) cc_final: 0.8367 (p) REVERT: f 41 TYR cc_start: 0.7905 (m-10) cc_final: 0.7682 (m-10) REVERT: f 48 ASN cc_start: 0.8524 (t0) cc_final: 0.8305 (t0) REVERT: f 55 GLU cc_start: 0.8555 (pp20) cc_final: 0.8081 (pp20) REVERT: f 57 ASP cc_start: 0.8906 (t70) cc_final: 0.8668 (t70) REVERT: f 103 ARG cc_start: 0.9066 (ttt90) cc_final: 0.8666 (ttt-90) REVERT: f 126 LEU cc_start: 0.9538 (mt) cc_final: 0.9153 (mt) REVERT: f 127 ILE cc_start: 0.9166 (mp) cc_final: 0.8795 (mt) REVERT: f 129 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8094 (mm-30) REVERT: f 142 TYR cc_start: 0.7170 (t80) cc_final: 0.6903 (t80) REVERT: f 149 ASN cc_start: 0.8501 (m-40) cc_final: 0.8201 (m110) REVERT: f 199 ASN cc_start: 0.8802 (t0) cc_final: 0.8558 (t0) REVERT: f 209 VAL cc_start: 0.9215 (t) cc_final: 0.8949 (p) REVERT: f 221 MET cc_start: 0.8959 (mmm) cc_final: 0.8616 (mmm) REVERT: g 12 GLN cc_start: 0.8764 (pp30) cc_final: 0.8233 (pp30) REVERT: g 85 SER cc_start: 0.9102 (m) cc_final: 0.8707 (p) REVERT: g 101 GLU cc_start: 0.8355 (tp30) cc_final: 0.7719 (mm-30) REVERT: g 112 SER cc_start: 0.8836 (m) cc_final: 0.7822 (p) REVERT: g 128 LYS cc_start: 0.7662 (mppt) cc_final: 0.6786 (mmtm) REVERT: g 148 MET cc_start: 0.6667 (ttm) cc_final: 0.6055 (ttt) REVERT: g 153 ILE cc_start: 0.9144 (pt) cc_final: 0.8900 (tp) REVERT: g 163 CYS cc_start: 0.8730 (p) cc_final: 0.8103 (p) REVERT: g 169 TRP cc_start: 0.8934 (t-100) cc_final: 0.7846 (t-100) REVERT: g 177 ARG cc_start: 0.8605 (mtt90) cc_final: 0.8312 (mtt-85) REVERT: g 181 ASP cc_start: 0.7609 (t0) cc_final: 0.7311 (t0) REVERT: g 216 CYS cc_start: 0.8583 (m) cc_final: 0.7973 (m) REVERT: g 225 ARG cc_start: 0.8836 (ptt90) cc_final: 0.8430 (ptt-90) REVERT: h 27 TYR cc_start: 0.8627 (p90) cc_final: 0.8271 (p90) REVERT: i 63 ASN cc_start: 0.8081 (t0) cc_final: 0.7657 (t0) REVERT: i 120 PHE cc_start: 0.8853 (m-80) cc_final: 0.8483 (m-10) REVERT: i 151 GLN cc_start: 0.9213 (tt0) cc_final: 0.8860 (tt0) REVERT: i 154 TYR cc_start: 0.9276 (t80) cc_final: 0.8998 (t80) REVERT: i 166 ASP cc_start: 0.8349 (p0) cc_final: 0.7787 (p0) REVERT: i 182 TYR cc_start: 0.9049 (t80) cc_final: 0.8200 (t80) REVERT: i 198 ASN cc_start: 0.8969 (m110) cc_final: 0.8669 (m110) REVERT: i 250 THR cc_start: 0.7806 (m) cc_final: 0.7394 (m) REVERT: i 264 TRP cc_start: 0.9173 (m-90) cc_final: 0.8688 (m-90) REVERT: j 55 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8360 (mm-30) REVERT: j 109 HIS cc_start: 0.8494 (t70) cc_final: 0.8128 (t-90) REVERT: j 132 MET cc_start: 0.8183 (mtt) cc_final: 0.7611 (mmt) REVERT: j 180 LEU cc_start: 0.9185 (mt) cc_final: 0.8923 (mt) REVERT: j 196 GLN cc_start: 0.8901 (tt0) cc_final: 0.8231 (tt0) REVERT: j 207 THR cc_start: 0.9296 (m) cc_final: 0.9048 (p) REVERT: j 213 VAL cc_start: 0.9230 (t) cc_final: 0.8890 (m) REVERT: j 227 TRP cc_start: 0.8439 (m100) cc_final: 0.8150 (m100) REVERT: j 259 GLU cc_start: 0.8836 (tt0) cc_final: 0.8546 (tt0) REVERT: k 13 PHE cc_start: 0.9348 (t80) cc_final: 0.9044 (t80) REVERT: k 27 ASN cc_start: 0.9075 (m110) cc_final: 0.8382 (m110) REVERT: k 29 ASP cc_start: 0.9423 (t0) cc_final: 0.8858 (t0) REVERT: k 36 ILE cc_start: 0.9319 (mt) cc_final: 0.8823 (mt) REVERT: k 43 MET cc_start: 0.9077 (mmm) cc_final: 0.8221 (mmm) REVERT: k 65 MET cc_start: 0.8151 (tpp) cc_final: 0.7947 (tpp) REVERT: k 69 GLN cc_start: 0.8699 (mt0) cc_final: 0.8347 (mt0) REVERT: k 112 SER cc_start: 0.9061 (m) cc_final: 0.8468 (p) REVERT: k 116 THR cc_start: 0.9166 (m) cc_final: 0.8819 (t) REVERT: k 124 MET cc_start: 0.7469 (mmm) cc_final: 0.7250 (mtt) REVERT: k 133 TYR cc_start: 0.8975 (t80) cc_final: 0.8528 (t80) REVERT: k 208 PHE cc_start: 0.8580 (m-80) cc_final: 0.8358 (m-80) REVERT: k 216 CYS cc_start: 0.8444 (m) cc_final: 0.7157 (m) REVERT: k 218 ASP cc_start: 0.8862 (p0) cc_final: 0.8635 (p0) REVERT: l 38 SER cc_start: 0.9588 (m) cc_final: 0.9274 (t) REVERT: l 64 THR cc_start: 0.8711 (p) cc_final: 0.8473 (p) REVERT: m 49 GLN cc_start: 0.8334 (mm-40) cc_final: 0.7557 (mm110) REVERT: m 70 SER cc_start: 0.9142 (p) cc_final: 0.8742 (t) REVERT: m 97 LYS cc_start: 0.8555 (pptt) cc_final: 0.7890 (ptmt) REVERT: m 105 ILE cc_start: 0.8950 (mm) cc_final: 0.8616 (tp) REVERT: m 110 THR cc_start: 0.8146 (p) cc_final: 0.7717 (p) REVERT: m 127 LEU cc_start: 0.9289 (tp) cc_final: 0.8912 (tp) REVERT: n 37 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8228 (mt-10) REVERT: n 61 ASN cc_start: 0.9184 (m-40) cc_final: 0.8871 (m-40) REVERT: n 74 THR cc_start: 0.8266 (p) cc_final: 0.8009 (t) REVERT: n 84 ASP cc_start: 0.8031 (t70) cc_final: 0.7565 (t0) REVERT: n 106 TYR cc_start: 0.8492 (m-80) cc_final: 0.8270 (m-80) REVERT: n 113 ASN cc_start: 0.7954 (m-40) cc_final: 0.7491 (t0) REVERT: n 178 ASP cc_start: 0.8419 (p0) cc_final: 0.8122 (p0) REVERT: n 183 SER cc_start: 0.9137 (p) cc_final: 0.8553 (t) REVERT: n 199 ASN cc_start: 0.8823 (t0) cc_final: 0.8439 (t0) REVERT: n 212 TYR cc_start: 0.9136 (t80) cc_final: 0.8800 (t80) REVERT: n 215 SER cc_start: 0.9503 (p) cc_final: 0.8932 (t) REVERT: n 216 LEU cc_start: 0.9390 (mt) cc_final: 0.9160 (mt) REVERT: n 219 ASP cc_start: 0.8864 (t0) cc_final: 0.8491 (m-30) REVERT: n 257 CYS cc_start: 0.8644 (m) cc_final: 0.8420 (m) REVERT: o 10 SER cc_start: 0.9061 (m) cc_final: 0.8429 (t) REVERT: o 39 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8134 (tm-30) REVERT: o 41 LYS cc_start: 0.8372 (mmtt) cc_final: 0.8072 (mmtp) REVERT: o 43 MET cc_start: 0.9010 (mmm) cc_final: 0.8734 (mmm) REVERT: o 48 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7357 (mt-10) REVERT: o 61 LYS cc_start: 0.8865 (mmtm) cc_final: 0.8605 (mmtt) REVERT: o 66 GLU cc_start: 0.8355 (pm20) cc_final: 0.8072 (pm20) REVERT: o 95 SER cc_start: 0.8689 (p) cc_final: 0.7584 (t) REVERT: o 101 GLU cc_start: 0.8256 (mm-30) cc_final: 0.8042 (mm-30) REVERT: o 104 ASN cc_start: 0.8238 (m-40) cc_final: 0.6953 (m-40) REVERT: o 128 LYS cc_start: 0.8607 (mmmt) cc_final: 0.8404 (mmmt) REVERT: o 156 ASP cc_start: 0.5004 (m-30) cc_final: 0.4672 (m-30) REVERT: o 163 CYS cc_start: 0.8296 (p) cc_final: 0.7868 (p) REVERT: o 191 CYS cc_start: 0.9031 (m) cc_final: 0.8689 (m) REVERT: o 216 CYS cc_start: 0.7856 (m) cc_final: 0.7002 (m) REVERT: o 226 ASP cc_start: 0.7882 (m-30) cc_final: 0.7597 (m-30) REVERT: p 21 ASN cc_start: 0.7791 (m110) cc_final: 0.7496 (m110) REVERT: q 95 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8049 (mm-30) REVERT: q 112 GLN cc_start: 0.7313 (tt0) cc_final: 0.7013 (tt0) REVERT: q 122 TYR cc_start: 0.9210 (m-80) cc_final: 0.8976 (m-10) REVERT: q 175 ASN cc_start: 0.8736 (m-40) cc_final: 0.8079 (m110) REVERT: q 189 MET cc_start: 0.8134 (ptt) cc_final: 0.7592 (ptm) REVERT: q 198 ASN cc_start: 0.9320 (m-40) cc_final: 0.9078 (m-40) REVERT: q 202 HIS cc_start: 0.8395 (m-70) cc_final: 0.7812 (m90) REVERT: q 218 ASP cc_start: 0.7390 (t70) cc_final: 0.7150 (t0) REVERT: q 256 MET cc_start: 0.7440 (mtm) cc_final: 0.6900 (mtm) REVERT: q 264 TRP cc_start: 0.9236 (m-90) cc_final: 0.8854 (m-90) REVERT: r 20 ASN cc_start: 0.8974 (p0) cc_final: 0.8729 (p0) REVERT: r 89 MET cc_start: 0.9233 (mmt) cc_final: 0.8982 (mmm) REVERT: r 122 LEU cc_start: 0.9451 (mt) cc_final: 0.9178 (mt) REVERT: r 200 LEU cc_start: 0.9531 (mt) cc_final: 0.9325 (mt) REVERT: s 18 ASP cc_start: 0.7694 (t0) cc_final: 0.7216 (t0) REVERT: s 34 ILE cc_start: 0.9061 (pt) cc_final: 0.8632 (pt) REVERT: s 44 MET cc_start: 0.9098 (mmm) cc_final: 0.8875 (mmm) REVERT: s 73 ASN cc_start: 0.9002 (p0) cc_final: 0.8683 (p0) REVERT: s 128 LYS cc_start: 0.7864 (mmtp) cc_final: 0.7588 (mmtm) REVERT: s 209 MET cc_start: 0.8472 (ttm) cc_final: 0.8085 (mtp) REVERT: s 218 ASP cc_start: 0.8721 (p0) cc_final: 0.8419 (p0) REVERT: s 219 PHE cc_start: 0.8914 (t80) cc_final: 0.8640 (t80) REVERT: s 226 ASP cc_start: 0.7607 (m-30) cc_final: 0.7137 (m-30) REVERT: t 26 ASN cc_start: 0.8961 (m110) cc_final: 0.8697 (m110) outliers start: 3 outliers final: 1 residues processed: 1534 average time/residue: 0.2222 time to fit residues: 555.8275 Evaluate side-chains 1237 residues out of total 3659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1236 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 253 optimal weight: 20.0000 chunk 114 optimal weight: 20.0000 chunk 291 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 chunk 226 optimal weight: 20.0000 chunk 402 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 195 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 overall best weight: 9.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 175 ASN ** e 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 43 ASN f 261 ASN ** g 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 152 HIS ** g 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 112 GLN ** i 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 184 ASN j 111 GLN j 149 ASN j 195 HIS j 226 ASN ** k 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 GLN m 32 ASN ** m 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 249 HIS ** n 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 27 ASN ** o 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 4 GLN ** p 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 148 GLN ** q 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 160 GLN ** s 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 44 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.110806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.099918 restraints weight = 79380.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.102639 restraints weight = 39989.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.104557 restraints weight = 24003.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.105808 restraints weight = 15952.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.106635 restraints weight = 11497.855| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.142 34734 Z= 0.359 Angle : 0.805 19.758 47379 Z= 0.420 Chirality : 0.050 0.230 5322 Planarity : 0.006 0.116 6150 Dihedral : 6.457 53.537 4820 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.11 % Allowed : 3.31 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.64 (0.12), residues: 4158 helix: -2.68 (0.20), residues: 424 sheet: 0.61 (0.16), residues: 1008 loop : -0.42 (0.11), residues: 2726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG i 188 TYR 0.030 0.003 TYR b 193 PHE 0.030 0.003 PHE q 120 TRP 0.023 0.002 TRP b 227 HIS 0.011 0.002 HIS q 99 Details of bonding type rmsd covalent geometry : bond 0.00797 (34734) covalent geometry : angle 0.80531 (47379) hydrogen bonds : bond 0.04703 ( 900) hydrogen bonds : angle 6.52558 ( 2583) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1441 residues out of total 3659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1437 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN b 272 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASN l 69 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 49 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8573 (mm110) REVERT: a 63 ASN cc_start: 0.8975 (t0) cc_final: 0.8708 (t0) REVERT: a 107 TYR cc_start: 0.9281 (p90) cc_final: 0.9068 (p90) REVERT: a 118 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7752 (mt-10) REVERT: a 126 ASP cc_start: 0.8811 (m-30) cc_final: 0.8494 (m-30) REVERT: a 127 LEU cc_start: 0.9188 (tp) cc_final: 0.8827 (tt) REVERT: a 170 TRP cc_start: 0.9259 (m100) cc_final: 0.9015 (m100) REVERT: a 205 ASP cc_start: 0.7783 (t70) cc_final: 0.7373 (t0) REVERT: a 256 MET cc_start: 0.8690 (mmm) cc_final: 0.8427 (tpp) REVERT: b 18 LEU cc_start: 0.9458 (mt) cc_final: 0.9224 (mt) REVERT: b 27 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7705 (tm-30) REVERT: b 84 ASP cc_start: 0.8454 (t70) cc_final: 0.7428 (t0) REVERT: b 156 GLU cc_start: 0.8865 (mp0) cc_final: 0.8472 (mp0) REVERT: b 174 PHE cc_start: 0.8644 (m-80) cc_final: 0.8270 (m-80) REVERT: b 216 LEU cc_start: 0.9021 (mt) cc_final: 0.8474 (mt) REVERT: b 260 PHE cc_start: 0.8886 (m-10) cc_final: 0.8677 (m-10) REVERT: c 2 LEU cc_start: 0.9410 (tp) cc_final: 0.9207 (tp) REVERT: c 17 ASP cc_start: 0.8389 (t70) cc_final: 0.8033 (t70) REVERT: c 20 GLN cc_start: 0.8426 (mt0) cc_final: 0.8117 (mt0) REVERT: c 43 MET cc_start: 0.9268 (mmm) cc_final: 0.9057 (mmm) REVERT: c 59 ASP cc_start: 0.8631 (m-30) cc_final: 0.8243 (m-30) REVERT: c 61 LYS cc_start: 0.8815 (mmtm) cc_final: 0.8603 (mmmt) REVERT: c 67 MET cc_start: 0.8919 (ptp) cc_final: 0.8597 (ptm) REVERT: c 69 GLN cc_start: 0.8436 (mt0) cc_final: 0.7981 (mp10) REVERT: c 139 LYS cc_start: 0.9167 (ptmm) cc_final: 0.8831 (ptpp) REVERT: c 222 ARG cc_start: 0.8382 (mmm-85) cc_final: 0.8132 (mmm160) REVERT: d 49 ASP cc_start: 0.9080 (t0) cc_final: 0.8826 (t0) REVERT: e 54 ASP cc_start: 0.8851 (m-30) cc_final: 0.8630 (m-30) REVERT: e 57 GLU cc_start: 0.5136 (mp0) cc_final: 0.4592 (mp0) REVERT: e 66 THR cc_start: 0.8740 (m) cc_final: 0.8381 (p) REVERT: e 91 SER cc_start: 0.8776 (p) cc_final: 0.8333 (m) REVERT: e 267 ARG cc_start: 0.9395 (mtp85) cc_final: 0.9046 (ttm110) REVERT: f 15 GLN cc_start: 0.7600 (tt0) cc_final: 0.6993 (mt0) REVERT: f 48 ASN cc_start: 0.8783 (t0) cc_final: 0.8411 (t0) REVERT: f 55 GLU cc_start: 0.8392 (pp20) cc_final: 0.7945 (pp20) REVERT: f 70 SER cc_start: 0.8722 (m) cc_final: 0.8421 (p) REVERT: f 84 ASP cc_start: 0.8024 (t70) cc_final: 0.7757 (t0) REVERT: f 100 TYR cc_start: 0.8753 (t80) cc_final: 0.8528 (t80) REVERT: f 126 LEU cc_start: 0.9447 (mt) cc_final: 0.9108 (mt) REVERT: f 127 ILE cc_start: 0.9303 (mp) cc_final: 0.8895 (mt) REVERT: f 149 ASN cc_start: 0.8309 (m-40) cc_final: 0.7870 (m-40) REVERT: f 209 VAL cc_start: 0.9359 (t) cc_final: 0.9128 (p) REVERT: f 212 TYR cc_start: 0.8854 (t80) cc_final: 0.8487 (t80) REVERT: f 217 VAL cc_start: 0.9017 (m) cc_final: 0.8505 (p) REVERT: f 221 MET cc_start: 0.8979 (mmm) cc_final: 0.8600 (mmm) REVERT: f 232 LEU cc_start: 0.9161 (mt) cc_final: 0.8740 (mp) REVERT: g 12 GLN cc_start: 0.8751 (pp30) cc_final: 0.8146 (pp30) REVERT: g 90 SER cc_start: 0.8102 (p) cc_final: 0.7711 (t) REVERT: g 101 GLU cc_start: 0.8458 (tp30) cc_final: 0.7808 (mm-30) REVERT: g 112 SER cc_start: 0.8937 (m) cc_final: 0.7986 (p) REVERT: g 133 TYR cc_start: 0.9410 (t80) cc_final: 0.9166 (t80) REVERT: g 148 MET cc_start: 0.6494 (ttm) cc_final: 0.5833 (ttt) REVERT: g 153 ILE cc_start: 0.9180 (pt) cc_final: 0.8933 (tp) REVERT: g 163 CYS cc_start: 0.8700 (p) cc_final: 0.8431 (p) REVERT: g 169 TRP cc_start: 0.9118 (t-100) cc_final: 0.7986 (t-100) REVERT: g 181 ASP cc_start: 0.7605 (t0) cc_final: 0.7345 (t0) REVERT: g 216 CYS cc_start: 0.8269 (m) cc_final: 0.7788 (m) REVERT: g 219 PHE cc_start: 0.9084 (t80) cc_final: 0.8849 (t80) REVERT: g 225 ARG cc_start: 0.8921 (ptt90) cc_final: 0.8348 (ptt-90) REVERT: g 234 LYS cc_start: 0.7102 (mtmt) cc_final: 0.6823 (mtmm) REVERT: h 8 GLN cc_start: 0.7975 (mt0) cc_final: 0.7369 (mt0) REVERT: i 120 PHE cc_start: 0.9023 (m-80) cc_final: 0.8707 (m-10) REVERT: i 151 GLN cc_start: 0.9361 (tt0) cc_final: 0.8896 (tt0) REVERT: i 166 ASP cc_start: 0.8472 (p0) cc_final: 0.7728 (p0) REVERT: i 171 GLN cc_start: 0.8373 (tt0) cc_final: 0.8087 (tt0) REVERT: i 173 SER cc_start: 0.9366 (t) cc_final: 0.8960 (p) REVERT: i 250 THR cc_start: 0.8117 (m) cc_final: 0.7787 (m) REVERT: i 264 TRP cc_start: 0.9169 (m-90) cc_final: 0.8915 (m-90) REVERT: j 59 SER cc_start: 0.9184 (m) cc_final: 0.8913 (p) REVERT: j 60 SER cc_start: 0.9128 (m) cc_final: 0.8397 (p) REVERT: j 129 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8471 (mm-30) REVERT: j 198 ILE cc_start: 0.9568 (mt) cc_final: 0.9350 (tt) REVERT: j 213 VAL cc_start: 0.9181 (t) cc_final: 0.8833 (m) REVERT: j 214 ASN cc_start: 0.9199 (t0) cc_final: 0.8907 (t0) REVERT: j 249 ILE cc_start: 0.8843 (mm) cc_final: 0.8598 (mm) REVERT: k 2 LEU cc_start: 0.9399 (tp) cc_final: 0.9152 (tp) REVERT: k 27 ASN cc_start: 0.8928 (m110) cc_final: 0.8627 (m-40) REVERT: k 29 ASP cc_start: 0.9397 (t0) cc_final: 0.9008 (t0) REVERT: k 36 ILE cc_start: 0.9356 (mt) cc_final: 0.9144 (mt) REVERT: k 66 GLU cc_start: 0.8355 (mp0) cc_final: 0.7949 (mp0) REVERT: k 69 GLN cc_start: 0.8913 (mt0) cc_final: 0.8363 (mt0) REVERT: k 84 LEU cc_start: 0.8787 (mp) cc_final: 0.8329 (mp) REVERT: k 112 SER cc_start: 0.9133 (m) cc_final: 0.8637 (p) REVERT: k 116 THR cc_start: 0.9191 (m) cc_final: 0.8973 (t) REVERT: k 133 TYR cc_start: 0.9022 (t80) cc_final: 0.8705 (t80) REVERT: k 156 ASP cc_start: 0.7876 (t0) cc_final: 0.7457 (t0) REVERT: k 169 TRP cc_start: 0.8029 (t-100) cc_final: 0.7718 (t-100) REVERT: k 188 PHE cc_start: 0.8836 (m-80) cc_final: 0.8314 (m-80) REVERT: k 199 VAL cc_start: 0.8652 (t) cc_final: 0.8048 (t) REVERT: k 208 PHE cc_start: 0.8631 (m-80) cc_final: 0.8378 (m-80) REVERT: k 216 CYS cc_start: 0.8501 (m) cc_final: 0.7504 (m) REVERT: k 218 ASP cc_start: 0.8838 (p0) cc_final: 0.8629 (p0) REVERT: l 25 ILE cc_start: 0.8784 (mm) cc_final: 0.8440 (mm) REVERT: l 38 SER cc_start: 0.9581 (m) cc_final: 0.9255 (t) REVERT: l 64 THR cc_start: 0.8791 (p) cc_final: 0.8490 (p) REVERT: m 70 SER cc_start: 0.9156 (p) cc_final: 0.8799 (t) REVERT: m 97 LYS cc_start: 0.8787 (pptt) cc_final: 0.8078 (ptmt) REVERT: m 105 ILE cc_start: 0.9204 (mm) cc_final: 0.8832 (tp) REVERT: m 146 ARG cc_start: 0.9367 (mmm160) cc_final: 0.9127 (mmm-85) REVERT: m 165 TRP cc_start: 0.8805 (p-90) cc_final: 0.8035 (p-90) REVERT: n 37 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8427 (mt-10) REVERT: n 61 ASN cc_start: 0.9179 (m-40) cc_final: 0.8949 (m-40) REVERT: n 66 LEU cc_start: 0.9065 (mt) cc_final: 0.8004 (mt) REVERT: n 74 THR cc_start: 0.8253 (p) cc_final: 0.7941 (t) REVERT: n 113 ASN cc_start: 0.7702 (m-40) cc_final: 0.7355 (t0) REVERT: n 149 ASN cc_start: 0.8970 (m-40) cc_final: 0.8650 (m-40) REVERT: n 183 SER cc_start: 0.9388 (p) cc_final: 0.8845 (t) REVERT: n 198 ILE cc_start: 0.9270 (mt) cc_final: 0.8742 (pt) REVERT: n 199 ASN cc_start: 0.8910 (t0) cc_final: 0.8303 (t0) REVERT: n 212 TYR cc_start: 0.9295 (t80) cc_final: 0.8580 (t80) REVERT: n 214 ASN cc_start: 0.9138 (t0) cc_final: 0.8587 (t0) REVERT: n 215 SER cc_start: 0.9460 (p) cc_final: 0.9153 (p) REVERT: n 216 LEU cc_start: 0.9466 (mt) cc_final: 0.9184 (mt) REVERT: n 217 VAL cc_start: 0.9452 (m) cc_final: 0.9224 (m) REVERT: n 219 ASP cc_start: 0.9150 (t0) cc_final: 0.8740 (t0) REVERT: o 17 ASP cc_start: 0.8805 (t0) cc_final: 0.6743 (t0) REVERT: o 39 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8120 (tm-30) REVERT: o 41 LYS cc_start: 0.8625 (mmtt) cc_final: 0.8273 (mmtp) REVERT: o 48 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7555 (mt-10) REVERT: o 61 LYS cc_start: 0.9003 (mmtm) cc_final: 0.8768 (mmtt) REVERT: o 66 GLU cc_start: 0.8566 (pm20) cc_final: 0.8116 (pm20) REVERT: o 120 CYS cc_start: 0.8773 (m) cc_final: 0.8447 (m) REVERT: o 148 MET cc_start: 0.5776 (ttt) cc_final: 0.5518 (ttt) REVERT: o 156 ASP cc_start: 0.4530 (m-30) cc_final: 0.4258 (m-30) REVERT: o 163 CYS cc_start: 0.8252 (p) cc_final: 0.7951 (p) REVERT: o 185 GLU cc_start: 0.7449 (mm-30) cc_final: 0.6967 (mm-30) REVERT: o 216 CYS cc_start: 0.8102 (m) cc_final: 0.7367 (m) REVERT: o 218 ASP cc_start: 0.8923 (p0) cc_final: 0.8701 (p0) REVERT: o 223 LEU cc_start: 0.8506 (tp) cc_final: 0.8282 (tp) REVERT: p 44 GLN cc_start: 0.8618 (pm20) cc_final: 0.8417 (mp10) REVERT: q 49 GLN cc_start: 0.7960 (mt0) cc_final: 0.7686 (mt0) REVERT: q 89 ASN cc_start: 0.9011 (t0) cc_final: 0.8723 (t0) REVERT: q 90 SER cc_start: 0.9048 (t) cc_final: 0.8821 (t) REVERT: q 95 GLU cc_start: 0.8714 (mm-30) cc_final: 0.7175 (mm-30) REVERT: q 98 LYS cc_start: 0.8950 (mtpt) cc_final: 0.7951 (mtpt) REVERT: q 112 GLN cc_start: 0.7435 (tt0) cc_final: 0.7155 (tt0) REVERT: q 182 TYR cc_start: 0.8759 (t80) cc_final: 0.8494 (t80) REVERT: q 189 MET cc_start: 0.8182 (ptt) cc_final: 0.7768 (ptm) REVERT: q 202 HIS cc_start: 0.8516 (m-70) cc_final: 0.7928 (m90) REVERT: q 209 ARG cc_start: 0.8110 (pmt-80) cc_final: 0.7785 (ptt-90) REVERT: q 264 TRP cc_start: 0.9224 (m-90) cc_final: 0.8797 (m-90) REVERT: r 91 MET cc_start: 0.5789 (mmt) cc_final: 0.5499 (mmt) REVERT: r 106 TYR cc_start: 0.8629 (m-80) cc_final: 0.8409 (m-80) REVERT: r 122 LEU cc_start: 0.9480 (mt) cc_final: 0.9239 (mt) REVERT: r 178 ASP cc_start: 0.9557 (p0) cc_final: 0.9203 (p0) REVERT: r 196 GLN cc_start: 0.8761 (mt0) cc_final: 0.8509 (mt0) REVERT: s 18 ASP cc_start: 0.7506 (t0) cc_final: 0.7303 (t0) REVERT: s 44 MET cc_start: 0.9142 (mmm) cc_final: 0.8939 (mmm) REVERT: s 98 MET cc_start: 0.9324 (tpp) cc_final: 0.8739 (tpp) REVERT: s 157 LEU cc_start: 0.9259 (mm) cc_final: 0.8937 (mt) REVERT: s 165 MET cc_start: 0.8869 (tmm) cc_final: 0.8640 (tmm) REVERT: s 209 MET cc_start: 0.8535 (ttm) cc_final: 0.7783 (mtp) REVERT: s 216 CYS cc_start: 0.8801 (m) cc_final: 0.8585 (m) REVERT: s 218 ASP cc_start: 0.8803 (p0) cc_final: 0.8563 (p0) REVERT: s 219 PHE cc_start: 0.9230 (t80) cc_final: 0.8959 (t80) REVERT: s 224 LEU cc_start: 0.9258 (mt) cc_final: 0.8968 (mt) REVERT: s 226 ASP cc_start: 0.7779 (m-30) cc_final: 0.7565 (m-30) REVERT: t 26 ASN cc_start: 0.9094 (m110) cc_final: 0.8852 (m110) REVERT: t 53 PHE cc_start: 0.9240 (m-80) cc_final: 0.8984 (m-80) outliers start: 4 outliers final: 2 residues processed: 1440 average time/residue: 0.2167 time to fit residues: 510.2912 Evaluate side-chains 1181 residues out of total 3659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1179 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 169 optimal weight: 8.9990 chunk 350 optimal weight: 8.9990 chunk 208 optimal weight: 5.9990 chunk 9 optimal weight: 50.0000 chunk 68 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 159 optimal weight: 7.9990 chunk 383 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 252 optimal weight: 20.0000 chunk 291 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 18 GLN a 23 GLN ** a 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 189 ASN ** b 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 271 HIS c 27 ASN ** c 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 171 GLN ** e 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 43 ASN ** g 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 35 HIS ** g 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 194 GLN ** g 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 112 GLN ** i 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 196 GLN j 224 HIS j 226 ASN ** k 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 32 ASN ** m 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 196 GLN ** n 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 35 HIS o 104 ASN ** o 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 4 GLN ** p 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 32 ASN ** q 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 260 HIS ** r 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.111506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.100143 restraints weight = 79591.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.103076 restraints weight = 39543.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.105060 restraints weight = 23230.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.106312 restraints weight = 15116.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.107224 restraints weight = 10710.926| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 34734 Z= 0.228 Angle : 0.681 8.248 47379 Z= 0.356 Chirality : 0.047 0.227 5322 Planarity : 0.006 0.090 6150 Dihedral : 6.231 53.403 4820 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.08 % Allowed : 2.43 % Favored : 97.49 % 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: -0.78 (0.12), residues: 4158 helix: -2.66 (0.20), residues: 438 sheet: 0.39 (0.15), residues: 1036 loop : -0.48 (0.12), residues: 2684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG r 264 TYR 0.027 0.002 TYR m 154 PHE 0.027 0.002 PHE g 212 TRP 0.034 0.002 TRP b 227 HIS 0.008 0.002 HIS f 195 Details of bonding type rmsd covalent geometry : bond 0.00515 (34734) covalent geometry : angle 0.68120 (47379) hydrogen bonds : bond 0.04155 ( 900) hydrogen bonds : angle 6.20037 ( 2583) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1450 residues out of total 3659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1447 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN b 272 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASN l 69 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 49 GLN cc_start: 0.8826 (mm-40) cc_final: 0.8516 (mm110) REVERT: a 63 ASN cc_start: 0.8882 (t0) cc_final: 0.8613 (t0) REVERT: a 98 LYS cc_start: 0.9132 (mmtt) cc_final: 0.8742 (mmmt) REVERT: a 118 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7680 (mt-10) REVERT: a 126 ASP cc_start: 0.8833 (m-30) cc_final: 0.8527 (m-30) REVERT: a 127 LEU cc_start: 0.9195 (tp) cc_final: 0.8864 (tt) REVERT: a 170 TRP cc_start: 0.9197 (m100) cc_final: 0.8940 (m100) REVERT: a 171 GLN cc_start: 0.8557 (mt0) cc_final: 0.8166 (mt0) REVERT: a 205 ASP cc_start: 0.7774 (t70) cc_final: 0.7242 (t0) REVERT: a 264 TRP cc_start: 0.9261 (m-90) cc_final: 0.8831 (m-90) REVERT: b 18 LEU cc_start: 0.9403 (mt) cc_final: 0.9182 (mt) REVERT: b 80 TRP cc_start: 0.9353 (m-90) cc_final: 0.9054 (m-90) REVERT: b 84 ASP cc_start: 0.8550 (t70) cc_final: 0.7713 (t0) REVERT: b 100 TYR cc_start: 0.8332 (t80) cc_final: 0.7522 (t80) REVERT: b 101 LEU cc_start: 0.9413 (mt) cc_final: 0.8871 (mt) REVERT: b 103 ARG cc_start: 0.8816 (ttt-90) cc_final: 0.8175 (tmm-80) REVERT: b 214 ASN cc_start: 0.8847 (t0) cc_final: 0.8527 (t0) REVERT: b 216 LEU cc_start: 0.8850 (mt) cc_final: 0.8427 (mt) REVERT: b 249 ILE cc_start: 0.9149 (mt) cc_final: 0.8882 (mm) REVERT: c 