Starting phenix.real_space_refine on Sun Jun 29 06:16:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tqs_26068/06_2025/7tqs_26068.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tqs_26068/06_2025/7tqs_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_26068/06_2025/7tqs_26068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tqs_26068/06_2025/7tqs_26068.map" model { file = "/net/cci-nas-00/data/ceres_data/7tqs_26068/06_2025/7tqs_26068.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tqs_26068/06_2025/7tqs_26068.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 19.44, per 1000 atoms: 0.57 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: 9.25 Conformation dependent library (CDL) restraints added in 4.1 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: 4.66 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: 14.12 Time building geometry restraints manager: 10.41 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 298 or resid 300)) selection = (chain 'i' and (resid 17 through 298 or resid 300)) selection = (chain 'm' and (resid 17 through 298 or resid 300)) selection = (chain 'q' and (resid 17 through 298 or resid 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.460 Check model and map are aligned: 0.260 Set scattering table: 0.330 Process input model: 76.860 Find NCS groups from input model: 2.260 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.360 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (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 TRP 0.047 0.007 TRP r 227 HIS 0.013 0.003 HIS q 246 PHE 0.030 0.006 PHE o 82 TYR 0.060 0.009 TYR i 168 ARG 0.013 0.001 ARG a 275 Details of bonding type rmsd hydrogen bonds : bond 0.15500 ( 924) hydrogen bonds : angle 8.60762 ( 2631) covalent geometry : bond 0.02119 (34975) covalent geometry : angle 1.80408 (47711) *********************** 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 : 3.516 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: 0.8948 (p) REVERT: a 49 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8311 (mm110) REVERT: a 105 ILE cc_start: 0.9599 (mt) cc_final: 0.9353 (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: 0.8289 (p) REVERT: a 174 SER cc_start: 0.9349 (m) cc_final: 0.8899 (t) REVERT: a 175 ASN cc_start: 0.8950 (m-40) cc_final: 0.8557 (m-40) 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: 0.7054 (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: 0.8378 (m-80) REVERT: b 104 SER cc_start: 0.9120 (t) cc_final: 0.8583 (p) REVERT: b 106 TYR cc_start: 0.9099 (m-80) cc_final: 0.8383 (m-80) REVERT: b 142 TYR cc_start: 0.7909 (t80) cc_final: 0.7703 (t80) REVERT: b 149 ASN cc_start: 0.8889 (m-40) cc_final: 0.8228 (m-40) REVERT: b 170 GLU cc_start: 0.7665 (mm-30) cc_final: 0.6639 (mm-30) REVERT: b 183 SER cc_start: 0.9111 (p) cc_final: 0.8754 (t) REVERT: b 193 TYR cc_start: 0.9072 (m-80) cc_final: 0.8863 (m-10) REVERT: b 198 ILE cc_start: 0.9456 (mt) cc_final: 0.9212 (tt) REVERT: b 249 ILE cc_start: 0.9584 (mt) cc_final: 0.9343 (mm) REVERT: c 10 SER cc_start: 0.9413 (t) cc_final: 0.9038 (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: 0.9348 (t0) REVERT: c 112 SER cc_start: 0.9560 (m) cc_final: 0.9252 (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: 0.7831 (m-30) REVERT: c 235 LEU cc_start: 0.8517 (mt) cc_final: 0.8201 (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: 0.8593 (pt) REVERT: e 163 SER cc_start: 0.8982 (p) cc_final: 0.8694 (p) REVERT: e 174 SER cc_start: 0.8993 (m) cc_final: 0.8571 (t) REVERT: e 182 TYR cc_start: 0.8653 (t80) cc_final: 0.8399 (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: 0.8720 (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: 0.7767 (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: 0.8655 (pttp) REVERT: f 122 LEU cc_start: 0.9410 (mt) cc_final: 0.9144 (mt) REVERT: f 145 TYR cc_start: 0.9071 (t80) cc_final: 0.8784 (t80) REVERT: g 6 ASN cc_start: 0.9067 (m-40) cc_final: 0.8866 (m-40) REVERT: g 42 ASN cc_start: 0.8498 (t0) cc_final: 0.8234 (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: 0.8332 (m-80) REVERT: g 112 SER cc_start: 0.9114 (m) cc_final: 0.8352 (p) REVERT: g 156 ASP cc_start: 0.8286 (t0) cc_final: 0.7672 (p0) REVERT: g 172 ASN cc_start: 0.9271 (p0) cc_final: 0.8941 (p0) REVERT: g 198 VAL cc_start: 0.9584 (t) cc_final: 0.9325 (p) REVERT: g 216 CYS cc_start: 0.8751 (m) cc_final: 0.7731 (m) REVERT: h 27 TYR cc_start: 0.9154 (p90) cc_final: 0.8822 (p90) REVERT: i 98 LYS cc_start: 0.8998 (mttt) cc_final: 0.8711 (mtpp) REVERT: i 101 ASN cc_start: 0.8468 (t0) cc_final: 0.8211 (t0) REVERT: i 105 ILE cc_start: 0.9092 (mm) cc_final: 0.8789 (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: 0.8519 (tp) REVERT: i 166 ASP cc_start: 0.7404 (p0) cc_final: 0.5743 (p0) REVERT: i 204 TYR cc_start: 0.8719 (t80) cc_final: 0.8185 (t80) REVERT: i 267 ARG cc_start: 0.9220 (mtp85) cc_final: 0.8767 (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: 0.7697 (t70) REVERT: j 91 MET cc_start: 0.8322 (mmm) cc_final: 0.8101 (mmt) REVERT: j 131 VAL cc_start: 0.9448 (t) cc_final: 0.9006 (p) REVERT: j 137 GLU cc_start: 0.7294 (pm20) cc_final: 0.6855 (tp30) REVERT: j 179 TYR cc_start: 0.8460 (p90) cc_final: 0.8065 (p90) REVERT: j 192 VAL cc_start: 0.9457 (m) cc_final: 0.9249 (t) REVERT: j 223 LYS cc_start: 0.9233 (mtmt) cc_final: 0.8603 (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: 0.7189 (pt0) REVERT: j 265 ASN cc_start: 0.7796 (t0) cc_final: 0.7528 (t0) REVERT: k 2 LEU cc_start: 0.9267 (tp) cc_final: 0.9015 (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: 0.8789 (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: 0.8160 (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: 0.8152 (m) REVERT: k 183 PHE cc_start: 0.8169 (t80) cc_final: 0.7947 (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: 0.7997 (m-30) REVERT: m 95 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7868 (mm-30) REVERT: m 105 ILE cc_start: 0.9163 (mt) cc_final: 0.8799 (mt) REVERT: m 127 LEU cc_start: 0.8930 (tp) cc_final: 0.8477 (tp) REVERT: m 166 ASP cc_start: 0.8803 (p0) cc_final: 0.8009 (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: 0.6482 (m-40) REVERT: m 218 ASP cc_start: 0.7770 (m-30) cc_final: 0.7450 (m-30) REVERT: n 13 VAL cc_start: 0.9589 (t) cc_final: 0.9229 (p) REVERT: n 33 VAL cc_start: 0.9639 (t) cc_final: 0.9413 (m) REVERT: n 60 SER cc_start: 0.9406 (m) cc_final: 0.8981 (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: 0.8735 (t-90) cc_final: 0.8235 (t-90) REVERT: o 87 SER cc_start: 0.9241 (m) cc_final: 0.8869 (p) REVERT: o 98 MET cc_start: 0.8622 (tpp) cc_final: 0.8422 (tpp) REVERT: o 128 LYS cc_start: 0.7191 (mttt) cc_final: 0.6957 (mttt) REVERT: o 153 ILE cc_start: 0.9226 (tt) cc_final: 0.8975 (tp) REVERT: p 46 LEU cc_start: 0.8599 (mt) cc_final: 0.8396 (mt) REVERT: p 64 THR cc_start: 0.9140 (p) cc_final: 0.8108 (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: 0.7447 (m-30) REVERT: q 126 ASP cc_start: 0.7917 (m-30) cc_final: 0.7589 (m-30) REVERT: q 127 LEU cc_start: 0.9435 (tp) cc_final: 0.9157 (tt) REVERT: q 137 TYR cc_start: 0.8886 (m-80) cc_final: 0.8682 (m-10) REVERT: q 165 TRP cc_start: 0.8400 (p-90) cc_final: 0.7190 (p-90) REVERT: q 168 TYR cc_start: 0.8878 (p90) cc_final: 0.8452 (p90) REVERT: q 171 GLN cc_start: 0.8570 (mt0) cc_final: 0.8051 (mt0) REVERT: q 221 ASP cc_start: 0.7322 (p0) cc_final: 0.7095 (p0) REVERT: q 244 ASN cc_start: 0.8648 (m-40) cc_final: 0.8411 (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: 0.8121 (m-80) REVERT: q 280 ASP cc_start: 0.8443 (m-30) cc_final: 0.8153 (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: 0.8811 (t0) REVERT: r 50 VAL cc_start: 0.9514 (m) cc_final: 0.9250 (p) REVERT: r 212 TYR cc_start: 0.8829 (t80) cc_final: 0.8364 (t80) REVERT: r 214 ASN cc_start: 0.9147 (t0) cc_final: 0.8902 (t0) REVERT: s 10 SER cc_start: 0.9560 (m) cc_final: 0.9273 (p) REVERT: s 42 ASN cc_start: 0.8446 (t0) cc_final: 0.8237 (t0) REVERT: s 43 MET cc_start: 0.9307 (mmm) cc_final: 0.8913 (tpp) REVERT: s 50 ASP cc_start: 0.8352 (m-30) cc_final: 0.8094 (m-30) REVERT: s 74 ASP cc_start: 0.8000 (p0) cc_final: 0.7467 (p0) REVERT: s 91 ASP cc_start: 0.8312 (t70) cc_final: 0.7889 (t0) REVERT: s 120 CYS cc_start: 0.8529 (m) cc_final: 0.8317 (m) REVERT: s 146 ASP cc_start: 0.8249 (m-30) cc_final: 0.8015 (m-30) REVERT: s 154 ILE cc_start: 0.9216 (mt) cc_final: 0.8854 (mt) REVERT: s 234 LYS cc_start: 0.8851 (mtmt) cc_final: 0.8422 (mttp) REVERT: t 28 THR cc_start: 0.9308 (m) cc_final: 0.9015 (p) REVERT: t 42 THR cc_start: 0.9125 (p) cc_final: 0.8781 (p) outliers start: 0 outliers final: 0 residues processed: 1664 average time/residue: 0.4894 time to fit residues: 1319.1853 Evaluate side-chains 1137 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1137 time to evaluate : 3.