Starting phenix.real_space_refine on Fri Mar 6 20:07:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tqs_26068/03_2026/7tqs_26068.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tqs_26068/03_2026/7tqs_26068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tqs_26068/03_2026/7tqs_26068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tqs_26068/03_2026/7tqs_26068.map" model { file = "/net/cci-nas-00/data/ceres_data/7tqs_26068/03_2026/7tqs_26068.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tqs_26068/03_2026/7tqs_26068.cif" } resolution = 3.9 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 211 5.16 5 C 21600 2.51 5 N 5788 2.21 5 O 6514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 34113 Number of models: 1 Model: "" Number of chains: 27 Chain: "L" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 480 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'TRANS': 95} Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 96 Planarities with less than four sites: {'UNK:plan-1': 96} Unresolved non-hydrogen planarities: 96 Chain: "H" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 530 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'TRANS': 105} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 318 Unresolved non-hydrogen dihedrals: 106 Planarities with less than four sites: {'UNK:plan-1': 106} Unresolved non-hydrogen planarities: 106 Chain: "a" 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: "b" Number of atoms: 2044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2044 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 16, 'TRANS': 246} Chain: "c" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1857 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 20, 'TRANS': 219} 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: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2226 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 20, 'TRANS': 262} Chain: "f" Number of atoms: 2036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2036 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 16, 'TRANS': 246} Chain breaks: 1 Chain: "g" 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: "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: 2030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2030 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 244} Chain breaks: 1 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: "k" 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: "l" 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: "m" 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: "n" Number of atoms: 2013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2013 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 242} Chain breaks: 1 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: "o" 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: "p" 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: "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: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2006 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 241} Chain breaks: 1 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: "s" 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: "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: 7.66, per 1000 atoms: 0.22 Number of scatterers: 34113 At special positions: 0 Unit cell: (126.445, 178.695, 157.795, 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 211 16.00 O 6514 8.00 N 5788 7.00 C 21600 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 1.2 seconds 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8382 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 66 sheets defined 15.9% alpha, 35.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'H' and resid 57 through 61 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 93 through 98 removed outlier: 4.308A pdb=" N LYS a 97 " --> pdb=" O SER a 93 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS a 98 " --> pdb=" O GLY a 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 93 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 229 Processing helix chain 'a' and resid 282 through 286 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 removed outlier: 3.855A pdb=" N LEU b 86 " --> pdb=" O LEU b 82 " (cutoff:3.500A) No H-bonds generated for '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: 4.029A pdb=" N ARG b 153 " --> pdb=" O PRO b 150 " (cutoff:3.500A) Processing helix chain 'b' and resid 186 through 193 removed outlier: 4.380A 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 93 through 96 removed outlier: 3.504A pdb=" N HIS c 96 " --> pdb=" O ARG c 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 93 through 96' Processing helix chain 'c' and resid 97 through 104 Processing helix chain 'c' and resid 143 through 148 Processing helix chain 'c' and resid 181 through 185 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 removed outlier: 3.757A pdb=" N VAL e 55 " --> pdb=" O ILE e 51 " (cutoff:3.500A) Processing helix chain 'e' and resid 71 through 76 Processing helix chain 'e' and resid 92 through 98 removed outlier: 4.882A pdb=" N LYS e 97 " --> pdb=" O GLY e 94 " (cutoff:3.500A) Processing helix chain 'e' and resid 110 through 118 Processing helix chain 'e' and resid 167 through 172 Processing helix chain 'e' and resid 225 through 230 Processing helix chain 'e' and resid 282 through 286 removed outlier: 4.034A pdb=" N ILE e 286 " --> pdb=" O SER e 283 " (cutoff:3.500A) 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 removed outlier: 3.803A pdb=" N LEU f 86 " --> pdb=" O LEU f 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 82 through 86' Processing helix chain 'f' and resid 91 through 98 Processing helix chain 'f' and resid 150 through 154 removed outlier: 3.877A pdb=" N ARG f 153 " --> pdb=" O PRO f 150 " (cutoff:3.500A) Processing helix chain 'f' and resid 168 through 172 removed outlier: 3.737A pdb=" N ARG f 172 " --> pdb=" O SER f 169 " (cutoff:3.500A) Processing helix chain 'f' and resid 186 through 193 removed outlier: 4.523A 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 93 through 96 removed outlier: 3.999A pdb=" N HIS g 96 " --> pdb=" O ARG g 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 93 through 96' Processing helix chain 'g' and resid 97 through 104 Processing helix chain 'g' and resid 143 through 148 Processing helix chain 'h' and resid 35 through 39 Processing helix chain 'h' and resid 50 through 55 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 92 through 98 removed outlier: 4.995A pdb=" N LYS i 97 " --> pdb=" O GLY i 94 " (cutoff:3.500A) Processing helix chain 'i' and resid 110 through 118 Processing helix chain 'i' and resid 167 through 172 Processing helix chain 'i' and resid 225 through 230 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 43 through 47 Processing helix chain 'j' and resid 56 through 61 Processing helix chain 'j' and resid 82 through 86 Processing helix chain 'j' and resid 87 through 89 No H-bonds generated for 'chain 'j' and resid 87 through 89' Processing helix chain 'j' and resid 92 through 99 Processing helix chain 'j' and resid 144 through 149 Processing helix chain 'j' and resid 186 through 193 removed outlier: 4.280A 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 'k' and resid 181 through 185 Processing helix chain 'l' and resid 22 through 24 No H-bonds generated for 'chain 'l' and resid 22 through 24' Processing helix chain 'l' and resid 35 through 39 Processing helix chain 'l' and resid 50 through 55 Processing helix chain 'm' and resid 51 through 55 Processing helix chain 'm' and resid 71 through 76 Processing helix chain 'm' and resid 92 through 98 removed outlier: 4.634A pdb=" N LYS m 97 " --> pdb=" O GLY m 94 " (cutoff:3.500A) Processing helix chain 'm' and resid 110 through 118 removed outlier: 4.384A pdb=" N LYS m 116 " --> pdb=" O GLN m 112 " (cutoff:3.500A) 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 43 through 47 removed outlier: 3.950A pdb=" N ALA n 47 " --> pdb=" O ASP n 44 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 60 Processing helix chain 'n' and resid 82 through 86 removed outlier: 3.882A 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 150 through 154 removed outlier: 4.223A pdb=" N ARG n 153 " --> pdb=" O PRO n 150 " (cutoff:3.500A) Processing helix chain 'n' and resid 169 through 173 removed outlier: 4.013A pdb=" N ARG n 172 " --> pdb=" O SER n 169 " (cutoff:3.500A) Processing helix chain 'n' and resid 186 through 193 removed outlier: 4.155A 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 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 41 through 45 Processing helix chain 'q' and resid 51 through 55 Processing helix chain 'q' and resid 71 through 76 Processing helix chain 'q' and resid 94 through 99 removed outlier: 3.664A pdb=" N LYS q 98 " --> pdb=" O GLY q 94 " (cutoff:3.500A) Processing helix chain 'q' and resid 110 through 118 Processing helix chain 'q' and resid 167 through 172 Processing helix chain 'q' and resid 220 through 224 Processing helix chain 'q' and resid 225 through 230 removed outlier: 3.858A pdb=" N ILE q 229 " --> pdb=" O GLY q 225 " (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 98 Processing helix chain 'r' and resid 144 through 149 Processing helix chain 'r' and resid 150 through 154 removed outlier: 4.174A pdb=" N ARG r 153 " --> pdb=" O PRO r 150 " (cutoff:3.500A) Processing helix chain 'r' and resid 186 through 193 removed outlier: 4.292A pdb=" N PHE r 191 " --> pdb=" O GLY r 188 " (cutoff:3.500A) Processing helix chain 's' and resid 42 through 49 Processing helix chain 's' and resid 64 through 69 Processing helix chain 's' and resid 93 through 96 Processing helix chain 's' and resid 97 through 104 Processing helix chain 's' and resid 143 through 148 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 23 through 24 Processing sheet with id=AA2, first strand: chain 'L' and resid 44 through 46 Processing sheet with id=AA3, first strand: chain 'H' and resid 7 through 8 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 53 through 55 removed outlier: 5.297A pdb=" N UNK H 43 " --> pdb=" O UNK H 39 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N UNK H 39 " --> pdb=" O UNK H 43 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N UNK H 45 " --> pdb=" O UNK H 37 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N UNK H 37 " --> pdb=" O UNK H 45 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N UNK H 47 " --> pdb=" O UNK H 35 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 39 through 40 Processing sheet with id=AA7, first strand: chain 'a' and resid 39 through 40 Processing sheet with id=AA8, first strand: chain 'a' and resid 80 through 83 removed outlier: 6.545A pdb=" N VAL a 254 " --> pdb=" O VAL a 82 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE a 261 " --> pdb=" O ARG a 124 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG a 124 " --> pdb=" O ILE a 261 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N CYS a 263 " --> pdb=" O TYR a 122 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TYR a 122 " --> pdb=" O CYS a 263 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'a' and resid 87 through 89 removed outlier: 4.296A pdb=" N ILE a 261 " --> pdb=" O ARG a 124 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG a 124 " --> pdb=" O ILE a 261 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N CYS a 263 " --> pdb=" O TYR a 122 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TYR a 122 " --> pdb=" O CYS a 263 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'a' and resid 100 through 104 Processing sheet with id=AB2, first strand: chain 'b' and resid 14 through 18 Processing sheet with id=AB3, first strand: chain 'b' and resid 32 through 33 removed outlier: 6.576A pdb=" N ILE b 32 " --> pdb=" O VAL b 209 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N HIS b 99 " --> pdb=" O GLY b 262 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLY b 262 " --> pdb=" O HIS b 99 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU b 101 " --> pdb=" O PHE b 260 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N PHE b 260 " --> pdb=" O LEU b 101 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ARG b 103 " --> pdb=" O THR b 258 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR b 258 " --> pdb=" O ARG b 103 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'b' and resid 32 through 33 removed outlier: 6.576A pdb=" N ILE b 32 " --> pdb=" O VAL b 209 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N HIS b 99 " --> pdb=" O GLY b 262 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLY b 262 " --> pdb=" O HIS b 99 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU b 101 " --> pdb=" O PHE b 260 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N PHE b 260 " --> pdb=" O LEU b 101 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ARG b 103 " --> pdb=" O THR b 258 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR b 258 " --> pdb=" O ARG b 103 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'b' and resid 155 through 156 removed outlier: 6.294A pdb=" N ALA b 121 " --> pdb=" O LEU b 234 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N GLN b 119 " --> pdb=" O PRO b 236 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'c' and resid 2 through 6 removed outlier: 7.695A pdb=" N THR g 4 " --> pdb=" O PRO c 3 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N MET c 5 " --> pdb=" O THR g 4 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ASN g 6 " --> pdb=" O MET c 5 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N THR k 4 " --> pdb=" O PRO g 3 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N MET g 5 " --> pdb=" O THR k 4 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ASN k 6 " --> pdb=" O MET g 5 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N THR o 4 " --> pdb=" O PRO k 3 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N MET k 5 " --> pdb=" O THR o 4 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ASN o 6 " --> pdb=" O MET k 5 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N THR s 4 " --> pdb=" O PRO o 3 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N MET o 5 " --> pdb=" O THR s 4 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ASN s 6 " --> pdb=" O MET o 5 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'c' and resid 13 through 14 Processing sheet with id=AB8, first strand: chain 'c' and resid 82 through 85 removed outlier: 4.012A pdb=" N PHE c 82 " --> pdb=" O CYS c 191 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'c' and resid 176 through 177 Processing sheet with id=AC1, first strand: chain 'd' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'e' and resid 39 through 40 Processing sheet with id=AC3, first strand: chain 'e' and resid 39 through 40 Processing sheet with id=AC4, first strand: chain 'e' and resid 80 through 89 removed outlier: 6.671A pdb=" N VAL e 254 " --> pdb=" O VAL e 82 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE e 84 " --> pdb=" O VAL e 252 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL e 252 " --> pdb=" O ILE e 84 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N SER e 86 " --> pdb=" O THR e 250 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR e 250 " --> pdb=" O SER e 86 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR e 88 " --> pdb=" O ILE e 248 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE e 248 " --> pdb=" O THR e 88 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE e 261 " --> pdb=" O ARG e 124 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG e 124 " --> pdb=" O ILE e 261 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N CYS e 263 " --> pdb=" O TYR e 122 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TYR e 122 " --> pdb=" O CYS e 263 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N CYS e 265 " --> pdb=" O PHE e 120 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N PHE e 120 " --> pdb=" O CYS e 265 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'e' and resid 188 through 191 removed outlier: 4.854A pdb=" N PHE e 120 " --> pdb=" O CYS e 265 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N CYS e 265 " --> pdb=" O PHE e 120 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TYR e 122 " --> pdb=" O CYS e 263 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N CYS e 263 " --> pdb=" O TYR e 122 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG e 124 " --> pdb=" O ILE e 261 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE e 261 " --> pdb=" O ARG e 124 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N CYS e 263 " --> pdb=" O VAL g 40 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'e' and resid 100 through 104 Processing sheet with id=AC7, first strand: chain 'f' and resid 14 through 18 Processing sheet with id=AC8, first strand: chain 'f' and resid 32 through 33 removed outlier: 6.395A pdb=" N ILE f 32 " --> pdb=" O VAL f 209 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N HIS f 99 " --> pdb=" O GLY f 262 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLY f 262 " --> pdb=" O HIS f 99 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU f 101 " --> pdb=" O PHE f 260 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N PHE f 260 " --> pdb=" O LEU f 101 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG f 103 " --> pdb=" O THR f 258 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N THR f 258 " --> pdb=" O ARG f 103 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'f' and resid 32 through 33 removed outlier: 6.395A pdb=" N ILE f 32 " --> pdb=" O VAL f 209 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N HIS f 99 " --> pdb=" O GLY f 262 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLY f 262 " --> pdb=" O HIS f 99 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU f 101 " --> pdb=" O PHE f 260 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N PHE f 260 " --> pdb=" O LEU f 101 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG f 103 " --> pdb=" O THR f 258 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N THR f 258 " --> pdb=" O ARG f 103 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'f' and resid 155 through 156 removed outlier: 6.385A pdb=" N ALA f 121 " --> pdb=" O LEU f 234 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N GLN f 119 " --> pdb=" O PRO f 236 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'g' and resid 82 through 85 removed outlier: 3.679A pdb=" N PHE g 82 " --> pdb=" O CYS g 191 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'g' and resid 108 through 109 Processing sheet with id=AD4, first strand: chain 'h' and resid 4 through 7 Processing sheet with id=AD5, first strand: chain 'i' and resid 80 through 89 removed outlier: 6.566A pdb=" N VAL i 254 " --> pdb=" O VAL i 82 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE i 84 " --> pdb=" O VAL i 252 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N VAL i 252 " --> pdb=" O ILE i 84 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER i 86 " --> pdb=" O THR i 250 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR i 250 " --> pdb=" O SER i 86 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR i 88 " --> pdb=" O ILE i 248 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE i 248 " --> pdb=" O THR i 88 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE i 261 " --> pdb=" O ARG i 124 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ARG i 124 " --> pdb=" O ILE i 261 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N CYS i 263 " --> pdb=" O TYR i 122 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N TYR i 122 " --> pdb=" O CYS i 263 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N CYS i 265 " --> pdb=" O PHE i 120 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N PHE i 120 " --> pdb=" O CYS i 265 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'i' and resid 188 through 191 removed outlier: 4.847A pdb=" N PHE i 120 " --> pdb=" O CYS i 265 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N CYS i 265 " --> pdb=" O PHE i 120 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N TYR i 122 " --> pdb=" O CYS i 263 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N CYS i 263 " --> pdb=" O TYR i 122 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ARG i 124 " --> pdb=" O ILE i 261 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE i 261 " --> pdb=" O ARG i 124 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N CYS i 263 " --> pdb=" O VAL k 40 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'i' and resid 100 through 104 Processing sheet with id=AD8, first strand: chain 'j' and resid 14 through 18 Processing sheet with id=AD9, first strand: chain 'j' and resid 32 through 33 removed outlier: 6.497A pdb=" N ILE j 32 " --> pdb=" O VAL j 209 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU j 101 " --> pdb=" O PHE j 260 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N PHE j 260 " --> pdb=" O LEU j 101 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG j 103 " --> pdb=" O THR j 258 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR j 258 " --> pdb=" O ARG j 103 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'j' and resid 32 through 33 removed outlier: 6.497A pdb=" N ILE j 32 " --> pdb=" O VAL j 209 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU j 101 " --> pdb=" O PHE j 260 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N PHE j 260 " --> pdb=" O LEU j 101 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG j 103 " --> pdb=" O THR j 258 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR j 258 " --> pdb=" O ARG j 103 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'j' and resid 155 through 156 removed outlier: 6.184A pdb=" N ALA j 121 " --> pdb=" O LEU j 234 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N GLN j 119 " --> pdb=" O PRO j 236 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'k' and resid 51 through 52 Processing sheet with id=AE4, first strand: chain 'k' and resid 51 through 52 Processing sheet with id=AE5, first strand: chain 'k' and resid 82 through 85 removed outlier: 3.571A pdb=" N PHE k 82 " --> pdb=" O CYS k 191 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LYS k 128 " --> pdb=" O GLN k 194 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ARG k 196 " --> pdb=" O THR k 126 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR k 126 " --> pdb=" O ARG k 196 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'k' and resid 176 through 177 Processing sheet with id=AE7, first strand: chain 'l' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'm' and resid 39 through 40 Processing sheet with id=AE9, first strand: chain 'm' and resid 39 through 40 Processing sheet with id=AF1, first strand: chain 'm' and resid 80 through 89 removed outlier: 6.732A pdb=" N VAL m 254 " --> pdb=" O VAL m 82 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE m 84 " --> pdb=" O VAL m 252 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL m 252 " --> pdb=" O ILE m 84 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER m 86 " --> pdb=" O THR m 250 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR m 250 " --> pdb=" O SER m 86 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N THR m 88 " --> pdb=" O ILE m 248 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE m 248 " --> pdb=" O THR m 88 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE m 261 " --> pdb=" O ARG m 124 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG m 124 " --> pdb=" O ILE m 261 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N CYS m 263 " --> pdb=" O TYR m 122 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N TYR m 122 " --> pdb=" O CYS m 263 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'm' and resid 80 through 89 removed outlier: 6.732A pdb=" N VAL m 254 " --> pdb=" O VAL m 82 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE m 84 " --> pdb=" O VAL m 252 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL m 252 " --> pdb=" O ILE m 84 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER m 86 " --> pdb=" O THR m 250 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR m 250 " --> pdb=" O SER m 86 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N THR m 88 " --> pdb=" O ILE m 248 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE m 248 " --> pdb=" O THR m 88 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE m 261 " --> pdb=" O ARG m 124 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG m 124 " --> pdb=" O ILE m 261 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N CYS m 263 " --> pdb=" O TYR m 122 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N TYR m 122 " --> pdb=" O CYS m 263 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'm' and resid 100 through 104 Processing sheet with id=AF4, first strand: chain 'n' and resid 14 through 18 Processing sheet with id=AF5, first strand: chain 'n' and resid 32 through 33 removed outlier: 6.850A pdb=" N ILE n 32 " --> pdb=" O VAL n 209 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N HIS n 99 " --> pdb=" O GLY n 262 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLY n 262 " --> pdb=" O HIS n 99 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU n 101 " --> pdb=" O PHE n 260 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N PHE n 260 " --> pdb=" O LEU n 101 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ARG n 103 " --> pdb=" O THR n 258 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N THR n 258 " --> pdb=" O ARG n 103 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'n' and resid 32 through 33 removed outlier: 6.850A pdb=" N ILE n 32 " --> pdb=" O VAL n 209 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N HIS n 99 " --> pdb=" O GLY n 262 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLY n 262 " --> pdb=" O HIS n 99 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU n 101 " --> pdb=" O PHE n 260 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N PHE n 260 " --> pdb=" O LEU n 101 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ARG n 103 " --> pdb=" O THR n 258 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N THR n 258 " --> pdb=" O ARG n 103 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'n' and resid 155 through 156 removed outlier: 6.257A pdb=" N ALA n 121 " --> pdb=" O LEU n 234 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N GLN n 119 " --> pdb=" O PRO n 236 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'o' and resid 82 through 85 removed outlier: 3.680A pdb=" N PHE o 82 " --> pdb=" O CYS o 191 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LYS o 128 " --> pdb=" O GLN o 194 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG o 196 " --> pdb=" O THR o 126 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR o 126 " --> pdb=" O ARG o 196 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'o' and resid 176 through 177 Processing sheet with id=AG1, first strand: chain 'p' and resid 4 through 7 Processing sheet with id=AG2, first strand: chain 'q' and resid 39 through 40 Processing sheet with id=AG3, first strand: chain 'q' and resid 39 through 40 Processing sheet with id=AG4, first strand: chain 'q' and resid 80 through 89 removed outlier: 6.623A pdb=" N VAL q 254 " --> pdb=" O VAL q 82 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE q 84 " --> pdb=" O VAL q 252 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL q 252 " --> pdb=" O ILE q 84 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER q 86 " --> pdb=" O THR q 250 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR q 250 " --> pdb=" O SER q 86 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N THR q 88 " --> pdb=" O ILE q 248 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE q 248 " --> pdb=" O THR q 88 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE q 261 " --> pdb=" O ARG q 124 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ARG q 124 " --> pdb=" O ILE q 261 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N CYS q 263 " --> pdb=" O TYR q 122 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N TYR q 122 " --> pdb=" O CYS q 263 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'q' and resid 80 through 89 removed outlier: 6.623A pdb=" N VAL q 254 " --> pdb=" O VAL q 82 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE q 84 " --> pdb=" O VAL q 252 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL q 252 " --> pdb=" O ILE q 84 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER q 86 " --> pdb=" O THR q 250 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR q 250 " --> pdb=" O SER q 86 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N THR q 88 " --> pdb=" O ILE q 248 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE q 248 " --> pdb=" O THR q 88 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE q 261 " --> pdb=" O ARG q 124 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ARG q 124 " --> pdb=" O ILE q 261 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N CYS q 263 " --> pdb=" O TYR q 122 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N TYR q 122 " --> pdb=" O CYS q 263 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'r' and resid 14 through 18 Processing sheet with id=AG7, first strand: chain 'r' and resid 28 through 33 removed outlier: 5.504A pdb=" N ALA r 28 " --> pdb=" O SER r 205 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N THR r 207 " --> pdb=" O ALA r 28 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN r 30 " --> pdb=" O THR r 207 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N VAL r 209 " --> pdb=" O ASN r 30 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE r 32 " --> pdb=" O VAL r 209 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N HIS r 99 " --> pdb=" O GLY r 262 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLY r 262 " --> pdb=" O HIS r 99 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU r 101 " --> pdb=" O PHE r 260 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N PHE r 260 " --> pdb=" O LEU r 101 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ARG r 103 " --> pdb=" O THR r 258 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR r 258 " --> pdb=" O ARG r 103 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'r' and resid 28 through 33 removed outlier: 5.504A pdb=" N ALA r 28 " --> pdb=" O SER r 205 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N THR r 207 " --> pdb=" O ALA r 28 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN r 30 " --> pdb=" O THR r 207 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N VAL r 209 " --> pdb=" O ASN r 30 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE r 32 " --> pdb=" O VAL r 209 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N HIS r 99 " --> pdb=" O GLY r 262 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLY r 262 " --> pdb=" O HIS r 99 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU r 101 " --> pdb=" O PHE r 260 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N PHE r 260 " --> pdb=" O LEU r 101 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ARG r 103 " --> pdb=" O THR r 258 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR r 258 " --> pdb=" O ARG r 103 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'r' and resid 155 through 156 removed outlier: 6.221A pdb=" N ALA r 121 " --> pdb=" O LEU r 234 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N GLN r 119 " --> pdb=" O PRO r 236 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 's' and resid 82 through 85 removed outlier: 3.614A pdb=" N PHE s 82 " --> pdb=" O CYS s 191 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LYS s 128 " --> pdb=" O GLN s 194 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ARG s 196 " --> pdb=" O THR s 126 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N THR s 126 " --> pdb=" O ARG s 196 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 's' and resid 176 through 177 Processing sheet with id=AH3, first strand: chain 't' and resid 4 through 7 1128 hydrogen bonds defined for protein. 2631 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: 6.65 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5819 1.30 - 1.44: 10161 1.44 - 1.57: 18578 1.57 - 1.71: 78 1.71 - 1.85: 339 Bond restraints: 34975 Sorted by residual: bond pdb=" CB HIS j 224 " pdb=" CG HIS j 224 " ideal model delta sigma weight residual 1.497 1.380 0.117 1.40e-02 5.10e+03 7.01e+01 bond pdb=" CB HIS r 224 " pdb=" CG HIS r 224 " ideal model delta sigma weight residual 1.497 1.395 0.102 1.40e-02 5.10e+03 5.31e+01 bond pdb=" CB PHE i 100 " pdb=" CG PHE i 100 " ideal model delta sigma weight residual 1.502 1.336 0.166 2.30e-02 1.89e+03 5.23e+01 bond pdb=" CB PHE q 100 " pdb=" CG PHE q 100 " ideal model delta sigma weight residual 1.502 1.340 0.162 2.30e-02 1.89e+03 4.96e+01 bond pdb=" CB HIS f 224 " pdb=" CG HIS f 224 " ideal model delta sigma weight residual 1.497 1.400 0.097 1.40e-02 5.10e+03 4.77e+01 ... (remaining 34970 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 39945 2.32 - 4.63: 6494 4.63 - 6.95: 1085 6.95 - 9.26: 157 9.26 - 11.58: 30 Bond angle restraints: 47711 Sorted by residual: angle pdb=" N VAL g 221 " pdb=" CA VAL g 221 " pdb=" C VAL g 221 " ideal model delta sigma weight residual 113.10 124.42 -11.32 9.70e-01 1.06e+00 1.36e+02 angle pdb=" C PRO o 135 " pdb=" N PRO o 136 " pdb=" CA PRO o 136 " ideal model delta sigma weight residual 120.21 129.62 -9.41 9.60e-01 1.09e+00 9.60e+01 angle pdb=" C PRO k 135 " pdb=" N PRO k 136 " pdb=" CA PRO k 136 " ideal model delta sigma weight residual 120.21 129.17 -8.96 9.60e-01 1.09e+00 8.71e+01 angle pdb=" C PRO s 135 " pdb=" N PRO s 136 " pdb=" CA PRO s 136 " ideal model delta sigma weight residual 120.21 129.13 -8.92 9.60e-01 1.09e+00 8.64e+01 angle pdb=" N LEU b 234 " pdb=" CA LEU b 234 " pdb=" C LEU b 234 " ideal model delta sigma weight residual 113.88 102.52 11.36 1.23e+00 6.61e-01 8.54e+01 ... (remaining 47706 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 20162 17.72 - 35.44: 519 35.44 - 53.16: 113 53.16 - 70.88: 51 70.88 - 88.60: 14 Dihedral angle restraints: 20859 sinusoidal: 7864 harmonic: 12995 Sorted by residual: dihedral pdb=" CA ASN l 15 " pdb=" C ASN l 15 " pdb=" N GLN l 16 " pdb=" CA GLN l 16 " ideal model delta harmonic sigma weight residual 180.00 157.02 22.98 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" C LEU r 82 " pdb=" N LEU r 82 " pdb=" CA LEU r 82 " pdb=" CB LEU r 82 " ideal model delta harmonic sigma weight residual -122.60 -133.44 10.84 0 2.50e+00 1.60e-01 1.88e+01 dihedral pdb=" CA ASP s 218 " pdb=" C ASP s 218 " pdb=" N PHE s 219 " pdb=" CA PHE s 219 " ideal model delta harmonic sigma weight residual 180.00 -160.91 -19.09 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 20856 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 3941 0.103 - 0.207: 1241 0.207 - 0.310: 152 0.310 - 0.414: 21 0.414 - 0.517: 8 Chirality restraints: 5363 Sorted by residual: chirality pdb=" CB VAL i 16 " pdb=" CA VAL i 16 " pdb=" CG1 VAL i 16 " pdb=" CG2 VAL i 16 " both_signs ideal model delta sigma weight residual False -2.63 -3.15 0.52 2.00e-01 2.50e+01 6.69e+00 chirality pdb=" CA TRP a 264 " pdb=" N TRP a 264 " pdb=" C TRP a 264 " pdb=" CB TRP a 264 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.42e+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 -3.13 0.50 2.00e-01 2.50e+01 6.30e+00 ... (remaining 5360 not shown) Planarity restraints: 6193 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR i 168 " -0.050 2.00e-02 2.50e+03 3.26e-02 2.13e+01 pdb=" CG TYR i 168 " 0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR i 168 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR i 168 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR i 168 " 0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR i 168 " 0.024 2.00e-02 2.50e+03 pdb=" CZ TYR i 168 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR i 168 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR b 179 " -0.054 2.00e-02 2.50e+03 3.15e-02 1.98e+01 pdb=" CG TYR b 179 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 TYR b 179 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR b 179 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR b 179 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR b 179 " 0.020 2.00e-02 2.50e+03 pdb=" CZ TYR b 179 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR b 179 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR e 255 " 0.051 2.00e-02 2.50e+03 3.05e-02 1.86e+01 pdb=" CG TYR e 255 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR e 255 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR e 255 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR e 255 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR e 255 " -0.023 2.00e-02 2.50e+03 pdb=" CZ TYR e 255 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR e 255 " 0.051 2.00e-02 2.50e+03 ... (remaining 6190 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 13147 2.87 - 3.38: 31983 3.38 - 3.89: 60789 3.89 - 4.39: 73811 4.39 - 4.90: 117677 Nonbonded interactions: 297407 Sorted by model distance: nonbonded pdb=" N ASP q 221 " pdb=" OD1 ASP q 221 " model vdw 2.363 3.120 nonbonded pdb=" N LEU b 234 " pdb=" N ALA b 235 " model vdw 2.408 2.560 nonbonded pdb=" NZ LYS i 257 " pdb=" O ASP k 17 " model vdw 2.409 3.120 nonbonded pdb=" O ALA d 41 " pdb=" NZ LYS t 34 " model vdw 2.409 3.120 nonbonded pdb=" N ASP k 218 " pdb=" N PHE k 219 " model vdw 2.411 2.560 ... (remaining 297402 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 13 through 108) selection = chain 'L' } ncs_group { reference = chain 'a' selection = (chain 'e' and resid 17 through 300) selection = (chain 'i' and resid 17 through 300) selection = (chain 'm' and resid 17 through 300) selection = (chain 'q' and resid 17 through 300) } ncs_group { reference = (chain 'b' and (resid 11 through 163 or resid 169 through 271)) selection = (chain 'f' and (resid 11 through 163 or resid 169 through 271)) selection = (chain 'j' and (resid 11 through 163 or resid 169 through 271)) selection = (chain 'n' and (resid 11 through 163 or resid 169 through 271)) selection = (chain 'r' and (resid 11 through 163 or resid 169 through 271)) } ncs_group { reference = (chain 'c' and resid 1 through 234) selection = (chain 'g' and resid 1 through 234) selection = chain 'k' selection = (chain 'o' and resid 1 through 234) selection = (chain 's' and resid 1 through 234) } ncs_group { reference = chain 'd' selection = chain 'h' selection = chain 'l' selection = chain 'p' selection = chain 't' } 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: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 30.860 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.090 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: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 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 0.166 34975 Z= 1.143 Angle : 1.804 11.580 47711 Z= 1.232 Chirality : 0.096 0.517 5363 Planarity : 0.009 0.052 6193 Dihedral : 9.827 88.605 12477 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.02 % 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: 0.58 (0.12), residues: 4201 helix: -2.79 (0.20), residues: 377 sheet: 1.63 (0.15), residues: 1032 loop : 0.46 (0.11), residues: 2792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG a 275 TYR 0.060 0.009 TYR i 168 PHE 0.030 0.006 PHE o 82 TRP 0.047 0.007 TRP r 227 HIS 0.013 0.003 HIS q 246 Details of bonding type rmsd covalent geometry : bond 0.02119 (34975) covalent geometry : angle 1.80408 (47711) hydrogen bonds : bond 0.15500 ( 924) hydrogen bonds : angle 8.60762 ( 2631) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1664 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1664 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN n 272 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN r 272 " (corrupted residue). Skipping it. REVERT: a 29 SER cc_start: 0.8666 (t) cc_final: 0.8350 (m) REVERT: a 47 SER cc_start: 0.9172 (m) cc_final: 0.8946 (p) REVERT: a 49 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8312 (mm110) REVERT: a 105 ILE cc_start: 0.9599 (mt) cc_final: 0.9356 (mt) REVERT: a 106 THR cc_start: 0.9279 (t) cc_final: 0.8955 (m) REVERT: a 110 THR cc_start: 0.8741 (p) cc_final: 0.8293 (p) REVERT: a 174 SER cc_start: 0.9349 (m) cc_final: 0.8890 (t) REVERT: a 175 ASN cc_start: 0.8950 (m-40) cc_final: 0.8644 (m-40) REVERT: a 179 PHE cc_start: 0.9022 (m-80) cc_final: 0.8794 (m-10) REVERT: a 205 ASP cc_start: 0.9055 (t0) cc_final: 0.8828 (t70) REVERT: a 267 ARG cc_start: 0.8815 (mtp85) cc_final: 0.8591 (mtt-85) REVERT: a 277 GLU cc_start: 0.7380 (mp0) cc_final: 0.7056 (mp0) REVERT: b 41 TYR cc_start: 0.8595 (m-80) cc_final: 0.8167 (m-10) REVERT: b 97 TYR cc_start: 0.8614 (m-80) cc_final: 0.8376 (m-80) REVERT: b 104 SER cc_start: 0.9120 (t) cc_final: 0.8584 (p) REVERT: b 106 TYR cc_start: 0.9099 (m-80) cc_final: 0.8384 (m-80) REVERT: b 142 TYR cc_start: 0.7909 (t80) cc_final: 0.7700 (t80) REVERT: b 149 ASN cc_start: 0.8889 (m-40) cc_final: 0.8222 (m-40) REVERT: b 170 GLU cc_start: 0.7665 (mm-30) cc_final: 0.6636 (mm-30) REVERT: b 183 SER cc_start: 0.9111 (p) cc_final: 0.8756 (t) REVERT: b 193 TYR cc_start: 0.9072 (m-80) cc_final: 0.8860 (m-10) REVERT: b 198 ILE cc_start: 0.9456 (mt) cc_final: 0.9211 (tt) REVERT: b 249 ILE cc_start: 0.9584 (mt) cc_final: 0.9342 (mm) REVERT: c 10 SER cc_start: 0.9413 (t) cc_final: 0.9036 (p) REVERT: c 21 SER cc_start: 0.9442 (p) cc_final: 0.8994 (m) REVERT: c 56 ASN cc_start: 0.9550 (t0) cc_final: 0.9349 (t0) REVERT: c 112 SER cc_start: 0.9560 (m) cc_final: 0.9254 (p) REVERT: c 146 ASP cc_start: 0.8907 (m-30) cc_final: 0.8689 (m-30) REVERT: c 226 ASP cc_start: 0.8482 (m-30) cc_final: 0.7828 (m-30) REVERT: c 235 LEU cc_start: 0.8517 (mt) cc_final: 0.8200 (mt) REVERT: d 21 ASN cc_start: 0.7786 (p0) cc_final: 0.7203 (p0) REVERT: e 51 ILE cc_start: 0.8917 (pt) cc_final: 0.8596 (pt) REVERT: e 163 SER cc_start: 0.8982 (p) cc_final: 0.8693 (p) REVERT: e 174 SER cc_start: 0.8993 (m) cc_final: 0.8573 (t) REVERT: e 182 TYR cc_start: 0.8653 (t80) cc_final: 0.8393 (t80) REVERT: e 204 TYR cc_start: 0.8645 (t80) cc_final: 0.8399 (t80) REVERT: e 205 ASP cc_start: 0.9146 (t0) cc_final: 0.8721 (t0) REVERT: e 229 ILE cc_start: 0.9062 (tt) cc_final: 0.8696 (tt) REVERT: e 282 ILE cc_start: 0.8007 (tp) cc_final: 0.7769 (pt) REVERT: f 13 VAL cc_start: 0.9581 (t) cc_final: 0.9345 (p) REVERT: f 87 LYS cc_start: 0.9084 (pttp) cc_final: 0.8651 (pttp) REVERT: f 122 LEU cc_start: 0.9410 (mt) cc_final: 0.9145 (mt) REVERT: f 145 TYR cc_start: 0.9071 (t80) cc_final: 0.8776 (t80) REVERT: g 6 ASN cc_start: 0.9067 (m-40) cc_final: 0.8864 (m-40) REVERT: g 42 ASN cc_start: 0.8498 (t0) cc_final: 0.8236 (t0) REVERT: g 74 ASP cc_start: 0.8720 (p0) cc_final: 0.8409 (p0) REVERT: g 85 SER cc_start: 0.8509 (t) cc_final: 0.8110 (m) REVERT: g 106 TYR cc_start: 0.9407 (m-80) cc_final: 0.8325 (m-80) REVERT: g 112 SER cc_start: 0.9114 (m) cc_final: 0.8353 (p) REVERT: g 156 ASP cc_start: 0.8286 (t0) cc_final: 0.7669 (p0) REVERT: g 172 ASN cc_start: 0.9271 (p0) cc_final: 0.8938 (p0) REVERT: g 198 VAL cc_start: 0.9584 (t) cc_final: 0.9323 (p) REVERT: g 216 CYS cc_start: 0.8751 (m) cc_final: 0.7730 (m) REVERT: h 27 TYR cc_start: 0.9154 (p90) cc_final: 0.8821 (p90) REVERT: i 98 LYS cc_start: 0.8998 (mttt) cc_final: 0.8710 (mtpp) REVERT: i 101 ASN cc_start: 0.8468 (t0) cc_final: 0.8213 (t0) REVERT: i 105 ILE cc_start: 0.9092 (mm) cc_final: 0.8788 (mm) REVERT: i 107 TYR cc_start: 0.9038 (p90) cc_final: 0.8729 (p90) REVERT: i 127 LEU cc_start: 0.9299 (tp) cc_final: 0.8520 (tp) REVERT: i 166 ASP cc_start: 0.7404 (p0) cc_final: 0.5746 (p0) REVERT: i 204 TYR cc_start: 0.8719 (t80) cc_final: 0.8186 (t80) REVERT: i 267 ARG cc_start: 0.9220 (mtp85) cc_final: 0.8768 (mtp180) REVERT: i 286 ILE cc_start: 0.8981 (pt) cc_final: 0.8711 (pt) REVERT: j 84 ASP cc_start: 0.8270 (t70) cc_final: 0.7695 (t70) REVERT: j 91 MET cc_start: 0.8322 (mmm) cc_final: 0.8102 (mmt) REVERT: j 131 VAL cc_start: 0.9448 (t) cc_final: 0.9005 (p) REVERT: j 137 GLU cc_start: 0.7294 (pm20) cc_final: 0.6850 (tp30) REVERT: j 179 TYR cc_start: 0.8460 (p90) cc_final: 0.8064 (p90) REVERT: j 192 VAL cc_start: 0.9457 (m) cc_final: 0.9250 (t) REVERT: j 223 LYS cc_start: 0.9233 (mtmt) cc_final: 0.8601 (mtmm) REVERT: j 227 TRP cc_start: 0.8856 (m100) cc_final: 0.8566 (m100) REVERT: j 259 GLU cc_start: 0.7692 (pt0) cc_final: 0.7188 (pt0) REVERT: j 265 ASN cc_start: 0.7796 (t0) cc_final: 0.7530 (t0) REVERT: k 2 LEU cc_start: 0.9267 (tp) cc_final: 0.9016 (tp) REVERT: k 42 ASN cc_start: 0.8708 (t0) cc_final: 0.8217 (t0) REVERT: k 55 MET cc_start: 0.9114 (tpp) cc_final: 0.8788 (tpt) REVERT: k 65 MET cc_start: 0.8380 (tpp) cc_final: 0.8150 (tpp) REVERT: k 107 THR cc_start: 0.9403 (p) cc_final: 0.9104 (t) REVERT: k 119 PHE cc_start: 0.8631 (t80) cc_final: 0.8159 (t80) REVERT: k 128 LYS cc_start: 0.8385 (mttm) cc_final: 0.7897 (mtmt) REVERT: k 155 TRP cc_start: 0.8381 (t60) cc_final: 0.7919 (t60) REVERT: k 169 TRP cc_start: 0.8774 (t-100) cc_final: 0.8125 (t-100) REVERT: k 178 CYS cc_start: 0.8403 (m) cc_final: 0.8153 (m) REVERT: k 183 PHE cc_start: 0.8169 (t80) cc_final: 0.7945 (t80) REVERT: k 196 ARG cc_start: 0.7584 (ttp80) cc_final: 0.6821 (ptt-90) REVERT: k 216 CYS cc_start: 0.8599 (m) cc_final: 0.8340 (m) REVERT: l 53 PHE cc_start: 0.9102 (m-80) cc_final: 0.8870 (m-80) REVERT: m 54 ASP cc_start: 0.8327 (m-30) cc_final: 0.7996 (m-30) REVERT: m 95 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7866 (mm-30) REVERT: m 105 ILE cc_start: 0.9163 (mt) cc_final: 0.8798 (mt) REVERT: m 127 LEU cc_start: 0.8930 (tp) cc_final: 0.8476 (tp) REVERT: m 166 ASP cc_start: 0.8803 (p0) cc_final: 0.8010 (p0) REVERT: m 205 ASP cc_start: 0.8639 (t0) cc_final: 0.7946 (t70) REVERT: m 216 ASN cc_start: 0.6964 (t0) cc_final: 0.6481 (m-40) REVERT: m 218 ASP cc_start: 0.7770 (m-30) cc_final: 0.7449 (m-30) REVERT: n 13 VAL cc_start: 0.9589 (t) cc_final: 0.9230 (p) REVERT: n 33 VAL cc_start: 0.9639 (t) cc_final: 0.9412 (m) REVERT: n 60 SER cc_start: 0.9406 (m) cc_final: 0.8980 (p) REVERT: n 71 TRP cc_start: 0.8653 (t60) cc_final: 0.8450 (t60) REVERT: n 129 GLU cc_start: 0.8406 (tp30) cc_final: 0.8052 (tp30) REVERT: n 180 LEU cc_start: 0.9073 (mt) cc_final: 0.8854 (mt) REVERT: n 213 VAL cc_start: 0.9786 (t) cc_final: 0.9439 (p) REVERT: n 216 LEU cc_start: 0.9249 (mt) cc_final: 0.8862 (mt) REVERT: n 224 HIS cc_start: 0.8734 (t-90) cc_final: 0.8235 (t-90) REVERT: o 87 SER cc_start: 0.9241 (m) cc_final: 0.8873 (p) REVERT: o 98 MET cc_start: 0.8622 (tpp) cc_final: 0.8421 (tpp) REVERT: o 128 LYS cc_start: 0.7191 (mttt) cc_final: 0.6956 (mttt) REVERT: o 153 ILE cc_start: 0.9226 (tt) cc_final: 0.8971 (tp) REVERT: p 46 LEU cc_start: 0.8599 (mt) cc_final: 0.8395 (mt) REVERT: p 64 THR cc_start: 0.9140 (p) cc_final: 0.8107 (p) REVERT: q 47 SER cc_start: 0.9110 (m) cc_final: 0.8871 (p) REVERT: q 62 VAL cc_start: 0.9606 (t) cc_final: 0.9346 (p) REVERT: q 105 ILE cc_start: 0.9088 (mt) cc_final: 0.8750 (mt) REVERT: q 109 ASP cc_start: 0.7807 (m-30) cc_final: 0.7448 (m-30) REVERT: q 126 ASP cc_start: 0.7917 (m-30) cc_final: 0.7588 (m-30) REVERT: q 127 LEU cc_start: 0.9435 (tp) cc_final: 0.9158 (tt) REVERT: q 137 TYR cc_start: 0.8886 (m-80) cc_final: 0.8681 (m-10) REVERT: q 165 TRP cc_start: 0.8400 (p-90) cc_final: 0.7189 (p-90) REVERT: q 168 TYR cc_start: 0.8878 (p90) cc_final: 0.8452 (p90) REVERT: q 171 GLN cc_start: 0.8569 (mt0) cc_final: 0.8050 (mt0) REVERT: q 244 ASN cc_start: 0.8648 (m-40) cc_final: 0.8413 (m110) REVERT: q 264 TRP cc_start: 0.9156 (m-90) cc_final: 0.8590 (m100) REVERT: q 274 TYR cc_start: 0.8411 (m-80) cc_final: 0.8124 (m-80) REVERT: q 280 ASP cc_start: 0.8443 (m-30) cc_final: 0.8152 (m-30) REVERT: r 40 THR cc_start: 0.9256 (p) cc_final: 0.8828 (t) REVERT: r 48 ASN cc_start: 0.9057 (t0) cc_final: 0.8812 (t0) REVERT: r 50 VAL cc_start: 0.9514 (m) cc_final: 0.9251 (p) REVERT: r 212 TYR cc_start: 0.8829 (t80) cc_final: 0.8365 (t80) REVERT: r 214 ASN cc_start: 0.9147 (t0) cc_final: 0.8903 (t0) REVERT: s 10 SER cc_start: 0.9560 (m) cc_final: 0.9272 (p) REVERT: s 42 ASN cc_start: 0.8446 (t0) cc_final: 0.8239 (t0) REVERT: s 43 MET cc_start: 0.9307 (mmm) cc_final: 0.8914 (tpp) REVERT: s 50 ASP cc_start: 0.8352 (m-30) cc_final: 0.8092 (m-30) REVERT: s 74 ASP cc_start: 0.8000 (p0) cc_final: 0.7471 (p0) REVERT: s 91 ASP cc_start: 0.8312 (t70) cc_final: 0.7888 (t0) REVERT: s 120 CYS cc_start: 0.8529 (m) cc_final: 0.8320 (m) REVERT: s 146 ASP cc_start: 0.8249 (m-30) cc_final: 0.8016 (m-30) REVERT: s 154 ILE cc_start: 0.9216 (mt) cc_final: 0.8839 (mt) REVERT: s 234 LYS cc_start: 0.8851 (mtmt) cc_final: 0.8421 (mttp) REVERT: t 28 THR cc_start: 0.9308 (m) cc_final: 0.9014 (p) REVERT: t 42 THR cc_start: 0.9125 (p) cc_final: 0.8782 (p) outliers start: 0 outliers final: 0 residues processed: 1664 average time/residue: 0.2118 time to fit residues: 571.3242 Evaluate side-chains 1135 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1135 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 401 optimal weight: 5.9990 chunk 424 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 204 ASN ** c 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 20 GLN ** c 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 13 HIS ** e 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 230 ASN e 249 HIS f 20 ASN ** f 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 56 ASN g 96 HIS h 13 HIS h 21 ASN h 44 GLN i 112 GLN ** i 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 118 HIS j 119 GLN ** k 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 160 GLN ** l 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 ASN m 89 ASN m 151 GLN ** m 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 249 HIS ** n 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 118 HIS n 119 GLN n 226 ASN ** o 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 27 ASN ** o 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 26 ASN p 31 ASN ** q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 184 ASN r 20 ASN ** r 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 4 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.112935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.100220 restraints weight = 65989.