61 LYS cc_start: 0.8725 (mmtm) cc_final: 0.8497 (mmmt) REVERT: c 65 MET cc_start: 0.8393 (mmp) cc_final: 0.8183 (tpp) REVERT: c 67 MET cc_start: 0.8933 (ptp) cc_final: 0.8636 (ptm) REVERT: c 69 GLN cc_start: 0.8380 (mt0) cc_final: 0.8030 (mp10) REVERT: c 139 LYS cc_start: 0.9143 (ptmm) cc_final: 0.8799 (ptmm) REVERT: c 209 MET cc_start: 0.7732 (ttp) cc_final: 0.7495 (ttp) REVERT: c 222 ARG cc_start: 0.8384 (mmm-85) cc_final: 0.8158 (mmm160) REVERT: d 34 LYS cc_start: 0.8399 (mtpt) cc_final: 0.7991 (mttt) REVERT: d 49 ASP cc_start: 0.9098 (t0) cc_final: 0.8853 (t0) REVERT: e 33 SER cc_start: 0.8534 (t) cc_final: 0.7593 (t) REVERT: e 35 GLU cc_start: 0.8819 (mp0) cc_final: 0.8219 (mp0) REVERT: e 49 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8107 (mm110) REVERT: e 57 GLU cc_start: 0.5024 (mp0) cc_final: 0.4454 (mp0) REVERT: e 66 THR cc_start: 0.8773 (m) cc_final: 0.8572 (p) REVERT: e 91 SER cc_start: 0.8673 (p) cc_final: 0.8282 (m) REVERT: e 200 TYR cc_start: 0.8788 (m-10) cc_final: 0.8574 (m-10) REVERT: e 267 ARG cc_start: 0.9299 (mtp85) cc_final: 0.9033 (ttm110) REVERT: f 15 GLN cc_start: 0.7512 (tt0) cc_final: 0.7125 (pt0) REVERT: f 48 ASN cc_start: 0.8648 (t0) cc_final: 0.8432 (t0) REVERT: f 55 GLU cc_start: 0.8477 (pp20) cc_final: 0.7985 (pp20) REVERT: f 57 ASP cc_start: 0.9025 (t70) cc_final: 0.8771 (t0) REVERT: f 70 SER cc_start: 0.8788 (m) cc_final: 0.8346 (p) REVERT: f 100 TYR cc_start: 0.8893 (t80) cc_final: 0.8674 (t80) REVERT: f 126 LEU cc_start: 0.9450 (mt) cc_final: 0.9075 (mt) REVERT: f 127 ILE cc_start: 0.9210 (mp) cc_final: 0.8832 (mt) REVERT: f 149 ASN cc_start: 0.8291 (m-40) cc_final: 0.7841 (m110) REVERT: f 217 VAL cc_start: 0.9136 (m) cc_final: 0.8886 (p) REVERT: f 219 ASP cc_start: 0.8938 (t0) cc_final: 0.8590 (t0) REVERT: f 221 MET cc_start: 0.9007 (mmm) cc_final: 0.8682 (mmm) REVERT: g 12 GLN cc_start: 0.8759 (pp30) cc_final: 0.8060 (pp30) REVERT: g 18 ASP cc_start: 0.7992 (t0) cc_final: 0.7411 (t0) REVERT: g 55 MET cc_start: 0.8357 (tpt) cc_final: 0.7679 (tpp) REVERT: g 101 GLU cc_start: 0.8407 (tp30) cc_final: 0.7754 (mm-30) REVERT: g 112 SER cc_start: 0.8913 (m) cc_final: 0.7891 (p) REVERT: g 139 LYS cc_start: 0.9005 (tptt) cc_final: 0.8748 (tppt) REVERT: g 148 MET cc_start: 0.6317 (ttm) cc_final: 0.5600 (ttt) REVERT: g 163 CYS cc_start: 0.8729 (p) cc_final: 0.8407 (p) REVERT: g 169 TRP cc_start: 0.9108 (t-100) cc_final: 0.7921 (t-100) REVERT: g 172 ASN cc_start: 0.9237 (p0) cc_final: 0.8872 (p0) REVERT: g 181 ASP cc_start: 0.7537 (t0) cc_final: 0.7226 (t0) REVERT: g 216 CYS cc_start: 0.8273 (m) cc_final: 0.7879 (m) REVERT: g 225 ARG cc_start: 0.8779 (ptt90) cc_final: 0.8418 (ptt-90) REVERT: h 8 GLN cc_start: 0.7933 (mt0) cc_final: 0.7237 (mt0) REVERT: i 63 ASN cc_start: 0.8411 (t0) cc_final: 0.8055 (t0) REVERT: i 120 PHE cc_start: 0.9067 (m-80) cc_final: 0.8828 (m-10) REVERT: i 151 GLN cc_start: 0.9344 (tt0) cc_final: 0.8939 (tt0) REVERT: i 166 ASP cc_start: 0.8542 (p0) cc_final: 0.7984 (p0) REVERT: i 180 TYR cc_start: 0.8356 (t80) cc_final: 0.8071 (t80) REVERT: i 264 TRP cc_start: 0.9175 (m-90) cc_final: 0.8972 (m-90) REVERT: j 59 SER cc_start: 0.9141 (m) cc_final: 0.8894 (p) REVERT: j 60 SER cc_start: 0.9109 (m) cc_final: 0.8367 (p) REVERT: j 99 HIS cc_start: 0.9139 (m90) cc_final: 0.8840 (m90) REVERT: j 129 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8386 (mm-30) REVERT: j 180 LEU cc_start: 0.9191 (mt) cc_final: 0.8881 (mt) REVERT: j 196 GLN cc_start: 0.8773 (tt0) cc_final: 0.8430 (tt0) REVERT: j 198 ILE cc_start: 0.9531 (mt) cc_final: 0.9216 (tt) REVERT: j 213 VAL cc_start: 0.8989 (t) cc_final: 0.8780 (m) REVERT: j 214 ASN cc_start: 0.9370 (t0) cc_final: 0.9017 (t0) REVERT: j 216 LEU cc_start: 0.8794 (mt) cc_final: 0.8575 (mt) REVERT: j 232 LEU cc_start: 0.9109 (mp) cc_final: 0.8849 (mp) REVERT: k 27 ASN cc_start: 0.8897 (m110) cc_final: 0.8619 (m-40) REVERT: k 29 ASP cc_start: 0.9318 (t0) cc_final: 0.8920 (t0) REVERT: k 64 THR cc_start: 0.7639 (t) cc_final: 0.7312 (p) REVERT: k 66 GLU cc_start: 0.8423 (mp0) cc_final: 0.8122 (mp0) REVERT: k 84 LEU cc_start: 0.8614 (mp) cc_final: 0.8258 (mp) REVERT: k 112 SER cc_start: 0.9071 (m) cc_final: 0.8337 (p) REVERT: k 118 LEU cc_start: 0.8599 (tp) cc_final: 0.8354 (tp) REVERT: k 124 MET cc_start: 0.7726 (mmm) cc_final: 0.7051 (mtt) REVERT: k 133 TYR cc_start: 0.9004 (t80) cc_final: 0.8573 (t80) REVERT: k 156 ASP cc_start: 0.7898 (t0) cc_final: 0.7517 (t0) REVERT: k 165 MET cc_start: 0.9098 (ttp) cc_final: 0.8898 (ttp) REVERT: k 188 PHE cc_start: 0.8924 (m-80) cc_final: 0.8374 (m-80) REVERT: k 208 PHE cc_start: 0.8512 (m-80) cc_final: 0.7934 (m-80) REVERT: k 216 CYS cc_start: 0.8511 (m) cc_final: 0.7414 (m) REVERT: k 226 ASP cc_start: 0.8457 (m-30) cc_final: 0.8086 (m-30) REVERT: l 25 ILE cc_start: 0.8758 (mm) cc_final: 0.8466 (mm) REVERT: l 38 SER cc_start: 0.9605 (m) cc_final: 0.9270 (t) REVERT: l 64 THR cc_start: 0.8863 (p) cc_final: 0.8588 (p) REVERT: m 49 GLN cc_start: 0.8503 (mm110) cc_final: 0.8012 (mm110) REVERT: m 97 LYS cc_start: 0.8778 (pptt) cc_final: 0.8071 (ptmt) REVERT: m 105 ILE cc_start: 0.9175 (mm) cc_final: 0.8789 (tp) REVERT: m 110 THR cc_start: 0.8312 (p) cc_final: 0.7739 (p) REVERT: m 127 LEU cc_start: 0.9183 (tp) cc_final: 0.8945 (tp) REVERT: m 146 ARG cc_start: 0.9402 (mmm160) cc_final: 0.9162 (mmm-85) REVERT: n 37 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8281 (mt-10) REVERT: n 61 ASN cc_start: 0.9145 (m-40) cc_final: 0.8889 (m-40) REVERT: n 74 THR cc_start: 0.8337 (p) cc_final: 0.8072 (t) REVERT: n 87 LYS cc_start: 0.8347 (pttt) cc_final: 0.8066 (pttt) REVERT: n 106 TYR cc_start: 0.8451 (m-10) cc_final: 0.7892 (m-10) REVERT: n 113 ASN cc_start: 0.7641 (m-40) cc_final: 0.7212 (t0) REVERT: n 132 MET cc_start: 0.8556 (mmp) cc_final: 0.8280 (mmp) REVERT: n 149 ASN cc_start: 0.8937 (m-40) cc_final: 0.8610 (m-40) REVERT: n 174 PHE cc_start: 0.8697 (m-10) cc_final: 0.8465 (m-80) REVERT: n 183 SER cc_start: 0.9388 (p) cc_final: 0.8908 (t) REVERT: n 198 ILE cc_start: 0.9177 (mt) cc_final: 0.8709 (pt) REVERT: n 199 ASN cc_start: 0.8777 (t0) cc_final: 0.8077 (t0) REVERT: n 212 TYR cc_start: 0.9341 (t80) cc_final: 0.8372 (t80) REVERT: n 214 ASN cc_start: 0.9080 (t0) cc_final: 0.8863 (t0) REVERT: n 215 SER cc_start: 0.9520 (p) cc_final: 0.9274 (p) REVERT: n 216 LEU cc_start: 0.9475 (mt) cc_final: 0.9141 (mt) REVERT: n 217 VAL cc_start: 0.9560 (m) cc_final: 0.9325 (m) REVERT: n 219 ASP cc_start: 0.8906 (t0) cc_final: 0.8673 (t0) REVERT: n 221 MET cc_start: 0.7467 (pmm) cc_final: 0.6948 (mtm) REVERT: n 257 CYS cc_start: 0.8762 (m) cc_final: 0.8477 (m) REVERT: o 17 ASP cc_start: 0.8718 (t0) cc_final: 0.7090 (t0) REVERT: o 39 GLU cc_start: 0.8748 (tm-30) cc_final: 0.8202 (tm-30) REVERT: o 48 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7587 (mt-10) REVERT: o 61 LYS cc_start: 0.8984 (mmtm) cc_final: 0.8729 (mmtt) REVERT: o 66 GLU cc_start: 0.8649 (pm20) cc_final: 0.8099 (pm20) REVERT: o 97 THR cc_start: 0.9474 (p) cc_final: 0.8712 (p) REVERT: o 101 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7951 (mm-30) REVERT: o 120 CYS cc_start: 0.8803 (m) cc_final: 0.8570 (m) REVERT: o 128 LYS cc_start: 0.8765 (mmtt) cc_final: 0.8530 (mmmt) REVERT: o 185 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6777 (mm-30) REVERT: o 191 CYS cc_start: 0.9109 (m) cc_final: 0.8758 (m) REVERT: o 216 CYS cc_start: 0.7999 (m) cc_final: 0.7210 (m) REVERT: o 218 ASP cc_start: 0.8914 (p0) cc_final: 0.8678 (p0) REVERT: q 83 THR cc_start: 0.8915 (t) cc_final: 0.8201 (m) REVERT: q 90 SER cc_start: 0.8979 (t) cc_final: 0.8717 (t) REVERT: q 95 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8060 (mm-30) REVERT: q 98 LYS cc_start: 0.8986 (mtpt) cc_final: 0.8529 (mtpt) REVERT: q 109 ASP cc_start: 0.7653 (m-30) cc_final: 0.7443 (m-30) REVERT: q 112 GLN cc_start: 0.7510 (tt0) cc_final: 0.7117 (tt0) REVERT: q 118 GLU cc_start: 0.8463 (mt-10) cc_final: 0.7876 (mt-10) REVERT: q 122 TYR cc_start: 0.9398 (m-80) cc_final: 0.9043 (m-10) REVERT: q 126 ASP cc_start: 0.8691 (m-30) cc_final: 0.7660 (m-30) REVERT: q 146 ARG cc_start: 0.8448 (mmm-85) cc_final: 0.7505 (mmm-85) REVERT: q 189 MET cc_start: 0.8270 (ptt) cc_final: 0.7894 (ptm) REVERT: q 198 ASN cc_start: 0.9488 (m110) cc_final: 0.9081 (m-40) REVERT: q 202 HIS cc_start: 0.8465 (m-70) cc_final: 0.7874 (m90) REVERT: q 209 ARG cc_start: 0.8015 (pmt-80) cc_final: 0.7740 (ptt90) REVERT: q 264 TRP cc_start: 0.9176 (m-90) cc_final: 0.8793 (m-90) REVERT: r 81 LYS cc_start: 0.8369 (mmmm) cc_final: 0.8061 (mmtp) REVERT: r 106 TYR cc_start: 0.8655 (m-80) cc_final: 0.8454 (m-80) REVERT: r 122 LEU cc_start: 0.9540 (mt) cc_final: 0.9255 (mt) REVERT: r 178 ASP cc_start: 0.9558 (p0) cc_final: 0.9131 (p0) REVERT: r 185 VAL cc_start: 0.9019 (t) cc_final: 0.8805 (t) REVERT: r 199 ASN cc_start: 0.8752 (t0) cc_final: 0.8546 (t0) REVERT: s 18 ASP cc_start: 0.7454 (t0) cc_final: 0.7225 (t0) REVERT: s 34 ILE cc_start: 0.9111 (pt) cc_final: 0.8546 (pt) REVERT: s 73 ASN cc_start: 0.9010 (p0) cc_final: 0.8696 (p0) REVERT: s 157 LEU cc_start: 0.9278 (mm) cc_final: 0.9000 (mt) REVERT: s 165 MET cc_start: 0.8752 (tmm) cc_final: 0.8506 (tmm) REVERT: s 209 MET cc_start: 0.8580 (ttm) cc_final: 0.8055 (mtp) REVERT: s 216 CYS cc_start: 0.8890 (m) cc_final: 0.8662 (m) REVERT: s 218 ASP cc_start: 0.8796 (p0) cc_final: 0.8573 (p0) REVERT: s 219 PHE cc_start: 0.9076 (t80) cc_final: 0.8728 (t80) REVERT: s 225 ARG cc_start: 0.8641 (ptt180) cc_final: 0.8378 (ptt90) REVERT: s 226 ASP cc_start: 0.7867 (m-30) cc_final: 0.7610 (m-30) REVERT: t 26 ASN cc_start: 0.9196 (m110) cc_final: 0.8885 (m110) REVERT: t 53 PHE cc_start: 0.9199 (m-80) cc_final: 0.8905 (m-80) outliers start: 3 outliers final: 1 residues processed: 1448 average time/residue: 0.2097 time to fit residues: 497.6963 Evaluate side-chains 1205 residues out of total 3659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1204 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 137 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 281 optimal weight: 7.9990 chunk 192 optimal weight: 9.9990 chunk 9 optimal weight: 50.0000 chunk 220 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 285 optimal weight: 20.0000 chunk 339 optimal weight: 5.9990 chunk 392 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 189 ASN ** b 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 8 GLN ** e 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 43 ASN ** g 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 232 GLN ** m 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 196 GLN ** n 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 27 ASN ** o 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 4 GLN ** p 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 162 ASN ** s 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 31 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.110703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.099507 restraints weight = 79509.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.102348 restraints weight = 39644.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.104299 restraints weight = 23357.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.105535 restraints weight = 15231.