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 365 optimal weight: 6.9990 chunk 328 optimal weight: 5.9990 chunk 182 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 221 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 chunk 339 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 206 optimal weight: 8.9990 chunk 252 optimal weight: 6.9990 chunk 393 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 ** p 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.113339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.100625 restraints weight = 65694.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.103629 restraints weight = 31072.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.105602 restraints weight = 18010.039| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 34975 Z= 0.274 Angle : 0.759 10.698 47711 Z= 0.399 Chirality : 0.049 0.243 5363 Planarity : 0.005 0.058 6193 Dihedral : 6.159 54.820 4860 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.69 % Allowed : 12.32 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.12), residues: 4201 helix: -2.52 (0.22), residues: 391 sheet: 1.18 (0.15), residues: 1042 loop : 0.04 (0.11), residues: 2768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP q 170 HIS 0.016 0.002 HIS k 96 PHE 0.028 0.003 PHE s 82 TYR 0.029 0.002 TYR i 154 ARG 0.010 0.001 ARG r 264 Details of bonding type rmsd hydrogen bonds : bond 0.04607 ( 924) hydrogen bonds : angle 6.50198 ( 2631) covalent geometry : bond 0.00618 (34975) covalent geometry : angle 0.75914 (47711) *********************** 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 1429 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 1293 time to evaluate : 3.833 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. 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: 0.8954 (mp0) cc_final: 0.8744 (mp0) REVERT: a 49 GLN cc_start: 0.8488 (mm-40) cc_final: 0.8136 (mm110) REVERT: a 105 ILE cc_start: 0.9626 (mt) cc_final: 0.9423 (mt) REVERT: a 120 PHE cc_start: 0.9431 (m-80) cc_final: 0.9158 (m-10) REVERT: a 205 ASP cc_start: 0.8739 (t0) cc_final: 0.8374 (t70) REVERT: a 215 GLU cc_start: 0.8729 (mp0) cc_final: 0.8516 (mp0) REVERT: a 277 GLU cc_start: 0.7856 (mp0) cc_final: 0.7340 (mp0) REVERT: b 16 ILE cc_start: 0.9282 (mp) cc_final: 0.9015 (mt) REVERT: b 64 TYR cc_start: 0.8871 (m-80) cc_final: 0.8466 (m-80) REVERT: b 84 ASP cc_start: 0.8308 (t0) cc_final: 0.7886 (t0) REVERT: b 97 TYR cc_start: 0.8623 (m-80) cc_final: 0.7933 (m-80) REVERT: b 104 SER cc_start: 0.9259 (t) cc_final: 0.8761 (p) REVERT: b 106 TYR cc_start: 0.9137 (m-80) cc_final: 0.7817 (m-80) REVERT: b 183 SER cc_start: 0.9370 (p) cc_final: 0.8916 (t) REVERT: b 214 ASN cc_start: 0.9249 (t0) cc_final: 0.8991 (t0) REVERT: b 215 SER cc_start: 0.9457 (p) cc_final: 0.9155 (p) REVERT: c 5 MET cc_start: 0.8748 (ttm) cc_final: 0.8489 (ttt) REVERT: c 17 ASP cc_start: 0.8542 (t70) cc_final: 0.8247 (t70) REVERT: c 101 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8010 (mm-30) REVERT: c 112 SER cc_start: 0.9437 (m) cc_final: 0.9119 (p) REVERT: c 131 LEU cc_start: 0.9069 (tp) cc_final: 0.8688 (tt) REVERT: c 226 ASP cc_start: 0.8565 (m-30) cc_final: 0.8283 (m-30) REVERT: d 21 ASN cc_start: 0.7466 (p0) cc_final: 0.7066 (p0) REVERT: e 101 ASN cc_start: 0.8827 (OUTLIER) cc_final: 0.7863 (m-40) REVERT: e 112 GLN cc_start: 0.8699 (mt0) cc_final: 0.8403 (mt0) REVERT: e 167 ASP cc_start: 0.9007 (t0) cc_final: 0.8800 (m-30) REVERT: e 173 SER cc_start: 0.9344 (p) cc_final: 0.8804 (p) REVERT: e 174 SER cc_start: 0.9386 (m) cc_final: 0.8855 (p) REVERT: e 182 TYR cc_start: 0.8973 (t80) cc_final: 0.8449 (t80) REVERT: e 205 ASP cc_start: 0.9041 (t0) cc_final: 0.8583 (t0) REVERT: e 229 ILE cc_start: 0.9007 (tt) cc_final: 0.8605 (tt) REVERT: e 291 LYS cc_start: 0.8976 (mtpt) cc_final: 0.8622 (mtpp) REVERT: f 145 TYR cc_start: 0.9048 (t80) cc_final: 0.8803 (t80) REVERT: f 173 LYS cc_start: 0.8916 (mptt) cc_final: 0.7143 (mttt) REVERT: g 44 MET cc_start: 0.8988 (mmm) cc_final: 0.8779 (mmm) REVERT: g 106 TYR cc_start: 0.9520 (m-80) cc_final: 0.9094 (m-80) REVERT: g 112 SER cc_start: 0.8934 (m) cc_final: 0.8082 (p) REVERT: g 154 ILE cc_start: 0.9219 (mm) cc_final: 0.8902 (mm) REVERT: g 156 ASP cc_start: 0.8123 (t0) cc_final: 0.7759 (p0) REVERT: g 194 GLN cc_start: 0.9038 (tp-100) cc_final: 0.8538 (tp40) REVERT: g 216 CYS cc_start: 0.8431 (m) cc_final: 0.7110 (m) REVERT: h 38 SER cc_start: 0.9256 (m) cc_final: 0.8972 (p) REVERT: i 25 THR cc_start: 0.9216 (m) cc_final: 0.8847 (t) REVERT: i 95 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7152 (mt-10) REVERT: i 98 LYS cc_start: 0.8896 (mttt) cc_final: 0.8537 (mtpp) REVERT: i 108 THR cc_start: 0.8528 (p) cc_final: 0.8241 (t) REVERT: i 127 LEU cc_start: 0.9241 (tp) cc_final: 0.9013 (tp) REVERT: i 129 MET cc_start: 0.8903 (mtm) cc_final: 0.8600 (mtm) REVERT: i 154 TYR cc_start: 0.8788 (t80) cc_final: 0.8533 (t80) REVERT: i 204 TYR cc_start: 0.8654 (t80) cc_final: 0.7936 (t80) REVERT: j 91 MET cc_start: 0.8523 (mmm) cc_final: 0.8283 (mmp) REVERT: j 110 VAL cc_start: 0.9630 (t) cc_final: 0.9415 (p) REVERT: j 129 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7504 (mm-30) REVERT: j 137 GLU cc_start: 0.7356 (pm20) cc_final: 0.7030 (pm20) REVERT: j 193 TYR cc_start: 0.8990 (m-80) cc_final: 0.8628 (m-10) REVERT: j 199 ASN cc_start: 0.9071 (t0) cc_final: 0.8696 (t0) REVERT: j 200 LEU cc_start: 0.9031 (mt) cc_final: 0.8772 (mt) REVERT: j 223 LYS cc_start: 0.9070 (mtmt) cc_final: 0.8177 (mtmm) REVERT: j 227 TRP cc_start: 0.8948 (m100) cc_final: 0.8732 (m100) REVERT: k 2 LEU cc_start: 0.9317 (tp) cc_final: 0.9105 (tp) REVERT: k 21 SER cc_start: 0.9672 (p) cc_final: 0.9438 (p) REVERT: k 39 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7887 (tm-30) REVERT: k 44 MET cc_start: 0.8856 (mmm) cc_final: 0.8538 (mmm) REVERT: k 55 MET cc_start: 0.9191 (tpp) cc_final: 0.8920 (tpt) REVERT: k 65 MET cc_start: 0.8571 (tpp) cc_final: 0.8273 (tpp) REVERT: k 84 LEU cc_start: 0.9029 (tt) cc_final: 0.8744 (tt) REVERT: k 87 SER cc_start: 0.9247 (t) cc_final: 0.8700 (p) REVERT: k 93 ARG cc_start: 0.8623 (mtm180) cc_final: 0.8376 (mtt180) REVERT: k 144 ARG cc_start: 0.8482 (ttm-80) cc_final: 0.7948 (ttm-80) REVERT: k 155 TRP cc_start: 0.8268 (t60) cc_final: 0.7587 (t60) REVERT: k 169 TRP cc_start: 0.8886 (t-100) cc_final: 0.7681 (t-100) REVERT: k 178 CYS cc_start: 0.8445 (m) cc_final: 0.7587 (m) REVERT: k 194 GLN cc_start: 0.9074 (tp40) cc_final: 0.8307 (tp40) REVERT: k 196 ARG cc_start: 0.7696 (ttp80) cc_final: 0.6528 (ptt-90) REVERT: k 216 CYS cc_start: 0.8522 (m) cc_final: 0.8090 (m) REVERT: m 166 ASP cc_start: 0.8607 (p0) cc_final: 0.7880 (p0) REVERT: m 204 TYR cc_start: 0.8924 (t80) cc_final: 0.8572 (t80) REVERT: m 205 ASP cc_start: 0.8299 (t0) cc_final: 0.7698 (t0) REVERT: m 216 ASN cc_start: 0.7565 (t0) cc_final: 0.7224 (m-40) REVERT: m 218 ASP cc_start: 0.8081 (m-30) cc_final: 0.7520 (m-30) REVERT: n 13 VAL cc_start: 0.9473 (t) cc_final: 0.9172 (p) REVERT: n 40 THR cc_start: 0.8991 (p) cc_final: 0.8584 (t) REVERT: n 51 ASP cc_start: 0.8664 (p0) cc_final: 0.7990 (p0) REVERT: n 60 SER cc_start: 0.9572 (m) cc_final: 0.9108 (p) REVERT: n 71 TRP cc_start: 0.8933 (t60) cc_final: 0.8494 (t60) REVERT: n 129 GLU cc_start: 0.8739 (tp30) cc_final: 0.8416 (tp30) REVERT: n 179 TYR cc_start: 0.8488 (p90) cc_final: 0.8253 (p90) REVERT: n 213 VAL cc_start: 0.9796 (t) cc_final: 0.9502 (p) REVERT: n 216 LEU cc_start: 0.9238 (mt) cc_final: 0.8726 (mt) REVERT: n 224 HIS cc_start: 0.8821 (t-90) cc_final: 0.8297 (t-170) REVERT: n 259 GLU cc_start: 0.7797 (tt0) cc_final: 0.7140 (tt0) REVERT: o 74 ASP cc_start: 0.8631 (p0) cc_final: 0.8418 (p0) REVERT: o 84 LEU cc_start: 0.8976 (mp) cc_final: 0.8649 (mp) REVERT: o 87 SER cc_start: 0.9114 (m) cc_final: 0.7929 (p) REVERT: o 91 ASP cc_start: 0.8018 (t0) cc_final: 0.7811 (t0) REVERT: o 128 LYS cc_start: 0.6610 (mttt) cc_final: 0.6348 (mttt) REVERT: o 146 ASP cc_start: 0.7897 (m-30) cc_final: 0.7675 (m-30) REVERT: o 175 TYR cc_start: 0.8870 (m-80) cc_final: 0.8409 (m-10) REVERT: o 207 MET cc_start: 0.8558 (ptp) cc_final: 0.8106 (ptp) REVERT: o 226 ASP cc_start: 0.7948 (m-30) cc_final: 0.7528 (m-30) REVERT: o 234 LYS cc_start: 0.7732 (tttt) cc_final: 0.7197 (tttt) REVERT: p 48 GLN cc_start: 0.8762 (pm20) cc_final: 0.8253 (pm20) REVERT: q 47 SER cc_start: 0.8942 (m) cc_final: 0.8644 (p) REVERT: q 61 VAL cc_start: 0.9464 (t) cc_final: 0.9221 (p) REVERT: q 62 VAL cc_start: 0.9598 (t) cc_final: 0.9298 (p) REVERT: q 90 SER cc_start: 0.8673 (t) cc_final: 0.8246 (t) REVERT: q 95 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7512 (mt-10) REVERT: q 105 ILE cc_start: 0.8986 (mt) cc_final: 0.8737 (mt) REVERT: q 122 TYR cc_start: 0.9223 (m-80) cc_final: 0.8839 (m-80) REVERT: q 126 ASP cc_start: 0.8174 (m-30) cc_final: 0.7771 (m-30) REVERT: q 137 TYR cc_start: 0.9167 (m-80) cc_final: 0.8910 (m-10) REVERT: q 154 TYR cc_start: 0.9249 (t80) cc_final: 0.8872 (t80) REVERT: q 171 GLN cc_start: 0.8408 (mt0) cc_final: 0.8132 (mt0) REVERT: q 173 SER cc_start: 0.9334 (m) cc_final: 0.9032 (p) REVERT: q 190 SER cc_start: 0.9540 (m) cc_final: 0.9310 (m) REVERT: q 274 TYR cc_start: 0.8423 (m-80) cc_final: 0.8127 (m-80) REVERT: q 280 ASP cc_start: 0.8504 (m-30) cc_final: 0.8260 (m-30) REVERT: r 48 ASN cc_start: 0.8917 (t0) cc_final: 0.8664 (t0) REVERT: r 50 VAL cc_start: 0.9438 (m) cc_final: 0.9184 (p) REVERT: r 112 CYS cc_start: 0.8047 (t) cc_final: 0.7798 (t) REVERT: r 116 LYS cc_start: 0.8907 (mttt) cc_final: 0.8131 (mtmt) REVERT: r 212 TYR cc_start: 0.8535 (t80) cc_final: 0.8136 (t80) REVERT: r 249 ILE cc_start: 0.9605 (mt) cc_final: 0.9312 (mm) REVERT: s 10 SER cc_start: 0.9451 (m) cc_final: 0.9221 (p) REVERT: s 11 ASN cc_start: 0.9327 (m-40) cc_final: 0.9122 (m-40) REVERT: s 50 ASP cc_start: 0.8501 (m-30) cc_final: 0.8277 (m-30) REVERT: s 74 ASP cc_start: 0.7998 (p0) cc_final: 0.7723 (p0) REVERT: s 156 ASP cc_start: 0.8680 (t0) cc_final: 0.8256 (t0) REVERT: s 214 SER cc_start: 0.9373 (p) cc_final: 0.9095 (t) REVERT: s 234 LYS cc_start: 0.8821 (mtmt) cc_final: 0.8168 (mttt) REVERT: s 235 LEU cc_start: 0.7963 (tp) cc_final: 0.7735 (tp) outliers start: 136 outliers final: 88 residues processed: 1355 average time/residue: 0.4583 time to fit residues: 1016.8903 Evaluate side-chains 1205 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 1116 time to evaluate : 3.550 ------------------------------------------------------------------------------- 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 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 173 SER 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 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 86 LEU 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 338 optimal weight: 10.0000 chunk 301 optimal weight: 8.9990 chunk 16 optimal weight: 50.0000 chunk 253 optimal weight: 3.9990 chunk 310 optimal weight: 9.9990 chunk 242 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 80 optimal weight: 0.0970 chunk 380 optimal weight: 9.9990 chunk 210 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 111 GLN 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 175 ASN ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 20 ASN ** f 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 135 ASN ** 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 61 ASN ** j 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 119 GLN ** k 69 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 ** 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 = 0.114098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.101463 restraints weight = 65803.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.104485 restraints weight = 30934.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.106462 restraints weight = 17784.450| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3676 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= 0.179 Angle : 0.654 8.648 47711 Z= 0.339 Chirality : 0.046 0.234 5363 Planarity : 0.004 0.041 6193 Dihedral : 5.823 52.986 4860 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.85 % Allowed : 16.42 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.12), residues: 4201 helix: -2.37 (0.22), residues: 392 sheet: 1.09 (0.15), residues: 1018 loop : -0.11 (0.11), residues: 2791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP o 169 HIS 0.008 0.001 HIS k 96 PHE 0.027 0.002 PHE o 82 TYR 0.022 0.002 TYR m 255 ARG 0.009 0.001 ARG c 176 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 924) hydrogen bonds : angle 6.00393 ( 2631) covalent geometry : bond 0.00404 (34975) covalent geometry : angle 0.65405 (47711) *********************** 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 1400 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 1258 time to evaluate : 3.585 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: symmetry clash REVERT: a 43 GLU cc_start: 0.8886 (mp0) cc_final: 0.8662 (mp0) REVERT: a 49 GLN cc_start: 0.8453 (mm-40) cc_final: 0.7973 (mm110) REVERT: a 54 ASP cc_start: 0.8631 (m-30) cc_final: 0.8398 (m-30) REVERT: a 120 PHE cc_start: 0.9347 (m-80) cc_final: 0.9112 (m-10) REVERT: a 179 PHE cc_start: 0.8927 (m-10) cc_final: 0.8601 (m-10) REVERT: a 205 ASP cc_start: 0.8741 (t0) cc_final: 0.8362 (t70) REVERT: a 215 GLU cc_start: 0.8704 (mp0) cc_final: 0.8248 (mp0) REVERT: a 277 GLU cc_start: 0.7746 (mp0) cc_final: 0.7384 (mp0) REVERT: b 84 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.8026 (t0) REVERT: b 97 TYR cc_start: 0.8568 (m-80) cc_final: 0.8149 (m-10) REVERT: b 104 SER cc_start: 0.9228 (t) cc_final: 0.8856 (p) REVERT: b 106 TYR cc_start: 0.9115 (m-80) cc_final: 0.7753 (m-80) REVERT: b 170 