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.103217 restraints weight = 31044.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.105234 restraints weight = 17960.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.106570 restraints weight = 11824.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.107497 restraints weight = 8569.172| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 34975 Z= 0.272 Angle : 0.762 10.641 47711 Z= 0.401 Chirality : 0.049 0.240 5363 Planarity : 0.005 0.058 6193 Dihedral : 6.145 54.806 4860 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.69 % Allowed : 12.16 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.06 (0.12), residues: 4201 helix: -2.51 (0.22), residues: 390 sheet: 1.18 (0.15), residues: 1042 loop : 0.04 (0.11), residues: 2769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG g 225 TYR 0.030 0.002 TYR i 154 PHE 0.025 0.002 PHE s 82 TRP 0.024 0.002 TRP q 170 HIS 0.015 0.002 HIS k 96 Details of bonding type rmsd covalent geometry : bond 0.00614 (34975) covalent geometry : angle 0.76191 (47711) hydrogen bonds : bond 0.04608 ( 924) hydrogen bonds : angle 6.48145 ( 2631) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1431 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 1295 time to evaluate : 1.060 Fit side-chains 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 n 272 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN r 272 " (corrupted residue). Skipping it. REVERT: a 43 GLU cc_start: 0.8959 (mp0) cc_final: 0.8692 (mp0) REVERT: a 49 GLN cc_start: 0.8499 (mm-40) cc_final: 0.8146 (mm110) REVERT: a 120 PHE cc_start: 0.9441 (m-80) cc_final: 0.9166 (m-10) REVERT: a 205 ASP cc_start: 0.8715 (t0) cc_final: 0.8323 (t70) REVERT: a 215 GLU cc_start: 0.8715 (mp0) cc_final: 0.8257 (mp0) REVERT: a 277 GLU cc_start: 0.7814 (mp0) cc_final: 0.7306 (mp0) REVERT: b 16 ILE cc_start: 0.9245 (mp) cc_final: 0.8986 (mt) REVERT: b 64 TYR cc_start: 0.8872 (m-80) cc_final: 0.8449 (m-80) REVERT: b 81 LYS cc_start: 0.8788 (mmtt) cc_final: 0.8567 (mmtt) REVERT: b 84 ASP cc_start: 0.8342 (t0) cc_final: 0.7927 (t0) REVERT: b 97 TYR cc_start: 0.8619 (m-80) cc_final: 0.7920 (m-80) REVERT: b 104 SER cc_start: 0.9247 (t) cc_final: 0.8753 (p) REVERT: b 106 TYR cc_start: 0.9139 (m-80) cc_final: 0.7722 (m-80) REVERT: b 173 LYS cc_start: 0.7484 (mttp) cc_final: 0.7187 (mttm) REVERT: b 183 SER cc_start: 0.9368 (p) cc_final: 0.8923 (t) REVERT: b 214 ASN cc_start: 0.9250 (t0) cc_final: 0.8989 (t0) REVERT: b 215 SER cc_start: 0.9463 (p) cc_final: 0.9164 (p) REVERT: c 5 MET cc_start: 0.8757 (ttm) cc_final: 0.8492 (ttt) REVERT: c 17 ASP cc_start: 0.8542 (t70) cc_final: 0.8243 (t70) REVERT: c 101 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8028 (mm-30) REVERT: c 112 SER cc_start: 0.9430 (m) cc_final: 0.9103 (p) REVERT: c 131 LEU cc_start: 0.9033 (tp) cc_final: 0.8626 (tt) REVERT: c 226 ASP cc_start: 0.8561 (m-30) cc_final: 0.8275 (m-30) REVERT: d 5 VAL cc_start: 0.9482 (t) cc_final: 0.9270 (m) REVERT: d 21 ASN cc_start: 0.7469 (p0) cc_final: 0.7070 (p0) REVERT: e 95 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7575 (mm-30) REVERT: e 101 ASN cc_start: 0.8816 (OUTLIER) cc_final: 0.7825 (m-40) REVERT: e 112 GLN cc_start: 0.8685 (mt0) cc_final: 0.8387 (mt0) REVERT: e 167 ASP cc_start: 0.9018 (t0) cc_final: 0.8816 (m-30) REVERT: e 173 SER cc_start: 0.9330 (p) cc_final: 0.8781 (p) REVERT: e 174 SER cc_start: 0.9380 (m) cc_final: 0.8868 (p) REVERT: e 182 TYR cc_start: 0.8974 (t80) cc_final: 0.8457 (t80) REVERT: e 205 ASP cc_start: 0.9052 (t0) cc_final: 0.8577 (t0) REVERT: e 229 ILE cc_start: 0.8998 (tt) cc_final: 0.8562 (tt) REVERT: e 231 ASP cc_start: 0.8245 (t0) cc_final: 0.8033 (t0) REVERT: e 259 LYS cc_start: 0.8954 (ptpt) cc_final: 0.8700 (ttpt) REVERT: e 291 LYS cc_start: 0.8965 (mtpt) cc_final: 0.8624 (mtpp) REVERT: f 101 LEU cc_start: 0.9168 (mt) cc_final: 0.8922 (mt) REVERT: f 145 TYR cc_start: 0.9034 (t80) cc_final: 0.8821 (t80) REVERT: g 44 MET cc_start: 0.8976 (mmm) cc_final: 0.8766 (mmm) REVERT: g 106 TYR cc_start: 0.9527 (m-80) cc_final: 0.9089 (m-80) REVERT: g 112 SER cc_start: 0.8889 (m) cc_final: 0.8033 (p) REVERT: g 154 ILE cc_start: 0.9209 (mm) cc_final: 0.8903 (mm) REVERT: g 156 ASP cc_start: 0.8101 (t0) cc_final: 0.7749 (p0) REVERT: g 194 GLN cc_start: 0.9050 (tp-100) cc_final: 0.8557 (tp40) REVERT: g 216 CYS cc_start: 0.8382 (m) cc_final: 0.7085 (m) REVERT: g 234 LYS cc_start: 0.8590 (pttp) cc_final: 0.8379 (ptpt) REVERT: h 38 SER cc_start: 0.9247 (m) cc_final: 0.8943 (p) REVERT: i 25 THR cc_start: 0.9214 (m) cc_final: 0.8862 (t) REVERT: i 95 GLU cc_start: 0.7323 (mt-10) cc_final: 0.7090 (mt-10) REVERT: i 98 LYS cc_start: 0.8898 (mttt) cc_final: 0.8547 (mtpp) REVERT: i 108 THR cc_start: 0.8505 (p) cc_final: 0.8205 (t) REVERT: i 127 LEU cc_start: 0.9239 (tp) cc_final: 0.9017 (tp) REVERT: i 129 MET cc_start: 0.8915 (mtm) cc_final: 0.8599 (mtm) REVERT: i 204 TYR cc_start: 0.8681 (t80) cc_final: 0.7950 (t80) REVERT: j 91 MET cc_start: 0.8528 (mmm) cc_final: 0.8269 (mmp) REVERT: j 110 VAL cc_start: 0.9626 (t) cc_final: 0.9425 (p) REVERT: j 129 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7519 (mm-30) REVERT: j 137 GLU cc_start: 0.7331 (pm20) cc_final: 0.6980 (pm20) REVERT: j 193 TYR cc_start: 0.8978 (m-80) cc_final: 0.8633 (m-10) REVERT: j 199 ASN cc_start: 0.9072 (t0) cc_final: 0.8730 (t0) REVERT: j 200 LEU cc_start: 0.9036 (mt) cc_final: 0.8773 (mt) REVERT: j 223 LYS cc_start: 0.9062 (mtmt) cc_final: 0.8170 (mtmm) REVERT: k 2 LEU cc_start: 0.9304 (tp) cc_final: 0.9064 (tp) REVERT: k 21 SER cc_start: 0.9672 (p) cc_final: 0.9438 (p) REVERT: k 39 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7899 (tm-30) REVERT: k 44 MET cc_start: 0.8868 (mmm) cc_final: 0.8565 (mmm) REVERT: k 65 MET cc_start: 0.8536 (tpp) cc_final: 0.8278 (tpp) REVERT: k 66 GLU cc_start: 0.9028 (mp0) cc_final: 0.8812 (mp0) REVERT: k 87 SER cc_start: 0.9240 (t) cc_final: 0.8702 (p) REVERT: k 93 ARG cc_start: 0.8605 (mtm180) cc_final: 0.8386 (mtt180) REVERT: k 144 ARG cc_start: 0.8504 (ttm-80) cc_final: 0.8006 (ttm-80) REVERT: k 155 TRP cc_start: 0.8248 (t60) cc_final: 0.7566 (t60) REVERT: k 169 TRP cc_start: 0.8878 (t-100) cc_final: 0.7653 (t-100) REVERT: k 177 ARG cc_start: 0.9010 (ttm110) cc_final: 0.8584 (ttm110) REVERT: k 178 CYS cc_start: 0.8413 (m) cc_final: 0.7483 (m) REVERT: k 194 GLN cc_start: 0.9074 (tp40) cc_final: 0.8335 (tp40) REVERT: k 216 CYS cc_start: 0.8478 (m) cc_final: 0.8006 (m) REVERT: m 105 ILE cc_start: 0.9174 (mt) cc_final: 0.8944 (mt) REVERT: m 166 ASP cc_start: 0.8611 (p0) cc_final: 0.7871 (p0) REVERT: m 204 TYR cc_start: 0.8914 (t80) cc_final: 0.8579 (t80) REVERT: m 205 ASP cc_start: 0.8338 (t0) cc_final: 0.7621 (t0) REVERT: m 209 ARG cc_start: 0.8729 (ttp80) cc_final: 0.7666 (ttp-110) REVERT: m 216 ASN cc_start: 0.7538 (t0) cc_final: 0.7201 (m-40) REVERT: m 218 ASP cc_start: 0.7967 (m-30) cc_final: 0.7402 (m-30) REVERT: n 13 VAL cc_start: 0.9485 (t) cc_final: 0.9184 (p) REVERT: n 40 THR cc_start: 0.8994 (p) cc_final: 0.8577 (t) REVERT: n 41 TYR cc_start: 0.8921 (m-80) cc_final: 0.8694 (m-10) REVERT: n 51 ASP cc_start: 0.8637 (p0) cc_final: 0.7953 (p0) REVERT: n 60 SER cc_start: 0.9565 (m) cc_final: 0.9089 (p) REVERT: n 71 TRP cc_start: 0.8938 (t60) cc_final: 0.8490 (t60) REVERT: n 129 GLU cc_start: 0.8763 (tp30) cc_final: 0.8432 (tp30) REVERT: n 179 TYR cc_start: 0.8481 (p90) cc_final: 0.8219 (p90) REVERT: n 213 VAL cc_start: 0.9796 (t) cc_final: 0.9497 (p) REVERT: n 216 LEU cc_start: 0.9244 (mt) cc_final: 0.8735 (mt) REVERT: n 224 HIS cc_start: 0.8820 (t-90) cc_final: 0.8365 (t-170) REVERT: n 226 ASN cc_start: 0.8809 (OUTLIER) cc_final: 0.8608 (m110) REVERT: o 74 ASP cc_start: 0.8553 (p0) cc_final: 0.8351 (p0) REVERT: o 87 SER cc_start: 0.9104 (m) cc_final: 0.7914 (p) REVERT: o 91 ASP cc_start: 0.7986 (t0) cc_final: 0.7764 (t0) REVERT: o 128 LYS cc_start: 0.6592 (mttt) cc_final: 0.6357 (mttt) REVERT: o 146 ASP cc_start: 0.7889 (m-30) cc_final: 0.7663 (m-30) REVERT: o 175 TYR cc_start: 0.8837 (m-80) cc_final: 0.8351 (m-10) REVERT: o 207 MET cc_start: 0.8534 (ptp) cc_final: 0.8103 (ptp) REVERT: o 226 ASP cc_start: 0.7929 (m-30) cc_final: 0.7498 (m-30) REVERT: o 234 LYS cc_start: 0.7698 (tttt) cc_final: 0.7184 (tttt) REVERT: p 32 TYR cc_start: 0.8876 (m-80) cc_final: 0.8554 (m-80) REVERT: p 48 GLN cc_start: 0.8747 (pm20) cc_final: 0.8240 (pm20) REVERT: q 47 SER cc_start: 0.8939 (m) cc_final: 0.8648 (p) REVERT: q 61 VAL cc_start: 0.9463 (t) cc_final: 0.9217 (p) REVERT: q 62 VAL cc_start: 0.9611 (t) cc_final: 0.9325 (p) REVERT: q 90 SER cc_start: 0.8668 (t) cc_final: 0.8234 (t) REVERT: q 95 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7500 (mt-10) REVERT: q 122 TYR cc_start: 0.9219 (m-80) cc_final: 0.8821 (m-80) REVERT: q 126 ASP cc_start: 0.8076 (m-30) cc_final: 0.7659 (m-30) REVERT: q 137 TYR cc_start: 0.9156 (m-80) cc_final: 0.8895 (m-10) REVERT: q 154 TYR cc_start: 0.9249 (t80) cc_final: 0.8874 (t80) REVERT: q 173 SER cc_start: 0.9321 (m) cc_final: 0.9025 (p) REVERT: q 190 SER cc_start: 0.9531 (m) cc_final: 0.9290 (m) REVERT: q 274 TYR cc_start: 0.8395 (m-80) cc_final: 0.8116 (m-80) REVERT: q 280 ASP cc_start: 0.8499 (m-30) cc_final: 0.8210 (m-30) REVERT: r 48 ASN cc_start: 0.8910 (t0) cc_final: 0.8685 (t0) REVERT: r 50 VAL cc_start: 0.9420 (m) cc_final: 0.9177 (p) REVERT: r 112 CYS cc_start: 0.8028 (t) cc_final: 0.7787 (t) REVERT: r 116 LYS cc_start: 0.8896 (mttt) cc_final: 0.8142 (mtmt) REVERT: r 212 TYR cc_start: 0.8534 (t80) cc_final: 0.8259 (t80) REVERT: r 249 ILE cc_start: 0.9594 (mt) cc_final: 0.9310 (mm) REVERT: s 10 SER cc_start: 0.9442 (m) cc_final: 0.9217 (p) REVERT: s 50 ASP cc_start: 0.8517 (m-30) cc_final: 0.8291 (m-30) REVERT: s 74 ASP cc_start: 0.7962 (p0) cc_final: 0.7686 (p0) REVERT: s 156 ASP cc_start: 0.8652 (t0) cc_final: 0.8217 (t0) REVERT: s 214 SER cc_start: 0.9363 (p) cc_final: 0.9058 (t) REVERT: s 234 LYS cc_start: 0.8816 (mtmt) cc_final: 0.8175 (mttt) REVERT: s 235 LEU cc_start: 0.7930 (tp) cc_final: 0.7700 (tp) REVERT: t 28 THR cc_start: 0.9467 (m) cc_final: 0.9262 (p) outliers start: 136 outliers final: 87 residues processed: 1359 average time/residue: 0.2007 time to fit residues: 449.4725 Evaluate side-chains 1193 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 1104 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 61 VAL Chi-restraints excluded: chain a residue 70 SER Chi-restraints excluded: chain a residue 134 THR Chi-restraints excluded: chain a residue 152 ILE Chi-restraints excluded: chain a residue 250 THR Chi-restraints excluded: chain a residue 282 ILE Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain b residue 202 THR Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain d residue 60 LEU Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 71 CYS Chi-restraints excluded: chain e residue 101 ASN Chi-restraints excluded: chain e residue 104 ASN Chi-restraints excluded: chain e residue 134 THR Chi-restraints excluded: chain e residue 237 VAL Chi-restraints excluded: chain e residue 248 ILE Chi-restraints excluded: chain e residue 293 ASP Chi-restraints excluded: chain f residue 20 ASN Chi-restraints excluded: chain f residue 40 THR Chi-restraints excluded: chain f residue 45 SER Chi-restraints excluded: chain f residue 88 ASP Chi-restraints excluded: chain f residue 112 CYS Chi-restraints excluded: chain f residue 126 LEU Chi-restraints excluded: chain f residue 263 LEU Chi-restraints excluded: chain g residue 56 ASN Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 203 THR Chi-restraints excluded: chain g residue 207 MET Chi-restraints excluded: chain h residue 7 THR Chi-restraints excluded: chain h residue 10 THR Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 88 THR Chi-restraints excluded: chain i residue 251 SER Chi-restraints excluded: chain i residue 296 THR Chi-restraints excluded: chain j residue 38 TRP Chi-restraints excluded: chain j residue 45 SER Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 119 GLN Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 246 GLN Chi-restraints excluded: chain k residue 10 SER Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 223 LEU Chi-restraints excluded: chain k residue 233 SER Chi-restraints excluded: chain l residue 24 THR Chi-restraints excluded: chain l residue 26 ASN Chi-restraints excluded: chain l residue 44 GLN Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 173 SER Chi-restraints excluded: chain m residue 272 VAL Chi-restraints excluded: chain m residue 282 ILE Chi-restraints excluded: chain n residue 54 THR Chi-restraints excluded: chain n residue 84 ASP Chi-restraints excluded: chain n residue 140 THR Chi-restraints excluded: chain n residue 226 ASN Chi-restraints excluded: chain o residue 27 ASN Chi-restraints excluded: chain o residue 30 VAL Chi-restraints excluded: chain o residue 51 THR Chi-restraints excluded: chain o residue 53 ILE Chi-restraints excluded: chain o residue 107 THR Chi-restraints excluded: chain o residue 122 SER Chi-restraints excluded: chain o residue 166 VAL Chi-restraints excluded: chain o residue 190 THR Chi-restraints excluded: chain o residue 198 VAL Chi-restraints excluded: chain p residue 7 THR Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain q residue 36 VAL Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 99 HIS Chi-restraints excluded: chain q residue 100 PHE Chi-restraints excluded: chain q residue 153 MET Chi-restraints excluded: chain q residue 265 CYS Chi-restraints excluded: chain r residue 18 LEU Chi-restraints excluded: chain r residue 25 THR Chi-restraints excluded: chain r residue 51 ASP Chi-restraints excluded: chain r residue 84 ASP Chi-restraints excluded: chain r residue 131 VAL Chi-restraints excluded: chain r residue 192 VAL Chi-restraints excluded: chain r residue 252 THR Chi-restraints excluded: chain s residue 5 MET Chi-restraints excluded: chain s residue 53 ILE Chi-restraints excluded: chain s residue 86 LEU Chi-restraints excluded: chain s residue 189 ILE Chi-restraints excluded: chain s residue 190 THR Chi-restraints excluded: chain s residue 203 THR Chi-restraints excluded: chain t residue 7 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 149 optimal weight: 0.8980 chunk 376 optimal weight: 7.9990 chunk 346 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 174 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 341 optimal weight: 10.0000 chunk 328 optimal weight: 1.9990 chunk 201 optimal weight: 4.9990 chunk 213 optimal weight: 0.0050 overall best weight: 2.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 111 GLN c 11 ASN d 4 GLN ** e 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 112 GLN e 151 GLN e 249 HIS f 20 ASN ** f 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 13 HIS h 21 ASN ** i 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 99 HIS ** j 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 119 GLN ** l 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 ASN ** m 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 119 GLN n 261 ASN ** o 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 27 ASN ** p 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 26 ASN q 101 ASN r 261 ASN ** s 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 4 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.114231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.101500 restraints weight = 65270.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.104538 restraints weight = 30613.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.106501 restraints weight = 17614.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.107841 restraints weight = 11648.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.108777 restraints weight = 8462.881| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 34975 Z= 0.160 Angle : 0.646 9.260 47711 Z= 0.336 Chirality : 0.046 0.233 5363 Planarity : 0.004 0.040 6193 Dihedral : 5.819 53.044 4860 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.47 % Allowed : 16.45 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.06 (0.12), residues: 4201 helix: -2.37 (0.22), residues: 396 sheet: 1.13 (0.15), residues: 1017 loop : -0.09 (0.11), residues: 2788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG c 176 TYR 0.027 0.002 TYR i 154 PHE 0.023 0.002 PHE c 13 TRP 0.018 0.001 TRP o 169 HIS 0.008 0.001 HIS k 96 Details of bonding type rmsd covalent geometry : bond 0.00363 (34975) covalent geometry : angle 0.64593 (47711) hydrogen bonds : bond 0.03904 ( 924) hydrogen bonds : angle 5.98682 ( 2631) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1391 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 1263 time to evaluate : 1.194 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 TARDY: cannot create tardy model for: "GLN n 272 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN r 272 " (corrupted residue). Skipping it. REVERT: a 43 GLU cc_start: 0.8860 (mp0) cc_final: 0.8538 (mp0) REVERT: a 49 GLN cc_start: 0.8508 (mm-40) cc_final: 0.7988 (mm110) REVERT: a 54 ASP cc_start: 0.8627 (m-30) cc_final: 0.8298 (m-30) REVERT: a 205 ASP cc_start: 0.8703 (t0) cc_final: 0.8405 (t70) REVERT: a 215 GLU cc_start: 0.8680 (mp0) cc_final: 0.8279 (mp0) REVERT: a 277 GLU cc_start: 0.7668 (mp0) cc_final: 0.7229 (mp0) REVERT: b 84 ASP cc_start: 0.8259 (t70) cc_final: 0.7706 (t0) REVERT: b 97 TYR cc_start: 0.8540 (m-80) cc_final: 0.8095 (m-10) REVERT: b 104 SER cc_start: 0.9193 (t) cc_final: 0.8845 (p) REVERT: b 106 TYR cc_start: 0.9115 (m-80) cc_final: 0.7757 (m-80) REVERT: b 170 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7893 (mm-30) REVERT: b 183 SER cc_start: 0.9351 (p) cc_final: 0.8973 (t) REVERT: b 246 GLN cc_start: 0.8155 (mt0) cc_final: 0.7749 (mt0) REVERT: c 48 GLU cc_start: 0.9240 (mt-10) cc_final: 0.8852 (mt-10) REVERT: c 56 ASN cc_start: 0.9575 (t0) cc_final: 0.9144 (t0) REVERT: c 74 ASP cc_start: 0.8341 (p0) cc_final: 0.8136 (p0) REVERT: c 112 SER cc_start: 0.9417 (m) cc_final: 0.9111 (p) REVERT: c 131 LEU cc_start: 0.9055 (tp) cc_final: 0.8562 (tt) REVERT: c 165 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8074 (ttm) REVERT: c 226 ASP cc_start: 0.8466 (m-30) cc_final: 0.8244 (m-30) REVERT: d 5 VAL cc_start: 0.9439 (t) cc_final: 0.9229 (m) REVERT: d 21 ASN cc_start: 0.7403 (p0) cc_final: 0.6983 (p0) REVERT: e 95 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7435 (mm-30) REVERT: e 173 SER cc_start: 0.9288 (p) cc_final: 0.8872 (p) REVERT: e 174 SER cc_start: 0.9217 (m) cc_final: 0.8665 (p) REVERT: e 182 TYR cc_start: 0.8895 (t80) cc_final: 0.8453 (t80) REVERT: e 204 TYR cc_start: 0.8747 (t80) cc_final: 0.8010 (t80) REVERT: e 205 ASP cc_start: 0.8979 (t0) cc_final: 0.8511 (t0) REVERT: e 229 ILE cc_start: 0.8942 (tt) cc_final: 0.8472 (tt) REVERT: e 231 ASP cc_start: 0.8232 (t0) cc_final: 0.8015 (t0) REVERT: e 257 LYS cc_start: 0.8970 (ttpp) cc_final: 0.8581 (tttp) REVERT: e 291 LYS cc_start: 0.9018 (mtpt) cc_final: 0.8043 (mtpp) REVERT: f 23 ILE cc_start: 0.9428 (mt) cc_final: 0.9052 (mm) REVERT: f 41 TYR cc_start: 0.8629 (m-80) cc_final: 0.8316 (m-80) REVERT: f 55 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8675 (mt-10) REVERT: f 87 LYS cc_start: 0.8958 (pttp) cc_final: 0.8562 (pttm) REVERT: f 97 TYR cc_start: 0.8725 (m-10) cc_final: 0.8525 (m-10) REVERT: f 116 LYS cc_start: 0.9175 (mttt) cc_final: 0.8822 (mttp) REVERT: f 145 TYR cc_start: 0.9136 (t80) cc_final: 0.8877 (t80) REVERT: f 191 PHE cc_start: 0.9221 (m-80) cc_final: 0.9014 (m-10) REVERT: f 193 TYR cc_start: 0.8973 (m-80) cc_final: 0.8259 (m-10) REVERT: f 196 GLN cc_start: 0.8837 (tt0) cc_final: 0.8025 (tp40) REVERT: f 214 ASN cc_start: 0.9045 (t0) cc_final: 0.8828 (t0) REVERT: f 250 THR cc_start: 0.8606 (m) cc_final: 0.8289 (p) REVERT: g 55 MET cc_start: 0.8804 (mmm) cc_final: 0.8406 (tpp) REVERT: g 98 MET cc_start: 0.9478 (tpt) cc_final: 0.9214 (tpt) REVERT: g 106 TYR cc_start: 0.9543 (m-80) cc_final: 0.9218 (m-80) REVERT: g 112 SER cc_start: 0.8875 (m) cc_final: 0.8495 (p) REVERT: g 154 ILE cc_start: 0.9233 (mm) cc_final: 0.8750 (mm) REVERT: g 156 ASP cc_start: 0.8307 (t0) cc_final: 0.7701 (p0) REVERT: g 194 GLN cc_start: 0.9052 (tp-100) cc_final: 0.8631 (tp40) REVERT: g 216 CYS cc_start: 0.8545 (m) cc_final: 0.7663 (m) REVERT: g 223 LEU cc_start: 0.7389 (mt) cc_final: 0.7178 (mt) REVERT: h 38 SER cc_start: 0.9251 (m) cc_final: 0.8999 (p) REVERT: i 23 GLN cc_start: 0.8992 (tt0) cc_final: 0.8507 (tt0) REVERT: i 25 THR cc_start: 0.9166 (m) cc_final: 0.8884 (t) REVERT: i 78 ARG cc_start: 0.8829 (mmt90) cc_final: 0.8575 (mmt90) REVERT: i 95 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7040 (tt0) REVERT: i 108 THR cc_start: 0.8373 (p) cc_final: 0.8161 (t) REVERT: i 150 TYR cc_start: 0.8443 (m-80) cc_final: 0.8094 (m-80) REVERT: i 154 TYR cc_start: 0.8608 (t80) cc_final: 0.8265 (t80) REVERT: i 168 TYR cc_start: 0.8247 (p90) cc_final: 0.7918 (p90) REVERT: i 200 TYR cc_start: 0.9294 (m-80) cc_final: 0.9031 (m-10) REVERT: i 204 TYR cc_start: 0.8632 (t80) cc_final: 0.8193 (t80) REVERT: j 91 MET cc_start: 0.8582 (mmm) cc_final: 0.8223 (mmp) REVERT: j 110 VAL cc_start: 0.9677 (t) cc_final: 0.9349 (p) REVERT: j 111 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7819 (tt0) REVERT: j 129 GLU cc_start: 0.8274 (mm-30) cc_final: 0.8047 (mm-30) REVERT: j 137 GLU cc_start: 0.7312 (pm20) cc_final: 0.6940 (pm20) REVERT: j 199 ASN cc_start: 0.9037 (t0) cc_final: 0.8582 (t0) REVERT: j 223 LYS cc_start: 0.9014 (mtmt) cc_final: 0.8255 (mttp) REVERT: k 21 SER cc_start: 0.9621 (p) cc_final: 0.9393 (p) REVERT: k 39 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7886 (tm-30) REVERT: k 55 MET cc_start: 0.8996 (tpt) cc_final: 0.8592 (tpt) REVERT: k 69 GLN cc_start: 0.8528 (mp10) cc_final: 0.7941 (mp10) REVERT: k 87 SER cc_start: 0.9234 (t) cc_final: 0.8723 (p) REVERT: k 144 ARG cc_start: 0.8469 (ttm-80) cc_final: 0.7321 (ttm-80) REVERT: k 169 TRP cc_start: 0.8874 (t-100) cc_final: 0.7870 (t-100) REVERT: k 177 ARG cc_start: 0.8931 (ttm110) cc_final: 0.8169 (mtm-85) REVERT: k 178 CYS cc_start: 0.8370 (m) cc_final: 0.7380 (m) REVERT: k 216 CYS cc_start: 0.8387 (m) cc_final: 0.7970 (m) REVERT: m 135 GLU cc_start: 0.8854 (pt0) cc_final: 0.8652 (pt0) REVERT: m 166 ASP cc_start: 0.8557 (p0) cc_final: 0.7864 (p0) REVERT: m 209 ARG cc_start: 0.8763 (ttp80) cc_final: 0.8533 (mtm110) REVERT: m 216 ASN cc_start: 0.7560 (t0) cc_final: 0.7121 (m-40) REVERT: m 218 ASP cc_start: 0.7925 (m-30) cc_final: 0.7429 (m-30) REVERT: n 13 VAL cc_start: 0.9500 (t) cc_final: 0.9232 (p) REVERT: n 46 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7513 (mt-10) REVERT: n 60 SER cc_start: 0.9493 (m) cc_final: 0.9045 (p) REVERT: n 71 TRP cc_start: 0.8797 (t60) cc_final: 0.8506 (t60) REVERT: n 213 VAL cc_start: 0.9700 (t) cc_final: 0.9487 (p) REVERT: n 216 LEU cc_start: 0.9222 (mt) cc_final: 0.8903 (mt) REVERT: n 249 ILE cc_start: 0.9335 (mt) cc_final: 0.9039 (mt) REVERT: o 20 GLN cc_start: 0.8698 (mt0) cc_final: 0.8473 (mt0) REVERT: o 66 GLU cc_start: 0.8777 (mp0) cc_final: 0.8452 (mp0) REVERT: o 87 SER cc_start: 0.9107 (m) cc_final: 0.7912 (p) REVERT: o 99 LEU cc_start: 0.9478 (tp) cc_final: 0.9232 (tt) REVERT: o 144 ARG cc_start: 0.7889 (ttp-170) cc_final: 0.7674 (ttp-170) REVERT: o 169 TRP cc_start: 0.9025 (t-100) cc_final: 0.8117 (t-100) REVERT: o 194 GLN cc_start: 0.8616 (mm-40) cc_final: 0.8379 (tt0) REVERT: o 207 MET cc_start: 0.8491 (ptp) cc_final: 0.8089 (ptp) REVERT: q 47 SER cc_start: 0.8990 (m) cc_final: 0.8710 (p) REVERT: q 66 THR cc_start: 0.8878 (m) cc_final: 0.8112 (p) REVERT: q 88 THR cc_start: 0.8931 (m) cc_final: 0.8119 (m) REVERT: q 90 SER cc_start: 0.8591 (t) cc_final: 0.8214 (t) REVERT: q 126 ASP cc_start: 0.8201 (m-30) cc_final: 0.7685 (m-30) REVERT: q 137 TYR cc_start: 0.9135 (m-80) cc_final: 0.8885 (m-10) REVERT: q 154 TYR cc_start: 0.9297 (t80) cc_final: 0.8974 (t80) REVERT: q 166 ASP cc_start: 0.7858 (p0) cc_final: 0.7587 (p0) REVERT: q 171 GLN cc_start: 0.8356 (mt0) cc_final: 0.8028 (mt0) REVERT: q 173 SER cc_start: 0.9318 (m) cc_final: 0.9004 (p) REVERT: q 190 SER cc_start: 0.9455 (m) cc_final: 0.9218 (m) REVERT: q 200 TYR cc_start: 0.9001 (m-80) cc_final: 0.8754 (m-80) REVERT: q 274 TYR cc_start: 0.8273 (m-80) cc_final: 0.7986 (m-80) REVERT: r 50 VAL cc_start: 0.9322 (m) cc_final: 0.9107 (p) REVERT: r 116 LYS cc_start: 0.8951 (mttt) cc_final: 0.8263 (mtmt) REVERT: r 210 VAL cc_start: 0.9440 (t) cc_final: 0.9131 (p) REVERT: r 212 TYR cc_start: 0.8442 (t80) cc_final: 0.8136 (t80) REVERT: r 249 ILE cc_start: 0.9604 (mt) cc_final: 0.9315 (mm) REVERT: s 10 SER cc_start: 0.9401 (m) cc_final: 0.9192 (p) REVERT: s 50 ASP cc_start: 0.8673 (m-30) cc_final: 0.8389 (m-30) REVERT: s 74 ASP cc_start: 0.7949 (p0) cc_final: 0.7634 (p0) REVERT: s 144 ARG cc_start: 0.9203 (ttm-80) cc_final: 0.8956 (ttm-80) REVERT: s 196 ARG cc_start: 0.8744 (ptt90) cc_final: 0.6513 (pmt170) REVERT: s 214 SER cc_start: 0.9307 (p) cc_final: 0.8999 (t) REVERT: s 234 LYS cc_start: 0.8800 (mtmt) cc_final: 0.8256 (mttt) REVERT: t 28 THR cc_start: 0.9489 (m) cc_final: 0.9272 (p) REVERT: t 62 LEU cc_start: 0.8600 (mp) cc_final: 0.8397 (mp) outliers start: 128 outliers final: 83 residues processed: 1317 average time/residue: 0.2047 time to fit residues: 442.0656 Evaluate side-chains 1215 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 1130 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 61 VAL Chi-restraints excluded: chain a residue 66 THR Chi-restraints excluded: chain a residue 70 SER Chi-restraints excluded: chain a residue 106 THR Chi-restraints excluded: chain a residue 110 THR Chi-restraints excluded: chain a residue 134 THR Chi-restraints excluded: chain a residue 295 ILE Chi-restraints excluded: chain b residue 15 GLN Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain b residue 172 ARG Chi-restraints excluded: chain b residue 202 THR Chi-restraints excluded: chain c residue 21 SER Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 159 LEU Chi-restraints excluded: chain c residue 165 MET Chi-restraints excluded: chain c residue 184 THR Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain c residue 213 VAL Chi-restraints excluded: chain d residue 60 LEU Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 104 ASN Chi-restraints excluded: chain e residue 135 GLU Chi-restraints excluded: chain f residue 40 THR Chi-restraints excluded: chain f residue 45 SER Chi-restraints excluded: chain f residue 88 ASP Chi-restraints excluded: chain f residue 126 LEU Chi-restraints excluded: chain f residue 140 THR Chi-restraints excluded: chain f residue 263 LEU Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 203 THR Chi-restraints excluded: chain g residue 207 MET Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 61 MET Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 88 THR Chi-restraints excluded: chain i residue 99 HIS Chi-restraints excluded: chain i residue 128 GLU Chi-restraints excluded: chain j residue 38 TRP Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 111 GLN Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 247 VAL Chi-restraints excluded: chain k residue 10 SER Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 181 ASP Chi-restraints excluded: chain k residue 189 ILE Chi-restraints excluded: chain k residue 223 LEU Chi-restraints excluded: chain l residue 26 ASN Chi-restraints excluded: chain l residue 44 GLN Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 173 SER Chi-restraints excluded: chain m residue 196 ILE Chi-restraints excluded: chain m residue 282 ILE Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 84 ASP Chi-restraints excluded: chain n residue 152 GLU Chi-restraints excluded: chain n residue 183 SER Chi-restraints excluded: chain o residue 30 VAL Chi-restraints excluded: chain o residue 51 THR Chi-restraints excluded: chain o residue 126 THR Chi-restraints excluded: chain o residue 132 SER Chi-restraints excluded: chain o residue 166 VAL Chi-restraints excluded: chain o residue 198 VAL Chi-restraints excluded: chain o residue 227 THR Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain q residue 35 GLU Chi-restraints excluded: chain q residue 36 VAL Chi-restraints excluded: chain q residue 68 SER Chi-restraints excluded: chain q residue 100 PHE Chi-restraints excluded: chain q residue 265 CYS Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 51 ASP Chi-restraints excluded: chain r residue 84 ASP Chi-restraints excluded: chain r residue 86 LEU Chi-restraints excluded: chain r residue 131 VAL Chi-restraints excluded: chain r residue 192 VAL Chi-restraints excluded: chain r residue 205 SER Chi-restraints excluded: chain r residue 252 THR Chi-restraints excluded: chain s residue 53 ILE Chi-restraints excluded: chain s residue 76 LEU Chi-restraints excluded: chain s residue 86 LEU Chi-restraints excluded: chain s residue 189 ILE Chi-restraints excluded: chain s residue 203 THR Chi-restraints excluded: chain t residue 7 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 193 optimal weight: 30.0000 chunk 230 optimal weight: 8.9990 chunk 258 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 430 optimal weight: 9.9990 chunk 283 optimal weight: 3.9990 chunk 18 optimal weight: 30.0000 chunk 29 optimal weight: 9.9990 chunk 427 optimal weight: 20.0000 chunk 211 optimal weight: 1.9990 chunk 152 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 ** a 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 147 ASN c 11 ASN ** c 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 112 GLN ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 135 ASN ** f 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 56 ASN h 21 ASN ** i 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 61 ASN j 265 ASN ** l 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 ASN ** m 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 119 GLN ** 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 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 26 ASN q 60 HIS ** r 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 271 HIS s 6 ASN s 12 GLN ** s 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 4 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.109827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.097278 restraints weight = 66917.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.100150 restraints weight = 31914.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.102059 restraints weight = 18722.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.103277 restraints weight = 12461.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.104217 restraints weight = 9238.268| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 34975 Z= 0.299 Angle : 0.707 8.976 47711 Z= 0.366 Chirality : 0.048 0.256 5363 Planarity : 0.005 0.061 6193 Dihedral : 5.926 55.770 4860 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 5.73 % Allowed : 16.34 % Favored : 77.93 % 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: -0.37 (0.12), residues: 4201 helix: -2.36 (0.22), residues: 391 sheet: 0.81 (0.15), residues: 1066 loop : -0.31 (0.11), residues: 2744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG a 262 TYR 0.030 0.002 TYR b 193 PHE 0.039 0.002 PHE g 212 TRP 0.023 0.002 TRP f 227 HIS 0.013 0.002 HIS o 229 Details of bonding type rmsd covalent geometry : bond 0.00683 (34975) covalent geometry : angle 0.70679 (47711) hydrogen bonds : bond 0.04003 ( 924) hydrogen bonds : angle 5.94377 ( 2631) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1383 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 211 poor density : 1172 time to evaluate : 1.392 Fit side-chains 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 n 272 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN r 272 " (corrupted residue). Skipping it. REVERT: a 43 GLU cc_start: 0.8860 (mp0) cc_final: 0.8275 (mp0) REVERT: a 120 PHE cc_start: 0.9088 (m-10) cc_final: 0.8759 (m-10) REVERT: a 135 GLU cc_start: 0.7572 (pt0) cc_final: 0.7337 (pt0) REVERT: a 161 ARG cc_start: 0.8588 (ttm170) cc_final: 0.8291 (ttm110) REVERT: a 179 PHE cc_start: 0.8981 (m-10) cc_final: 0.8627 (m-10) REVERT: b 81 LYS cc_start: 0.8920 (mmtp) cc_final: 0.8687 (mmtt) REVERT: b 87 LYS cc_start: 0.8467 (pttp) cc_final: 0.8020 (ptmt) REVERT: b 97 TYR cc_start: 0.8658 (m-80) cc_final: 0.7932 (m-10) REVERT: b 183 SER cc_start: 0.9396 (p) cc_final: 0.9082 (t) REVERT: b 246 GLN cc_start: 0.8153 (mt0) cc_final: 0.7706 (mt0) REVERT: b 264 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7414 (ptt90) REVERT: c 48 GLU cc_start: 0.9246 (mt-10) cc_final: 0.8851 (mt-10) REVERT: c 112 SER cc_start: 0.9367 (m) cc_final: 0.8992 (p) REVERT: c 131 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8914 (tp) REVERT: c 156 ASP cc_start: 0.8018 (t0) cc_final: 0.7548 (t0) REVERT: c 177 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.7643 (mpt-90) REVERT: d 21 ASN cc_start: 0.7551 (p0) cc_final: 0.7009 (p0) REVERT: e 173 SER cc_start: 0.9297 (p) cc_final: 0.9036 (p) REVERT: e 174 SER cc_start: 0.9104 (m) cc_final: 0.8792 (p) REVERT: e 182 TYR cc_start: 0.9016 (t80) cc_final: 0.8443 (t80) REVERT: e 204 TYR cc_start: 0.8887 (t80) cc_final: 0.8193 (t80) REVERT: e 205 ASP cc_start: 0.8928 (t0) cc_final: 0.8451 (t0) REVERT: e 257 LYS cc_start: 0.8974 (ttpp) cc_final: 0.8585 (tttp) REVERT: f 23 ILE cc_start: 0.9418 (mt) cc_final: 0.9089 (mm) REVERT: f 41 TYR cc_start: 0.8648 (m-80) cc_final: 0.8370 (m-10) REVERT: f 46 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8859 (mt-10) REVERT: f 55 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8782 (mt-10) REVERT: f 116 LYS cc_start: 0.9137 (mttt) cc_final: 0.8706 (mttp) REVERT: f 196 GLN cc_start: 0.8907 (tt0) cc_final: 0.8270 (tp40) REVERT: f 214 ASN cc_start: 0.9056 (t0) cc_final: 0.8842 (t0) REVERT: f 250 THR cc_start: 0.8616 (m) cc_final: 0.8323 (p) REVERT: f 259 GLU cc_start: 0.8578 (tt0) cc_final: 0.8356 (tt0) REVERT: g 55 MET cc_start: 0.8705 (mmm) cc_final: 0.8492 (tpp) REVERT: g 59 ASP cc_start: 0.8289 (t0) cc_final: 0.8036 (t70) REVERT: g 106 TYR cc_start: 0.9580 (m-80) cc_final: 0.9157 (m-80) REVERT: g 154 ILE cc_start: 0.9307 (mm) cc_final: 0.8810 (mm) REVERT: g 156 ASP cc_start: 0.8327 (t0) cc_final: 0.7712 (p0) REVERT: g 194 GLN cc_start: 0.9166 (tp40) cc_final: 0.8664 (tp40) REVERT: g 216 CYS cc_start: 0.8678 (m) cc_final: 0.8095 (m) REVERT: g 218 ASP cc_start: 0.8541 (p0) cc_final: 0.8280 (p0) REVERT: i 25 THR cc_start: 0.9144 (m) cc_final: 0.8902 (t) REVERT: i 78 ARG cc_start: 0.8863 (mmt90) cc_final: 0.8571 (mmt90) REVERT: i 98 LYS cc_start: 0.8920 (mttt) cc_final: 0.8537 (mtpp) REVERT: i 135 GLU cc_start: 0.8297 (mt-10) cc_final: 0.8041 (mt-10) REVERT: i 154 TYR cc_start: 0.8684 (t80) cc_final: 0.8189 (t80) REVERT: i 166 ASP cc_start: 0.7957 (t70) cc_final: 0.7700 (t70) REVERT: i 204 TYR cc_start: 0.8822 (t80) cc_final: 0.8054 (t80) REVERT: j 87 LYS cc_start: 0.8309 (ptpp) cc_final: 0.8073 (ptpp) REVERT: j 91 MET cc_start: 0.8585 (mmm) cc_final: 0.8119 (mmt) REVERT: j 110 VAL cc_start: 0.9661 (t) cc_final: 0.9342 (p) REVERT: j 111 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7933 (tt0) REVERT: j 137 GLU cc_start: 0.7279 (pm20) cc_final: 0.6898 (pm20) REVERT: j 223 LYS cc_start: 0.9194 (mtmt) cc_final: 0.8334 (mtmm) REVERT: j 224 HIS cc_start: 0.8598 (t-90) cc_final: 0.8308 (t-90) REVERT: j 227 TRP cc_start: 0.9117 (m100) cc_final: 0.8809 (m100) REVERT: j 266 ILE cc_start: 0.9281 (tp) cc_final: 0.8828 (tt) REVERT: k 55 MET cc_start: 0.9035 (tpt) cc_final: 0.8542 (tpt) REVERT: k 66 GLU cc_start: 0.9027 (mp0) cc_final: 0.8679 (mp0) REVERT: k 67 MET cc_start: 0.9079 (ptm) cc_final: 0.8866 (ptp) REVERT: k 69 GLN cc_start: 0.8320 (mp10) cc_final: 0.7459 (mp10) REVERT: k 87 SER cc_start: 0.9219 (t) cc_final: 0.8791 (p) REVERT: k 92 LYS cc_start: 0.8974 (mmtm) cc_final: 0.8559 (mtpp) REVERT: k 144 ARG cc_start: 0.8585 (ttm-80) cc_final: 0.7706 (ttm-80) REVERT: k 155 TRP cc_start: 0.8420 (t60) cc_final: 0.7618 (t60) REVERT: k 177 ARG cc_start: 0.8946 (ttm110) cc_final: 0.8065 (mtm-85) REVERT: k 178 CYS cc_start: 0.8391 (m) cc_final: 0.7532 (m) REVERT: k 194 GLN cc_start: 0.9108 (tp40) cc_final: 0.8507 (mm-40) REVERT: k 216 CYS cc_start: 0.8477 (m) cc_final: 0.8012 (m) REVERT: l 53 PHE cc_start: 0.9188 (m-80) cc_final: 0.8878 (m-80) REVERT: m 95 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8017 (mm-30) REVERT: m 111 VAL cc_start: 0.8696 (m) cc_final: 0.8415 (p) REVERT: m 122 TYR cc_start: 0.9118 (m-80) cc_final: 0.8779 (m-80) REVERT: m 166 ASP cc_start: 0.8561 (p0) cc_final: 0.7845 (p0) REVERT: m 216 ASN cc_start: 0.7661 (t0) cc_final: 0.7091 (m-40) REVERT: m 218 ASP cc_start: 0.8089 (m-30) cc_final: 0.7582 (m-30) REVERT: m 240 VAL cc_start: 0.9564 (OUTLIER) cc_final: 0.9275 (t) REVERT: n 13 VAL cc_start: 0.9523 (t) cc_final: 0.9248 (p) REVERT: n 60 SER cc_start: 0.9539 (m) cc_final: 0.9088 (p) REVERT: n 71 TRP cc_start: 0.8801 (t60) cc_final: 0.8488 (t60) REVERT: n 216 LEU cc_start: 0.9383 (mt) cc_final: 0.8997 (mt) REVERT: n 226 ASN cc_start: 0.8458 (m-40) cc_final: 0.8243 (m110) REVERT: n 249 ILE cc_start: 0.9414 (mt) cc_final: 0.9117 (mt) REVERT: o 66 GLU cc_start: 0.8786 (mp0) cc_final: 0.8489 (mp0) REVERT: o 87 SER cc_start: 0.9121 (m) cc_final: 0.7926 (p) REVERT: o 144 ARG cc_start: 0.8163 (ttp-170) cc_final: 0.7685 (ttp-170) REVERT: o 157 LEU cc_start: 0.8382 (mt) cc_final: 0.8097 (mt) REVERT: o 169 TRP cc_start: 0.9060 (t-100) cc_final: 0.8142 (t-100) REVERT: o 194 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8357 (tp40) REVERT: o 207 MET cc_start: 0.8649 (ptp) cc_final: 0.8188 (ptp) REVERT: p 4 GLN cc_start: 0.8035 (mt0) cc_final: 0.7678 (mp10) REVERT: q 47 SER cc_start: 0.9016 (m) cc_final: 0.8708 (p) REVERT: q 88 THR cc_start: 0.8848 (m) cc_final: 0.8509 (m) REVERT: q 105 ILE cc_start: 0.9061 (mt) cc_final: 0.8629 (tt) REVERT: q 126 ASP cc_start: 0.8274 (m-30) cc_final: 0.8058 (m-30) REVERT: q 154 TYR cc_start: 0.9319 (t80) cc_final: 0.9003 (t80) REVERT: q 173 SER cc_start: 0.9338 (m) cc_final: 0.9026 (p) REVERT: q 190 SER cc_start: 0.9390 (m) cc_final: 0.9160 (m) REVERT: q 231 ASP cc_start: 0.7702 (t0) cc_final: 0.7419 (t0) REVERT: r 50 VAL cc_start: 0.9376 (m) cc_final: 0.9160 (p) REVERT: r 116 LYS cc_start: 0.8789 (mttt) cc_final: 0.8383 (mtmt) REVERT: r 249 ILE cc_start: 0.9592 (mt) cc_final: 0.9326 (mm) REVERT: s 10 SER cc_start: 0.9411 (m) cc_final: 0.9151 (p) REVERT: s 50 ASP cc_start: 0.8874 (m-30) cc_final: 0.8592 (m-30) REVERT: s 74 ASP cc_start: 0.7939 (p0) cc_final: 0.7635 (p0) REVERT: s 144 ARG cc_start: 0.9314 (tmm-80) cc_final: 0.8988 (ttm-80) REVERT: s 175 TYR cc_start: 0.8519 (m-80) cc_final: 0.8267 (m-80) REVERT: s 234 LYS cc_start: 0.8717 (mtmt) cc_final: 0.8195 (mttp) REVERT: t 28 THR cc_start: 0.9511 (m) cc_final: 0.9232 (p) outliers start: 211 outliers final: 162 residues processed: 1276 average time/residue: 0.2043 time to fit residues: 427.0924 Evaluate side-chains 1262 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 1095 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 55 VAL Chi-restraints excluded: chain a residue 61 VAL Chi-restraints excluded: chain a residue 66 THR Chi-restraints excluded: chain a residue 71 CYS Chi-restraints excluded: chain a residue 106 THR Chi-restraints excluded: chain a residue 110 THR Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 129 MET Chi-restraints excluded: chain a residue 134 THR Chi-restraints excluded: chain a residue 164 SER Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain a residue 295 ILE Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain b residue 26 GLN Chi-restraints excluded: chain b residue 60 SER Chi-restraints excluded: chain b residue 172 ARG Chi-restraints excluded: chain b residue 202 THR Chi-restraints excluded: chain b residue 264 ARG Chi-restraints excluded: chain b residue 268 VAL Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 17 ASP Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 131 LEU Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 159 LEU Chi-restraints excluded: chain c residue 177 ARG Chi-restraints excluded: chain c residue 184 THR Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain c residue 209 MET Chi-restraints excluded: chain c residue 213 VAL Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 60 LEU Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 104 ASN Chi-restraints excluded: chain e residue 134 THR Chi-restraints excluded: chain e residue 237 VAL Chi-restraints excluded: chain e residue 282 ILE Chi-restraints excluded: chain f residue 40 THR Chi-restraints excluded: chain f residue 45 SER Chi-restraints excluded: chain f residue 60 SER Chi-restraints excluded: chain f residue 88 ASP Chi-restraints excluded: chain f residue 126 LEU Chi-restraints excluded: chain f residue 140 THR Chi-restraints excluded: chain f residue 146 ILE Chi-restraints excluded: chain f residue 180 LEU Chi-restraints excluded: chain f residue 208 ILE Chi-restraints excluded: chain f residue 263 LEU Chi-restraints excluded: chain f residue 265 ASN Chi-restraints excluded: chain g residue 56 ASN Chi-restraints excluded: chain g residue 67 MET Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 153 ILE Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 203 THR Chi-restraints excluded: chain g residue 205 THR Chi-restraints excluded: chain g residue 207 MET Chi-restraints excluded: chain g residue 224 LEU Chi-restraints excluded: chain h residue 7 THR Chi-restraints excluded: chain h residue 9 LYS Chi-restraints excluded: chain h residue 10 THR Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 44 THR Chi-restraints excluded: chain i residue 88 THR Chi-restraints excluded: chain i residue 99 HIS Chi-restraints excluded: chain i residue 117 LEU Chi-restraints excluded: chain i residue 128 GLU Chi-restraints excluded: chain i residue 132 VAL Chi-restraints excluded: chain i residue 248 ILE Chi-restraints excluded: chain i residue 296 THR Chi-restraints excluded: chain j residue 25 THR Chi-restraints excluded: chain j residue 38 TRP Chi-restraints excluded: chain j residue 40 THR Chi-restraints excluded: chain j residue 45 SER Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain j residue 67 GLU Chi-restraints excluded: chain j residue 111 GLN Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 181 LEU Chi-restraints excluded: chain j residue 183 SER Chi-restraints excluded: chain j residue 246 GLN Chi-restraints excluded: chain j residue 247 VAL Chi-restraints excluded: chain k residue 5 MET Chi-restraints excluded: chain k residue 10 SER Chi-restraints excluded: chain k residue 30 VAL Chi-restraints excluded: chain k residue 81 ILE Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain k residue 189 ILE Chi-restraints excluded: chain k residue 203 THR Chi-restraints excluded: chain k residue 223 LEU Chi-restraints excluded: chain k residue 233 SER Chi-restraints excluded: chain l residue 24 THR Chi-restraints excluded: chain l residue 26 ASN Chi-restraints excluded: chain l residue 44 GLN Chi-restraints excluded: chain m residue 117 LEU Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 173 SER Chi-restraints excluded: chain m residue 177 SER Chi-restraints excluded: chain m residue 196 ILE Chi-restraints excluded: chain m residue 221 ASP Chi-restraints excluded: chain m residue 240 VAL Chi-restraints excluded: chain m residue 251 SER Chi-restraints excluded: chain m residue 272 VAL Chi-restraints excluded: chain m residue 282 ILE Chi-restraints excluded: chain n residue 40 THR Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 54 THR Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 84 ASP Chi-restraints excluded: chain n residue 126 LEU Chi-restraints excluded: chain n residue 140 THR Chi-restraints excluded: chain n residue 152 GLU Chi-restraints excluded: chain n residue 183 SER Chi-restraints excluded: chain n residue 198 ILE Chi-restraints excluded: chain o residue 30 VAL Chi-restraints excluded: chain o residue 51 THR Chi-restraints excluded: chain o residue 53 ILE Chi-restraints excluded: chain o residue 118 LEU Chi-restraints excluded: chain o residue 122 SER Chi-restraints excluded: chain o residue 126 THR Chi-restraints excluded: chain o residue 132 SER Chi-restraints excluded: chain o residue 153 ILE Chi-restraints excluded: chain o residue 166 VAL Chi-restraints excluded: chain o residue 190 THR Chi-restraints excluded: chain o residue 198 VAL Chi-restraints excluded: chain o residue 199 VAL Chi-restraints excluded: chain o residue 209 MET Chi-restraints excluded: chain o residue 214 SER Chi-restraints excluded: chain p residue 7 THR Chi-restraints excluded: chain p residue 25 ILE Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain q residue 71 CYS Chi-restraints excluded: chain q residue 99 HIS Chi-restraints excluded: chain q residue 100 PHE Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain q residue 178 ILE Chi-restraints excluded: chain q residue 217 THR Chi-restraints excluded: chain q residue 265 CYS Chi-restraints excluded: chain q residue 296 THR Chi-restraints excluded: chain r residue 18 LEU Chi-restraints excluded: chain r residue 32 ILE Chi-restraints excluded: chain r residue 44 ASP Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 51 ASP Chi-restraints excluded: chain r residue 84 ASP Chi-restraints excluded: chain r residue 85 CYS Chi-restraints excluded: chain r residue 86 LEU Chi-restraints excluded: chain r residue 131 VAL Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain r residue 192 VAL Chi-restraints excluded: chain r residue 205 SER Chi-restraints excluded: chain r residue 252 THR Chi-restraints excluded: chain s residue 53 ILE Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 76 LEU Chi-restraints excluded: chain s residue 86 LEU Chi-restraints excluded: chain s residue 173 THR Chi-restraints excluded: chain s residue 189 ILE Chi-restraints excluded: chain s residue 195 THR Chi-restraints excluded: chain s residue 203 THR Chi-restraints excluded: chain s residue 205 THR Chi-restraints excluded: chain t residue 7 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 12 optimal weight: 40.0000 chunk 55 optimal weight: 6.9990 chunk 305 optimal weight: 10.0000 chunk 307 optimal weight: 10.0000 chunk 244 optimal weight: 0.9990 chunk 429 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 3 optimal weight: 50.0000 chunk 288 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 266 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 99 HIS ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 232 GLN ** e 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 112 GLN h 15 ASN h 21 ASN ** i 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 196 GLN j 265 ASN ** k 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 ASN l 39 ASN ** m 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 26 ASN ** r 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 69 GLN ** s 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 4 GLN t 44 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.111912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.099376 restraints weight = 66389.