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.106451 restraints weight = 10836.472| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.5450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 34734 Z= 0.265 Angle : 0.712 8.523 47379 Z= 0.369 Chirality : 0.048 0.249 5322 Planarity : 0.006 0.077 6150 Dihedral : 6.274 52.635 4820 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.03 % Allowed : 1.97 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.89 (0.12), residues: 4158 helix: -2.64 (0.20), residues: 432 sheet: 0.24 (0.15), residues: 1018 loop : -0.53 (0.12), residues: 2708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG s 114 TYR 0.032 0.002 TYR a 137 PHE 0.037 0.002 PHE a 120 TRP 0.053 0.002 TRP b 227 HIS 0.009 0.002 HIS g 96 Details of bonding type rmsd covalent geometry : bond 0.00604 (34734) covalent geometry : angle 0.71197 (47379) hydrogen bonds : bond 0.04207 ( 900) hydrogen bonds : angle 6.19925 ( 2583) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1419 residues out of total 3659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1418 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN b 272 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASN l 69 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 49 GLN cc_start: 0.8754 (mm-40) cc_final: 0.8395 (mm110) REVERT: a 63 ASN cc_start: 0.8750 (t0) cc_final: 0.8533 (t0) REVERT: a 98 LYS cc_start: 0.9158 (mmtt) cc_final: 0.8716 (mmmt) REVERT: a 118 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7987 (mt-10) REVERT: a 126 ASP cc_start: 0.8840 (m-30) cc_final: 0.8505 (m-30) REVERT: a 127 LEU cc_start: 0.9261 (tp) cc_final: 0.8794 (tt) REVERT: a 135 GLU cc_start: 0.8180 (pt0) cc_final: 0.7034 (pt0) REVERT: a 171 GLN cc_start: 0.8543 (mt0) cc_final: 0.8159 (mt0) REVERT: a 205 ASP cc_start: 0.7578 (t70) cc_final: 0.6971 (t0) REVERT: a 264 TRP cc_start: 0.9207 (m-90) cc_final: 0.8830 (m-90) REVERT: b 27 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7493 (tm-30) REVERT: b 80 TRP cc_start: 0.9375 (m-90) cc_final: 0.9046 (m-90) REVERT: b 84 ASP cc_start: 0.8581 (t70) cc_final: 0.7714 (t0) REVERT: b 100 TYR cc_start: 0.8333 (t80) cc_final: 0.7546 (t80) REVERT: b 101 LEU cc_start: 0.9454 (mt) cc_final: 0.8940 (mt) REVERT: b 103 ARG cc_start: 0.8820 (ttt-90) cc_final: 0.8246 (tmm-80) REVERT: b 249 ILE cc_start: 0.9152 (mt) cc_final: 0.8875 (mm) REVERT: c 5 MET cc_start: 0.7703 (mtp) cc_final: 0.7459 (mtp) REVERT: c 17 ASP cc_start: 0.8373 (t70) cc_final: 0.8042 (t70) REVERT: c 61 LYS cc_start: 0.8814 (mmtm) cc_final: 0.8598 (mmmt) REVERT: c 63 ASN cc_start: 0.9055 (m-40) cc_final: 0.8780 (m-40) REVERT: c 65 MET cc_start: 0.8452 (mmp) cc_final: 0.7950 (tpp) REVERT: c 67 MET cc_start: 0.8946 (ptp) cc_final: 0.8495 (ptm) REVERT: c 69 GLN cc_start: 0.8277 (mt0) cc_final: 0.7957 (mp10) REVERT: c 123 MET cc_start: 0.9041 (tpp) cc_final: 0.8738 (tpp) REVERT: c 139 LYS cc_start: 0.9116 (ptmm) cc_final: 0.8760 (ptmm) REVERT: c 163 CYS cc_start: 0.7551 (p) cc_final: 0.7115 (p) REVERT: c 209 MET cc_start: 0.7734 (ttp) cc_final: 0.7355 (ttp) REVERT: e 33 SER cc_start: 0.8479 (t) cc_final: 0.7467 (t) REVERT: e 35 GLU cc_start: 0.8851 (mp0) cc_final: 0.8002 (mp0) REVERT: e 57 GLU cc_start: 0.5085 (mp0) cc_final: 0.4501 (mp0) REVERT: e 66 THR cc_start: 0.8728 (m) cc_final: 0.8523 (p) REVERT: e 91 SER cc_start: 0.8701 (p) cc_final: 0.8303 (m) REVERT: e 257 LYS cc_start: 0.9144 (ttpp) cc_final: 0.8871 (mtpt) REVERT: e 267 ARG cc_start: 0.9345 (mtp85) cc_final: 0.9027 (ttm110) REVERT: f 15 GLN cc_start: 0.7579 (tt0) cc_final: 0.7113 (pt0) REVERT: f 48 ASN cc_start: 0.8684 (t0) cc_final: 0.8452 (t0) REVERT: f 55 GLU cc_start: 0.8315 (pp20) cc_final: 0.7928 (pp20) REVERT: f 70 SER cc_start: 0.8770 (m) cc_final: 0.8422 (p) REVERT: f 84 ASP cc_start: 0.8421 (t70) cc_final: 0.8049 (t0) REVERT: f 126 LEU cc_start: 0.9436 (mt) cc_final: 0.9079 (mt) REVERT: f 127 ILE cc_start: 0.9216 (mp) cc_final: 0.8876 (mt) REVERT: f 129 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8170 (mm-30) REVERT: f 149 ASN cc_start: 0.8479 (m-40) cc_final: 0.7920 (m-40) REVERT: f 199 ASN cc_start: 0.8909 (t0) cc_final: 0.8619 (t0) REVERT: f 217 VAL cc_start: 0.9236 (m) cc_final: 0.8935 (p) REVERT: f 221 MET cc_start: 0.9051 (mmm) cc_final: 0.8684 (mmm) REVERT: f 265 ASN cc_start: 0.7623 (t0) cc_final: 0.6531 (t0) REVERT: g 12 GLN cc_start: 0.8812 (pp30) cc_final: 0.8072 (pp30) REVERT: g 13 PHE cc_start: 0.9232 (t80) cc_final: 0.8861 (t80) REVERT: g 55 MET cc_start: 0.8363 (tpt) cc_final: 0.7699 (tpp) REVERT: g 69 GLN cc_start: 0.8479 (pm20) cc_final: 0.8052 (pm20) REVERT: g 112 SER cc_start: 0.8831 (m) cc_final: 0.7877 (p) REVERT: g 139 LYS cc_start: 0.8964 (tptt) cc_final: 0.8726 (tppt) REVERT: g 148 MET cc_start: 0.6341 (ttm) cc_final: 0.5798 (ttt) REVERT: g 163 CYS cc_start: 0.8785 (p) cc_final: 0.8398 (p) REVERT: g 169 TRP cc_start: 0.9114 (t-100) cc_final: 0.7983 (t-100) REVERT: g 181 ASP cc_start: 0.7500 (t0) cc_final: 0.7232 (t0) REVERT: g 208 PHE cc_start: 0.8641 (m-80) cc_final: 0.8353 (m-10) REVERT: g 216 CYS cc_start: 0.8273 (m) cc_final: 0.7929 (m) REVERT: h 27 TYR cc_start: 0.8460 (p90) cc_final: 0.8200 (p90) REVERT: i 120 PHE cc_start: 0.9121 (m-80) cc_final: 0.8871 (m-10) REVERT: i 151 GLN cc_start: 0.9352 (tt0) cc_final: 0.8918 (tt0) REVERT: i 166 ASP cc_start: 0.8570 (p0) cc_final: 0.7787 (p0) REVERT: i 180 TYR cc_start: 0.8424 (t80) cc_final: 0.8166 (t80) REVERT: i 251 SER cc_start: 0.8184 (p) cc_final: 0.7915 (t) REVERT: i 262 ARG cc_start: 0.9002 (ttp80) cc_final: 0.8256 (ttm170) REVERT: j 59 SER cc_start: 0.9164 (m) cc_final: 0.8927 (p) REVERT: j 60 SER cc_start: 0.9138 (m) cc_final: 0.8488 (p) REVERT: j 81 LYS cc_start: 0.8367 (mptt) cc_final: 0.7708 (mmtp) REVERT: j 88 ASP cc_start: 0.8310 (t70) cc_final: 0.8087 (t70) REVERT: j 129 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8476 (mm-30) REVERT: j 180 LEU cc_start: 0.9209 (mt) cc_final: 0.8965 (mt) REVERT: j 198 ILE cc_start: 0.9499 (mt) cc_final: 0.9163 (tt) REVERT: j 214 ASN cc_start: 0.9331 (t0) cc_final: 0.8979 (t0) REVERT: j 216 LEU cc_start: 0.8766 (mt) cc_final: 0.8475 (mt) REVERT: j 232 LEU cc_start: 0.9112 (mp) cc_final: 0.8864 (mp) REVERT: j 260 PHE cc_start: 0.9187 (m-80) cc_final: 0.8889 (m-80) REVERT: k 29 ASP cc_start: 0.9334 (t0) cc_final: 0.8990 (t0) REVERT: k 64 THR cc_start: 0.7828 (t) cc_final: 0.7247 (p) REVERT: k 112 SER cc_start: 0.8975 (m) cc_final: 0.8398 (p) REVERT: k 118 LEU cc_start: 0.8837 (tp) cc_final: 0.8570 (tp) REVERT: k 119 PHE cc_start: 0.8633 (t80) cc_final: 0.8040 (t80) REVERT: k 133 TYR cc_start: 0.9067 (t80) cc_final: 0.8615 (t80) REVERT: k 146 ASP cc_start: 0.7925 (m-30) cc_final: 0.7574 (m-30) REVERT: k 156 ASP cc_start: 0.8034 (t0) cc_final: 0.7600 (t0) REVERT: k 165 MET cc_start: 0.9128 (ttp) cc_final: 0.8911 (ttp) REVERT: k 188 PHE cc_start: 0.9006 (m-80) cc_final: 0.8408 (m-80) REVERT: k 216 CYS cc_start: 0.8540 (m) cc_final: 0.7440 (m) REVERT: k 226 ASP cc_start: 0.8483 (m-30) cc_final: 0.8171 (m-30) REVERT: l 25 ILE cc_start: 0.8701 (mm) cc_final: 0.8428 (mm) REVERT: l 38 SER cc_start: 0.9611 (m) cc_final: 0.9247 (t) REVERT: m 34 GLN cc_start: 0.8387 (pm20) cc_final: 0.7308 (tm-30) REVERT: m 66 THR cc_start: 0.8709 (m) cc_final: 0.8428 (p) REVERT: m 97 LYS cc_start: 0.8507 (pptt) cc_final: 0.8193 (ptmt) REVERT: m 105 ILE cc_start: 0.9240 (mm) cc_final: 0.8867 (tp) REVERT: m 110 THR cc_start: 0.8226 (p) cc_final: 0.8017 (p) REVERT: m 146 ARG cc_start: 0.9398 (mmm160) cc_final: 0.9092 (mmm-85) REVERT: m 165 TRP cc_start: 0.8534 (p-90) cc_final: 0.7823 (p-90) REVERT: n 61 ASN cc_start: 0.9104 (m-40) cc_final: 0.8887 (m-40) REVERT: n 74 THR cc_start: 0.8340 (p) cc_final: 0.8062 (t) REVERT: n 84 ASP cc_start: 0.8590 (t70) cc_final: 0.7594 (t0) REVERT: n 85 CYS cc_start: 0.8626 (t) cc_final: 0.8073 (t) REVERT: n 113 ASN cc_start: 0.7525 (m-40) cc_final: 0.7139 (t0) REVERT: n 132 MET cc_start: 0.8614 (mmp) cc_final: 0.8309 (mmp) REVERT: n 174 PHE cc_start: 0.8642 (m-10) cc_final: 0.8341 (m-80) REVERT: n 183 SER cc_start: 0.9340 (p) cc_final: 0.9033 (t) REVERT: n 198 ILE cc_start: 0.9198 (mt) cc_final: 0.8732 (pt) REVERT: n 199 ASN cc_start: 0.8656 (t0) cc_final: 0.7947 (t0) REVERT: n 212 TYR cc_start: 0.9367 (t80) cc_final: 0.8264 (t80) REVERT: n 214 ASN cc_start: 0.9121 (t0) cc_final: 0.8590 (t0) REVERT: n 216 LEU cc_start: 0.9489 (mt) cc_final: 0.9052 (mt) REVERT: n 217 VAL cc_start: 0.9513 (m) cc_final: 0.9156 (m) REVERT: n 219 ASP cc_start: 0.8907 (t0) cc_final: 0.8667 (t0) REVERT: n 221 MET cc_start: 0.7614 (pmm) cc_final: 0.7317 (mtm) REVERT: n 223 LYS cc_start: 0.9076 (mtmm) cc_final: 0.8784 (mtmm) REVERT: n 257 CYS cc_start: 0.8726 (m) cc_final: 0.8520 (m) REVERT: o 17 ASP cc_start: 0.8913 (t0) cc_final: 0.7039 (t0) REVERT: o 39 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8182 (tm-30) REVERT: o 43 MET cc_start: 0.9100 (mmm) cc_final: 0.8759 (mmm) REVERT: o 48 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7508 (mt-10) REVERT: o 61 LYS cc_start: 0.8985 (mmtm) cc_final: 0.8750 (mmtt) REVERT: o 66 GLU cc_start: 0.8624 (pm20) cc_final: 0.8212 (pm20) REVERT: o 97 THR cc_start: 0.9468 (p) cc_final: 0.8571 (p) REVERT: o 120 CYS cc_start: 0.8884 (m) cc_final: 0.8639 (m) REVERT: o 154 ILE cc_start: 0.8143 (mm) cc_final: 0.7358 (pt) REVERT: o 185 GLU cc_start: 0.7390 (mm-30) cc_final: 0.6829 (mm-30) REVERT: o 191 CYS cc_start: 0.9046 (m) cc_final: 0.8686 (m) REVERT: o 216 CYS cc_start: 0.8040 (m) cc_final: 0.7277 (m) REVERT: o 218 ASP cc_start: 0.8904 (p0) cc_final: 0.8671 (p0) REVERT: q 23 GLN cc_start: 0.8446 (tp40) cc_final: 0.8170 (tp-100) REVERT: q 83 THR cc_start: 0.8977 (t) cc_final: 0.8213 (m) REVERT: q 90 SER cc_start: 0.8944 (t) cc_final: 0.8709 (t) REVERT: q 95 GLU cc_start: 0.8697 (mm-30) cc_final: 0.7995 (mm-30) REVERT: q 98 LYS cc_start: 0.8975 (mtpt) cc_final: 0.8452 (mtpt) REVERT: q 112 GLN cc_start: 0.7537 (tt0) cc_final: 0.7106 (tt0) REVERT: q 118 GLU cc_start: 0.8447 (mt-10) cc_final: 0.7803 (mt-10) REVERT: q 127 LEU cc_start: 0.9264 (tp) cc_final: 0.8968 (tp) REVERT: q 135 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6426 (mt-10) REVERT: q 146 ARG cc_start: 0.8459 (mmm-85) cc_final: 0.7574 (mmm-85) REVERT: q 148 GLN cc_start: 0.8419 (mt0) cc_final: 0.8034 (mt0) REVERT: q 189 MET cc_start: 0.8481 (ptt) cc_final: 0.8119 (ptm) REVERT: q 198 ASN cc_start: 0.9496 (m110) cc_final: 0.9118 (m-40) REVERT: q 202 HIS cc_start: 0.8455 (m-70) cc_final: 0.7785 (m90) REVERT: q 209 ARG cc_start: 0.8084 (pmt-80) cc_final: 0.7712 (pmt-80) REVERT: q 264 TRP cc_start: 0.9172 (m-90) cc_final: 0.8963 (m-90) REVERT: r 122 LEU cc_start: 0.9555 (mt) cc_final: 0.9285 (mt) REVERT: r 178 ASP cc_start: 0.9569 (p0) cc_final: 0.9187 (p0) REVERT: r 199 ASN cc_start: 0.8766 (t0) cc_final: 0.8419 (t0) REVERT: s 8 PRO cc_start: 0.9347 (Cg_exo) cc_final: 0.9034 (Cg_endo) REVERT: s 18 ASP cc_start: 0.7416 (t0) cc_final: 0.7196 (t0) REVERT: s 34 ILE cc_start: 0.9173 (pt) cc_final: 0.8610 (pt) REVERT: s 73 ASN cc_start: 0.9098 (p0) cc_final: 0.8878 (p0) REVERT: s 157 LEU cc_start: 0.9325 (mm) cc_final: 0.8925 (mt) REVERT: s 165 MET cc_start: 0.8777 (tmm) cc_final: 0.8430 (tmm) REVERT: s 209 MET cc_start: 0.8525 (ttm) cc_final: 0.7921 (mtp) REVERT: s 218 ASP cc_start: 0.8847 (p0) cc_final: 0.8632 (p0) REVERT: s 219 PHE cc_start: 0.9119 (t80) cc_final: 0.8897 (t80) REVERT: s 226 ASP cc_start: 0.7924 (m-30) cc_final: 0.7642 (m-30) outliers start: 1 outliers final: 0 residues processed: 1419 average time/residue: 0.2122 time to fit residues: 494.5246 Evaluate side-chains 1172 residues out of total 3659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1172 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 279 optimal weight: 0.9980 chunk 202 optimal weight: 10.0000 chunk 247 optimal weight: 10.0000 chunk 352 optimal weight: 0.0020 chunk 269 optimal weight: 5.9990 chunk 380 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 325 optimal weight: 7.9990 chunk 389 optimal weight: 20.0000 chunk 76 optimal weight: 0.5980 overall best weight: 1.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 226 ASN ** c 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 89 ASN ** e 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 244 ASN f 43 ASN ** g 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 112 GLN ** i 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 195 HIS j 224 HIS j 226 ASN ** l 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 32 ASN ** m 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 94 GLN ** n 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 27 ASN o 35 HIS ** o 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 49 GLN ** q 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.115315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.104013 restraints weight = 78341.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.107012 restraints weight = 38876.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.108977 restraints weight = 22700.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.110271 restraints weight = 14744.