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8041 (mm-30) REVERT: b 183 SER cc_start: 0.9376 (p) cc_final: 0.8974 (t) REVERT: b 246 GLN cc_start: 0.8168 (mt0) cc_final: 0.7750 (mt0) REVERT: c 48 GLU cc_start: 0.9251 (mt-10) cc_final: 0.8857 (mt-10) REVERT: c 56 ASN cc_start: 0.9583 (t0) cc_final: 0.9167 (t0) REVERT: c 74 ASP cc_start: 0.8390 (p0) cc_final: 0.8181 (p0) REVERT: c 101 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8059 (mm-30) REVERT: c 112 SER cc_start: 0.9420 (m) cc_final: 0.9094 (p) REVERT: c 131 LEU cc_start: 0.9117 (tp) cc_final: 0.8740 (tt) REVERT: d 21 ASN cc_start: 0.7443 (p0) cc_final: 0.7017 (p0) REVERT: e 95 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7242 (mm-30) REVERT: e 98 LYS cc_start: 0.9124 (mtpt) cc_final: 0.8896 (mtpt) REVERT: e 173 SER cc_start: 0.9302 (p) cc_final: 0.8891 (p) REVERT: e 174 SER cc_start: 0.9238 (m) cc_final: 0.8682 (p) REVERT: e 182 TYR cc_start: 0.8900 (t80) cc_final: 0.8405 (t80) REVERT: e 204 TYR cc_start: 0.8755 (t80) cc_final: 0.8028 (t80) REVERT: e 205 ASP cc_start: 0.8982 (t0) cc_final: 0.8534 (t0) REVERT: e 229 ILE cc_start: 0.8971 (tt) cc_final: 0.8494 (tt) REVERT: e 257 LYS cc_start: 0.8978 (ttpp) cc_final: 0.8602 (tttp) REVERT: e 291 LYS cc_start: 0.9032 (mtpt) cc_final: 0.8032 (mtpp) REVERT: f 23 ILE cc_start: 0.9387 (mt) cc_final: 0.9034 (mm) REVERT: f 41 TYR cc_start: 0.8633 (m-80) cc_final: 0.8337 (m-80) REVERT: f 55 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8702 (mt-10) REVERT: f 87 LYS cc_start: 0.8943 (pttp) cc_final: 0.8565 (pttm) REVERT: f 116 LYS cc_start: 0.9192 (mttt) cc_final: 0.8806 (mttp) REVERT: f 145 TYR cc_start: 0.9130 (t80) cc_final: 0.8867 (t80) REVERT: f 173 LYS cc_start: 0.8591 (mptt) cc_final: 0.8301 (mptt) REVERT: f 191 PHE cc_start: 0.9210 (m-80) cc_final: 0.8985 (m-10) REVERT: f 196 GLN cc_start: 0.8828 (tt0) cc_final: 0.8026 (tp40) REVERT: f 214 ASN cc_start: 0.9013 (t0) cc_final: 0.8791 (t0) REVERT: f 250 THR cc_start: 0.8622 (m) cc_final: 0.8311 (p) REVERT: f 264 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7484 (ptt90) REVERT: f 267 THR cc_start: 0.9200 (m) cc_final: 0.8994 (m) REVERT: g 91 ASP cc_start: 0.8473 (t0) cc_final: 0.8142 (t0) REVERT: g 98 MET cc_start: 0.9497 (tpt) cc_final: 0.9239 (tpt) REVERT: g 106 TYR cc_start: 0.9544 (m-80) cc_final: 0.9210 (m-80) REVERT: g 112 SER cc_start: 0.8960 (m) cc_final: 0.8504 (p) REVERT: g 154 ILE cc_start: 0.9254 (mm) cc_final: 0.8764 (mm) REVERT: g 156 ASP cc_start: 0.8347 (t0) cc_final: 0.7727 (p0) REVERT: g 194 GLN cc_start: 0.9072 (tp-100) cc_final: 0.8637 (tp40) REVERT: g 216 CYS cc_start: 0.8613 (m) cc_final: 0.7716 (m) REVERT: g 223 LEU cc_start: 0.7487 (mt) cc_final: 0.7263 (mt) REVERT: h 38 SER cc_start: 0.9237 (m) cc_final: 0.8969 (p) REVERT: i 23 GLN cc_start: 0.9010 (tt0) cc_final: 0.8473 (tt0) REVERT: i 25 THR cc_start: 0.9168 (m) cc_final: 0.8876 (t) REVERT: i 78 ARG cc_start: 0.8813 (mmt90) cc_final: 0.8570 (mmt90) REVERT: i 95 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7199 (mt-10) REVERT: i 98 LYS cc_start: 0.8872 (mttt) cc_final: 0.8531 (mtpp) REVERT: i 122 TYR cc_start: 0.9317 (m-80) cc_final: 0.9024 (m-80) REVERT: i 135 GLU cc_start: 0.8192 (pt0) cc_final: 0.7868 (mt-10) REVERT: i 150 TYR cc_start: 0.8467 (m-80) cc_final: 0.8216 (m-80) REVERT: i 154 TYR cc_start: 0.8787 (t80) cc_final: 0.8325 (t80) REVERT: i 168 TYR cc_start: 0.8308 (p90) cc_final: 0.7934 (p90) REVERT: i 190 SER cc_start: 0.9422 (OUTLIER) cc_final: 0.9172 (p) REVERT: i 200 TYR cc_start: 0.9327 (m-80) cc_final: 0.9009 (m-10) REVERT: i 204 TYR cc_start: 0.8661 (t80) cc_final: 0.8169 (t80) REVERT: j 91 MET cc_start: 0.8520 (mmm) cc_final: 0.8171 (mmp) REVERT: j 110 VAL cc_start: 0.9662 (t) cc_final: 0.9347 (p) REVERT: j 137 GLU cc_start: 0.7357 (pm20) cc_final: 0.6996 (pm20) REVERT: j 199 ASN cc_start: 0.9052 (t0) cc_final: 0.8672 (t0) REVERT: j 223 LYS cc_start: 0.9043 (mtmt) cc_final: 0.8249 (mttp) REVERT: k 21 SER cc_start: 0.9633 (p) cc_final: 0.9294 (p) REVERT: k 39 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7923 (tm-30) REVERT: k 55 MET cc_start: 0.9174 (tpp) cc_final: 0.8812 (tpt) REVERT: k 65 MET cc_start: 0.8629 (tpp) cc_final: 0.8300 (tpp) REVERT: k 67 MET cc_start: 0.9088 (ptm) cc_final: 0.8747 (ptp) REVERT: k 87 SER cc_start: 0.9237 (t) cc_final: 0.8709 (p) REVERT: k 93 ARG cc_start: 0.8646 (mtm180) cc_final: 0.8424 (mtt180) REVERT: k 169 TRP cc_start: 0.8908 (t-100) cc_final: 0.7896 (t-100) REVERT: k 177 ARG cc_start: 0.8936 (ttm110) cc_final: 0.8186 (mtm-85) REVERT: k 178 CYS cc_start: 0.8402 (m) cc_final: 0.7571 (m) REVERT: k 216 CYS cc_start: 0.8498 (m) cc_final: 0.7990 (m) REVERT: m 129 MET cc_start: 0.8748 (mtm) cc_final: 0.8525 (mtp) REVERT: m 166 ASP cc_start: 0.8560 (p0) cc_final: 0.7871 (p0) REVERT: m 204 TYR cc_start: 0.8948 (t80) cc_final: 0.8644 (t80) REVERT: m 205 ASP cc_start: 0.8348 (t0) cc_final: 0.7599 (t70) REVERT: m 209 ARG cc_start: 0.8829 (ttp80) cc_final: 0.8606 (mtm110) REVERT: m 216 ASN cc_start: 0.7626 (t0) cc_final: 0.7185 (m-40) REVERT: m 218 ASP cc_start: 0.8070 (m-30) cc_final: 0.7588 (m-30) REVERT: n 13 VAL cc_start: 0.9488 (t) cc_final: 0.9218 (p) REVERT: n 41 TYR cc_start: 0.8714 (m-80) cc_final: 0.8511 (m-10) REVERT: n 60 SER cc_start: 0.9496 (m) cc_final: 0.9060 (p) REVERT: n 71 TRP cc_start: 0.8816 (t60) cc_final: 0.8490 (t60) REVERT: n 129 GLU cc_start: 0.8572 (tp30) cc_final: 0.8042 (tp30) REVERT: n 213 VAL cc_start: 0.9766 (t) cc_final: 0.9493 (p) REVERT: n 216 LEU cc_start: 0.9240 (mt) cc_final: 0.8892 (mt) REVERT: n 224 HIS cc_start: 0.8555 (t-90) cc_final: 0.8168 (t-170) REVERT: o 20 GLN cc_start: 0.8708 (mt0) cc_final: 0.8481 (mt0) REVERT: o 66 GLU cc_start: 0.8797 (mp0) cc_final: 0.8473 (mp0) REVERT: o 87 SER cc_start: 0.9140 (m) cc_final: 0.7928 (p) REVERT: o 144 ARG cc_start: 0.7896 (ttp-170) cc_final: 0.7681 (ttp-170) REVERT: o 169 TRP cc_start: 0.9010 (t-100) cc_final: 0.8168 (t-100) REVERT: o 194 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8420 (tt0) REVERT: o 207 MET cc_start: 0.8575 (ptp) cc_final: 0.8251 (ptp) REVERT: q 47 SER cc_start: 0.8990 (m) cc_final: 0.8708 (p) REVERT: q 66 THR cc_start: 0.8912 (m) cc_final: 0.8172 (p) REVERT: q 88 THR cc_start: 0.8956 (m) cc_final: 0.8158 (m) REVERT: q 90 SER cc_start: 0.8621 (t) cc_final: 0.8263 (t) REVERT: q 126 ASP cc_start: 0.8214 (m-30) cc_final: 0.7698 (m-30) REVERT: q 137 TYR cc_start: 0.9189 (m-80) cc_final: 0.8945 (m-10) REVERT: q 167 ASP cc_start: 0.8993 (t0) cc_final: 0.8759 (t0) REVERT: q 190 SER cc_start: 0.9499 (m) cc_final: 0.9236 (m) REVERT: q 274 TYR cc_start: 0.8315 (m-80) cc_final: 0.8012 (m-80) REVERT: r 50 VAL cc_start: 0.9356 (m) cc_final: 0.9138 (p) REVERT: r 116 LYS cc_start: 0.8879 (mttt) cc_final: 0.8322 (mtmt) REVERT: r 210 VAL cc_start: 0.9483 (t) cc_final: 0.9204 (p) REVERT: r 212 TYR cc_start: 0.8464 (t80) cc_final: 0.8206 (t80) REVERT: r 249 ILE cc_start: 0.9618 (mt) cc_final: 0.9322 (mm) REVERT: s 10 SER cc_start: 0.9437 (m) cc_final: 0.9187 (p) REVERT: s 50 ASP cc_start: 0.8642 (m-30) cc_final: 0.8414 (m-30) REVERT: s 74 ASP cc_start: 0.7936 (p0) cc_final: 0.7631 (p0) REVERT: s 144 ARG cc_start: 0.9210 (ttm-80) cc_final: 0.8960 (ttm-80) REVERT: s 154 ILE cc_start: 0.8956 (mt) cc_final: 0.8669 (pt) REVERT: s 196 ARG cc_start: 0.8753 (ptt90) cc_final: 0.6448 (pmt170) REVERT: s 214 SER cc_start: 0.9320 (p) cc_final: 0.9019 (t) REVERT: s 234 LYS cc_start: 0.8785 (mtmt) cc_final: 0.8187 (mttt) REVERT: t 62 LEU cc_start: 0.8691 (mp) cc_final: 0.8456 (mp) outliers start: 142 outliers final: 101 residues processed: 1319 average time/residue: 0.5239 time to fit residues: 1145.3916 Evaluate side-chains 1224 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 1120 time to evaluate : 4.355 ------------------------------------------------------------------------------- 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 134 THR Chi-restraints excluded: chain a residue 295 ILE Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain b residue 84 ASP Chi-restraints excluded: chain b residue 172 ARG Chi-restraints excluded: chain b residue 202 THR Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 10 SER 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 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 110 THR 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 180 LEU Chi-restraints excluded: chain f residue 263 LEU Chi-restraints excluded: chain f residue 264 ARG Chi-restraints excluded: chain g residue 190 THR 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 h residue 10 THR 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 44 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 i residue 190 SER Chi-restraints excluded: chain j residue 38 TRP Chi-restraints excluded: chain j residue 50 VAL 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 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 181 ASP Chi-restraints excluded: chain k residue 189 ILE Chi-restraints excluded: chain k residue 223 LEU 