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.102319 restraints weight = 31416.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.104243 restraints weight = 18179.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.105553 restraints weight = 12041.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.106455 restraints weight = 8758.443| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 34975 Z= 0.180 Angle : 0.637 9.861 47711 Z= 0.326 Chirality : 0.046 0.278 5363 Planarity : 0.004 0.055 6193 Dihedral : 5.771 59.726 4860 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.18 % Allowed : 19.14 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.41 (0.12), residues: 4201 helix: -2.24 (0.22), residues: 415 sheet: 0.78 (0.15), residues: 1039 loop : -0.33 (0.11), residues: 2747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG c 222 TYR 0.033 0.002 TYR o 175 PHE 0.022 0.002 PHE c 212 TRP 0.022 0.001 TRP f 227 HIS 0.010 0.001 HIS o 229 Details of bonding type rmsd covalent geometry : bond 0.00417 (34975) covalent geometry : angle 0.63692 (47711) hydrogen bonds : bond 0.03589 ( 924) hydrogen bonds : angle 5.71771 ( 2631) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1351 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 1197 time to evaluate : 1.000 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 TARDY: cannot create tardy model for: "GLN n 272 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN r 272 " (corrupted residue). Skipping it. REVERT: a 43 GLU cc_start: 0.8836 (mp0) cc_final: 0.8247 (mp0) REVERT: a 54 ASP cc_start: 0.8598 (m-30) cc_final: 0.8306 (m-30) REVERT: a 69 GLU cc_start: 0.7768 (tt0) cc_final: 0.7425 (tt0) REVERT: a 74 SER cc_start: 0.9398 (m) cc_final: 0.9183 (t) REVERT: a 78 ARG cc_start: 0.8505 (mmm-85) cc_final: 0.8301 (mmm-85) REVERT: a 120 PHE cc_start: 0.8924 (m-80) cc_final: 0.8693 (m-10) REVERT: a 135 GLU cc_start: 0.7408 (pt0) cc_final: 0.7110 (pt0) REVERT: a 161 ARG cc_start: 0.8504 (ttm170) cc_final: 0.8240 (ttm110) REVERT: a 179 PHE cc_start: 0.8991 (m-10) cc_final: 0.8697 (m-10) REVERT: a 205 ASP cc_start: 0.8782 (t70) cc_final: 0.8541 (t70) REVERT: a 215 GLU cc_start: 0.8750 (mp0) cc_final: 0.8358 (mp0) REVERT: a 277 GLU cc_start: 0.7647 (mp0) cc_final: 0.7253 (mp0) REVERT: b 87 LYS cc_start: 0.8459 (pttp) cc_final: 0.7840 (ttpt) REVERT: b 97 TYR cc_start: 0.8583 (m-80) cc_final: 0.7896 (m-80) REVERT: b 100 TYR cc_start: 0.8995 (t80) cc_final: 0.8749 (t80) REVERT: b 172 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7307 (mtt90) REVERT: b 183 SER cc_start: 0.9347 (p) cc_final: 0.9063 (t) REVERT: b 191 PHE cc_start: 0.9278 (m-80) cc_final: 0.8943 (m-80) REVERT: b 237 LEU cc_start: 0.9268 (tp) cc_final: 0.9015 (tp) REVERT: b 246 GLN cc_start: 0.8088 (mt0) cc_final: 0.7579 (mt0) REVERT: b 264 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7432 (ptt90) REVERT: c 48 GLU cc_start: 0.9238 (mt-10) cc_final: 0.8812 (mt-10) REVERT: c 91 ASP cc_start: 0.8291 (t0) cc_final: 0.7957 (t0) REVERT: c 112 SER cc_start: 0.9364 (m) cc_final: 0.9016 (p) REVERT: c 131 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8954 (tp) REVERT: c 148 MET cc_start: 0.6833 (ttm) cc_final: 0.6596 (ttt) REVERT: c 225 ARG cc_start: 0.8514 (ptt-90) cc_final: 0.8310 (ptt180) REVERT: d 21 ASN cc_start: 0.7475 (p0) cc_final: 0.6927 (p0) REVERT: e 83 THR cc_start: 0.9345 (t) cc_final: 0.9062 (p) REVERT: e 120 PHE cc_start: 0.9313 (m-80) cc_final: 0.9026 (m-10) REVERT: e 173 SER cc_start: 0.9216 (p) cc_final: 0.8933 (p) REVERT: e 174 SER cc_start: 0.9046 (m) cc_final: 0.8783 (p) REVERT: e 181 MET cc_start: 0.8356 (ptm) cc_final: 0.7796 (ptt) REVERT: e 182 TYR cc_start: 0.8987 (t80) cc_final: 0.8500 (t80) REVERT: e 204 TYR cc_start: 0.8853 (t80) cc_final: 0.8158 (t80) REVERT: e 231 ASP cc_start: 0.8296 (t0) cc_final: 0.8043 (t0) REVERT: e 257 LYS cc_start: 0.8989 (ttpp) cc_final: 0.8604 (tttp) REVERT: e 291 LYS cc_start: 0.8890 (mtpt) cc_final: 0.8467 (mttm) REVERT: f 23 ILE cc_start: 0.9374 (mt) cc_final: 0.9057 (mm) REVERT: f 41 TYR cc_start: 0.8607 (m-80) cc_final: 0.8332 (m-10) REVERT: f 46 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8824 (mt-10) REVERT: f 55 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8681 (mt-10) REVERT: f 116 LYS cc_start: 0.9127 (mttt) cc_final: 0.8682 (mttp) REVERT: f 132 MET cc_start: 0.8747 (mtm) cc_final: 0.8542 (mtp) REVERT: f 196 GLN cc_start: 0.8858 (tt0) cc_final: 0.8302 (tp40) REVERT: f 250 THR cc_start: 0.8610 (m) cc_final: 0.8301 (p) REVERT: g 5 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8465 (ttt) REVERT: g 53 ILE cc_start: 0.9594 (mt) cc_final: 0.9235 (mp) REVERT: g 55 MET cc_start: 0.8624 (mmm) cc_final: 0.8262 (tpp) REVERT: g 59 ASP cc_start: 0.8122 (t0) cc_final: 0.7741 (t70) REVERT: g 91 ASP cc_start: 0.8297 (t0) cc_final: 0.7959 (t0) REVERT: g 99 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9161 (tt) REVERT: g 106 TYR cc_start: 0.9559 (m-80) cc_final: 0.9110 (m-80) REVERT: g 112 SER cc_start: 0.9010 (m) cc_final: 0.8080 (p) REVERT: g 123 MET cc_start: 0.8240 (tpp) cc_final: 0.8012 (tpp) REVERT: g 154 ILE cc_start: 0.9284 (mm) cc_final: 0.8790 (mm) REVERT: g 156 ASP cc_start: 0.8384 (t0) cc_final: 0.7737 (p0) REVERT: g 194 GLN cc_start: 0.9151 (tp40) cc_final: 0.8622 (tp40) REVERT: g 216 CYS cc_start: 0.8661 (m) cc_final: 0.7007 (m) REVERT: g 218 ASP cc_start: 0.8597 (p0) cc_final: 0.8371 (p0) REVERT: i 25 THR cc_start: 0.9097 (m) cc_final: 0.8857 (t) REVERT: i 67 ARG cc_start: 0.8232 (mtt180) cc_final: 0.7946 (mtt180) REVERT: i 78 ARG cc_start: 0.8818 (mmt90) cc_final: 0.8568 (mmt90) REVERT: i 95 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7170 (tt0) REVERT: i 154 TYR cc_start: 0.8659 (t80) cc_final: 0.8005 (t80) REVERT: i 168 TYR cc_start: 0.8491 (p90) cc_final: 0.8242 (p90) REVERT: i 200 TYR cc_start: 0.9236 (m-80) cc_final: 0.9036 (m-10) REVERT: i 204 TYR cc_start: 0.8811 (t80) cc_final: 0.8185 (t80) REVERT: j 91 MET cc_start: 0.8598 (mmm) cc_final: 0.7935 (mmt) REVERT: j 110 VAL cc_start: 0.9652 (t) cc_final: 0.9328 (p) REVERT: j 137 GLU cc_start: 0.7312 (pm20) cc_final: 0.6896 (pm20) REVERT: j 193 TYR cc_start: 0.8903 (m-80) cc_final: 0.8612 (m-10) REVERT: j 196 GLN cc_start: 0.9022 (tt0) cc_final: 0.8640 (tt0) REVERT: j 223 LYS cc_start: 0.9061 (mtmt) cc_final: 0.8206 (mtmm) REVERT: j 227 TRP cc_start: 0.9089 (m100) cc_final: 0.8759 (m100) REVERT: j 264 ARG cc_start: 0.8408 (ptt90) cc_final: 0.8199 (ptt180) REVERT: j 266 ILE cc_start: 0.9239 (tp) cc_final: 0.8823 (tt) REVERT: k 39 GLU cc_start: 0.8263 (tm-30) cc_final: 0.8007 (tm-30) REVERT: k 66 GLU cc_start: 0.9103 (mp0) cc_final: 0.8752 (mp0) REVERT: k 69 GLN cc_start: 0.8166 (mp10) cc_final: 0.7574 (mp10) REVERT: k 81 ILE cc_start: 0.9392 (OUTLIER) cc_final: 0.9158 (mp) REVERT: k 87 SER cc_start: 0.9243 (t) cc_final: 0.8803 (p) REVERT: k 92 LYS cc_start: 0.8964 (mmtm) cc_final: 0.8638 (mtpp) REVERT: k 144 ARG cc_start: 0.8558 (ttm-80) cc_final: 0.7774 (ttm-80) REVERT: k 155 TRP cc_start: 0.8448 (t60) cc_final: 0.7676 (t60) REVERT: k 178 CYS cc_start: 0.8325 (m) cc_final: 0.7687 (m) REVERT: k 194 GLN cc_start: 0.9153 (tp40) cc_final: 0.8690 (mm-40) REVERT: k 216 CYS cc_start: 0.8503 (m) cc_final: 0.8177 (m) REVERT: l 53 PHE cc_start: 0.9211 (m-80) cc_final: 0.8855 (m-80) REVERT: m 111 VAL cc_start: 0.8663 (m) cc_final: 0.8386 (p) REVERT: m 129 MET cc_start: 0.9027 (mmt) cc_final: 0.8662 (mmt) REVERT: m 166 ASP cc_start: 0.8615 (p0) cc_final: 0.7853 (p0) REVERT: m 216 ASN cc_start: 0.7710 (t0) cc_final: 0.7096 (m-40) REVERT: m 218 ASP cc_start: 0.8055 (m-30) cc_final: 0.7555 (m-30) REVERT: n 13 VAL cc_start: 0.9505 (t) cc_final: 0.9246 (p) REVERT: n 46 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7598 (mt-10) REVERT: n 60 SER cc_start: 0.9531 (m) cc_final: 0.9072 (p) REVERT: n 71 TRP cc_start: 0.8744 (t60) cc_final: 0.8473 (t60) REVERT: n 226 ASN cc_start: 0.8407 (m-40) cc_final: 0.8194 (m110) REVERT: n 249 ILE cc_start: 0.9392 (mt) cc_final: 0.9108 (mt) REVERT: o 66 GLU cc_start: 0.8716 (mp0) cc_final: 0.8472 (mp0) REVERT: o 87 SER cc_start: 0.9102 (m) cc_final: 0.7981 (p) REVERT: o 157 LEU cc_start: 0.8300 (mt) cc_final: 0.8075 (mt) REVERT: o 194 GLN cc_start: 0.8754 (mm-40) cc_final: 0.8456 (tt0) REVERT: o 207 MET cc_start: 0.8628 (ptp) cc_final: 0.8137 (ptp) REVERT: o 227 THR cc_start: 0.9204 (OUTLIER) cc_final: 0.8955 (m) REVERT: p 4 GLN cc_start: 0.7990 (mt0) cc_final: 0.7617 (mp10) REVERT: p 48 GLN cc_start: 0.8545 (pm20) cc_final: 0.8240 (pt0) REVERT: q 47 SER cc_start: 0.8999 (m) cc_final: 0.8687 (p) REVERT: q 105 ILE cc_start: 0.9051 (mt) cc_final: 0.8625 (tt) REVERT: q 126 ASP cc_start: 0.8322 (m-30) cc_final: 0.8063 (m-30) REVERT: q 154 TYR cc_start: 0.9356 (t80) cc_final: 0.9038 (t80) REVERT: q 190 SER cc_start: 0.9341 (m) cc_final: 0.9005 (m) REVERT: q 242 ARG cc_start: 0.8580 (ttm110) cc_final: 0.8247 (mtp-110) REVERT: r 41 TYR cc_start: 0.8921 (m-80) cc_final: 0.8148 (m-10) REVERT: r 50 VAL cc_start: 0.9305 (m) cc_final: 0.9084 (p) REVERT: r 116 LYS cc_start: 0.8834 (mttt) cc_final: 0.8333 (mtmt) REVERT: r 221 MET cc_start: 0.8221 (mtt) cc_final: 0.7897 (mtt) REVERT: r 249 ILE cc_start: 0.9600 (mt) cc_final: 0.9331 (mm) REVERT: r 264 ARG cc_start: 0.8241 (ptt180) cc_final: 0.7963 (ptm160) REVERT: s 10 SER cc_start: 0.9393 (m) cc_final: 0.9104 (p) REVERT: s 50 ASP cc_start: 0.8857 (m-30) cc_final: 0.8588 (m-30) REVERT: s 74 ASP cc_start: 0.7841 (p0) cc_final: 0.7536 (p0) REVERT: s 144 ARG cc_start: 0.9292 (tmm-80) cc_final: 0.8991 (ttm-80) REVERT: s 175 TYR cc_start: 0.8497 (m-80) cc_final: 0.8223 (m-10) REVERT: s 234 LYS cc_start: 0.8592 (mtmt) cc_final: 0.8052 (mttp) REVERT: s 235 LEU cc_start: 0.7975 (tp) cc_final: 0.7646 (tp) REVERT: t 28 THR cc_start: 0.9480 (m) cc_final: 0.9252 (p) outliers start: 154 outliers final: 119 residues processed: 1271 average time/residue: 0.2092 time to fit residues: 436.2206 Evaluate side-chains 1240 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 1114 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 61 VAL Chi-restraints excluded: chain a residue 66 THR Chi-restraints excluded: chain a residue 106 THR Chi-restraints excluded: chain a residue 129 MET Chi-restraints excluded: chain a residue 134 THR Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain a residue 293 ASP Chi-restraints excluded: chain a residue 295 ILE Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain b residue 60 SER Chi-restraints excluded: chain b residue 172 ARG Chi-restraints excluded: chain b residue 202 THR Chi-restraints excluded: chain b residue 234 LEU Chi-restraints excluded: chain b residue 264 ARG Chi-restraints excluded: chain b residue 268 VAL Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 131 LEU Chi-restraints excluded: chain c residue 159 LEU Chi-restraints excluded: chain c residue 184 THR Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain d residue 60 LEU Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 104 ASN Chi-restraints excluded: chain e residue 237 VAL Chi-restraints excluded: chain f residue 40 THR Chi-restraints excluded: chain f residue 88 ASP Chi-restraints excluded: chain f residue 126 LEU Chi-restraints excluded: chain f residue 140 THR Chi-restraints excluded: chain f residue 146 ILE Chi-restraints excluded: chain f residue 152 GLU Chi-restraints excluded: chain f residue 263 LEU Chi-restraints excluded: chain g residue 5 MET Chi-restraints excluded: chain g residue 99 LEU Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 203 THR Chi-restraints excluded: chain g residue 207 MET Chi-restraints excluded: chain g residue 224 LEU Chi-restraints excluded: chain h residue 9 LYS Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 44 THR Chi-restraints excluded: chain i residue 88 THR Chi-restraints excluded: chain i residue 99 HIS Chi-restraints excluded: chain i residue 100 PHE Chi-restraints excluded: chain i residue 117 LEU Chi-restraints excluded: chain i residue 128 GLU Chi-restraints excluded: chain i residue 132 VAL Chi-restraints excluded: chain i residue 296 THR Chi-restraints excluded: chain j residue 25 THR Chi-restraints excluded: chain j residue 38 TRP Chi-restraints excluded: chain j residue 82 LEU Chi-restraints excluded: chain j residue 84 ASP Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 181 LEU Chi-restraints excluded: chain j residue 246 GLN Chi-restraints excluded: chain j residue 247 VAL Chi-restraints excluded: chain k residue 5 MET Chi-restraints excluded: chain k residue 10 SER Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 76 LEU Chi-restraints excluded: chain k residue 81 ILE Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain k residue 189 ILE Chi-restraints excluded: chain k residue 199 VAL Chi-restraints excluded: chain k residue 223 LEU Chi-restraints excluded: chain k residue 227 THR Chi-restraints excluded: chain k residue 233 SER Chi-restraints excluded: chain l residue 26 ASN Chi-restraints excluded: chain l residue 44 GLN Chi-restraints excluded: chain m residue 83 THR Chi-restraints excluded: chain m residue 84 ILE Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 173 SER Chi-restraints excluded: chain m residue 196 ILE Chi-restraints excluded: chain n residue 84 ASP Chi-restraints excluded: chain n residue 152 GLU Chi-restraints excluded: chain n residue 183 SER Chi-restraints excluded: chain n residue 186 LEU Chi-restraints excluded: chain o residue 27 ASN Chi-restraints excluded: chain o residue 30 VAL Chi-restraints excluded: chain o residue 53 ILE Chi-restraints excluded: chain o residue 118 LEU Chi-restraints excluded: chain o residue 126 THR Chi-restraints excluded: chain o residue 132 SER Chi-restraints excluded: chain o residue 153 ILE Chi-restraints excluded: chain o residue 198 VAL Chi-restraints excluded: chain o residue 199 VAL Chi-restraints excluded: chain o residue 209 MET Chi-restraints excluded: chain o residue 213 VAL Chi-restraints excluded: chain o residue 227 THR Chi-restraints excluded: chain p residue 25 ILE Chi-restraints excluded: chain p residue 32 TYR Chi-restraints excluded: chain p residue 40 SER Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain p residue 64 THR Chi-restraints excluded: chain q residue 36 VAL Chi-restraints excluded: chain q residue 99 HIS Chi-restraints excluded: chain q residue 100 PHE Chi-restraints excluded: chain q residue 178 ILE Chi-restraints excluded: chain q residue 217 THR Chi-restraints excluded: chain r residue 18 LEU Chi-restraints excluded: chain r residue 32 ILE Chi-restraints excluded: chain r residue 40 THR Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 51 ASP Chi-restraints excluded: chain r residue 84 ASP Chi-restraints excluded: chain r residue 85 CYS Chi-restraints excluded: chain r residue 86 LEU Chi-restraints excluded: chain r residue 111 GLN Chi-restraints excluded: chain r residue 131 VAL Chi-restraints excluded: chain r residue 192 VAL Chi-restraints excluded: chain r residue 205 SER Chi-restraints excluded: chain s residue 53 ILE Chi-restraints excluded: chain s residue 76 LEU Chi-restraints excluded: chain s residue 86 LEU Chi-restraints excluded: chain s residue 148 MET Chi-restraints excluded: chain s residue 173 THR Chi-restraints excluded: chain s residue 189 ILE Chi-restraints excluded: chain s residue 195 THR Chi-restraints excluded: chain s residue 203 THR Chi-restraints excluded: chain s residue 205 THR Chi-restraints excluded: chain t residue 7 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 356 optimal weight: 20.0000 chunk 189 optimal weight: 0.6980 chunk 74 optimal weight: 9.9990 chunk 266 optimal weight: 9.9990 chunk 261 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 313 optimal weight: 8.9990 chunk 299 optimal weight: 2.9990 chunk 404 optimal weight: 9.9990 chunk 117 optimal weight: 8.9990 chunk 238 optimal weight: 9.9990 overall best weight: 6.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 99 HIS ** b 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 224 HIS ** c 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 ASN ** i 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 30 ASN ** j 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 232 GLN ** l 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 ASN m 18 GLN ** m 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 6 ASN ** o 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 26 ASN ** r 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 4 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.109539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.097082 restraints weight = 67193.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.099938 restraints weight = 31987.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.101835 restraints weight = 18666.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.103128 restraints weight = 12420.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.104011 restraints weight = 9076.364| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 34975 Z= 0.267 Angle : 0.687 9.629 47711 Z= 0.351 Chirality : 0.048 0.307 5363 Planarity : 0.005 0.052 6193 Dihedral : 5.822 58.350 4860 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 5.13 % Allowed : 19.49 % Favored : 75.38 % 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: -0.55 (0.12), residues: 4201 helix: -2.19 (0.23), residues: 392 sheet: 0.61 (0.15), residues: 1045 loop : -0.45 (0.11), residues: 2764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG q 238 TYR 0.032 0.002 TYR o 175 PHE 0.036 0.002 PHE c 212 TRP 0.027 0.002 TRP f 227 HIS 0.010 0.002 HIS o 229 Details of bonding type rmsd covalent geometry : bond 0.00614 (34975) covalent geometry : angle 0.68699 (47711) hydrogen bonds : bond 0.03776 ( 924) hydrogen bonds : angle 5.77408 ( 2631) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1314 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 1125 time to evaluate : 1.284 Fit side-chains 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 n 272 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN r 272 " (corrupted residue). Skipping it. REVERT: a 43 GLU cc_start: 0.8831 (mp0) cc_final: 0.8252 (mp0) REVERT: a 54 ASP cc_start: 0.8620 (m-30) cc_final: 0.8406 (m-30) REVERT: a 74 SER cc_start: 0.9404 (m) cc_final: 0.9142 (p) REVERT: a 120 PHE cc_start: 0.8997 (m-80) cc_final: 0.8735 (m-10) REVERT: a 161 ARG cc_start: 0.8590 (ttm170) cc_final: 0.8266 (ttm110) REVERT: a 205 ASP cc_start: 0.8808 (t70) cc_final: 0.8222 (t70) REVERT: b 84 ASP cc_start: 0.8374 (t0) cc_final: 0.7744 (t0) REVERT: b 87 LYS cc_start: 0.8508 (pttp) cc_final: 0.8064 (ttpt) REVERT: b 97 TYR cc_start: 0.8634 (m-80) cc_final: 0.7944 (m-80) REVERT: b 170 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7931 (mm-30) REVERT: b 172 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7138 (mtt90) REVERT: b 183 SER cc_start: 0.9347 (p) cc_final: 0.9045 (t) REVERT: b 246 GLN cc_start: 0.8157 (mt0) cc_final: 0.7687 (mt0) REVERT: b 264 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7505 (ptt90) REVERT: c 48 GLU cc_start: 0.9234 (mt-10) cc_final: 0.8809 (mt-10) REVERT: c 95 SER cc_start: 0.8988 (p) cc_final: 0.8719 (t) REVERT: c 112 SER cc_start: 0.9329 (m) cc_final: 0.8978 (p) REVERT: c 148 MET cc_start: 0.6907 (ttm) cc_final: 0.6645 (ttt) REVERT: c 175 TYR cc_start: 0.9275 (m-80) cc_final: 0.9058 (m-10) REVERT: c 177 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7636 (mpt-90) REVERT: d 21 ASN cc_start: 0.7511 (p0) cc_final: 0.6955 (p0) REVERT: e 83 THR cc_start: 0.9352 (t) cc_final: 0.9051 (p) REVERT: e 120 PHE cc_start: 0.9331 (m-80) cc_final: 0.9022 (m-10) REVERT: e 174 SER cc_start: 0.9092 (m) cc_final: 0.8743 (p) REVERT: e 182 TYR cc_start: 0.9037 (t80) cc_final: 0.8615 (t80) REVERT: e 204 TYR cc_start: 0.8890 (t80) cc_final: 0.8217 (t80) REVERT: e 205 ASP cc_start: 0.8952 (t0) cc_final: 0.8219 (t0) REVERT: e 231 ASP cc_start: 0.8389 (t0) cc_final: 0.8142 (t0) REVERT: e 257 LYS cc_start: 0.9004 (ttpp) cc_final: 0.8593 (tttp) REVERT: e 291 LYS cc_start: 0.8943 (mtpt) cc_final: 0.8526 (mttm) REVERT: f 23 ILE cc_start: 0.9352 (mt) cc_final: 0.9061 (mm) REVERT: f 30 ASN cc_start: 0.8525 (t0) cc_final: 0.8197 (t0) REVERT: f 32 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.8938 (mp) REVERT: f 41 TYR cc_start: 0.8569 (m-80) cc_final: 0.8260 (m-10) REVERT: f 46 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8841 (mt-10) REVERT: f 55 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8684 (mt-10) REVERT: f 116 LYS cc_start: 0.9118 (mttt) cc_final: 0.8669 (mttp) REVERT: f 170 GLU cc_start: 0.7190 (tp30) cc_final: 0.6833 (tp30) REVERT: f 196 GLN cc_start: 0.8843 (tt0) cc_final: 0.8249 (tp40) REVERT: f 250 THR cc_start: 0.8589 (m) cc_final: 0.8312 (p) REVERT: g 5 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8477 (ttt) REVERT: g 59 ASP cc_start: 0.8127 (t0) cc_final: 0.7736 (t70) REVERT: g 91 ASP cc_start: 0.8369 (t0) cc_final: 0.8113 (t0) REVERT: g 99 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9105 (tt) REVERT: g 106 TYR cc_start: 0.9548 (m-80) cc_final: 0.9087 (m-80) REVERT: g 123 MET cc_start: 0.8338 (tpp) cc_final: 0.8113 (tpp) REVERT: g 154 ILE cc_start: 0.9312 (mm) cc_final: 0.8943 (mm) REVERT: g 156 ASP cc_start: 0.8358 (t0) cc_final: 0.7726 (p0) REVERT: g 216 CYS cc_start: 0.8705 (m) cc_final: 0.8197 (m) REVERT: i 34 GLN cc_start: 0.8816 (mp10) cc_final: 0.7755 (tt0) REVERT: i 95 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7268 (tt0) REVERT: i 98 LYS cc_start: 0.9002 (mttt) cc_final: 0.8514 (mtpp) REVERT: i 168 TYR cc_start: 0.8612 (p90) cc_final: 0.7554 (p90) REVERT: i 171 GLN cc_start: 0.8848 (mp10) cc_final: 0.8546 (mp10) REVERT: i 204 TYR cc_start: 0.8785 (t80) cc_final: 0.8145 (t80) REVERT: j 44 ASP cc_start: 0.8900 (m-30) cc_final: 0.8593 (m-30) REVERT: j 91 MET cc_start: 0.8625 (mmm) cc_final: 0.7970 (mmt) REVERT: j 137 GLU cc_start: 0.7276 (pm20) cc_final: 0.6834 (pm20) REVERT: j 196 GLN cc_start: 0.8999 (tt0) cc_final: 0.8775 (tt0) REVERT: j 223 LYS cc_start: 0.9064 (mtmt) cc_final: 0.8283 (mttp) REVERT: j 227 TRP cc_start: 0.9137 (m100) cc_final: 0.8781 (m100) REVERT: k 39 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7995 (tm-30) REVERT: k 41 LYS cc_start: 0.8650 (mttm) cc_final: 0.8423 (mttm) REVERT: k 55 MET cc_start: 0.9313 (tpp) cc_final: 0.8948 (tpt) REVERT: k 69 GLN cc_start: 0.8325 (mp10) cc_final: 0.7559 (mp10) REVERT: k 87 SER cc_start: 0.9222 (t) cc_final: 0.8919 (m) REVERT: k 117 PHE cc_start: 0.9160 (m-80) cc_final: 0.8779 (m-80) REVERT: k 144 ARG cc_start: 0.8611 (ttm-80) cc_final: 0.7783 (ttm-80) REVERT: k 155 TRP cc_start: 0.8535 (t60) cc_final: 0.7674 (t60) REVERT: k 178 CYS cc_start: 0.8372 (m) cc_final: 0.7738 (m) REVERT: k 194 GLN cc_start: 0.9183 (tp40) cc_final: 0.8688 (mm-40) REVERT: k 216 CYS cc_start: 0.8561 (m) cc_final: 0.8234 (m) REVERT: l 53 PHE cc_start: 0.9309 (m-80) cc_final: 0.9002 (m-80) REVERT: m 95 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8430 (mm-30) REVERT: m 111 VAL cc_start: 0.8713 (m) cc_final: 0.8456 (p) REVERT: m 122 TYR cc_start: 0.8836 (m-80) cc_final: 0.8296 (m-80) REVERT: m 166 ASP cc_start: 0.8614 (p0) cc_final: 0.7848 (p0) REVERT: m 205 ASP cc_start: 0.8289 (t0) cc_final: 0.8089 (t0) REVERT: m 216 ASN cc_start: 0.7686 (t0) cc_final: 0.7071 (m-40) REVERT: m 218 ASP cc_start: 0.8152 (m-30) cc_final: 0.7654 (m-30) REVERT: n 13 VAL cc_start: 0.9523 (t) cc_final: 0.9261 (p) REVERT: n 41 TYR cc_start: 0.8643 (m-10) cc_final: 0.8439 (m-10) REVERT: n 46 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7640 (mt-10) REVERT: n 60 SER cc_start: 0.9517 (m) cc_final: 0.9065 (p) REVERT: n 129 GLU cc_start: 0.8589 (tp30) cc_final: 0.7630 (tp30) REVERT: n 226 ASN cc_start: 0.8389 (m-40) cc_final: 0.8093 (m110) REVERT: n 249 ILE cc_start: 0.9412 (mt) cc_final: 0.9075 (mt) REVERT: o 87 SER cc_start: 0.9084 (m) cc_final: 0.7948 (p) REVERT: o 144 ARG