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.111211 restraints weight = 10370.758| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.5567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34734 Z= 0.142 Angle : 0.649 8.740 47379 Z= 0.336 Chirality : 0.046 0.219 5322 Planarity : 0.005 0.059 6150 Dihedral : 6.012 58.164 4820 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.03 % Allowed : 1.01 % Favored : 98.96 % 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: -0.78 (0.12), residues: 4158 helix: -2.58 (0.20), residues: 419 sheet: 0.31 (0.15), residues: 1013 loop : -0.46 (0.12), residues: 2726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG m 209 TYR 0.026 0.002 TYR a 154 PHE 0.035 0.002 PHE a 120 TRP 0.044 0.002 TRP b 227 HIS 0.010 0.001 HIS j 109 Details of bonding type rmsd covalent geometry : bond 0.00331 (34734) covalent geometry : angle 0.64944 (47379) hydrogen bonds : bond 0.03749 ( 900) hydrogen bonds : angle 5.98584 ( 2583) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1478 residues out of total 3659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1477 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN b 272 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASN l 69 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 43 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8300 (mt-10) REVERT: a 98 LYS cc_start: 0.9051 (mmtt) cc_final: 0.8833 (mmtt) REVERT: a 118 GLU cc_start: 0.8408 (mt-10) cc_final: 0.7916 (mt-10) REVERT: a 120 PHE cc_start: 0.8488 (m-10) cc_final: 0.8030 (m-10) REVERT: a 126 ASP cc_start: 0.8823 (m-30) cc_final: 0.8448 (m-30) REVERT: a 171 GLN cc_start: 0.8503 (mt0) cc_final: 0.8148 (mt0) REVERT: a 205 ASP cc_start: 0.7578 (t70) cc_final: 0.6930 (t0) REVERT: a 241 ASN cc_start: 0.7564 (t0) cc_final: 0.7360 (t0) REVERT: a 264 TRP cc_start: 0.9235 (m-90) cc_final: 0.8867 (m-90) REVERT: a 286 ILE cc_start: 0.9168 (pt) cc_final: 0.8602 (pt) REVERT: b 16 ILE cc_start: 0.8721 (mt) cc_final: 0.8388 (mt) REVERT: b 84 ASP cc_start: 0.8503 (t70) cc_final: 0.7735 (t0) REVERT: b 103 ARG cc_start: 0.8622 (ttt-90) cc_final: 0.8361 (ttt-90) REVERT: b 129 GLU cc_start: 0.8479 (mm-30) cc_final: 0.7764 (mm-30) REVERT: b 130 PHE cc_start: 0.8425 (t80) cc_final: 0.8143 (t80) REVERT: b 223 LYS cc_start: 0.8901 (mtmt) cc_final: 0.8594 (mttp) REVERT: b 249 ILE cc_start: 0.9076 (mt) cc_final: 0.8808 (mm) REVERT: c 43 MET cc_start: 0.9487 (mmm) cc_final: 0.9033 (mmm) REVERT: c 63 ASN cc_start: 0.9009 (m-40) cc_final: 0.8803 (m-40) REVERT: c 69 GLN cc_start: 0.8323 (mt0) cc_final: 0.8013 (mp10) REVERT: c 139 LYS cc_start: 0.9094 (ptmm) cc_final: 0.8732 (ptmm) REVERT: c 163 CYS cc_start: 0.7526 (p) cc_final: 0.7261 (p) REVERT: c 197 ILE cc_start: 0.8638 (pt) cc_final: 0.8426 (pt) REVERT: c 225 ARG cc_start: 0.7883 (ptt90) cc_final: 0.7453 (ptm-80) REVERT: d 34 LYS cc_start: 0.8473 (mtpt) cc_final: 0.8267 (mttt) REVERT: e 33 SER cc_start: 0.8488 (t) cc_final: 0.7433 (t) REVERT: e 35 GLU cc_start: 0.8848 (mp0) cc_final: 0.8110 (mp0) REVERT: e 57 GLU cc_start: 0.4938 (mp0) cc_final: 0.4422 (mp0) REVERT: e 257 LYS cc_start: 0.9182 (ttpp) cc_final: 0.8874 (mtpt) REVERT: e 267 ARG cc_start: 0.9215 (mtp85) cc_final: 0.8876 (ttm110) REVERT: f 15 GLN cc_start: 0.7550 (tt0) cc_final: 0.7095 (pt0) REVERT: f 21 SER cc_start: 0.8961 (t) cc_final: 0.8412 (p) REVERT: f 55 GLU cc_start: 0.8288 (pp20) cc_final: 0.7991 (pp20) REVERT: f 70 SER cc_start: 0.8715 (m) cc_final: 0.8380 (p) REVERT: f 126 LEU cc_start: 0.9439 (mt) cc_final: 0.9096 (mt) REVERT: f 129 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8009 (mm-30) REVERT: f 199 ASN cc_start: 0.8873 (t0) cc_final: 0.8557 (t0) REVERT: f 221 MET cc_start: 0.9052 (mmm) cc_final: 0.8711 (mmm) REVERT: g 11 ASN cc_start: 0.8839 (m-40) cc_final: 0.8592 (m-40) REVERT: g 12 GLN cc_start: 0.8755 (pp30) cc_final: 0.7930 (pp30) REVERT: g 13 PHE cc_start: 0.9243 (t80) cc_final: 0.8837 (t80) REVERT: g 18 ASP cc_start: 0.7879 (t0) cc_final: 0.7301 (t0) REVERT: g 55 MET cc_start: 0.8334 (tpt) cc_final: 0.7724 (tpp) REVERT: g 69 GLN cc_start: 0.8432 (pm20) cc_final: 0.8187 (pm20) REVERT: g 101 GLU cc_start: 0.8479 (mm-30) cc_final: 0.7688 (mm-30) REVERT: g 112 SER cc_start: 0.8974 (m) cc_final: 0.7971 (p) REVERT: g 148 MET cc_start: 0.6275 (ttm) cc_final: 0.5576 (ttt) REVERT: g 163 CYS cc_start: 0.8678 (p) cc_final: 0.8263 (p) REVERT: g 169 TRP cc_start: 0.9057 (t-100) cc_final: 0.7853 (t-100) REVERT: g 181 ASP cc_start: 0.7431 (t0) cc_final: 0.7157 (t0) REVERT: g 208 PHE cc_start: 0.8575 (m-80) cc_final: 0.8250 (m-10) REVERT: g 216 CYS cc_start: 0.8332 (m) cc_final: 0.7869 (m) REVERT: i 120 PHE cc_start: 0.9032 (m-80) cc_final: 0.8741 (m-10) REVERT: i 151 GLN cc_start: 0.9318 (tt0) cc_final: 0.8668 (tt0) REVERT: i 154 TYR cc_start: 0.9270 (t80) cc_final: 0.9030 (t80) REVERT: i 166 ASP cc_start: 0.8570 (p0) cc_final: 0.8164 (p0) REVERT: i 203 PHE cc_start: 0.9198 (m-80) cc_final: 0.8435 (m-80) REVERT: i 250 THR cc_start: 0.7846 (m) cc_final: 0.7584 (m) REVERT: i 262 ARG cc_start: 0.8938 (ttp80) cc_final: 0.8025 (ttm170) REVERT: i 264 TRP cc_start: 0.9154 (m-90) cc_final: 0.8604 (m-10) REVERT: j 59 SER cc_start: 0.9151 (m) cc_final: 0.8944 (p) REVERT: j 60 SER cc_start: 0.9093 (m) cc_final: 0.8464 (p) REVERT: j 81 LYS cc_start: 0.8383 (mptt) cc_final: 0.7778 (mmtp) REVERT: j 88 ASP cc_start: 0.8257 (t70) cc_final: 0.7969 (t70) REVERT: j 129 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8393 (mm-30) REVERT: j 198 ILE cc_start: 0.9440 (mt) cc_final: 0.9214 (tt) REVERT: j 214 ASN cc_start: 0.9306 (t0) cc_final: 0.9061 (t0) REVERT: j 216 LEU cc_start: 0.8707 (mt) cc_final: 0.8477 (mt) REVERT: j 227 TRP cc_start: 0.8396 (m100) cc_final: 0.7687 (m-10) REVERT: j 260 PHE cc_start: 0.9083 (m-80) cc_final: 0.8780 (m-80) REVERT: k 29 ASP cc_start: 0.9235 (t0) cc_final: 0.8875 (t0) REVERT: k 43 MET cc_start: 0.8891 (mmm) cc_final: 0.8412 (mmm) REVERT: k 64 THR cc_start: 0.7734 (t) cc_final: 0.7198 (p) REVERT: k 69 GLN cc_start: 0.8662 (mt0) cc_final: 0.8246 (mt0) REVERT: k 112 SER cc_start: 0.8917 (m) cc_final: 0.8199 (p) REVERT: k 124 MET cc_start: 0.7543 (mmm) cc_final: 0.7251 (mtt) REVERT: k 188 PHE cc_start: 0.8996 (m-80) cc_final: 0.8414 (m-80) REVERT: k 208 PHE cc_start: 0.8432 (m-80) cc_final: 0.7972 (m-80) REVERT: k 216 CYS cc_start: 0.8427 (m) cc_final: 0.7486 (m) REVERT: k 226 ASP cc_start: 0.8465 (m-30) cc_final: 0.8085 (m-30) REVERT: l 25 ILE cc_start: 0.8622 (mm) cc_final: 0.8300 (mm) REVERT: l 38 SER cc_start: 0.9658 (m) cc_final: 0.9323 (t) REVERT: l 64 THR cc_start: 0.8970 (p) cc_final: 0.8717 (p) REVERT: m 34 GLN cc_start: 0.8348 (pm20) cc_final: 0.7283 (tm-30) REVERT: m 97 LYS cc_start: 0.8475 (pptt) cc_final: 0.8186 (ptmt) REVERT: m 105 ILE cc_start: 0.9215 (mm) cc_final: 0.8830 (tp) REVERT: m 118 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8388 (mt-10) REVERT: m 165 TRP cc_start: 0.8368 (p-90) cc_final: 0.7731 (p-90) REVERT: m 209 ARG cc_start: 0.7670 (ttp80) cc_final: 0.7311 (ttp80) REVERT: m 274 TYR cc_start: 0.7920 (m-80) cc_final: 0.7668 (m-80) REVERT: n 37 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8179 (mt-10) REVERT: n 61 ASN cc_start: 0.9083 (m-40) cc_final: 0.8809 (m-40) REVERT: n 74 THR cc_start: 0.8284 (p) cc_final: 0.8045 (t) REVERT: n 84 ASP cc_start: 0.8348 (t70) cc_final: 0.7965 (t0) REVERT: n 113 ASN cc_start: 0.7696 (m-40) cc_final: 0.7171 (t0) REVERT: n 183 SER cc_start: 0.9181 (p) cc_final: 0.8714 (t) REVERT: n 198 ILE cc_start: 0.9190 (mt) cc_final: 0.8751 (pt) REVERT: n 199 ASN cc_start: 0.8573 (t0) cc_final: 0.7883 (t0) REVERT: n 212 TYR cc_start: 0.9238 (t80) cc_final: 0.8206 (t80) REVERT: n 216 LEU cc_start: 0.9510 (mt) cc_final: 0.9197 (mt) REVERT: n 217 VAL cc_start: 0.9596 (m) cc_final: 0.9348 (m) REVERT: n 223 LYS cc_start: 0.9016 (mtmm) cc_final: 0.8725 (mtmm) REVERT: n 257 CYS cc_start: 0.8670 (m) cc_final: 0.8407 (m) REVERT: n 259 GLU cc_start: 0.8256 (pt0) cc_final: 0.7226 (pm20) REVERT: o 17 ASP cc_start: 0.8690 (t0) cc_final: 0.6903 (t0) REVERT: o 39 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8193 (tm-30) REVERT: o 43 MET cc_start: 0.9000 (mmm) cc_final: 0.8625 (mmm) REVERT: o 48 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7407 (mt-10) REVERT: o 97 THR cc_start: 0.9415 (p) cc_final: 0.8891 (p) REVERT: o 120 CYS cc_start: 0.8828 (m) cc_final: 0.8556 (m) REVERT: o 154 ILE cc_start: 0.8208 (mm) cc_final: 0.7280 (pt) REVERT: o 185 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6918 (mm-30) REVERT: o 191 CYS cc_start: 0.9003 (m) cc_final: 0.8556 (m) REVERT: o 216 CYS cc_start: 0.7900 (m) cc_final: 0.7096 (m) REVERT: o 218 ASP cc_start: 0.8868 (p0) cc_final: 0.8643 (p0) REVERT: q 23 GLN cc_start: 0.8421 (tp40) cc_final: 0.8168 (tp-100) REVERT: q 83 THR cc_start: 0.8902 (t) cc_final: 0.8304 (m) REVERT: q 90 SER cc_start: 0.8817 (t) cc_final: 0.8550 (t) REVERT: q 95 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8043 (mm-30) REVERT: q 98 LYS cc_start: 0.8956 (mtpt) cc_final: 0.8465 (mtpt) REVERT: q 101 ASN cc_start: 0.7522 (m110) cc_final: 0.7100 (m110) REVERT: q 112 GLN cc_start: 0.7421 (tt0) cc_final: 0.7034 (tt0) REVERT: q 118 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8113 (mt-10) REVERT: q 146 ARG cc_start: 0.8319 (mmm-85) cc_final: 0.7408 (mmm-85) REVERT: q 175 ASN cc_start: 0.8427 (m-40) cc_final: 0.7977 (m110) REVERT: q 189 MET cc_start: 0.8200 (ptt) cc_final: 0.7887 (ptm) REVERT: q 196 ILE cc_start: 0.9349 (pt) cc_final: 0.8886 (pt) REVERT: q 198 ASN cc_start: 0.9448 (m110) cc_final: 0.9029 (m-40) REVERT: q 202 HIS cc_start: 0.8536 (m-70) cc_final: 0.7894 (m90) REVERT: q 209 ARG cc_start: 0.8039 (pmt-80) cc_final: 0.7612 (ptt90) REVERT: q 286 ILE cc_start: 0.9194 (pt) cc_final: 0.8631 (mt) REVERT: r 55 GLU cc_start: 0.8429 (mm-30) cc_final: 0.7608 (pm20) REVERT: r 122 LEU cc_start: 0.9523 (mt) cc_final: 0.9226 (mt) REVERT: r 178 ASP cc_start: 0.9512 (p0) cc_final: 0.9084 (p0) REVERT: r 196 GLN cc_start: 0.9046 (mm-40) cc_final: 0.8786 (mm-40) REVERT: r 199 ASN cc_start: 0.8705 (t0) cc_final: 0.8402 (t0) REVERT: s 8 PRO cc_start: 0.9257 (Cg_exo) cc_final: 0.8946 (Cg_endo) REVERT: s 18 ASP cc_start: 0.7410 (t0) cc_final: 0.7108 (t0) REVERT: s 34 ILE cc_start: 0.9147 (pt) cc_final: 0.8573 (pt) REVERT: s 43 MET cc_start: 0.8670 (mmm) cc_final: 0.8349 (mtt) REVERT: s 84 LEU cc_start: 0.9200 (mt) cc_final: 0.8985 (mt) REVERT: s 128 LYS cc_start: 0.7960 (mmtp) cc_final: 0.7659 (mmtm) REVERT: s 157 LEU cc_start: 0.9276 (mm) cc_final: 0.8947 (mt) REVERT: s 209 MET cc_start: 0.8375 (ttm) cc_final: 0.7844 (mtp) REVERT: s 216 CYS cc_start: 0.8925 (m) cc_final: 0.8629 (m) REVERT: s 218 ASP cc_start: 0.8791 (p0) cc_final: 0.8571 (p0) REVERT: s 219 PHE cc_start: 0.9039 (t80) cc_final: 0.8724 (t80) REVERT: s 226 ASP cc_start: 0.7757 (m-30) cc_final: 0.7462 (m-30) REVERT: t 7 THR cc_start: 0.9334 (p) cc_final: 0.9094 (t) REVERT: t 39 ASN cc_start: 0.8937 (m-40) cc_final: 0.8516 (m110) REVERT: t 40 SER cc_start: 0.9231 (p) cc_final: 0.9024 (p) outliers start: 1 outliers final: 1 residues processed: 1478 average time/residue: 0.2136 time to fit residues: 518.1832 Evaluate side-chains 1215 residues out of total 3659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1214 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 87 optimal weight: 5.9990 chunk 7 optimal weight: 50.0000 chunk 157 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 143 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 347 optimal weight: 5.9990 chunk 288 optimal weight: 20.0000 chunk 240 optimal weight: 6.9990 chunk 225 optimal weight: 20.0000 chunk 248 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 175 ASN ** a 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 111 GLN c 63 ASN ** e 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 198 ASN ** e 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 149 ASN f 225 ASN ** g 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 195 HIS ** j 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 224 HIS j 226 ASN ** k 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 4 GLN ** p 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 49 GLN ** q 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 162 ASN ** s 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.111708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.100400 restraints weight = 79777.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.103311 restraints weight = 39933.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.105269 restraints weight = 23531.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.106513 restraints weight = 15353.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.107451 restraints weight = 11011.413| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.5751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.118 34734 Z= 0.266 Angle : 0.715 8.580 47379 Z= 0.370 Chirality : 0.047 0.239 5322 Planarity : 0.006 0.054 6150 Dihedral : 6.216 59.852 4820 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.03 % Allowed : 1.45 % Favored : 98.52 % 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: -0.94 (0.12), residues: 4158 helix: -2.64 (0.20), residues: 429 sheet: 0.20 (0.15), residues: 1006 loop : -0.58 (0.12), residues: 2723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG i 188 TYR 0.029 0.002 TYR a 137 PHE 0.032 0.002 PHE e 179 TRP 0.058 0.002 TRP b 227 HIS 0.012 0.002 HIS c 96 Details of bonding type rmsd covalent geometry : bond 0.00609 (34734) covalent geometry : angle 0.71471 (47379) hydrogen bonds : bond 0.04088 ( 900) hydrogen bonds : angle 6.06810 ( 2583) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1387 residues out of total 3659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1386 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN b 272 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASN l 69 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 49 GLN cc_start: 0.8772 (mm-40) cc_final: 0.8373 (mm110) REVERT: a 120 PHE cc_start: 0.8619 (m-10) cc_final: 0.8251 (m-10) REVERT: a 126 ASP cc_start: 0.8912 (m-30) cc_final: 0.8625 (m-30) REVERT: a 127 LEU cc_start: 0.9258 (tt) cc_final: 0.8994 (tp) REVERT: a 171 GLN cc_start: 0.8527 (mt0) cc_final: 0.8133 (mt0) REVERT: a 205 ASP cc_start: 0.7519 (t70) cc_final: 0.6996 (t0) REVERT: a 264 TRP cc_start: 0.9231 (m-90) cc_final: 0.8789 (m-90) REVERT: b 16 ILE cc_start: 0.8668 (mt) cc_final: 0.8379 (mt) REVERT: b 18 LEU cc_start: 0.9433 (mt) cc_final: 0.8962 (mp) REVERT: b 27 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7859 (tm-30) REVERT: b 84 ASP cc_start: 0.8378 (t70) cc_final: 0.7428 (t70) REVERT: b 100 TYR cc_start: 0.8343 (t80) cc_final: 0.7850 (t80) REVERT: b 101 LEU cc_start: 0.9391 (mt) cc_final: 0.9135 (mt) REVERT: b 103 ARG cc_start: 0.8800 (ttt-90) cc_final: 0.8370 (ttt-90) REVERT: b 130 PHE cc_start: 0.8456 (t80) cc_final: 0.8121 (t80) REVERT: b 249 ILE cc_start: 0.9103 (mt) cc_final: 0.8826 (mm) REVERT: c 65 MET cc_start: 0.8397 (mmp) cc_final: 0.8141 (mmp) REVERT: c 67 MET cc_start: 0.8817 (ptm) cc_final: 0.8427 (ptm) REVERT: c 69 GLN cc_start: 0.8291 (mt0) cc_final: 0.7921 (mp10) REVERT: c 82 PHE cc_start: 0.8862 (p90) cc_final: 0.8506 (p90) REVERT: c 123 MET cc_start: 0.9036 (tpp) cc_final: 0.8809 (tpp) REVERT: c 159 LEU cc_start: 0.9021 (mt) cc_final: 0.8800 (mt) REVERT: c 163 CYS cc_start: 0.7559 (p) cc_final: 0.7311 (p) REVERT: c 209 MET cc_start: 0.7883 (ttp) cc_final: 0.7573 (ttp) REVERT: e 57 GLU cc_start: 0.5252 (mp0) cc_final: 0.4627 (mp0) REVERT: e 91 SER cc_start: 0.8791 (p) cc_final: 0.8336 (m) REVERT: e 128 GLU cc_start: 0.7786 (tt0) cc_final: 0.7495 (tt0) REVERT: e 267 ARG cc_start: 0.9192 (mtp85) cc_final: 0.8828 (ttm110) REVERT: e 281 MET cc_start: 0.8823 (mpp) cc_final: 0.8594 (mtt) REVERT: e 282 ILE cc_start: 0.9093 (tp) cc_final: 0.8880 (tp) REVERT: f 15 GLN cc_start: 0.7598 (tt0) cc_final: 0.7129 (pt0) REVERT: f 55 GLU cc_start: 0.8346 (pp20) cc_final: 0.7924 (pp20) REVERT: f 70 SER cc_start: 0.8733 (m) cc_final: 0.8480 (p) REVERT: f 84 ASP cc_start: 0.8467 (t0) cc_final: 0.6353 (t0) REVERT: f 103 ARG cc_start: 0.9261 (ttm-80) cc_final: 0.8809 (ttp80) REVERT: f 126 LEU cc_start: 0.9454 (mt) cc_final: 0.9005 (mt) REVERT: f 127 ILE cc_start: 0.9165 (mp) cc_final: 0.8865 (mt) REVERT: f 129 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8095 (mm-30) REVERT: f 149 ASN cc_start: 0.8421 (m110) cc_final: 0.8200 (t0) REVERT: f 199 ASN cc_start: 0.8898 (t0) cc_final: 0.8581 (t0) REVERT: f 217 VAL cc_start: 0.9260 (m) cc_final: 0.8848 (p) REVERT: f 221 MET cc_start: 0.9079 (mmm) cc_final: 0.8667 (mmm) REVERT: f 249 ILE cc_start: 0.9046 (mm) cc_final: 0.8640 (mm) REVERT: g 2 LEU cc_start: 0.9450 (tp) cc_final: 0.9243 (tp) REVERT: g 12 GLN cc_start: 0.8881 (pp30) cc_final: 0.8172 (pp30) REVERT: g 55 MET cc_start: 0.8363 (tpt) cc_final: 0.7972 (tpt) REVERT: g 67 MET cc_start: 0.8892 (ptp) cc_final: 0.8576 (ptp) REVERT: g 68 TYR cc_start: 0.9105 (m-10) cc_final: 0.8890 (m-10) REVERT: g 112 SER cc_start: 0.8975 (m) cc_final: 0.7947 (p) REVERT: g 163 CYS cc_start: 0.8759 (p) cc_final: 0.8412 (p) REVERT: g 169 TRP cc_start: 0.9107 (t-100) cc_final: 0.7960 (t-100) REVERT: g 181 ASP cc_start: 0.7482 (t0) cc_final: 0.7177 (t0) REVERT: g 185 GLU cc_start: 0.7572 (tp30) cc_final: 0.7324 (tp30) REVERT: g 216 CYS cc_start: 0.8331 (m) cc_final: 0.7871 (m) REVERT: h 8 GLN cc_start: 0.7830 (mt0) cc_final: 0.7132 (mt0) REVERT: i 120 PHE cc_start: 0.9171 (m-80) cc_final: 0.8919 (m-10) REVERT: i 146 ARG cc_start: 0.8490 (mmm160) cc_final: 0.8265 (mmp-170) REVERT: i 151 GLN cc_start: 0.9400 (tt0) cc_final: 0.8974 (tt0) REVERT: i 154 TYR cc_start: 0.9240 (t80) cc_final: 0.8736 (t80) REVERT: i 182 TYR cc_start: 0.9139 (t80) cc_final: 0.8921 (t80) REVERT: i 189 MET cc_start: 0.8703 (ptt) cc_final: 0.8060 (pmm) REVERT: i 262 ARG cc_start: 0.9014 (ttp80) cc_final: 0.8388 (ttm170) REVERT: i 264 TRP cc_start: 0.9184 (m-90) cc_final: 0.8923 (m-90) REVERT: j 59 SER cc_start: 0.9116 (m) cc_final: 0.8907 (p) REVERT: j 60 SER cc_start: 0.9160 (m) cc_final: 0.8488 (p) REVERT: j 81 LYS cc_start: 0.8574 (mptt) cc_final: 0.7881 (mmtp) REVERT: j 117 PHE cc_start: 0.8622 (m-80) cc_final: 0.7665 (m-80) REVERT: j 129 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8613 (mm-30) REVERT: j 198 ILE cc_start: 0.9472 (mt) cc_final: 0.9160 (tt) REVERT: j 214 ASN cc_start: 0.9399 (t0) cc_final: 0.9020 (t0) REVERT: j 232 LEU cc_start: 0.9170 (mp) cc_final: 0.8943 (mp) REVERT: j 260 PHE cc_start: 0.9131 (m-80) cc_final: 0.8818 (m-80) REVERT: k 27 ASN cc_start: 0.8807 (m110) cc_final: 0.8541 (m110) REVERT: k 69 GLN cc_start: 0.8798 (mt0) cc_final: 0.8301 (mt0) REVERT: k 93 ARG cc_start: 0.9254 (mpp80) cc_final: 0.8803 (mtt180) REVERT: k 112 SER cc_start: 0.9039 (m) cc_final: 0.8287 (p) REVERT: k 119 PHE cc_start: 0.8696 (t80) cc_final: 0.8447 (t80) REVERT: k 124 MET cc_start: 0.7683 (mmm) cc_final: 0.7201 (mtt) REVERT: k 188 PHE cc_start: 0.9019 (m-80) cc_final: 0.8469 (m-80) REVERT: k 216 CYS cc_start: 0.8546 (m) cc_final: 0.7329 (m) REVERT: k 218 ASP cc_start: 0.8776 (p0) cc_final: 0.8570 (p0) REVERT: k 226 ASP cc_start: 0.8506 (m-30) cc_final: 0.8121 (m-30) REVERT: l 25 ILE cc_start: 0.8750 (mm) cc_final: 0.8524 (mm) REVERT: l 38 SER cc_start: 0.9652 (m) cc_final: 0.9287 (t) REVERT: m 34 GLN cc_start: 0.8476 (pm20) cc_final: 0.7357 (tm-30) REVERT: m 97 LYS cc_start: 0.8604 (pptt) cc_final: 0.8272 (ptmt) REVERT: m 105 ILE cc_start: 0.9277 (mm) cc_final: 0.8903 (tp) REVERT: m 146 ARG cc_start: 0.9391 (mmm160) cc_final: 0.9111 (mmm-85) REVERT: m 165 TRP cc_start: 0.8449 (p-90) cc_final: 0.7693 (p-90) REVERT: m 281 MET cc_start: 0.8791 (mtt) cc_final: 0.8533 (mtt) REVERT: n 37 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8183 (mt-10) REVERT: n 74 THR cc_start: 0.8364 (p) cc_final: 0.8121 (t) REVERT: n 84 ASP cc_start: 0.8267 (t70) cc_final: 0.7728 (t0) REVERT: n 85 CYS cc_start: 0.8589 (t) cc_final: 0.8235 (t) REVERT: n 106 TYR cc_start: 0.8867 (m-80) cc_final: 0.8394 (m-80) REVERT: n 113 ASN cc_start: 0.7617 (m-40) cc_final: 0.7278 (t0) REVERT: n 183 SER cc_start: 0.9242 (p) cc_final: 0.8801 (t) REVERT: n 198 ILE cc_start: 0.9199 (mt) cc_final: 0.8664 (pt) REVERT: n 199 ASN cc_start: 0.8589 (t0) cc_final: 0.7790 (t0) REVERT: n 212 TYR cc_start: 0.9279 (t80) cc_final: 0.8102 (t80) REVERT: n 214 ASN cc_start: 0.9063 (t0) cc_final: 0.8641 (t0) REVERT: n 216 LEU cc_start: 0.9448 (mt) cc_final: 0.8950 (mt) REVERT: n 217 VAL cc_start: 0.9520 (m) cc_final: 0.9126 (m) REVERT: n 219 ASP cc_start: 0.9083 (t0) cc_final: 0.8650 (t0) REVERT: n 232 LEU cc_start: 0.9471 (mt) cc_final: 0.9248 (mt) REVERT: n 257 CYS cc_start: 0.8735 (m) cc_final: 0.8456 (m) REVERT: n 259 GLU cc_start: 0.8489 (pt0) cc_final: 0.7250 (pm20) REVERT: o 17 ASP cc_start: 0.8878 (t0) cc_final: 0.7130 (t0) REVERT: o 39 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8248 (tm-30) REVERT: o 43 MET cc_start: 0.9095 (mmm) cc_final: 0.8751 (mmm) REVERT: o 48 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7542 (mt-10) REVERT: o 120 CYS cc_start: 0.8800 (m) cc_final: 0.8498 (m) REVERT: o 154 ILE cc_start: 0.8630 (mm) cc_final: 0.7768 (pt) REVERT: o 185 GLU cc_start: 0.7442 (mm-30) cc_final: 0.6738 (mm-30) REVERT: o 191 CYS cc_start: 0.8968 (m) cc_final: 0.8609 (m) REVERT: o 216 CYS cc_start: 0.7948 (m) cc_final: 0.7143 (m) REVERT: o 218 ASP cc_start: 0.8940 (p0) cc_final: 0.8625 (p0) REVERT: q 23 GLN cc_start: 0.8410 (tp40) cc_final: 0.8162 (tp-100) REVERT: q 83 THR cc_start: 0.8978 (t) cc_final: 0.8287 (m) REVERT: q 90 SER cc_start: 0.8917 (t) cc_final: 0.8622 (t) REVERT: q 95 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8055 (mm-30) REVERT: q 98 LYS cc_start: 0.9026 (mtpt) cc_final: 0.8621 (mtpt) REVERT: q 109 ASP cc_start: 0.7869 (m-30) cc_final: 0.7629 (m-30) REVERT: q 112 GLN cc_start: 0.7377 (tt0) cc_final: 0.7023 (tt0) REVERT: q 118 GLU cc_start: 0.8528 (mt-10) cc_final: 0.7962 (mt-10) REVERT: q 135 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6422 (mt-10) REVERT: q 148 GLN cc_start: 0.8690 (mm110) cc_final: 0.8134 (mm110) REVERT: q 175 ASN cc_start: 0.9011 (m-40) cc_final: 0.8093 (m110) REVERT: q 189 MET cc_start: 0.8341 (ptt) cc_final: 0.7980 (ptm) REVERT: q 198 ASN cc_start: 0.9489 (m110) cc_final: 0.9100 (m-40) REVERT: q 202 HIS cc_start: 0.8524 (m-70) cc_final: 0.7911 (m90) REVERT: q 209 ARG cc_start: 0.8059 (pmt-80) cc_final: 0.7689 (ptt90) REVERT: q 264 TRP cc_start: 0.9219 (m-90) cc_final: 0.8972 (m-90) REVERT: q 286 ILE cc_start: 0.9268 (pt) cc_final: 0.8678 (mt) REVERT: r 55 GLU cc_start: 0.8460 (mm-30) cc_final: 0.7672 (pm20) REVERT: r 122 LEU cc_start: 0.9535 (mt) cc_final: 0.9194 (mt) REVERT: r 132 MET cc_start: 0.8639 (mtm) cc_final: 0.7371 (mtm) REVERT: r 178 ASP cc_start: 0.9550 (p0) cc_final: 0.9110 (p0) REVERT: r 196 GLN cc_start: 0.9011 (mm-40) cc_final: 0.8769 (mm-40) REVERT: r 199 ASN cc_start: 0.8749 (t0) cc_final: 0.8408 (t0) REVERT: r 264 ARG cc_start: 0.7814 (ptp90) cc_final: 0.7052 (ptp90) REVERT: s 8 PRO cc_start: 0.9189 (Cg_exo) cc_final: 0.8868 (Cg_endo) REVERT: s 18 ASP cc_start: 0.7491 (t0) cc_final: 0.7130 (t0) REVERT: s 34 ILE cc_start: 0.9201 (pt) cc_final: 0.8627 (pt) REVERT: s 157 LEU cc_start: 0.9286 (mm) cc_final: 0.8983 (mt) REVERT: s 165 MET cc_start: 0.8822 (tmm) cc_final: 0.8582 (tmm) REVERT: s 209 MET cc_start: 0.8448 (ttm) cc_final: 0.7583 (mtp) REVERT: s 216 CYS cc_start: 0.9035 (m) cc_final: 0.8742 (m) REVERT: s 218 ASP cc_start: 0.8792 (p0) cc_final: 0.8585 (p0) REVERT: s 219 PHE cc_start: 0.9161 (t80) cc_final: 0.8835 (t80) REVERT: s 226 ASP cc_start: 0.7805 (m-30) cc_final: 0.7529 (m-30) REVERT: t 7 THR cc_start: 0.9404 (p) cc_final: 0.9134 (t) outliers start: 1 outliers final: 0 residues processed: 1387 average time/residue: 0.2183 time to fit residues: 497.6155 Evaluate side-chains 1177 residues out of total 3659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1177 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 309 optimal weight: 10.0000 chunk 403 optimal weight: 7.9990 chunk 414 optimal weight: 8.9990 chunk 395 optimal weight: 10.0000 chunk 276 optimal weight: 0.6980 chunk 334 optimal weight: 5.9990 chunk 196 optimal weight: 6.9990 chunk 355 optimal weight: 5.9990 chunk 3 optimal weight: 50.0000 chunk 167 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 119 GLN d 4 GLN ** d 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 108 HIS g 194 GLN ** h 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 34 GLN i 112 GLN ** i 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 195 HIS j 224 HIS j 226 ASN ** m 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 49 GLN q 136 ASN ** q 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 44 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.114502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.103230 restraints weight = 78563.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.106174 restraints weight = 38983.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.108140 restraints weight = 22784.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.109401 restraints weight = 14834.