cc_start: 0.7800 (ttp-170) cc_final: 0.7584 (ttp-170) REVERT: o 148 MET cc_start: 0.5500 (ttm) cc_final: 0.5288 (ttt) REVERT: o 157 LEU cc_start: 0.8355 (mt) cc_final: 0.8021 (mt) REVERT: o 207 MET cc_start: 0.8642 (ptp) cc_final: 0.8150 (ptp) REVERT: o 227 THR cc_start: 0.9247 (OUTLIER) cc_final: 0.9013 (m) REVERT: p 4 GLN cc_start: 0.8000 (mt0) cc_final: 0.7594 (mp10) REVERT: q 47 SER cc_start: 0.9018 (m) cc_final: 0.8788 (p) REVERT: q 61 VAL cc_start: 0.9331 (t) cc_final: 0.9094 (p) REVERT: q 126 ASP cc_start: 0.8338 (m-30) cc_final: 0.8094 (m-30) REVERT: q 190 SER cc_start: 0.9177 (m) cc_final: 0.8933 (m) REVERT: q 231 ASP cc_start: 0.7623 (t0) cc_final: 0.7223 (t0) REVERT: r 26 GLN cc_start: 0.7416 (mt0) cc_final: 0.7007 (mt0) REVERT: r 50 VAL cc_start: 0.9359 (m) cc_final: 0.9127 (p) REVERT: r 116 LYS cc_start: 0.8884 (mttt) cc_final: 0.8426 (mtmt) REVERT: r 210 VAL cc_start: 0.9600 (p) cc_final: 0.9204 (m) REVERT: r 249 ILE cc_start: 0.9603 (mt) cc_final: 0.9323 (mm) REVERT: s 10 SER cc_start: 0.9411 (m) cc_final: 0.9113 (p) REVERT: s 50 ASP cc_start: 0.8914 (m-30) cc_final: 0.8686 (m-30) REVERT: s 74 ASP cc_start: 0.7879 (p0) cc_final: 0.7674 (p0) REVERT: s 144 ARG cc_start: 0.9307 (tmm-80) cc_final: 0.8980 (ttm-80) REVERT: s 175 TYR cc_start: 0.8574 (m-80) cc_final: 0.8195 (m-10) REVERT: s 234 LYS cc_start: 0.8554 (mtmt) cc_final: 0.7919 (mttp) REVERT: s 235 LEU cc_start: 0.8355 (tp) cc_final: 0.8131 (tp) REVERT: t 28 THR cc_start: 0.9483 (m) cc_final: 0.9237 (p) outliers start: 189 outliers final: 154 residues processed: 1212 average time/residue: 0.2074 time to fit residues: 411.3554 Evaluate side-chains 1260 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 1099 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 61 VAL Chi-restraints excluded: chain a residue 66 THR Chi-restraints excluded: chain a residue 106 THR Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 129 MET Chi-restraints excluded: chain a residue 130 THR Chi-restraints excluded: chain a residue 134 THR Chi-restraints excluded: chain a residue 293 ASP Chi-restraints excluded: chain a residue 295 ILE Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain b residue 26 GLN Chi-restraints excluded: chain b residue 60 SER Chi-restraints excluded: chain b residue 172 ARG Chi-restraints excluded: chain b residue 200 LEU Chi-restraints excluded: chain b residue 202 THR Chi-restraints excluded: chain b residue 234 LEU Chi-restraints excluded: chain b residue 242 THR Chi-restraints excluded: chain b residue 256 MET Chi-restraints excluded: chain b residue 264 ARG Chi-restraints excluded: chain b residue 268 VAL Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 17 ASP Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 159 LEU Chi-restraints excluded: chain c residue 177 ARG Chi-restraints excluded: chain c residue 184 THR Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain c residue 213 VAL Chi-restraints excluded: chain d residue 60 LEU Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 104 ASN Chi-restraints excluded: chain e residue 134 THR Chi-restraints excluded: chain e residue 135 GLU Chi-restraints excluded: chain e residue 237 VAL Chi-restraints excluded: chain e residue 282 ILE Chi-restraints excluded: chain f residue 32 ILE Chi-restraints excluded: chain f residue 40 THR Chi-restraints excluded: chain f residue 88 ASP Chi-restraints excluded: chain f residue 126 LEU Chi-restraints excluded: chain f residue 146 ILE Chi-restraints excluded: chain f residue 180 LEU Chi-restraints excluded: chain f residue 208 ILE Chi-restraints excluded: chain f residue 263 LEU Chi-restraints excluded: chain f residue 265 ASN Chi-restraints excluded: chain f residue 268 VAL Chi-restraints excluded: chain g residue 4 THR Chi-restraints excluded: chain g residue 5 MET Chi-restraints excluded: chain g residue 67 MET Chi-restraints excluded: chain g residue 99 LEU Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain g residue 153 ILE Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 203 THR Chi-restraints excluded: chain g residue 205 THR Chi-restraints excluded: chain g residue 207 MET Chi-restraints excluded: chain g residue 224 LEU Chi-restraints excluded: chain h residue 7 THR Chi-restraints excluded: chain h residue 9 LYS Chi-restraints excluded: chain h residue 10 THR Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 88 THR Chi-restraints excluded: chain i residue 99 HIS Chi-restraints excluded: chain i residue 100 PHE Chi-restraints excluded: chain i residue 117 LEU Chi-restraints excluded: chain i residue 132 VAL Chi-restraints excluded: chain i residue 296 THR Chi-restraints excluded: chain j residue 25 THR Chi-restraints excluded: chain j residue 38 TRP Chi-restraints excluded: chain j residue 40 THR Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain j residue 84 ASP Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 181 LEU Chi-restraints excluded: chain j residue 183 SER Chi-restraints excluded: chain j residue 246 GLN Chi-restraints excluded: chain j residue 247 VAL Chi-restraints excluded: chain k residue 5 MET Chi-restraints excluded: chain k residue 10 SER Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 76 LEU Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain k residue 189 ILE Chi-restraints excluded: chain k residue 199 VAL Chi-restraints excluded: chain k residue 223 LEU Chi-restraints excluded: chain k residue 227 THR Chi-restraints excluded: chain k residue 233 SER Chi-restraints excluded: chain l residue 26 ASN Chi-restraints excluded: chain l residue 44 GLN Chi-restraints excluded: chain m residue 83 THR Chi-restraints excluded: chain m residue 84 ILE Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 173 SER Chi-restraints excluded: chain m residue 196 ILE Chi-restraints excluded: chain m residue 221 ASP Chi-restraints excluded: chain m residue 229 ILE Chi-restraints excluded: chain m residue 251 SER Chi-restraints excluded: chain m residue 265 CYS Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 69 VAL Chi-restraints excluded: chain n residue 84 ASP Chi-restraints excluded: chain n residue 152 GLU Chi-restraints excluded: chain n residue 183 SER Chi-restraints excluded: chain n residue 186 LEU Chi-restraints excluded: chain n residue 198 ILE Chi-restraints excluded: chain o residue 6 ASN Chi-restraints excluded: chain o residue 27 ASN Chi-restraints excluded: chain o residue 30 VAL Chi-restraints excluded: chain o residue 51 THR Chi-restraints excluded: chain o residue 53 ILE Chi-restraints excluded: chain o residue 118 LEU Chi-restraints excluded: chain o residue 126 THR Chi-restraints excluded: chain o residue 132 SER Chi-restraints excluded: chain o residue 153 ILE Chi-restraints excluded: chain o residue 198 VAL Chi-restraints excluded: chain o residue 199 VAL Chi-restraints excluded: chain o residue 209 MET Chi-restraints excluded: chain o residue 214 SER Chi-restraints excluded: chain o residue 227 THR Chi-restraints excluded: chain p residue 25 ILE Chi-restraints excluded: chain p residue 32 TYR Chi-restraints excluded: chain p residue 40 SER Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain p residue 64 THR Chi-restraints excluded: chain q residue 36 VAL Chi-restraints excluded: chain q residue 68 SER Chi-restraints excluded: chain q residue 99 HIS Chi-restraints excluded: chain q residue 100 PHE Chi-restraints excluded: chain q residue 178 ILE Chi-restraints excluded: chain q residue 217 THR Chi-restraints excluded: chain r residue 18 LEU Chi-restraints excluded: chain r residue 32 ILE Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 51 ASP Chi-restraints excluded: chain r residue 54 THR Chi-restraints excluded: chain r residue 84 ASP Chi-restraints excluded: chain r residue 85 CYS Chi-restraints excluded: chain r residue 86 LEU Chi-restraints excluded: chain r residue 111 GLN Chi-restraints excluded: chain r residue 131 VAL Chi-restraints excluded: chain r residue 192 VAL Chi-restraints excluded: chain r residue 205 SER Chi-restraints excluded: chain r residue 218 ILE Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 76 LEU Chi-restraints excluded: chain s residue 85 SER Chi-restraints excluded: chain s residue 86 LEU Chi-restraints excluded: chain s residue 148 MET Chi-restraints excluded: chain s residue 173 THR Chi-restraints excluded: chain s residue 189 ILE Chi-restraints excluded: chain s residue 195 THR Chi-restraints excluded: chain s residue 203 THR Chi-restraints excluded: chain s residue 205 THR Chi-restraints excluded: chain s residue 213 VAL Chi-restraints excluded: chain t residue 7 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 150 optimal weight: 10.0000 chunk 366 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 431 optimal weight: 20.0000 chunk 164 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 381 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 223 optimal weight: 9.9990 chunk 353 optimal weight: 3.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 232 GLN e 23 GLN ** e 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 ASN ** i 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 30 ASN j 265 ASN ** k 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 ASN l 39 ASN m 202 HIS ** n 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 26 ASN r 261 ASN ** s 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 4 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.112818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.100394 restraints weight = 66384.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.103316 restraints weight = 31387.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.105249 restraints weight = 18186.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.106518 restraints weight = 12020.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.107427 restraints weight = 8796.686| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 34975 Z= 0.151 Angle : 0.634 9.525 47711 Z= 0.323 Chirality : 0.046 0.308 5363 Planarity : 0.004 0.047 6193 Dihedral : 5.686 58.085 4860 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.13 % Allowed : 21.01 % Favored : 74.86 % 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: -0.45 (0.12), residues: 4201 helix: -2.00 (0.23), residues: 392 sheet: 0.66 (0.15), residues: 1042 loop : -0.39 (0.11), residues: 2767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG g 222 TYR 0.040 0.002 TYR b 179 PHE 0.028 0.002 PHE c 212 TRP 0.023 0.001 TRP f 227 HIS 0.008 0.001 HIS o 229 Details of bonding type rmsd covalent geometry : bond 0.00351 (34975) covalent geometry : angle 0.63409 (47711) hydrogen bonds : bond 0.03464 ( 924) hydrogen bonds : angle 5.59978 ( 2631) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1346 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 1194 time to evaluate : 1.305 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 TARDY: cannot create tardy model for: "GLN n 272 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN r 272 " (corrupted residue). Skipping it. REVERT: a 43 GLU cc_start: 0.8792 (mp0) cc_final: 0.8252 (mp0) REVERT: a 54 ASP cc_start: 0.8429 (m-30) cc_final: 0.8123 (m-30) REVERT: a 74 SER cc_start: 0.9420 (m) cc_final: 0.9105 (p) REVERT: a 161 ARG cc_start: 0.8560 (ttm170) cc_final: 0.8259 (ttm110) REVERT: a 167 ASP cc_start: 0.8153 (m-30) cc_final: 0.7912 (m-30) REVERT: a 205 ASP cc_start: 0.8703 (t70) cc_final: 0.8260 (t70) REVERT: a 277 GLU cc_start: 0.7699 (mp0) cc_final: 0.7236 (mp0) REVERT: b 87 LYS cc_start: 0.8521 (pttp) cc_final: 0.8193 (ttpt) REVERT: b 97 TYR cc_start: 0.8624 (m-80) cc_final: 0.7795 (m-80) REVERT: b 183 SER cc_start: 0.9305 (p) cc_final: 0.9049 (t) REVERT: b 246 GLN cc_start: 0.8151 (mt0) cc_final: 0.7680 (mt0) REVERT: c 48 GLU cc_start: 0.9212 (mt-10) cc_final: 0.8737 (mt-10) REVERT: c 76 LEU cc_start: 0.8449 (tp) cc_final: 0.8212 (tp) REVERT: c 95 SER cc_start: 0.8924 (p) cc_final: 0.8651 (t) REVERT: c 112 SER cc_start: 0.9308 (m) cc_final: 0.9008 (p) REVERT: c 225 ARG cc_start: 0.8581 (ptt180) cc_final: 0.7885 (ptt180) REVERT: e 83 THR cc_start: 0.9350 (t) cc_final: 0.9027 (p) REVERT: e 120 PHE cc_start: 0.9286 (m-80) cc_final: 0.8921 (m-80) REVERT: e 182 TYR cc_start: 0.8988 (t80) cc_final: 0.8581 (t80) REVERT: e 204 TYR cc_start: 0.8861 (t80) cc_final: 0.8155 (t80) REVERT: e 231 ASP cc_start: 0.8405 (t0) cc_final: 0.8200 (t0) REVERT: e 257 LYS cc_start: 0.9032 (ttpp) cc_final: 0.8675 (tttp) REVERT: e 291 LYS cc_start: 0.8891 (mtpt) cc_final: 0.8508 (mttm) REVERT: f 23 ILE cc_start: 0.9340 (mt) cc_final: 0.9065 (mm) REVERT: f 30 ASN cc_start: 0.8467 (t0) cc_final: 0.8104 (t0) REVERT: f 41 TYR cc_start: 0.8490 (m-80) cc_final: 0.8019 (m-10) REVERT: f 55 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8595 (mt-10) REVERT: f 91 MET cc_start: 0.8290 (mmm) cc_final: 0.7865 (tpp) REVERT: f 116 LYS cc_start: 0.9127 (mttt) cc_final: 0.8692 (mttp) REVERT: f 170 GLU cc_start: 0.7371 (tp30) cc_final: 0.7031 (tp30) REVERT: f 196 GLN cc_start: 0.8855 (tt0) cc_final: 0.8343 (tp40) REVERT: f 250 THR cc_start: 0.8506 (m) cc_final: 0.8247 (p) REVERT: g 59 ASP cc_start: 0.8128 (t0) cc_final: 0.7715 (t70) REVERT: g 91 ASP cc_start: 0.8406 (t0) cc_final: 0.8095 (t0) REVERT: g 99 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9139 (tt) REVERT: g 112 SER cc_start: 0.9008 (m) cc_final: 0.8413 (p) REVERT: g 123 MET cc_start: 0.8207 (tpp) cc_final: 0.7998 (tpp) REVERT: g 154 ILE cc_start: 0.9278 (mm) cc_final: 0.8934 (mm) REVERT: g 156 ASP cc_start: 0.8363 (t0) cc_final: 0.7742 (p0) REVERT: g 194 GLN cc_start: 0.9126 (tp40) cc_final: 0.8820 (tp-100) REVERT: g 216 CYS cc_start: 0.8690 (m) cc_final: 0.7800 (m) REVERT: g 218 ASP cc_start: 0.8506 (p0) cc_final: 0.8085 (p0) REVERT: i 95 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7238 (tt0) REVERT: i 96 GLU cc_start: 0.8273 (tm-30) cc_final: 0.8053 (tt0) REVERT: i 168 TYR cc_start: 0.8601 (p90) cc_final: 0.7439 (p90) REVERT: i 171 GLN cc_start: 0.8823 (mp10) cc_final: 0.8483 (mp10) REVERT: i 204 TYR cc_start: 0.8749 (t80) cc_final: 0.8174 (t80) REVERT: j 44 ASP cc_start: 0.8893 (m-30) cc_final: 0.8631 (m-30) REVERT: j 91 MET cc_start: 0.8553 (mmm) cc_final: 0.7785 (mmt) REVERT: j 110 VAL cc_start: 0.9667 (t) cc_final: 0.9378 (p) REVERT: j 111 GLN cc_start: 0.8342 (pm20) cc_final: 0.7711 (tt0) REVERT: j 137 GLU cc_start: 0.7210 (pm20) cc_final: 0.6760 (pm20) REVERT: j 196 GLN cc_start: 0.8995 (tt0) cc_final: 0.8739 (tt0) REVERT: j 223 LYS cc_start: 0.8959 (mtmt) cc_final: 0.8285 (mttp) REVERT: j 227 TRP cc_start: 0.9101 (m100) cc_final: 0.8696 (m100) REVERT: j 259 GLU cc_start: 0.7831 (pt0) cc_final: 0.7585 (pt0) REVERT: j 266 ILE cc_start: 0.9182 (tp) cc_final: 0.8763 (tt) REVERT: k 39 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7905 (tm-30) REVERT: k 55 MET cc_start: 0.9316 (tpp) cc_final: 0.8940 (tpt) REVERT: k 67 MET cc_start: 0.9187 (ptm) cc_final: 0.8985 (ptp) REVERT: k 69 GLN cc_start: 0.8261 (mp10) cc_final: 0.7786 (mp10) REVERT: k 87 SER cc_start: 0.9199 (t) cc_final: 0.8866 (m) REVERT: k 92 LYS cc_start: 0.8922 (mmtm) cc_final: 0.8547 (mtpp) REVERT: k 144 ARG cc_start: 0.8470 (ttm-80) cc_final: 0.7415 (ttm-80) REVERT: k 155 TRP cc_start: 0.8482 (t60) cc_final: 0.7651 (t60) REVERT: k 178 CYS cc_start: 0.8292 (m) cc_final: 0.7642 (m) REVERT: k 194 GLN cc_start: 0.9191 (tp40) cc_final: 0.8459 (mm-40) REVERT: k 216 CYS cc_start: 0.8528 (m) cc_final: 0.8207 (m) REVERT: l 53 PHE cc_start: 0.9294 (m-80) cc_final: 0.8972 (m-80) REVERT: m 95 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8435 (mm-30) REVERT: m 111 VAL cc_start: 0.8665 (m) cc_final: 0.8384 (p) REVERT: m 122 TYR cc_start: 0.8737 (m-80) cc_final: 0.8316 (m-80) REVERT: m 135 GLU cc_start: 0.8848 (pt0) cc_final: 0.8647 (pt0) REVERT: m 166 ASP cc_start: 0.8625 (p0) cc_final: 0.7918 (p0) REVERT: m 205 ASP cc_start: 0.8187 (t0) cc_final: 0.7985 (t0) REVERT: m 216 ASN cc_start: 0.7719 (t0) cc_final: 0.7071 (m-40) REVERT: m 218 ASP cc_start: 0.8109 (m-30) cc_final: 0.7623 (m-30) REVERT: m 240 VAL cc_start: 0.9573 (OUTLIER) cc_final: 0.9254 (t) REVERT: n 13 VAL cc_start: 0.9492 (t) cc_final: 0.9254 (p) REVERT: n 46 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7565 (mt-10) REVERT: n 60 SER cc_start: 0.9462 (m) cc_final: 0.9062 (p) REVERT: n 129 GLU cc_start: 0.8608 (tp30) cc_final: 0.7732 (tp30) REVERT: n 226 ASN cc_start: 0.8282 (m-40) cc_final: 0.8071 (m110) REVERT: n 249 ILE cc_start: 0.9353 (mt) cc_final: 0.9046 (mt) REVERT: n 259 GLU cc_start: 0.7709 (tt0) cc_final: 0.7109 (tt0) REVERT: o 5 MET cc_start: 0.8572 (ttp) cc_final: 0.8324 (ttt) REVERT: o 87 SER cc_start: 0.9062 (m) cc_final: 0.7957 (p) REVERT: o 144 ARG cc_start: 0.7743 (ttp-170) cc_final: 0.7451 (ttp-170) REVERT: o 146 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7420 (t0) REVERT: o 155 TRP cc_start: 0.8761 (t60) cc_final: 0.7641 (t60) REVERT: o 157 LEU cc_start: 0.8261 (mt) cc_final: 0.7826 (mt) REVERT: o 194 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8365 (tt0) REVERT: o 207 MET cc_start: 0.8568 (ptp) cc_final: 0.8015 (ptp) REVERT: o 227 THR cc_start: 0.9208 (OUTLIER) cc_final: 0.8955 (m) REVERT: p 4 GLN cc_start: 0.7861 (mt0) cc_final: 0.7403 (mp10) REVERT: q 47 SER cc_start: 0.8996 (m) cc_final: 0.8642 (p) REVERT: q 126 ASP cc_start: 0.8479 (m-30) cc_final: 0.8180 (m-30) REVERT: q 190 SER cc_start: 0.9141 (m) cc_final: 0.8889 (m) REVERT: q 242 ARG cc_start: 0.8518 (ttm110) cc_final: 0.8283 (mtp-110) REVERT: r 50 VAL cc_start: 0.9276 (m) cc_final: 0.9031 (p) REVERT: r 116 LYS cc_start: 0.8862 (mttt) cc_final: 0.8402 (mtmm) REVERT: r 210 VAL cc_start: 0.9595 (p) cc_final: 0.9221 (m) REVERT: r 249 ILE cc_start: 0.9579 (mt) cc_final: 0.9292 (mm) REVERT: s 10 SER cc_start: 0.9359 (m) cc_final: 0.9084 (p) REVERT: s 50 ASP cc_start: 0.8837 (m-30) cc_final: 0.8620 (m-30) REVERT: s 73 ASN cc_start: 0.9022 (p0) cc_final: 0.8803 (p0) REVERT: s 143 ASN cc_start: 0.8400 (t0) cc_final: 0.8106 (t0) REVERT: s 144 ARG cc_start: 0.9227 (tmm-80) cc_final: 0.8989 (ttm-80) REVERT: s 175 TYR cc_start: 0.8567 (m-80) cc_final: 0.8130 (m-10) REVERT: t 28 THR cc_start: 0.9493 (m) cc_final: 0.9255 (p) outliers start: 152 outliers final: 118 residues processed: 1263 average time/residue: 0.1995 time to fit residues: 415.7648 Evaluate side-chains 1249 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 1126 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 61 VAL Chi-restraints excluded: chain a residue 66 THR Chi-restraints excluded: chain a residue 106 THR Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 129 MET Chi-restraints excluded: chain a residue 134 THR Chi-restraints excluded: chain a residue 293 ASP Chi-restraints excluded: chain a residue 295 ILE Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain b residue 26 GLN Chi-restraints excluded: chain b residue 60 SER Chi-restraints excluded: chain b residue 200 LEU Chi-restraints excluded: chain b residue 234 LEU Chi-restraints excluded: chain b residue 242 THR Chi-restraints excluded: chain b residue 268 VAL Chi-restraints excluded: chain c residue 17 ASP Chi-restraints excluded: chain c residue 74 ASP Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 159 LEU Chi-restraints excluded: chain c residue 184 THR Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain c residue 213 VAL Chi-restraints excluded: chain d residue 60 LEU Chi-restraints excluded: chain d residue 62 LEU Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 104 ASN Chi-restraints excluded: chain e residue 229 ILE Chi-restraints excluded: chain e residue 237 VAL Chi-restraints excluded: chain f residue 88 ASP Chi-restraints excluded: chain f residue 126 LEU Chi-restraints excluded: chain f residue 146 ILE Chi-restraints excluded: chain f residue 180 LEU Chi-restraints excluded: chain f residue 263 LEU Chi-restraints excluded: chain f residue 268 VAL Chi-restraints excluded: chain g residue 4 THR Chi-restraints excluded: chain g residue 67 MET Chi-restraints excluded: chain g residue 99 LEU Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 203 THR Chi-restraints excluded: chain g residue 207 MET Chi-restraints excluded: chain g residue 224 LEU Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 88 THR Chi-restraints excluded: chain i residue 99 HIS Chi-restraints excluded: chain i residue 100 PHE Chi-restraints excluded: chain i residue 132 VAL Chi-restraints excluded: chain j residue 25 THR Chi-restraints excluded: chain j residue 38 TRP Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 82 LEU Chi-restraints excluded: chain j residue 84 ASP Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 181 LEU Chi-restraints excluded: chain j residue 204 ASN Chi-restraints excluded: chain j residue 246 GLN Chi-restraints excluded: chain j residue 247 VAL Chi-restraints excluded: chain k residue 10 SER Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain k residue 199 VAL Chi-restraints excluded: chain k residue 223 LEU Chi-restraints excluded: chain k residue 226 ASP Chi-restraints excluded: chain k residue 227 THR Chi-restraints excluded: chain k residue 233 SER Chi-restraints excluded: chain l residue 26 ASN Chi-restraints excluded: chain m residue 61 VAL Chi-restraints excluded: chain m residue 83 THR Chi-restraints excluded: chain m residue 117 LEU Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 196 ILE Chi-restraints excluded: chain m residue 221 ASP Chi-restraints excluded: chain m residue 240 VAL Chi-restraints excluded: chain m residue 265 CYS Chi-restraints excluded: chain n residue 40 THR Chi-restraints excluded: chain n residue 84 ASP Chi-restraints excluded: chain n residue 152 GLU Chi-restraints excluded: chain n residue 183 SER Chi-restraints excluded: chain o residue 6 ASN Chi-restraints excluded: chain o residue 30 VAL Chi-restraints excluded: chain o residue 126 THR Chi-restraints excluded: chain o residue 132 SER Chi-restraints excluded: chain o residue 146 ASP Chi-restraints excluded: chain o residue 194 GLN Chi-restraints excluded: chain o residue 199 VAL Chi-restraints excluded: chain o residue 213 VAL Chi-restraints excluded: chain o residue 214 SER Chi-restraints excluded: chain o residue 227 THR Chi-restraints excluded: chain p residue 25 ILE Chi-restraints excluded: chain p residue 32 TYR Chi-restraints excluded: chain p residue 40 SER Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain p residue 64 THR Chi-restraints excluded: chain q residue 36 VAL Chi-restraints excluded: chain q residue 71 CYS Chi-restraints excluded: chain q residue 100 PHE Chi-restraints excluded: chain q residue 110 THR Chi-restraints excluded: chain q residue 178 ILE Chi-restraints excluded: chain r residue 18 LEU Chi-restraints excluded: chain r residue 24 THR Chi-restraints excluded: chain r residue 32 ILE Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 51 ASP Chi-restraints excluded: chain r residue 84 ASP Chi-restraints excluded: chain r residue 86 LEU Chi-restraints excluded: chain r residue 131 VAL Chi-restraints excluded: chain r residue 192 VAL Chi-restraints excluded: chain r residue 205 SER Chi-restraints excluded: chain r residue 226 ASN Chi-restraints excluded: chain s residue 76 LEU Chi-restraints excluded: chain s residue 85 SER Chi-restraints excluded: chain s residue 86 LEU Chi-restraints excluded: chain s residue 97 THR Chi-restraints excluded: chain s residue 148 MET Chi-restraints excluded: chain s residue 173 THR Chi-restraints excluded: chain s residue 189 ILE Chi-restraints excluded: chain s residue 205 THR Chi-restraints excluded: chain t residue 7 THR Chi-restraints excluded: chain t residue 44 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 115 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 136 optimal weight: 10.0000 chunk 226 optimal weight: 8.9990 chunk 204 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 261 optimal weight: 9.9990 chunk 390 optimal weight: 10.0000 chunk 247 optimal weight: 3.9990 chunk 134 optimal weight: 20.0000 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 99 HIS ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 ASN ** i 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 ASN l 39 ASN ** n 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 196 GLN ** n 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 6 ASN ** o 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 26 ASN ** r 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 226 ASN ** s 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 4 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.110014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.097675 restraints weight = 67357.