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.110337 restraints weight = 10526.785| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.5886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 34734 Z= 0.171 Angle : 0.673 9.428 47379 Z= 0.348 Chirality : 0.047 0.219 5322 Planarity : 0.005 0.063 6150 Dihedral : 6.097 59.941 4820 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.03 % Allowed : 0.66 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.87 (0.13), residues: 4158 helix: -2.59 (0.21), residues: 425 sheet: 0.35 (0.16), residues: 969 loop : -0.57 (0.12), residues: 2764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG c 222 TYR 0.034 0.002 TYR s 105 PHE 0.028 0.002 PHE c 13 TRP 0.052 0.002 TRP b 227 HIS 0.007 0.001 HIS c 96 Details of bonding type rmsd covalent geometry : bond 0.00394 (34734) covalent geometry : angle 0.67306 (47379) hydrogen bonds : bond 0.03820 ( 900) hydrogen bonds : angle 5.98390 ( 2583) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1414 residues out of total 3659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1413 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN b 272 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASN l 69 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 43 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8140 (mt-10) REVERT: a 118 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8156 (mt-10) REVERT: a 120 PHE cc_start: 0.8533 (m-10) cc_final: 0.8020 (m-10) REVERT: a 126 ASP cc_start: 0.8932 (m-30) cc_final: 0.8608 (m-30) REVERT: a 171 GLN cc_start: 0.8526 (mt0) cc_final: 0.8148 (mt0) REVERT: a 205 ASP cc_start: 0.7574 (t70) cc_final: 0.7014 (t0) REVERT: a 241 ASN cc_start: 0.7606 (t0) cc_final: 0.7395 (t0) REVERT: a 264 TRP cc_start: 0.9266 (m-90) cc_final: 0.8826 (m-90) REVERT: b 16 ILE cc_start: 0.8727 (mt) cc_final: 0.8466 (mt) REVERT: b 84 ASP cc_start: 0.8276 (t70) cc_final: 0.7331 (t70) REVERT: b 96 MET cc_start: 0.9035 (tpt) cc_final: 0.8443 (tpt) REVERT: b 103 ARG cc_start: 0.8664 (ttt-90) cc_final: 0.8248 (ttt-90) REVERT: b 130 PHE cc_start: 0.8457 (t80) cc_final: 0.8148 (t80) REVERT: b 223 LYS cc_start: 0.9078 (mtmt) cc_final: 0.8706 (mttp) REVERT: b 249 ILE cc_start: 0.9067 (mt) cc_final: 0.8789 (mm) REVERT: b 266 ILE cc_start: 0.8955 (tp) cc_final: 0.8523 (tp) REVERT: c 43 MET cc_start: 0.9430 (mmm) cc_final: 0.8916 (mmm) REVERT: c 62 VAL cc_start: 0.9494 (p) cc_final: 0.9271 (p) REVERT: c 65 MET cc_start: 0.8336 (mmp) cc_final: 0.7546 (mmp) REVERT: c 67 MET cc_start: 0.8806 (ptm) cc_final: 0.8377 (ptm) REVERT: c 69 GLN cc_start: 0.8309 (mt0) cc_final: 0.8040 (mp10) REVERT: c 82 PHE cc_start: 0.8808 (p90) cc_final: 0.8475 (p90) REVERT: c 93 ARG cc_start: 0.8408 (mtm180) cc_final: 0.7923 (mtm-85) REVERT: c 207 MET cc_start: 0.8954 (pmm) cc_final: 0.8558 (pmm) REVERT: e 33 SER cc_start: 0.8413 (t) cc_final: 0.7362 (t) REVERT: e 35 GLU cc_start: 0.8874 (mp0) cc_final: 0.8148 (mp0) REVERT: e 57 GLU cc_start: 0.5150 (mp0) cc_final: 0.4531 (mp0) REVERT: e 91 SER cc_start: 0.8729 (p) cc_final: 0.8317 (m) REVERT: e 122 TYR cc_start: 0.9160 (m-80) cc_final: 0.8877 (m-10) REVERT: e 128 GLU cc_start: 0.7704 (tt0) cc_final: 0.7344 (tt0) REVERT: e 257 LYS cc_start: 0.9124 (ttpt) cc_final: 0.8867 (ttpp) REVERT: f 15 GLN cc_start: 0.7570 (tt0) cc_final: 0.7135 (pt0) REVERT: f 55 GLU cc_start: 0.8305 (pp20) cc_final: 0.7895 (pp20) REVERT: f 70 SER cc_start: 0.8699 (m) cc_final: 0.8451 (p) REVERT: f 84 ASP cc_start: 0.8541 (t0) cc_final: 0.6446 (t0) REVERT: f 126 LEU cc_start: 0.9414 (mt) cc_final: 0.8933 (mt) REVERT: f 127 ILE cc_start: 0.9223 (mp) cc_final: 0.8851 (mt) REVERT: f 129 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8151 (mm-30) REVERT: f 149 ASN cc_start: 0.8495 (m110) cc_final: 0.8251 (t0) REVERT: f 199 ASN cc_start: 0.8837 (t0) cc_final: 0.8528 (t0) REVERT: f 221 MET cc_start: 0.9018 (mmm) cc_final: 0.8649 (mmm) REVERT: f 249 ILE cc_start: 0.9049 (mm) cc_final: 0.8623 (mm) REVERT: g 2 LEU cc_start: 0.9386 (tp) cc_final: 0.9183 (tp) REVERT: g 11 ASN cc_start: 0.8946 (m-40) cc_final: 0.8667 (m-40) REVERT: g 12 GLN cc_start: 0.8861 (pp30) cc_final: 0.8115 (pp30) REVERT: g 44 MET cc_start: 0.8929 (mmm) cc_final: 0.8361 (mmp) REVERT: g 68 TYR cc_start: 0.9112 (m-10) cc_final: 0.8900 (m-10) REVERT: g 101 GLU cc_start: 0.8509 (mm-30) cc_final: 0.7748 (mm-30) REVERT: g 112 SER cc_start: 0.8904 (m) cc_final: 0.7925 (p) REVERT: g 163 CYS cc_start: 0.8815 (p) cc_final: 0.8130 (p) REVERT: g 169 TRP cc_start: 0.9081 (t-100) cc_final: 0.8099 (t-100) REVERT: g 181 ASP cc_start: 0.7389 (t0) cc_final: 0.7091 (t0) REVERT: g 216 CYS cc_start: 0.8361 (m) cc_final: 0.7918 (m) REVERT: h 9 LYS cc_start: 0.9055 (ttmm) cc_final: 0.8852 (ttpp) REVERT: i 120 PHE cc_start: 0.9120 (m-80) cc_final: 0.8864 (m-10) REVERT: i 146 ARG cc_start: 0.8353 (mmm160) cc_final: 0.7907 (mmp-170) REVERT: i 151 GLN cc_start: 0.9373 (tt0) cc_final: 0.8863 (tt0) REVERT: i 154 TYR cc_start: 0.9243 (t80) cc_final: 0.8852 (t80) REVERT: i 250 THR cc_start: 0.7936 (m) cc_final: 0.7652 (m) REVERT: i 264 TRP cc_start: 0.9158 (m-90) cc_final: 0.8677 (m-90) REVERT: j 23 ILE cc_start: 0.8198 (tp) cc_final: 0.7943 (tt) REVERT: j 60 SER cc_start: 0.9027 (m) cc_final: 0.8359 (p) REVERT: j 81 LYS cc_start: 0.8247 (mptt) cc_final: 0.7732 (mmtp) REVERT: j 109 HIS cc_start: 0.8254 (t-90) cc_final: 0.7815 (t-90) REVERT: j 129 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8383 (mm-30) REVERT: j 179 TYR cc_start: 0.6321 (t80) cc_final: 0.6053 (t80) REVERT: j 198 ILE cc_start: 0.9468 (mt) cc_final: 0.9174 (tt) REVERT: j 232 LEU cc_start: 0.9157 (mp) cc_final: 0.8956 (mp) REVERT: j 260 PHE cc_start: 0.9077 (m-80) cc_final: 0.8765 (m-80) REVERT: k 27 ASN cc_start: 0.8777 (m110) cc_final: 0.8573 (m110) REVERT: k 29 ASP cc_start: 0.9173 (t0) cc_final: 0.8843 (t0) REVERT: k 36 ILE cc_start: 0.9336 (mt) cc_final: 0.9013 (mt) REVERT: k 43 MET cc_start: 0.8901 (mmm) cc_final: 0.8405 (mmm) REVERT: k 69 GLN cc_start: 0.8875 (mt0) cc_final: 0.8413 (mt0) REVERT: k 93 ARG cc_start: 0.9190 (mpp80) cc_final: 0.8782 (mtt180) REVERT: k 112 SER cc_start: 0.8817 (m) cc_final: 0.7980 (p) REVERT: k 188 PHE cc_start: 0.8988 (m-80) cc_final: 0.8522 (m-80) REVERT: k 216 CYS cc_start: 0.8488 (m) cc_final: 0.7483 (m) REVERT: k 226 ASP cc_start: 0.8474 (m-30) cc_final: 0.8077 (m-30) REVERT: l 25 ILE cc_start: 0.8703 (mm) cc_final: 0.8430 (mm) REVERT: l 38 SER cc_start: 0.9652 (m) cc_final: 0.9292 (t) REVERT: m 34 GLN cc_start: 0.8448 (pm20) cc_final: 0.7350 (tm-30) REVERT: m 49 GLN cc_start: 0.8362 (mm110) cc_final: 0.8135 (mm110) REVERT: m 105 ILE cc_start: 0.9246 (mm) cc_final: 0.8840 (tp) REVERT: m 118 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8549 (mt-10) REVERT: m 129 MET cc_start: 0.8399 (mmm) cc_final: 0.8069 (mtp) REVERT: m 165 TRP cc_start: 0.8328 (p-90) cc_final: 0.7646 (p-90) REVERT: m 281 MET cc_start: 0.8678 (mtt) cc_final: 0.8419 (mtt) REVERT: n 37 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8111 (mt-10) REVERT: n 72 LYS cc_start: 0.7719 (tttm) cc_final: 0.7496 (mtpt) REVERT: n 74 THR cc_start: 0.8287 (p) cc_final: 0.8019 (t) REVERT: n 84 ASP cc_start: 0.8251 (t70) cc_final: 0.7764 (t0) REVERT: n 106 TYR cc_start: 0.8779 (m-80) cc_final: 0.8380 (m-80) REVERT: n 113 ASN cc_start: 0.7717 (m-40) cc_final: 0.7413 (t0) REVERT: n 132 MET cc_start: 0.8801 (mmm) cc_final: 0.8398 (mmm) REVERT: n 178 ASP cc_start: 0.8498 (p0) cc_final: 0.7629 (p0) REVERT: n 183 SER cc_start: 0.9150 (p) cc_final: 0.8607 (t) REVERT: n 198 ILE cc_start: 0.9205 (mt) cc_final: 0.8798 (pt) REVERT: n 199 ASN cc_start: 0.8566 (t0) cc_final: 0.7817 (t0) REVERT: n 212 TYR cc_start: 0.9284 (t80) cc_final: 0.8059 (t80) REVERT: n 214 ASN cc_start: 0.9025 (t0) cc_final: 0.8649 (t0) REVERT: n 216 LEU cc_start: 0.9435 (mt) cc_final: 0.8984 (mt) REVERT: n 217 VAL cc_start: 0.9529 (m) cc_final: 0.9227 (m) REVERT: n 219 ASP cc_start: 0.9002 (t0) cc_final: 0.8680 (t70) REVERT: n 257 CYS cc_start: 0.8717 (m) cc_final: 0.8417 (m) REVERT: n 259 GLU cc_start: 0.8441 (pt0) cc_final: 0.7280 (pm20) REVERT: o 17 ASP cc_start: 0.8851 (t0) cc_final: 0.7084 (t0) REVERT: o 39 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8227 (tm-30) REVERT: o 43 MET cc_start: 0.9015 (mmm) cc_final: 0.8717 (mmm) REVERT: o 48 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7492 (mt-10) REVERT: o 61 LYS cc_start: 0.9013 (mmmt) cc_final: 0.8752 (mmtt) REVERT: o 65 MET cc_start: 0.8365 (tpp) cc_final: 0.7977 (tpp) REVERT: o 70 ILE cc_start: 0.9415 (mt) cc_final: 0.9007 (mt) REVERT: o 97 THR cc_start: 0.9444 (p) cc_final: 0.9018 (p) REVERT: o 120 CYS cc_start: 0.8837 (m) cc_final: 0.8524 (m) REVERT: o 128 LYS cc_start: 0.8640 (mmmt) cc_final: 0.8109 (mmmt) REVERT: o 154 ILE cc_start: 0.8461 (mm) cc_final: 0.7540 (pt) REVERT: o 185 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6931 (mm-30) REVERT: o 191 CYS cc_start: 0.9015 (m) cc_final: 0.8547 (m) REVERT: o 216 CYS cc_start: 0.7903 (m) cc_final: 0.7120 (m) REVERT: o 218 ASP cc_start: 0.8828 (p0) cc_final: 0.8560 (p0) REVERT: o 223 LEU cc_start: 0.8283 (tp) cc_final: 0.8019 (tp) REVERT: q 23 GLN cc_start: 0.8392 (tp40) cc_final: 0.8149 (tp-100) REVERT: q 54 ASP cc_start: 0.8366 (m-30) cc_final: 0.8108 (m-30) REVERT: q 83 THR cc_start: 0.8929 (t) cc_final: 0.8304 (m) REVERT: q 90 SER cc_start: 0.8795 (t) cc_final: 0.8475 (t) REVERT: q 95 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8056 (mm-30) REVERT: q 98 LYS cc_start: 0.9034 (mtpt) cc_final: 0.8683 (mtpt) REVERT: q 109 ASP cc_start: 0.7858 (m-30) cc_final: 0.7637 (m-30) REVERT: q 112 GLN cc_start: 0.7511 (tt0) cc_final: 0.7174 (tt0) REVERT: q 118 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8088 (mt-10) REVERT: q 148 GLN cc_start: 0.8572 (mm110) cc_final: 0.8248 (mm110) REVERT: q 175 ASN cc_start: 0.8898 (m-40) cc_final: 0.8085 (m-40) REVERT: q 189 MET cc_start: 0.8370 (ptt) cc_final: 0.8041 (ptm) REVERT: q 198 ASN cc_start: 0.9456 (m110) cc_final: 0.9014 (m-40) REVERT: q 202 HIS cc_start: 0.8471 (m-70) cc_final: 0.7924 (m90) REVERT: q 209 ARG cc_start: 0.8114 (pmt-80) cc_final: 0.7715 (ptt90) REVERT: q 212 LEU cc_start: 0.8858 (pt) cc_final: 0.8522 (pt) REVERT: q 264 TRP cc_start: 0.9153 (m-90) cc_final: 0.8714 (m-90) REVERT: q 286 ILE cc_start: 0.9139 (pt) cc_final: 0.8779 (mt) REVERT: q 293 ASP cc_start: 0.8288 (m-30) cc_final: 0.8078 (t0) REVERT: r 55 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7581 (pm20) REVERT: r 122 LEU cc_start: 0.9548 (mt) cc_final: 0.9280 (mt) REVERT: r 170 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7966 (tp30) REVERT: r 178 ASP cc_start: 0.9557 (p0) cc_final: 0.8971 (p0) REVERT: r 196 GLN cc_start: 0.9116 (mm-40) cc_final: 0.8891 (mm-40) REVERT: r 199 ASN cc_start: 0.8727 (t0) cc_final: 0.8388 (t0) REVERT: r 224 HIS cc_start: 0.8831 (t-170) cc_final: 0.8483 (t-170) REVERT: s 8 PRO cc_start: 0.9123 (Cg_exo) cc_final: 0.8794 (Cg_endo) REVERT: s 18 ASP cc_start: 0.7458 (t0) cc_final: 0.7134 (t0) REVERT: s 34 ILE cc_start: 0.9208 (pt) cc_final: 0.8656 (pt) REVERT: s 128 LYS cc_start: 0.8063 (mmtp) cc_final: 0.7807 (mmtp) REVERT: s 209 MET cc_start: 0.8217 (ttm) cc_final: 0.7787 (mtp) REVERT: s 216 CYS cc_start: 0.8982 (m) cc_final: 0.8623 (m) REVERT: s 218 ASP cc_start: 0.8783 (p0) cc_final: 0.8523 (p0) REVERT: s 219 PHE cc_start: 0.9077 (t80) cc_final: 0.8680 (t80) REVERT: s 226 ASP cc_start: 0.7697 (m-30) cc_final: 0.7434 (m-30) REVERT: t 7 THR cc_start: 0.9400 (p) cc_final: 0.9133 (t) outliers start: 1 outliers final: 0 residues processed: 1414 average time/residue: 0.2164 time to fit residues: 503.7631 Evaluate side-chains 1194 residues out of total 3659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1194 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 117 optimal weight: 7.9990 chunk 327 optimal weight: 6.9990 chunk 384 optimal weight: 9.9990 chunk 221 optimal weight: 10.0000 chunk 161 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 139 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 4 GLN e 49 GLN ** e 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 26 ASN i 112 GLN ** j 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 195 HIS j 224 HIS k 229 HIS ** k 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 94 GLN ** n 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 49 GLN ** q 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 162 ASN ** s 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.114926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.103515 restraints weight = 79833.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.106455 restraints weight = 39966.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.108428 restraints weight = 23501.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.109677 restraints weight = 15367.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.110616 restraints weight = 11032.245| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 34734 Z= 0.190 Angle : 0.686 8.970 47379 Z= 0.354 Chirality : 0.047 0.318 5322 Planarity : 0.005 0.068 6150 Dihedral : 6.053 59.094 4820 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.05 % Allowed : 0.41 % Favored : 99.54 % 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: -0.82 (0.13), residues: 4158 helix: -2.52 (0.21), residues: 415 sheet: 0.29 (0.16), residues: 1000 loop : -0.52 (0.12), residues: 2743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG m 209 TYR 0.035 0.002 TYR a 180 PHE 0.028 0.002 PHE a 75 TRP 0.108 0.002 TRP n 227 HIS 0.008 0.002 HIS g 96 Details of bonding type rmsd covalent geometry : bond 0.00443 (34734) covalent geometry : angle 0.68581 (47379) hydrogen bonds : bond 0.03887 ( 900) hydrogen bonds : angle 5.98252 ( 2583) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1383 residues out of total 3659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1381 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN b 272 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASN l 69 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 120 PHE cc_start: 0.8580 (m-10) cc_final: 0.8069 (m-10) REVERT: a 126 ASP cc_start: 0.8957 (m-30) cc_final: 0.8592 (m-30) REVERT: a 130 THR cc_start: 0.9440 (m) cc_final: 0.9210 (p) REVERT: a 171 GLN cc_start: 0.8554 (mt0) cc_final: 0.8164 (mt0) REVERT: a 205 ASP cc_start: 0.7514 (t70) cc_final: 0.6904 (t0) REVERT: a 241 ASN cc_start: 0.7645 (t0) cc_final: 0.7396 (t0) REVERT: a 264 TRP cc_start: 0.9266 (m-90) cc_final: 0.8757 (m-90) REVERT: b 16 ILE cc_start: 0.8757 (mt) cc_final: 0.8433 (mt) REVERT: b 18 LEU cc_start: 0.9451 (mt) cc_final: 0.9240 (mt) REVERT: b 67 GLU cc_start: 0.8557 (tm-30) cc_final: 0.7836 (tm-30) REVERT: b 84 ASP cc_start: 0.8334 (t70) cc_final: 0.7387 (t70) REVERT: b 103 ARG cc_start: 0.8428 (ttt-90) cc_final: 0.8035 (ttt-90) REVERT: b 104 SER cc_start: 0.8593 (p) cc_final: 0.7936 (m) REVERT: b 130 PHE cc_start: 0.8427 (t80) cc_final: 0.8053 (t80) REVERT: b 249 ILE cc_start: 0.9071 (mt) cc_final: 0.8770 (mm) REVERT: b 266 ILE cc_start: 0.8915 (tp) cc_final: 0.8501 (tp) REVERT: c 19 PHE cc_start: 0.9069 (m-10) cc_final: 0.8860 (m-10) REVERT: c 43 MET cc_start: 0.9426 (mmm) cc_final: 0.8898 (mmm) REVERT: c 52 LEU cc_start: 0.9629 (mt) cc_final: 0.9320 (mp) REVERT: c 62 VAL cc_start: 0.9483 (p) cc_final: 0.9279 (p) REVERT: c 65 MET cc_start: 0.8395 (mmp) cc_final: 0.7967 (mmp) REVERT: c 67 MET cc_start: 0.8714 (ptm) cc_final: 0.8368 (ptm) REVERT: c 69 GLN cc_start: 0.8254 (mt0) cc_final: 0.7853 (mp10) REVERT: c 93 ARG cc_start: 0.8408 (mtm180) cc_final: 0.7910 (mtm-85) REVERT: c 159 LEU cc_start: 0.8960 (mt) cc_final: 0.8727 (mt) REVERT: c 163 CYS cc_start: 0.7273 (p) cc_final: 0.6497 (p) REVERT: e 49 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8690 (mm-40) REVERT: e 57 GLU cc_start: 0.5138 (mp0) cc_final: 0.4541 (mp0) REVERT: e 91 SER cc_start: 0.8700 (p) cc_final: 0.8314 (m) REVERT: e 128 GLU cc_start: 0.7680 (tt0) cc_final: 0.7234 (tt0) REVERT: e 191 ILE cc_start: 0.8703 (mt) cc_final: 0.8486 (mt) REVERT: e 257 LYS cc_start: 0.9119 (ttpt) cc_final: 0.8817 (mtpt) REVERT: f 12 ARG cc_start: 0.8065 (ptm160) cc_final: 0.7760 (ptm160) REVERT: f 15 GLN cc_start: 0.7581 (tt0) cc_final: 0.7168 (pt0) REVERT: f 70 SER cc_start: 0.8669 (m) cc_final: 0.8419 (p) REVERT: f 84 ASP cc_start: 0.8552 (t0) cc_final: 0.7879 (t0) REVERT: f 87 LYS cc_start: 0.8924 (pttp) cc_final: 0.8378 (ptpt) REVERT: f 89 MET cc_start: 0.9018 (pmm) cc_final: 0.8817 (pmm) REVERT: f 129 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8150 (mm-30) REVERT: f 149 ASN cc_start: 0.8503 (m110) cc_final: 0.8100 (m-40) REVERT: f 199 ASN cc_start: 0.8860 (t0) cc_final: 0.8519 (t0) REVERT: f 221 MET cc_start: 0.9043 (mmm) cc_final: 0.8672 (mmm) REVERT: f 249 ILE cc_start: 0.9066 (mm) cc_final: 0.8665 (mm) REVERT: g 2 LEU cc_start: 0.9438 (tp) cc_final: 0.9207 (tp) REVERT: g 11 ASN cc_start: 0.9004 (m-40) cc_final: 0.8599 (m-40) REVERT: g 12 GLN cc_start: 0.8883 (pp30) cc_final: 0.8168 (pp30) REVERT: g 44 MET cc_start: 0.8978 (mmm) cc_final: 0.8360 (mmp) REVERT: g 55 MET cc_start: 0.8319 (tpt) cc_final: 0.7593 (tpp) REVERT: g 112 SER cc_start: 0.8894 (m) cc_final: 0.8034 (p) REVERT: g 113 ILE cc_start: 0.9176 (mm) cc_final: 0.8903 (mm) REVERT: g 114 ARG cc_start: 0.8862 (ttm110) cc_final: 0.8075 (ttm170) REVERT: g 163 CYS cc_start: 0.8846 (p) cc_final: 0.8247 (p) REVERT: g 169 TRP cc_start: 0.9026 (t-100) cc_final: 0.8165 (t-100) REVERT: g 216 CYS cc_start: 0.8471 (m) cc_final: 0.7911 (m) REVERT: h 53 PHE cc_start: 0.9044 (m-80) cc_final: 0.8743 (m-80) REVERT: i 120 PHE cc_start: 0.9130 (m-80) cc_final: 0.8837 (m-10) REVERT: i 146 ARG cc_start: 0.8287 (mmm160) cc_final: 0.7871 (mmp-170) REVERT: i 151 GLN cc_start: 0.9377 (tt0) cc_final: 0.8664 (tt0) REVERT: i 154 TYR cc_start: 0.9254 (t80) cc_final: 0.8876 (t80) REVERT: i 250 THR cc_start: 0.7916 (m) cc_final: 0.7659 (m) REVERT: i 264 TRP cc_start: 0.9209 (m-90) cc_final: 0.8678 (m-90) REVERT: j 23 ILE cc_start: 0.8237 (tp) cc_final: 0.7807 (tt) REVERT: j 37 GLU cc_start: 0.8002 (tt0) cc_final: 0.7757 (tt0) REVERT: j 81 LYS cc_start: 0.8521 (mptt) cc_final: 0.8216 (mptt) REVERT: j 84 ASP cc_start: 0.7854 (t70) cc_final: 0.7638 (t0) REVERT: j 109 HIS cc_start: 0.8306 (t-90) cc_final: 0.7529 (t-170) REVERT: j 129 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8439 (mm-30) REVERT: j 179 TYR cc_start: 0.6453 (t80) cc_final: 0.6248 (t80) REVERT: j 195 HIS cc_start: 0.8916 (p-80) cc_final: 0.8525 (p-80) REVERT: j 198 ILE cc_start: 0.9504 (mt) cc_final: 0.9093 (tt) REVERT: j 214 ASN cc_start: 0.9441 (t0) cc_final: 0.9097 (t0) REVERT: j 260 PHE cc_start: 0.9118 (m-80) cc_final: 0.8871 (m-80) REVERT: k 29 ASP cc_start: 0.9195 (t0) cc_final: 0.8843 (t0) REVERT: k 36 ILE cc_start: 0.9265 (mt) cc_final: 0.8880 (mt) REVERT: k 43 MET cc_start: 0.8961 (mmm) cc_final: 0.8030 (mmm) REVERT: k 44 MET cc_start: 0.8352 (mmm) cc_final: 0.7932 (mmm) REVERT: k 64 THR cc_start: 0.7751 (p) cc_final: 0.7508 (p) REVERT: k 73 ASN cc_start: 0.8343 (t0) cc_final: 0.8090 (t0) REVERT: k 93 ARG cc_start: 0.9181 (mpp80) cc_final: 0.8807 (mtt180) REVERT: k 112 SER cc_start: 0.8822 (m) cc_final: 0.7995 (p) REVERT: k 188 PHE cc_start: 0.8995 (m-80) cc_final: 0.8541 (m-80) REVERT: k 216 CYS cc_start: 0.8608 (m) cc_final: 0.7455 (m) REVERT: k 226 ASP cc_start: 0.8473 (m-30) cc_final: 0.8088 (m-30) REVERT: l 25 ILE cc_start: 0.8740 (mm) cc_final: 0.8506 (mm) REVERT: l 38 SER cc_start: 0.9655 (m) cc_final: 0.9291 (t) REVERT: m 34 GLN cc_start: 0.8471 (pm20) cc_final: 0.7367 (tm-30) REVERT: m 98 LYS cc_start: 0.9165 (mptt) cc_final: 0.8926 (mmtm) REVERT: m 110 THR cc_start: 0.8195 (p) cc_final: 0.7991 (p) REVERT: m 118 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8447 (mt-10) REVERT: m 127 LEU cc_start: 0.9183 (tp) cc_final: 0.8609 (tp) REVERT: m 165 TRP cc_start: 0.8499 (p-90) cc_final: 0.7681 (p-90) REVERT: m 281 MET cc_start: 0.8726 (mtt) cc_final: 0.8472 (mtt) REVERT: n 37 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8013 (mt-10) REVERT: n 54 THR cc_start: 0.8533 (m) cc_final: 0.8174 (t) REVERT: n 72 LYS cc_start: 0.7751 (tttm) cc_final: 0.7497 (mtpt) REVERT: n 74 THR cc_start: 0.8305 (p) cc_final: 0.8037 (t) REVERT: n 84 ASP cc_start: 0.8178 (t70) cc_final: 0.7573 (t0) REVERT: n 106 TYR cc_start: 0.8344 (m-80) cc_final: 0.8129 (m-80) REVERT: n 113 ASN cc_start: 0.7754 (m-40) cc_final: 0.7469 (t0) REVERT: n 129 GLU cc_start: 0.8512 (mp0) cc_final: 0.8123 (mp0) REVERT: n 132 MET cc_start: 0.8699 (mmm) cc_final: 0.8275 (mmm) REVERT: n 178 ASP cc_start: 0.8544 (p0) cc_final: 0.7717 (p0) REVERT: n 183 SER cc_start: 0.9030 (p) cc_final: 0.8577 (t) REVERT: n 199 ASN cc_start: 0.8575 (t0) cc_final: 0.7799 (t0) REVERT: n 212 TYR cc_start: 0.9134 (t80) cc_final: 0.8029 (t80) REVERT: n 214 ASN cc_start: 0.9112 (t0) cc_final: 0.8705 (t0) REVERT: n 216 LEU cc_start: 0.9407 (mt) cc_final: 0.9076 (mt) REVERT: n 217 VAL cc_start: 0.9501 (m) cc_final: 0.9175 (m) REVERT: n 257 CYS cc_start: 0.8631 (m) cc_final: 0.8400 (m) REVERT: n 259 GLU cc_start: 0.8507 (pt0) cc_final: 0.7293 (pm20) REVERT: o 17 ASP cc_start: 0.8679 (t0) cc_final: 0.6917 (t0) REVERT: o 39 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8267 (tm-30) REVERT: o 43 MET cc_start: 0.9017 (mmm) cc_final: 0.8700 (mmm) REVERT: o 48 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7520 (mt-10) REVERT: o 61 LYS cc_start: 0.8984 (mmmt) cc_final: 0.8763 (mmtt) REVERT: o 65 MET cc_start: 0.8357 (tpp) cc_final: 0.8091 (tpp) REVERT: o 70 ILE cc_start: 0.9395 (mt) cc_final: 0.9094 (mt) REVERT: o 72 LEU cc_start: 0.8574 (mt) cc_final: 0.7726 (mt) REVERT: o 97 THR cc_start: 0.9430 (p) cc_final: 0.8981 (p) REVERT: o 101 GLU cc_start: 0.8548 (mp0) cc_final: 0.8208 (mp0) REVERT: o 120 CYS cc_start: 0.8817 (m) cc_final: 0.8508 (m) REVERT: o 128 LYS cc_start: 0.8603 (mmmt) cc_final: 0.8062 (mmmt) REVERT: o 154 ILE cc_start: 0.8517 (mm) cc_final: 0.7615 (pt) REVERT: o 185 GLU cc_start: 0.7325 (mm-30) cc_final: 0.6909 (mm-30) REVERT: o 191 CYS cc_start: 0.9005 (m) cc_final: 0.8529 (m) REVERT: o 209 MET cc_start: 0.8236 (ptt) cc_final: 0.7894 (ptt) REVERT: o 216 CYS cc_start: 0.7856 (m) cc_final: 0.7057 (m) REVERT: o 218 ASP cc_start: 0.8877 (p0) cc_final: 0.8634 (p0) REVERT: q 23 GLN cc_start: 0.8304 (tp40) cc_final: 0.8057 (tp-100) REVERT: q 83 THR cc_start: 0.8939 (t) cc_final: 0.8292 (m) REVERT: q 90 SER cc_start: 0.8795 (t) cc_final: 0.8525 (t) REVERT: q 101 ASN cc_start: 0.7430 (m110) cc_final: 0.6989 (m110) REVERT: q 112 GLN cc_start: 0.7698 (tt0) cc_final: 0.7365 (tt0) REVERT: q 118 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8102 (mt-10) REVERT: q 127 LEU cc_start: 0.9354 (tp) cc_final: 0.8512 (tp) REVERT: q 148 GLN cc_start: 0.8637 (mm110) cc_final: 0.8225 (mm110) REVERT: q 165 TRP cc_start: 0.8790 (p-90) cc_final: 0.8323 (p-90) REVERT: q 175 ASN cc_start: 0.8895 (m-40) cc_final: 0.8020 (m-40) REVERT: q 189 MET cc_start: 0.8434 (ptt) cc_final: 0.8143 (ptm) REVERT: q 198 ASN cc_start: 0.9430 (m110) cc_final: 0.9032 (m-40) REVERT: q 202 HIS cc_start: 0.8453 (m-70) cc_final: 0.7989 (m90) REVERT: q 209 ARG cc_start: 0.8076 (pmt-80) cc_final: 0.7818 (ptt90) REVERT: q 264 TRP cc_start: 0.9194 (m-90) cc_final: 0.8747 (m-90) REVERT: q 274 TYR cc_start: 0.8422 (m-80) cc_final: 0.8107 (m-10) REVERT: q 286 ILE cc_start: 0.9231 (pt) cc_final: 0.8710 (mt) REVERT: r 55 GLU cc_start: 0.8431 (mm-30) cc_final: 0.7559 (pm20) REVERT: r 122 LEU cc_start: 0.9533 (mt) cc_final: 0.9253 (mt) REVERT: r 170 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8000 (tp30) REVERT: r 178 ASP cc_start: 0.9535 (p0) cc_final: 0.9053 (p0) REVERT: r 196 GLN cc_start: 0.9132 (mm-40) cc_final: 0.8903 (mm-40) REVERT: r 199 ASN cc_start: 0.8680 (t0) cc_final: 0.8342 (t0) REVERT: r 224 HIS cc_start: 0.8924 (t-170) cc_final: 0.8573 (t-170) REVERT: r 259 GLU cc_start: 0.9084 (tp30) cc_final: 0.8858 (tp30) REVERT: s 8 PRO cc_start: 0.9068 (Cg_exo) cc_final: 0.8730 (Cg_endo) REVERT: s 17 ASP cc_start: 0.7988 (t70) cc_final: 0.7704 (t70) REVERT: s 18 ASP cc_start: 0.7626 (t0) cc_final: 0.7406 (t0) REVERT: s 34 ILE cc_start: 0.9186 (pt) cc_final: 0.8643 (pt) REVERT: s 84 LEU cc_start: 0.9192 (mt) cc_final: 0.8980 (mp) REVERT: s 128 LYS cc_start: 0.8102 (mmtp) cc_final: 0.7822 (mmtp) REVERT: s 175 TYR cc_start: 0.9238 (m-80) cc_final: 0.8710 (m-80) REVERT: s 209 MET cc_start: 0.8317 (ttm) cc_final: 0.7851 (mtp) REVERT: s 216 CYS cc_start: 0.8951 (m) cc_final: 0.8659 (m) REVERT: s 218 ASP cc_start: 0.8756 (p0) cc_final: 0.8511 (p0) REVERT: s 219 PHE cc_start: 0.9019 (t80) cc_final: 0.8683 (t80) REVERT: s 226 ASP cc_start: 0.7793 (m-30) cc_final: 0.7494 (m-30) REVERT: t 7 THR cc_start: 0.9401 (p) cc_final: 0.9137 (t) outliers start: 2 outliers final: 1 residues processed: 1383 average time/residue: 0.2089 time to fit residues: 475.5697 Evaluate side-chains 1173 residues out of total 3659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1171 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 330 optimal weight: 9.9990 chunk 422 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 129 optimal weight: 6.9990 chunk 381 optimal weight: 20.0000 chunk 357 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 193 optimal weight: 0.0270 chunk 88 optimal weight: 7.9990 chunk 143 optimal weight: 20.0000 overall best weight: 5.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 43 ASN ** g 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 112 GLN ** i 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 99 HIS j 224 HIS j 226 ASN ** k 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 13 HIS ** p 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 49 GLN ** q 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 232 GLN t 31 ASN t 39 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.113476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.102174 restraints weight = 79977.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.105066 restraints weight = 40407.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.107027 restraints weight = 23926.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.108317 restraints weight = 15665.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.109187 restraints weight = 11119.504| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.6104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 34734 Z= 0.228 Angle : 0.708 9.490 47379 Z= 0.366 Chirality : 0.047 0.260 5322 Planarity : 0.006 0.065 6150 Dihedral : 6.106 58.064 4820 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: -0.96 (0.13), residues: 4158 helix: -2.62 (0.20), residues: 434 sheet: 0.21 (0.16), residues: 1001 loop : -0.61 (0.12), residues: 2723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG s 222 TYR 0.032 0.002 TYR a 154 PHE 0.041 0.002 PHE f 130 TRP 0.084 0.002 TRP n 227 HIS 0.024 0.002 HIS o 108 Details of bonding type rmsd covalent geometry : bond 0.00523 (34734) covalent geometry : angle 0.70850 (47379) hydrogen bonds : bond 0.03949 ( 900) hydrogen bonds : angle 6.03094 ( 2583) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8374.95 seconds wall clock time: 145 minutes 7.54 seconds (8707.54 seconds total)