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.100512 restraints weight = 32033.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.102388 restraints weight = 18684.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.103657 restraints weight = 12434.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.104536 restraints weight = 9125.635| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 34975 Z= 0.264 Angle : 0.700 13.428 47711 Z= 0.356 Chirality : 0.048 0.319 5363 Planarity : 0.005 0.075 6193 Dihedral : 5.810 55.351 4860 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.42 % Allowed : 21.15 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.12), residues: 4201 helix: -1.92 (0.24), residues: 369 sheet: 0.47 (0.15), residues: 1053 loop : -0.49 (0.11), residues: 2779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG a 262 TYR 0.052 0.002 TYR o 175 PHE 0.035 0.002 PHE a 120 TRP 0.047 0.002 TRP f 227 HIS 0.009 0.001 HIS o 229 Details of bonding type rmsd covalent geometry : bond 0.00610 (34975) covalent geometry : angle 0.70018 (47711) hydrogen bonds : bond 0.03706 ( 924) hydrogen bonds : angle 5.71288 ( 2631) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1291 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 1128 time to evaluate : 1.187 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 TARDY: cannot create tardy model for: "GLN n 272 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN r 272 " (corrupted residue). Skipping it. REVERT: a 43 GLU cc_start: 0.8827 (mp0) cc_final: 0.8249 (mp0) REVERT: a 69 GLU cc_start: 0.7892 (tt0) cc_final: 0.7660 (tt0) REVERT: a 74 SER cc_start: 0.9451 (m) cc_final: 0.9235 (p) REVERT: a 161 ARG cc_start: 0.8568 (ttm170) cc_final: 0.8272 (ttm110) REVERT: a 205 ASP cc_start: 0.8808 (t70) cc_final: 0.8360 (t70) REVERT: a 277 GLU cc_start: 0.7687 (mp0) cc_final: 0.7205 (mp0) REVERT: b 87 LYS cc_start: 0.8593 (pttp) cc_final: 0.8328 (ttpt) REVERT: b 97 TYR cc_start: 0.8600 (m-80) cc_final: 0.7845 (m-10) REVERT: b 183 SER cc_start: 0.9262 (p) cc_final: 0.8935 (t) REVERT: b 246 GLN cc_start: 0.8160 (mt0) cc_final: 0.7693 (mt0) REVERT: c 48 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8786 (mt-10) REVERT: c 95 SER cc_start: 0.8936 (p) cc_final: 0.8703 (t) REVERT: c 112 SER cc_start: 0.9269 (m) cc_final: 0.8953 (p) REVERT: c 225 ARG cc_start: 0.8693 (ptt180) cc_final: 0.8057 (ptt180) REVERT: d 21 ASN cc_start: 0.7846 (p0) cc_final: 0.6962 (p0) REVERT: e 83 THR cc_start: 0.9299 (t) cc_final: 0.9020 (p) REVERT: e 120 PHE cc_start: 0.9320 (m-80) cc_final: 0.8952 (m-80) REVERT: e 182 TYR cc_start: 0.9010 (t80) cc_final: 0.8635 (t80) REVERT: e 257 LYS cc_start: 0.9026 (ttpp) cc_final: 0.8657 (tttp) REVERT: e 291 LYS cc_start: 0.8940 (mtpt) cc_final: 0.8533 (mttm) REVERT: f 23 ILE cc_start: 0.9334 (mt) cc_final: 0.9079 (mm) REVERT: f 30 ASN cc_start: 0.8595 (t0) cc_final: 0.8294 (t0) REVERT: f 32 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.9129 (mp) REVERT: f 116 LYS cc_start: 0.9096 (mttt) cc_final: 0.8587 (mttp) REVERT: f 170 GLU cc_start: 0.7367 (tp30) cc_final: 0.7025 (tp30) REVERT: f 193 TYR cc_start: 0.9022 (m-80) cc_final: 0.8293 (m-10) REVERT: f 250 THR cc_start: 0.8593 (m) cc_final: 0.8319 (p) REVERT: g 59 ASP cc_start: 0.8117 (t0) cc_final: 0.7679 (t70) REVERT: g 91 ASP cc_start: 0.8381 (t0) cc_final: 0.8117 (t0) REVERT: g 99 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9108 (tt) REVERT: g 123 MET cc_start: 0.8320 (tpp) cc_final: 0.8108 (tpp) REVERT: g 154 ILE cc_start: 0.9314 (mm) cc_final: 0.8950 (mm) REVERT: g 216 CYS cc_start: 0.8743 (m) cc_final: 0.8240 (m) REVERT: i 34 GLN cc_start: 0.8853 (mp10) cc_final: 0.7862 (tt0) REVERT: i 69 GLU cc_start: 0.8501 (mp0) cc_final: 0.8277 (mm-30) REVERT: i 95 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7366 (tt0) REVERT: i 98 LYS cc_start: 0.8950 (mttt) cc_final: 0.8460 (mtpp) REVERT: i 154 TYR cc_start: 0.8709 (t80) cc_final: 0.8021 (t80) REVERT: i 168 TYR cc_start: 0.8704 (p90) cc_final: 0.7603 (p90) REVERT: i 171 GLN cc_start: 0.8843 (mp10) cc_final: 0.8531 (mp10) REVERT: j 44 ASP cc_start: 0.8989 (m-30) cc_final: 0.8517 (m-30) REVERT: j 71 TRP cc_start: 0.9274 (t60) cc_final: 0.9026 (t60) REVERT: j 91 MET cc_start: 0.8560 (mmm) cc_final: 0.7863 (mmt) REVERT: j 110 VAL cc_start: 0.9658 (t) cc_final: 0.9381 (p) REVERT: j 137 GLU cc_start: 0.7344 (pm20) cc_final: 0.6867 (pm20) REVERT: j 196 GLN cc_start: 0.8967 (tt0) cc_final: 0.8733 (tt0) REVERT: j 223 LYS cc_start: 0.9078 (mtmt) cc_final: 0.8176 (mtmm) REVERT: j 227 TRP cc_start: 0.9172 (m100) cc_final: 0.8830 (m100) REVERT: j 266 ILE cc_start: 0.9198 (tp) cc_final: 0.8810 (tt) REVERT: k 18 ASP cc_start: 0.7832 (t70) cc_final: 0.7613 (t70) REVERT: k 39 GLU cc_start: 0.8331 (tm-30) cc_final: 0.8012 (tm-30) REVERT: k 55 MET cc_start: 0.9357 (tpp) cc_final: 0.9051 (tpt) REVERT: k 69 GLN cc_start: 0.8355 (mp10) cc_final: 0.7609 (mp10) REVERT: k 87 SER cc_start: 0.9199 (t) cc_final: 0.8939 (m) REVERT: k 92 LYS cc_start: 0.8952 (mmtm) cc_final: 0.8590 (mtpp) REVERT: k 144 ARG cc_start: 0.8588 (ttm-80) cc_final: 0.7445 (ttm-80) REVERT: k 155 TRP cc_start: 0.8585 (t60) cc_final: 0.7702 (t60) REVERT: k 164 SER cc_start: 0.9415 (m) cc_final: 0.8782 (t) REVERT: k 178 CYS cc_start: 0.8348 (m) cc_final: 0.7646 (m) REVERT: k 194 GLN cc_start: 0.9180 (tp40) cc_final: 0.8502 (mm-40) REVERT: k 216 CYS cc_start: 0.8545 (m) cc_final: 0.8215 (m) REVERT: l 53 PHE cc_start: 0.9362 (m-80) cc_final: 0.9065 (m-80) REVERT: l 55 GLU cc_start: 0.8374 (tt0) cc_final: 0.7993 (tt0) REVERT: m 95 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8431 (mm-30) REVERT: m 111 VAL cc_start: 0.8715 (m) cc_final: 0.8473 (p) REVERT: m 119 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8483 (t80) REVERT: m 135 GLU cc_start: 0.8823 (pt0) cc_final: 0.8612 (pt0) REVERT: m 166 ASP cc_start: 0.8595 (p0) cc_final: 0.7792 (p0) REVERT: m 216 ASN cc_start: 0.7684 (t0) cc_final: 0.7073 (m-40) REVERT: m 218 ASP cc_start: 0.8155 (m-30) cc_final: 0.7694 (m-30) REVERT: m 240 VAL cc_start: 0.9603 (OUTLIER) cc_final: 0.9287 (t) REVERT: m 256 MET cc_start: 0.8411 (tpp) cc_final: 0.8166 (mmt) REVERT: n 13 VAL cc_start: 0.9518 (t) cc_final: 0.9278 (p) REVERT: n 46 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7631 (mt-10) REVERT: n 54 THR cc_start: 0.8912 (m) cc_final: 0.8667 (t) REVERT: n 60 SER cc_start: 0.9423 (m) cc_final: 0.9088 (p) REVERT: n 129 GLU cc_start: 0.8656 (tp30) cc_final: 0.7865 (tp30) REVERT: n 226 ASN cc_start: 0.8295 (m-40) cc_final: 0.8032 (m110) REVERT: n 249 ILE cc_start: 0.9396 (mt) cc_final: 0.9120 (mt) REVERT: o 87 SER cc_start: 0.9088 (m) cc_final: 0.7972 (p) REVERT: o 155 TRP cc_start: 0.8823 (t60) cc_final: 0.7772 (t60) REVERT: o 156 ASP cc_start: 0.3847 (m-30) cc_final: 0.3128 (m-30) REVERT: o 194 GLN cc_start: 0.8648 (mm-40) cc_final: 0.8283 (tt0) REVERT: o 207 MET cc_start: 0.8622 (ptp) cc_final: 0.8029 (ptp) REVERT: p 4 GLN cc_start: 0.7945 (mt0) cc_final: 0.7567 (mp10) REVERT: q 61 VAL cc_start: 0.9266 (t) cc_final: 0.9038 (p) REVERT: q 68 SER cc_start: 0.9186 (OUTLIER) cc_final: 0.8776 (t) REVERT: q 126 ASP cc_start: 0.8525 (m-30) cc_final: 0.8185 (m-30) REVERT: q 242 ARG cc_start: 0.8579 (ttm110) cc_final: 0.8338 (mtp-110) REVERT: r 26 GLN cc_start: 0.7060 (mt0) cc_final: 0.6618 (mt0) REVERT: r 50 VAL cc_start: 0.9341 (m) cc_final: 0.9110 (p) REVERT: r 210 VAL cc_start: 0.9604 (p) cc_final: 0.9242 (m) REVERT: r 249 ILE cc_start: 0.9590 (mt) cc_final: 0.9302 (mm) REVERT: s 73 ASN cc_start: 0.9010 (p0) cc_final: 0.8789 (p0) REVERT: s 92 LYS cc_start: 0.8875 (mtmm) cc_final: 0.8615 (mtmm) REVERT: s 143 ASN cc_start: 0.8478 (t0) cc_final: 0.8186 (t0) REVERT: s 144 ARG cc_start: 0.9276 (tmm-80) cc_final: 0.9017 (ttm-80) REVERT: s 165 MET cc_start: 0.7973 (ttm) cc_final: 0.7708 (mtm) REVERT: t 28 THR cc_start: 0.9481 (m) cc_final: 0.9225 (p) outliers start: 163 outliers final: 142 residues processed: 1209 average time/residue: 0.2052 time to fit residues: 407.9210 Evaluate side-chains 1229 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 1082 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 61 VAL Chi-restraints excluded: chain a residue 66 THR Chi-restraints excluded: chain a residue 106 THR Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 129 MET Chi-restraints excluded: chain a residue 130 THR Chi-restraints excluded: chain a residue 134 THR Chi-restraints excluded: chain a residue 293 ASP Chi-restraints excluded: chain a residue 295 ILE Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain b residue 26 GLN Chi-restraints excluded: chain b residue 60 SER Chi-restraints excluded: chain b residue 200 LEU Chi-restraints excluded: chain b residue 234 LEU Chi-restraints excluded: chain b residue 242 THR Chi-restraints excluded: chain b residue 256 MET Chi-restraints excluded: chain b residue 268 VAL Chi-restraints excluded: chain c residue 50 ASP Chi-restraints excluded: chain c residue 74 ASP Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 159 LEU Chi-restraints excluded: chain c residue 184 THR Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain c residue 213 VAL Chi-restraints excluded: chain d residue 60 LEU Chi-restraints excluded: chain d residue 62 LEU Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 104 ASN Chi-restraints excluded: chain e residue 134 THR Chi-restraints excluded: chain e residue 229 ILE Chi-restraints excluded: chain e residue 237 VAL Chi-restraints excluded: chain f residue 32 ILE Chi-restraints excluded: chain f residue 40 THR Chi-restraints excluded: chain f residue 88 ASP Chi-restraints excluded: chain f residue 126 LEU Chi-restraints excluded: chain f residue 146 ILE Chi-restraints excluded: chain f residue 180 LEU Chi-restraints excluded: chain f residue 208 ILE Chi-restraints excluded: chain f residue 249 ILE Chi-restraints excluded: chain f residue 263 LEU Chi-restraints excluded: chain f residue 265 ASN Chi-restraints excluded: chain f residue 268 VAL Chi-restraints excluded: chain g residue 4 THR Chi-restraints excluded: chain g residue 67 MET Chi-restraints excluded: chain g residue 99 LEU Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 203 THR Chi-restraints excluded: chain g residue 207 MET Chi-restraints excluded: chain g residue 224 LEU Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 88 THR Chi-restraints excluded: chain i residue 99 HIS Chi-restraints excluded: chain i residue 100 PHE Chi-restraints excluded: chain i residue 132 VAL Chi-restraints excluded: chain j residue 25 THR Chi-restraints excluded: chain j residue 38 TRP Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 82 LEU Chi-restraints excluded: chain j residue 84 ASP Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 181 LEU Chi-restraints excluded: chain j residue 183 SER Chi-restraints excluded: chain j residue 204 ASN Chi-restraints excluded: chain j residue 246 GLN Chi-restraints excluded: chain j residue 247 VAL Chi-restraints excluded: chain k residue 5 MET Chi-restraints excluded: chain k residue 10 SER Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 30 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain k residue 199 VAL Chi-restraints excluded: chain k residue 223 LEU Chi-restraints excluded: chain k residue 226 ASP Chi-restraints excluded: chain k residue 227 THR Chi-restraints excluded: chain k residue 233 SER Chi-restraints excluded: chain l residue 26 ASN Chi-restraints excluded: chain l residue 44 GLN Chi-restraints excluded: chain m residue 61 VAL Chi-restraints excluded: chain m residue 83 THR Chi-restraints excluded: chain m residue 117 LEU Chi-restraints excluded: chain m residue 119 PHE Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 196 ILE Chi-restraints excluded: chain m residue 221 ASP Chi-restraints excluded: chain m residue 229 ILE Chi-restraints excluded: chain m residue 240 VAL Chi-restraints excluded: chain m residue 251 SER Chi-restraints excluded: chain m residue 265 CYS Chi-restraints excluded: chain n residue 84 ASP Chi-restraints excluded: chain n residue 152 GLU Chi-restraints excluded: chain n residue 183 SER Chi-restraints excluded: chain n residue 186 LEU Chi-restraints excluded: chain n residue 198 ILE Chi-restraints excluded: chain o residue 6 ASN Chi-restraints excluded: chain o residue 27 ASN Chi-restraints excluded: chain o residue 30 VAL Chi-restraints excluded: chain o residue 107 THR Chi-restraints excluded: chain o residue 126 THR Chi-restraints excluded: chain o residue 132 SER Chi-restraints excluded: chain o residue 153 ILE Chi-restraints excluded: chain o residue 198 VAL Chi-restraints excluded: chain o residue 199 VAL Chi-restraints excluded: chain o residue 214 SER Chi-restraints excluded: chain o residue 227 THR Chi-restraints excluded: chain p residue 25 ILE Chi-restraints excluded: chain p residue 40 SER Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain p residue 64 THR Chi-restraints excluded: chain q residue 36 VAL Chi-restraints excluded: chain q residue 68 SER Chi-restraints excluded: chain q residue 71 CYS Chi-restraints excluded: chain q residue 100 PHE Chi-restraints excluded: chain q residue 110 THR Chi-restraints excluded: chain q residue 178 ILE Chi-restraints excluded: chain q residue 217 THR Chi-restraints excluded: chain r residue 18 LEU Chi-restraints excluded: chain r residue 24 THR Chi-restraints excluded: chain r residue 32 ILE Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 51 ASP Chi-restraints excluded: chain r residue 84 ASP Chi-restraints excluded: chain r residue 85 CYS Chi-restraints excluded: chain r residue 86 LEU Chi-restraints excluded: chain r residue 131 VAL Chi-restraints excluded: chain r residue 205 SER Chi-restraints excluded: chain r residue 226 ASN Chi-restraints excluded: chain r residue 268 VAL Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 76 LEU Chi-restraints excluded: chain s residue 85 SER Chi-restraints excluded: chain s residue 86 LEU Chi-restraints excluded: chain s residue 97 THR Chi-restraints excluded: chain s residue 148 MET Chi-restraints excluded: chain s residue 173 THR Chi-restraints excluded: chain s residue 189 ILE Chi-restraints excluded: chain s residue 205 THR Chi-restraints excluded: chain t residue 7 THR Chi-restraints excluded: chain t residue 44 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 121 optimal weight: 10.0000 chunk 146 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 347 optimal weight: 9.9990 chunk 415 optimal weight: 10.0000 chunk 326 optimal weight: 10.0000 chunk 318 optimal weight: 10.0000 chunk 229 optimal weight: 0.9980 chunk 227 optimal weight: 0.8980 chunk 125 optimal weight: 10.0000 chunk 325 optimal weight: 2.9990 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 112 GLN ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 44 GLN i 23 GLN ** i 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 ASN ** n 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 6 ASN ** o 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 8 GLN ** p 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 26 ASN q 18 GLN q 112 GLN ** r 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 4 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.111571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.099244 restraints weight = 66833.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.102103 restraints weight = 31742.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.103997 restraints weight = 18501.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.105262 restraints weight = 12288.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.106145 restraints weight = 9012.266| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.5165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 34975 Z= 0.200 Angle : 0.680 10.600 47711 Z= 0.345 Chirality : 0.048 0.333 5363 Planarity : 0.005 0.053 6193 Dihedral : 5.803 56.508 4860 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.10 % Allowed : 22.20 % Favored : 73.70 % 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: -0.62 (0.12), residues: 4201 helix: -1.88 (0.25), residues: 363 sheet: 0.44 (0.15), residues: 1055 loop : -0.52 (0.11), residues: 2783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG i 67 TYR 0.036 0.002 TYR o 175 PHE 0.031 0.002 PHE c 212 TRP 0.043 0.002 TRP f 227 HIS 0.009 0.001 HIS k 96 Details of bonding type rmsd covalent geometry : bond 0.00464 (34975) covalent geometry : angle 0.68030 (47711) hydrogen bonds : bond 0.03553 ( 924) hydrogen bonds : angle 5.65253 ( 2631) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1266 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 1115 time to evaluate : 1.307 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 n 272 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN r 272 " (corrupted residue). Skipping it. REVERT: a 43 GLU cc_start: 0.8836 (mp0) cc_final: 0.8274 (mp0) REVERT: a 74 SER cc_start: 0.9413 (m) cc_final: 0.9205 (p) REVERT: a 161 ARG cc_start: 0.8553 (ttm170) cc_final: 0.8264 (ttm110) REVERT: a 167 ASP cc_start: 0.8177 (m-30) cc_final: 0.7935 (m-30) REVERT: a 205 ASP cc_start: 0.8782 (t70) cc_final: 0.8464 (t70) REVERT: a 277 GLU cc_start: 0.7623 (mp0) cc_final: 0.7249 (mp0) REVERT: b 87 LYS cc_start: 0.8591 (pttp) cc_final: 0.8290 (ttpt) REVERT: b 97 TYR cc_start: 0.8578 (m-80) cc_final: 0.7785 (m-80) REVERT: b 183 SER cc_start: 0.9209 (p) cc_final: 0.8886 (t) REVERT: b 246 GLN cc_start: 0.8150 (mt0) cc_final: 0.7679 (mt0) REVERT: c 48 GLU cc_start: 0.9199 (mt-10) cc_final: 0.8773 (mt-10) REVERT: c 56 ASN cc_start: 0.9536 (t0) cc_final: 0.9277 (t0) REVERT: c 91 ASP cc_start: 0.8239 (t0) cc_final: 0.7957 (t0) REVERT: c 95 SER cc_start: 0.8934 (p) cc_final: 0.8714 (t) REVERT: c 112 SER cc_start: 0.9269 (m) cc_final: 0.8967 (p) REVERT: c 128 LYS cc_start: 0.8723 (mptt) cc_final: 0.8500 (mptt) REVERT: c 225 ARG cc_start: 0.8710 (ptt180) cc_final: 0.8071 (ptt180) REVERT: d 21 ASN cc_start: 0.7853 (p0) cc_final: 0.6981 (p0) REVERT: e 83 THR cc_start: 0.9297 (t) cc_final: 0.9012 (p) REVERT: e 120 PHE cc_start: 0.9296 (m-80) cc_final: 0.8919 (m-80) REVERT: e 182 TYR cc_start: 0.8939 (t80) cc_final: 0.8490 (t80) REVERT: e 204 TYR cc_start: 0.8881 (t80) cc_final: 0.8440 (t80) REVERT: e 230 ASN cc_start: 0.7921 (t0) cc_final: 0.7688 (t0) REVERT: e 257 LYS cc_start: 0.9061 (ttpp) cc_final: 0.8694 (tttp) REVERT: e 291 LYS cc_start: 0.8935 (mtpt) cc_final: 0.8530 (mttm) REVERT: f 23 ILE cc_start: 0.9327 (mt) cc_final: 0.9083 (mm) REVERT: f 30 ASN cc_start: 0.8565 (t0) cc_final: 0.8187 (t0) REVERT: f 55 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8609 (mt-10) REVERT: f 87 LYS cc_start: 0.9041 (ptmm) cc_final: 0.8443 (ptpp) REVERT: f 91 MET cc_start: 0.8273 (mmm) cc_final: 0.7891 (tpp) REVERT: f 116 LYS cc_start: 0.9128 (mttt) cc_final: 0.8616 (mttp) REVERT: f 170 GLU cc_start: 0.7420 (tp30) cc_final: 0.7043 (tp30) REVERT: f 250 THR cc_start: 0.8555 (m) cc_final: 0.8253 (p) REVERT: g 59 ASP cc_start: 0.8076 (t0) cc_final: 0.7614 (t70) REVERT: g 91 ASP cc_start: 0.8339 (t0) cc_final: 0.8043 (t0) REVERT: g 99 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9136 (tt) REVERT: g 154 ILE cc_start: 0.9299 (mm) cc_final: 0.8940 (mm) REVERT: g 156 ASP cc_start: 0.8380 (t0) cc_final: 0.7574 (p0) REVERT: g 216 CYS cc_start: 0.8722 (m) cc_final: 0.8216 (m) REVERT: g 218 ASP cc_start: 0.8504 (p0) cc_final: 0.8248 (p0) REVERT: h 38 SER cc_start: 0.9262 (m) cc_final: 0.8919 (t) REVERT: i 23 GLN cc_start: 0.8961 (tt0) cc_final: 0.8566 (tt0) REVERT: i 34 GLN cc_start: 0.8857 (mp10) cc_final: 0.7882 (tt0) REVERT: i 95 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7354 (tt0) REVERT: i 96 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7931 (tt0) REVERT: i 154 TYR cc_start: 0.8617 (t80) cc_final: 0.8046 (t80) REVERT: i 168 TYR cc_start: 0.8722 (p90) cc_final: 0.7458 (p90) REVERT: i 171 GLN cc_start: 0.8843 (mp10) cc_final: 0.8506 (mp10) REVERT: j 30 ASN cc_start: 0.7894 (m-40) cc_final: 0.7654 (t0) REVERT: j 44 ASP cc_start: 0.8976 (m-30) cc_final: 0.8504 (m-30) REVERT: j 71 TRP cc_start: 0.9268 (t60) cc_final: 0.9026 (t60) REVERT: j 91 MET cc_start: 0.8558 (mmm) cc_final: 0.7829 (mmt) REVERT: j 110 VAL cc_start: 0.9649 (t) cc_final: 0.9397 (p) REVERT: j 129 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8226 (mm-30) REVERT: j 137 GLU cc_start: 0.7355 (pm20) cc_final: 0.6740 (pm20) REVERT: j 196 GLN cc_start: 0.8962 (tt0) cc_final: 0.8760 (tt0) REVERT: j 223 LYS cc_start: 0.9079 (mtmt) cc_final: 0.8312 (mttp) REVERT: j 227 TRP cc_start: 0.9135 (m100) cc_final: 0.8778 (m100) REVERT: k 18 ASP cc_start: 0.7877 (t70) cc_final: 0.7653 (t70) REVERT: k 39 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7914 (tm-30) REVERT: k 55 MET cc_start: 0.9367 (tpp) cc_final: 0.8767 (tpt) REVERT: k 69 GLN cc_start: 0.8300 (mp10) cc_final: 0.7624 (mp10) REVERT: k 87 SER cc_start: 0.9165 (t) cc_final: 0.8900 (m) REVERT: k 92 LYS cc_start: 0.8959 (mmtm) cc_final: 0.8588 (mtpp) REVERT: k 144 ARG cc_start: 0.8571 (ttm-80) cc_final: 0.7438 (ttm-80) REVERT: k 155 TRP cc_start: 0.8588 (t60) cc_final: 0.7740 (t60) REVERT: k 164 SER cc_start: 0.9430 (m) cc_final: 0.8827 (t) REVERT: k 178 CYS cc_start: 0.8313 (m) cc_final: 0.7460 (m) REVERT: k 194 GLN cc_start: 0.9148 (tp40) cc_final: 0.8530 (mm-40) REVERT: k 216 CYS cc_start: 0.8580 (m) cc_final: 0.8266 (m) REVERT: l 53 PHE cc_start: 0.9417 (m-80) cc_final: 0.9085 (m-80) REVERT: l 55 GLU cc_start: 0.8311 (tt0) cc_final: 0.7925 (tt0) REVERT: m 111 VAL cc_start: 0.8693 (m) cc_final: 0.8431 (p) REVERT: m 119 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.8408 (t80) REVERT: m 122 TYR cc_start: 0.8859 (m-80) cc_final: 0.8432 (m-80) REVERT: m 166 ASP cc_start: 0.8610 (p0) cc_final: 0.7919 (p0) REVERT: m 216 ASN cc_start: 0.7737 (t0) cc_final: 0.7119 (m-40) REVERT: m 218 ASP cc_start: 0.8139 (m-30) cc_final: 0.7686 (m-30) REVERT: m 240 VAL cc_start: 0.9581 (OUTLIER) cc_final: 0.9234 (t) REVERT: n 13 VAL cc_start: 0.9496 (t) cc_final: 0.9264 (p) REVERT: n 46 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7624 (mt-10) REVERT: n 60 SER cc_start: 0.9387 (m) cc_final: 0.9102 (p) REVERT: n 129 GLU cc_start: 0.8668 (tp30) cc_final: 0.7824 (tp30) REVERT: n 186 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8221 (mp) REVERT: n 226 ASN cc_start: 0.8265 (m-40) cc_final: 0.8046 (m110) REVERT: n 249 ILE cc_start: 0.9369 (mt) cc_final: 0.9087 (mt) REVERT: o 87 SER cc_start: 0.9093 (m) cc_final: 0.7997 (p) REVERT: o 144 ARG cc_start: 0.7559 (ttp-170) cc_final: 0.7219 (ttp-170) REVERT: o 148 MET cc_start: 0.5938 (ttm) cc_final: 0.5575 (ttt) REVERT: o 155 TRP cc_start: 0.8839 (t60) cc_final: 0.7840 (t60) REVERT: o 156 ASP cc_start: 0.3821 (m-30) cc_final: 0.3096 (m-30) REVERT: o 194 GLN cc_start: 0.8648 (mm-40) cc_final: 0.8344 (tt0) REVERT: o 207 MET cc_start: 0.8589 (ptp) cc_final: 0.8122 (ptp) REVERT: p 4 GLN cc_start: 0.7935 (mt0) cc_final: 0.7624 (mp10) REVERT: q 126 ASP cc_start: 0.8575 (m-30) cc_final: 0.8224 (m-30) REVERT: q 242 ARG cc_start: 0.8570 (ttm110) cc_final: 0.8322 (mtp-110) REVERT: r 26 GLN cc_start: 0.7125 (mt0) cc_final: 0.6651 (mt0) REVERT: r 50 VAL cc_start: 0.9316 (m) cc_final: 0.9096 (p) REVERT: r 210 VAL cc_start: 0.9606 (p) cc_final: 0.9245 (m) REVERT: r 249 ILE cc_start: 0.9576 (mt) cc_final: 0.9287 (mm) REVERT: s 44 MET cc_start: 0.8388 (mmm) cc_final: 0.8143 (tpp) REVERT: s 92 LYS cc_start: 0.8859 (mtmm) cc_final: 0.8640 (mtmm) REVERT: s 143 ASN cc_start: 0.8485 (t0) cc_final: 0.8205 (t0) REVERT: s 144 ARG cc_start: 0.9251 (tmm-80) cc_final: 0.9005 (ttm-80) REVERT: s 175 TYR cc_start: 0.8606 (m-80) cc_final: 0.8392 (m-10) REVERT: s 191 CYS cc_start: 0.9115 (t) cc_final: 0.8620 (t) REVERT: t 28 THR cc_start: 0.9472 (m) cc_final: 0.9235 (p) outliers start: 151 outliers final: 132 residues processed: 1191 average time/residue: 0.2005 time to fit residues: 393.2945 Evaluate side-chains 1224 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 1088 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 61 VAL Chi-restraints excluded: chain a residue 66 THR Chi-restraints excluded: chain a residue 106 THR Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 129 MET Chi-restraints excluded: chain a residue 130 THR Chi-restraints excluded: chain a residue 134 THR Chi-restraints excluded: chain a residue 227 VAL Chi-restraints excluded: chain a residue 293 ASP Chi-restraints excluded: chain a residue 295 ILE Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain b residue 26 GLN Chi-restraints excluded: chain b residue 60 SER Chi-restraints excluded: chain b residue 200 LEU Chi-restraints excluded: chain b residue 242 THR Chi-restraints excluded: chain b residue 256 MET Chi-restraints excluded: chain b residue 268 VAL Chi-restraints excluded: chain c residue 17 ASP Chi-restraints excluded: chain c residue 50 ASP Chi-restraints excluded: chain c residue 74 ASP Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 159 LEU Chi-restraints excluded: chain c residue 184 THR Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain c residue 213 VAL Chi-restraints excluded: chain d residue 62 LEU Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 104 ASN Chi-restraints excluded: chain e residue 134 THR Chi-restraints excluded: chain e residue 229 ILE Chi-restraints excluded: chain e residue 237 VAL Chi-restraints excluded: chain f residue 88 ASP Chi-restraints excluded: chain f residue 126 LEU Chi-restraints excluded: chain f residue 146 ILE Chi-restraints excluded: chain f residue 180 LEU Chi-restraints excluded: chain f residue 249 ILE Chi-restraints excluded: chain f residue 263 LEU Chi-restraints excluded: chain f residue 268 VAL Chi-restraints excluded: chain g residue 67 MET Chi-restraints excluded: chain g residue 99 LEU Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 203 THR Chi-restraints excluded: chain g residue 207 MET Chi-restraints excluded: chain g residue 224 LEU Chi-restraints excluded: chain g residue 227 THR Chi-restraints excluded: chain h residue 7 THR Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 88 THR Chi-restraints excluded: chain i residue 99 HIS Chi-restraints excluded: chain i residue 100 PHE Chi-restraints excluded: chain i residue 132 VAL Chi-restraints excluded: chain i residue 227 VAL Chi-restraints excluded: chain i residue 248 ILE Chi-restraints excluded: chain j residue 25 THR Chi-restraints excluded: chain j residue 38 TRP Chi-restraints excluded: chain j residue 40 THR Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 82 LEU Chi-restraints excluded: chain j residue 84 ASP Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 181 LEU Chi-restraints excluded: chain j residue 204 ASN Chi-restraints excluded: chain j residue 246 GLN Chi-restraints excluded: chain k residue 10 SER Chi-restraints excluded: chain k residue 30 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain k residue 189 ILE Chi-restraints excluded: chain k residue 199 VAL Chi-restraints excluded: chain k residue 223 LEU Chi-restraints excluded: chain k residue 227 THR Chi-restraints excluded: chain m residue 61 VAL Chi-restraints excluded: chain m residue 83 THR Chi-restraints excluded: chain m residue 117 LEU Chi-restraints excluded: chain m residue 119 PHE Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 173 SER Chi-restraints excluded: chain m residue 196 ILE Chi-restraints excluded: chain m residue 221 ASP Chi-restraints excluded: chain m residue 240 VAL Chi-restraints excluded: chain m residue 251 SER Chi-restraints excluded: chain m residue 265 CYS Chi-restraints excluded: chain n residue 40 THR Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 84 ASP Chi-restraints excluded: chain n residue 152 GLU Chi-restraints excluded: chain n residue 183 SER Chi-restraints excluded: chain n residue 186 LEU Chi-restraints excluded: chain n residue 198 ILE Chi-restraints excluded: chain o residue 27 ASN Chi-restraints excluded: chain o residue 30 VAL Chi-restraints excluded: chain o residue 53 ILE Chi-restraints excluded: chain o residue 107 THR Chi-restraints excluded: chain o residue 126 THR Chi-restraints excluded: chain o residue 132 SER Chi-restraints excluded: chain o residue 198 VAL Chi-restraints excluded: chain o residue 199 VAL Chi-restraints excluded: chain o residue 214 SER Chi-restraints excluded: chain p residue 25 ILE Chi-restraints excluded: chain p residue 40 SER Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain q residue 36 VAL Chi-restraints excluded: chain q residue 68 SER Chi-restraints excluded: chain q residue 71 CYS Chi-restraints excluded: chain q residue 100 PHE Chi-restraints excluded: chain q residue 110 THR Chi-restraints excluded: chain q residue 178 ILE Chi-restraints excluded: chain q residue 217 THR Chi-restraints excluded: chain r residue 32 ILE Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 51 ASP Chi-restraints excluded: chain r residue 84 ASP Chi-restraints excluded: chain r residue 85 CYS Chi-restraints excluded: chain r residue 86 LEU Chi-restraints excluded: chain r residue 111 GLN Chi-restraints excluded: chain r residue 131 VAL Chi-restraints excluded: chain r residue 192 VAL Chi-restraints excluded: chain r residue 205 SER Chi-restraints excluded: chain r residue 268 VAL Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 76 LEU Chi-restraints excluded: chain s residue 85 SER Chi-restraints excluded: chain s residue 86 LEU Chi-restraints excluded: chain s residue 97 THR Chi-restraints excluded: chain s residue 148 MET Chi-restraints excluded: chain s residue 173 THR Chi-restraints excluded: chain s residue 189 ILE Chi-restraints excluded: chain s residue 205 THR Chi-restraints excluded: chain t residue 7 THR Chi-restraints excluded: chain t residue 44 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 60 optimal weight: 7.9990 chunk 171 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 325 optimal weight: 8.9990 chunk 160 optimal weight: 7.9990 chunk 153 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 chunk 344 optimal weight: 7.9990 chunk 264 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 294 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 6 ASN c 11 ASN ** e 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 ASN ** i 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 ASN ** m 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 6 ASN ** o 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 26 ASN ** p 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 4 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.110684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.098385 restraints weight = 67408.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.101284 restraints weight = 31990.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.103197 restraints weight = 18495.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.104440 restraints weight = 12300.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.105312 restraints weight = 9024.843| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 34975 Z= 0.214 Angle : 0.698 12.246 47711 Z= 0.352 Chirality : 0.048 0.339 5363 Planarity : 0.005 0.056 6193 Dihedral : 5.846 59.925 4860 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.18 % Allowed : 22.42 % Favored : 73.40 % 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: -0.74 (0.12), residues: 4201 helix: -1.98 (0.24), residues: 387 sheet: 0.35 (0.15), residues: 1063 loop : -0.59 (0.11), residues: 2751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG i 67 TYR 0.038 0.002 TYR b 179 PHE 0.044 0.002 PHE c 19 TRP 0.053 0.002 TRP n 71 HIS 0.009 0.001 HIS k 96 Details of bonding type rmsd covalent geometry : bond 0.00496 (34975) covalent geometry : angle 0.69773 (47711) hydrogen bonds : bond 0.03573 ( 924) hydrogen bonds : angle 5.65704 ( 2631) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1272 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 1118 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN n 272 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN r 272 " (corrupted residue). Skipping it. REVERT: a 43 GLU cc_start: 0.8859 (mp0) cc_final: 0.8308 (mp0) REVERT: a 54 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.8359 (m-30) REVERT: a 69 GLU cc_start: 0.7861 (tt0) cc_final: 0.7627 (tt0) REVERT: a 161 ARG cc_start: 0.8594 (ttm170) cc_final: 0.8298 (ttm110) REVERT: a 167 ASP cc_start: 0.8187 (m-30) cc_final: 0.7934 (m-30) REVERT: a 205 ASP cc_start: 0.8651 (t70) cc_final: 0.8197 (t70) REVERT: a 277 GLU cc_start: 0.7618 (mp0) cc_final: 0.7238 (mp0) REVERT: b 87 LYS cc_start: 0.8571 (pttp) cc_final: 0.8355 (ttpt) REVERT: b 97 TYR cc_start: 0.8600 (m-80) cc_final: 0.7728 (m-80) REVERT: b 183 SER cc_start: 0.9269 (p) cc_final: 0.8939 (t) REVERT: b 227 TRP cc_start: 0.8830 (m100) cc_final: 0.8414 (m100) REVERT: b 246 GLN cc_start: 0.8131 (mt0) cc_final: 0.7658 (mt0) REVERT: c 48 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8763 (mt-10) REVERT: c 56 ASN cc_start: 0.9528 (t0) cc_final: 0.9175 (t0) REVERT: c 95 SER cc_start: 0.8979 (p) cc_final: 0.8747 (t) REVERT: c 112 SER cc_start: 0.9245 (m) cc_final: 0.8962 (p) REVERT: c 128 LYS cc_start: 0.8693 (mptt) cc_final: 0.8481 (mptt) REVERT: c 225 ARG cc_start: 0.8697 (ptt180) cc_final: 0.8129 (ptt180) REVERT: d 21 ASN cc_start: 0.7895 (p0) cc_final: 0.6980 (p0) REVERT: e 83 THR cc_start: 0.9291 (t) cc_final: 0.9014 (p) REVERT: e 120 PHE cc_start: 0.9300 (m-80) cc_final: 0.8922 (m-80) REVERT: e 182 TYR cc_start: 0.8915 (t80) cc_final: 0.8533 (t80) REVERT: e 204 TYR cc_start: 0.8903 (t80) cc_final: 0.8371 (t80) REVERT: e 230 ASN cc_start: 0.7983 (t0) cc_final: 0.7645 (t0) REVERT: e 257 LYS cc_start: 0.9065 (ttpp) cc_final: 0.8691 (tttp) REVERT: e 286 ILE cc_start: 0.8896 (pt) cc_final: 0.8601 (mt) REVERT: e 291 LYS cc_start: 0.8939 (mtpt) cc_final: 0.8560 (mttm) REVERT: f 23 ILE cc_start: 0.9325 (mt) cc_final: 0.9068 (mm) REVERT: f 30 ASN cc_start: 0.8485 (t0) cc_final: 0.8134 (t0) REVERT: f 55 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8588 (mt-10) REVERT: f 87 LYS cc_start: 0.9068 (ptmm) cc_final: 0.8448 (ptpp) REVERT: f 91 MET cc_start: 0.8196 (mmm) cc_final: 0.7809 (tpp) REVERT: f 116 LYS cc_start: 0.9129 (mttt) cc_final: 0.8633 (mttp) REVERT: f 170 GLU cc_start: 0.7395 (tp30) cc_final: 0.7074 (tp30) REVERT: f 193 TYR cc_start: 0.9027 (m-80) cc_final: 0.8255 (m-10) REVERT: f 250 THR cc_start: 0.8538 (m) cc_final: 0.8227 (p) REVERT: f 264 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.7126 (ptt180) REVERT: g 59 ASP cc_start: 0.8052 (t0) cc_final: 0.7658 (t70) REVERT: g 91 ASP cc_start: 0.8334 (t0) cc_final: 0.8042 (t0) REVERT: g 99 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9127 (tt) REVERT: g 123 MET cc_start: 0.8242 (tpp) cc_final: 0.7971 (tpt) REVERT: g 216 CYS cc_start: 0.8742 (m) cc_final: 0.8296 (m) REVERT: g 218 ASP cc_start: 0.8498 (p0) cc_final: 0.8228 (p0) REVERT: h 38 SER cc_start: 0.9256 (m) cc_final: 0.8914 (t) REVERT: i 23 GLN cc_start: 0.8974 (tt0) cc_final: 0.8567 (tt0) REVERT: i 34 GLN cc_start: 0.8829 (mp10) cc_final: 0.7882 (tt0) REVERT: i 95 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7402 (tt0) REVERT: i 98 LYS cc_start: 0.8912 (mttt) cc_final: 0.8634 (mtpt) REVERT: i 154 TYR cc_start: 0.8659 (t80) cc_final: 0.8204 (t80) REVERT: i 168 TYR cc_start: 0.8763 (p90) cc_final: 0.7529 (p90) REVERT: i 171 GLN cc_start: 0.8810 (mp10) cc_final: 0.8501 (mp10) REVERT: j 44 ASP cc_start: 0.8987 (m-30) cc_final: 0.8504 (m-30) REVERT: j 71 TRP cc_start: 0.9296 (t60) cc_final: 0.9022 (t60) REVERT: j 91 MET cc_start: 0.8536 (mmm) cc_final: 0.8082 (mmp) REVERT: j 110 VAL cc_start: 0.9643 (t) cc_final: 0.9393 (p) REVERT: j 129 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8193 (mm-30) REVERT: j 137 GLU cc_start: 0.7349 (pm20) cc_final: 0.6742 (pm20) REVERT: j 196 GLN cc_start: 0.8928 (tt0) cc_final: 0.8718 (tt0) REVERT: j 223 LYS cc_start: 0.9093 (mtmt) cc_final: 0.8353 (mttp) REVERT: j 227 TRP cc_start: 0.9131 (m100) cc_final: 0.8787 (m100) REVERT: k 39 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7940 (tm-30) REVERT: k 55 MET cc_start: 0.9387 (tpp) cc_final: 0.8902 (tpt) REVERT: k 69 GLN cc_start: 0.8300 (mp10) cc_final: 0.7614 (mp10) REVERT: k 87 SER cc_start: 0.9109 (t) cc_final: 0.8873 (m) REVERT: k 92 LYS cc_start: 0.8963 (mmtm) cc_final: 0.8621 (mtpp) REVERT: k 144 ARG cc_start: 0.8577 (ttm-80) cc_final: 0.7387 (ttm-80) REVERT: k 155 TRP cc_start: 0.8594 (t60) cc_final: 0.7729 (t60) REVERT: k 164 SER cc_start: 0.9408 (m) cc_final: 0.8802 (t) REVERT: k 178 CYS cc_start: 0.8341 (m) cc_final: 0.7426 (m) REVERT: k 194 GLN cc_start: 0.9131 (tp40) cc_final: 0.8566 (mm-40) REVERT: k 216 CYS cc_start: 0.8583 (m) cc_final: 0.8285 (m) REVERT: l 53 PHE cc_start: 0.9430 (m-80) cc_final: 0.9139 (m-80) REVERT: l 55 GLU cc_start: 0.8354 (tt0) cc_final: 0.7980 (tt0) REVERT: m 111 VAL cc_start: 0.8717 (m) cc_final: 0.8469 (p) REVERT: m 119 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.8450 (t80) REVERT: m 122 TYR cc_start: 0.8881 (m-80) cc_final: 0.8545 (m-80) REVERT: m 166 ASP cc_start: 0.8644 (p0) cc_final: 0.7814 (p0) REVERT: m 209 ARG cc_start: 0.8925 (ttp80) cc_final: 0.8594 (ptm-80) REVERT: m 216 ASN cc_start: 0.7613 (t0) cc_final: 0.7297 (m-40) REVERT: m 218 ASP cc_start: 0.8191 (m-30) cc_final: 0.7762 (m-30) REVERT: m 240 VAL cc_start: 0.9574 (OUTLIER) cc_final: 0.9230 (t) REVERT: m 256 MET cc_start: 0.8352 (tpp) cc_final: 0.8025 (mmp) REVERT: n 13 VAL cc_start: 0.9498 (t) cc_final: 0.9262 (p) REVERT: n 46 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7638 (mt-10) REVERT: n 60 SER cc_start: 0.9370 (m) cc_final: 0.9097 (p) REVERT: n 129 GLU cc_start: 0.8672 (tp30) cc_final: 0.7898 (tp30) REVERT: n 226 ASN cc_start: 0.8247 (m-40) cc_final: 0.7996 (m110) REVERT: n 249 ILE cc_start: 0.9378 (mt) cc_final: 0.9087 (mt) REVERT: o 87 SER cc_start: 0.9095 (m) cc_final: 0.8004 (p) REVERT: o 105 TYR cc_start: 0.8919 (m-80) cc_final: 0.8598 (m-80) REVERT: o 144 ARG cc_start: 0.7571 (ttp-170) cc_final: 0.7204 (ttp-170) REVERT: o 148 MET cc_start: 0.5985 (ttm) cc_final: 0.5654 (ttt) REVERT: o 155 TRP cc_start: 0.8849 (t60) cc_final: 0.7865 (t60) REVERT: o 156 ASP cc_start: 0.3874 (m-30) cc_final: 0.3143 (m-30) REVERT: o 194 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8304 (tt0) REVERT: o 207 MET cc_start: 0.8564 (ptp) cc_final: 0.8091 (ptp) REVERT: p 4 GLN cc_start: 0.7903 (mt0) cc_final: 0.7579 (mp10) REVERT: q 68 SER cc_start: 0.9149 (OUTLIER) cc_final: 0.8714 (t) REVERT: q 126 ASP cc_start: 0.8541 (m-30) cc_final: 0.8159 (m-30) REVERT: r 26 GLN cc_start: 0.7076 (mt0) cc_final: 0.6588 (mt0) REVERT: r 50 VAL cc_start: 0.9321 (m) cc_final: 0.9108 (p) REVERT: r 210 VAL cc_start: 0.9599 (p) cc_final: 0.9245 (m) REVERT: r 249 ILE cc_start: 0.9574 (mt) cc_final: 0.9240 (mm) REVERT: s 44 MET cc_start: 0.8344 (mmm) cc_final: 0.8111 (tpp) REVERT: s 92 LYS cc_start: 0.8867 (mtmm) cc_final: 0.8665 (mtmm) REVERT: s 143 ASN cc_start: 0.8523 (t0) cc_final: 0.8244 (t0) REVERT: s 144 ARG cc_start: 0.9253 (tmm-80) cc_final: 0.9022 (ttm-80) REVERT: s 175 TYR cc_start: 0.8563 (m-80) cc_final: 0.8271 (m-10) REVERT: s 191 CYS cc_start: 0.9124 (t) cc_final: 0.8704 (t) REVERT: s 193 TYR cc_start: 0.8760 (m-10) cc_final: 0.8547 (m-10) REVERT: t 28 THR cc_start: 0.9469 (m) cc_final: 0.9224 (p) outliers start: 154 outliers final: 139 residues processed: 1191 average time/residue: 0.2027 time to fit residues: 395.8237 Evaluate side-chains 1221 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 1076 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 54 ASP Chi-restraints excluded: chain a residue 61 VAL Chi-restraints excluded: chain a residue 66 THR Chi-restraints excluded: chain a residue 106 THR Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 129 MET Chi-restraints excluded: chain a residue 130 THR Chi-restraints excluded: chain a residue 134 THR Chi-restraints excluded: chain a residue 227 VAL Chi-restraints excluded: chain a residue 293 ASP Chi-restraints excluded: chain a residue 295 ILE Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain b residue 26 GLN Chi-restraints excluded: chain b residue 60 SER Chi-restraints excluded: chain b residue 200 LEU Chi-restraints excluded: chain b residue 234 LEU Chi-restraints excluded: chain b residue 242 THR Chi-restraints excluded: chain b residue 256 MET Chi-restraints excluded: chain b residue 268 VAL Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 17 ASP Chi-restraints excluded: chain c residue 50 ASP Chi-restraints excluded: chain c residue 74 ASP Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 159 LEU Chi-restraints excluded: chain c residue 184 THR Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain c residue 213 VAL Chi-restraints excluded: chain d residue 62 LEU Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 104 ASN Chi-restraints excluded: chain e residue 134 THR Chi-restraints excluded: chain e residue 229 ILE Chi-restraints excluded: chain e residue 237 VAL Chi-restraints excluded: chain f residue 88 ASP Chi-restraints excluded: chain f residue 126 LEU Chi-restraints excluded: chain f residue 146 ILE Chi-restraints excluded: chain f residue 180 LEU Chi-restraints excluded: chain f residue 249 ILE Chi-restraints excluded: chain f residue 263 LEU Chi-restraints excluded: chain f residue 264 ARG Chi-restraints excluded: chain f residue 268 VAL Chi-restraints excluded: chain g residue 67 MET Chi-restraints excluded: chain g residue 99 LEU Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 203 THR Chi-restraints excluded: chain g residue 207 MET Chi-restraints excluded: chain g residue 224 LEU Chi-restraints excluded: chain g residue 227 THR Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 88 THR Chi-restraints excluded: chain i residue 99 HIS Chi-restraints excluded: chain i residue 100 PHE Chi-restraints excluded: chain i residue 132 VAL Chi-restraints excluded: chain i residue 227 VAL Chi-restraints excluded: chain i residue 248 ILE Chi-restraints excluded: chain j residue 25 THR Chi-restraints excluded: chain j residue 38 TRP Chi-restraints excluded: chain j residue 40 THR Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 82 LEU Chi-restraints excluded: chain j residue 84 ASP Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 181 LEU Chi-restraints excluded: chain j residue 183 SER Chi-restraints excluded: chain j residue 204 ASN Chi-restraints excluded: chain j residue 246 GLN Chi-restraints excluded: chain k residue 10 SER Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 30 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain k residue 189 ILE Chi-restraints excluded: chain k residue 199 VAL Chi-restraints excluded: chain k residue 223 LEU Chi-restraints excluded: chain k residue 227 THR Chi-restraints excluded: chain l residue 44 GLN Chi-restraints excluded: chain m residue 61 VAL Chi-restraints excluded: chain m residue 83 THR Chi-restraints excluded: chain m residue 117 LEU Chi-restraints excluded: chain m residue 119 PHE Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 173 SER Chi-restraints excluded: chain m residue 196 ILE Chi-restraints excluded: chain m residue 221 ASP Chi-restraints excluded: chain m residue 240 VAL Chi-restraints excluded: chain m residue 251 SER Chi-restraints excluded: chain m residue 265 CYS Chi-restraints excluded: chain n residue 84 ASP Chi-restraints excluded: chain n residue 152 GLU Chi-restraints excluded: chain n residue 183 SER Chi-restraints excluded: chain n residue 186 LEU Chi-restraints excluded: chain n residue 198 ILE Chi-restraints excluded: chain o residue 6 ASN Chi-restraints excluded: chain o residue 30 VAL Chi-restraints excluded: chain o residue 53 ILE Chi-restraints excluded: chain o residue 107 THR Chi-restraints excluded: chain o residue 126 THR Chi-restraints excluded: chain o residue 132 SER Chi-restraints excluded: chain o residue 198 VAL Chi-restraints excluded: chain o residue 199 VAL Chi-restraints excluded: chain o residue 213 VAL Chi-restraints excluded: chain o residue 214 SER Chi-restraints excluded: chain p residue 25 ILE Chi-restraints excluded: chain p residue 40 SER Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain q residue 36 VAL Chi-restraints excluded: chain q residue 68 SER Chi-restraints excluded: chain q residue 71 CYS Chi-restraints excluded: chain q residue 100 PHE Chi-restraints excluded: chain q residue 110 THR Chi-restraints excluded: chain q residue 178 ILE Chi-restraints excluded: chain q residue 217 THR Chi-restraints excluded: chain r residue 32 ILE Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 51 ASP Chi-restraints excluded: chain r residue 84 ASP Chi-restraints excluded: chain r residue 85 CYS Chi-restraints excluded: chain r residue 86 LEU Chi-restraints excluded: chain r residue 111 GLN Chi-restraints excluded: chain r residue 131 VAL Chi-restraints excluded: chain r residue 173 LYS Chi-restraints excluded: chain r residue 192 VAL Chi-restraints excluded: chain r residue 205 SER Chi-restraints excluded: chain r residue 252 THR Chi-restraints excluded: chain r residue 268 VAL Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 74 ASP Chi-restraints excluded: chain s residue 76 LEU Chi-restraints excluded: chain s residue 85 SER Chi-restraints excluded: chain s residue 86 LEU Chi-restraints excluded: chain s residue 97 THR Chi-restraints excluded: chain s residue 148 MET Chi-restraints excluded: chain s residue 173 THR Chi-restraints excluded: chain s residue 177 ARG Chi-restraints excluded: chain s residue 189 ILE Chi-restraints excluded: chain s residue 195 THR Chi-restraints excluded: chain s residue 205 THR Chi-restraints excluded: chain t residue 7 THR Chi-restraints excluded: chain t residue 44 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 154 optimal weight: 9.9990 chunk 353 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 306 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 184 optimal weight: 10.0000 chunk 239 optimal weight: 6.9990 chunk 375 optimal weight: 4.9990 chunk 391 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 196 GLN ** h 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 ASN ** i 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 31 ASN l 39 ASN ** m 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 202 HIS ** n 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 6 ASN ** o 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 8 GLN ** p 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 26 ASN ** p 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 63 ASN ** r 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 12 GLN ** s 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 229 HIS ** 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 = 0.3197 r_free = 0.3197 target = 0.112718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.100524 restraints weight = 66708.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.103423 restraints weight = 31521.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.105342 restraints weight = 18226.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.106606 restraints weight = 12061.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.107474 restraints weight = 8783.638| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.5365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 34975 Z= 0.166 Angle : 0.686 12.217 47711 Z= 0.345 Chirality : 0.047 0.349 5363 Planarity : 0.004 0.051 6193 Dihedral : 5.797 58.873 4860 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.85 % Allowed : 23.13 % Favored : 73.02 % 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: -0.69 (0.12), residues: 4201 helix: -1.92 (0.23), residues: 393 sheet: 0.43 (0.15), residues: 1048 loop : -0.58 (0.12), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG i 67 TYR 0.033 0.002 TYR g 106 PHE 0.040 0.002 PHE c 19 TRP 0.060 0.002 TRP n 71 HIS 0.009 0.001 HIS k 96 Details of bonding type rmsd covalent geometry : bond 0.00389 (34975) covalent geometry : angle 0.68557 (47711) hydrogen bonds : bond 0.03440 ( 924) hydrogen bonds : angle 5.59441 ( 2631) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7352.33 seconds wall clock time: 127 minutes 25.74 seconds (7645.74 seconds total)