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 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 54 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 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 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 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 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 r residue 268 VAL 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 s residue 205 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 375 optimal weight: 8.9990 chunk 148 optimal weight: 9.9990 chunk 348 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 291 optimal weight: 20.0000 chunk 319 optimal weight: 10.0000 chunk 300 optimal weight: 8.9990 chunk 358 optimal weight: 20.0000 chunk 283 optimal weight: 5.9990 chunk 221 optimal weight: 10.0000 chunk 317 optimal weight: 10.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- 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 232 GLN ** e 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 135 ASN g 73 ASN h 21 ASN h 44 GLN i 23 GLN ** i 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 265 ASN ** k 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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** o 27 ASN ** o 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 108 HIS ** 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 ** 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 t 44 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.107991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.095430 restraints weight = 67992.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.098297 restraints weight = 32408.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.100195 restraints weight = 18927.909| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 34975 Z= 0.350 Angle : 0.747 9.346 47711 Z= 0.388 Chirality : 0.049 0.271 5363 Planarity : 0.005 0.049 6193 Dihedral : 6.003 55.003 4860 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 6.08 % Allowed : 16.40 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.12), residues: 4201 helix: -2.41 (0.22), residues: 392 sheet: 0.71 (0.15), residues: 1066 loop : -0.43 (0.11), residues: 2743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP f 227 HIS 0.013 0.002 HIS o 229 PHE 0.040 0.003 PHE g 212 TYR 0.026 0.003 TYR i 193 ARG 0.007 0.001 ARG r 264 Details of bonding type rmsd hydrogen bonds : bond 0.04163 ( 924) hydrogen bonds : angle 6.07547 ( 2631) covalent geometry : bond 0.00794 (34975) covalent geometry : angle 0.74749 (47711) *********************** 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 1400 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 1176 time to evaluate : 3.649 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. revert: symmetry clash TARDY: cannot create tardy model for: "GLN r 272 " (corrupted residue). Skipping it. REVERT: a 43 GLU cc_start: 0.8934 (mp0) cc_final: 0.8587 (mp0) REVERT: a 135 GLU cc_start: 0.7656 (pt0) cc_final: 0.7450 (pt0) REVERT: a 161 ARG cc_start: 0.8608 (ttm170) cc_final: 0.8321 (ttm110) REVERT: b 87 LYS cc_start: 0.8543 (pttp) cc_final: 0.8056 (ptmt) REVERT: b 97 TYR cc_start: 0.8710 (m-80) cc_final: 0.7970 (m-10) REVERT: b 183 SER cc_start: 0.9406 (p) cc_final: 0.9043 (t) REVERT: b 196 GLN cc_start: 0.8811 (tt0) cc_final: 0.7964 (mt0) REVERT: b 264 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7398 (ptt90) REVERT: c 48 GLU cc_start: 0.9254 (mt-10) cc_final: 0.8868 (mt-10) REVERT: c 69 GLN cc_start: 0.8549 (mt0) cc_final: 0.8288 (mt0) REVERT: c 101 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8174 (mm-30) REVERT: c 112 SER cc_start: 0.9353 (m) cc_final: 0.8972 (p) REVERT: c 131 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8807 (tp) REVERT: c 156 ASP cc_start: 0.7836 (t0) cc_final: 0.7387 (t0) REVERT: c 177 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7490 (mpt-90) REVERT: d 21 ASN cc_start: 0.7650 (p0) cc_final: 0.7110 (p0) REVERT: e 95 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7142 (mm-30) REVERT: e 98 LYS cc_start: 0.9152 (mtpt) cc_final: 0.8589 (mtpt) REVERT: e 173 SER cc_start: 0.9306 (p) cc_final: 0.8913 (p) REVERT: e 174 SER cc_start: 0.9136 (m) cc_final: 0.8779 (p) REVERT: e 182 TYR cc_start: 0.9073 (t80) cc_final: 0.8511 (t80) REVERT: e 204 TYR cc_start: 0.8922 (t80) cc_final: 0.8202 (t80) REVERT: e 205 ASP cc_start: 0.8943 (t0) cc_final: 0.8375 (t0) REVERT: e 257 LYS cc_start: 0.8998 (ttpp) cc_final: 0.8613 (tttp) REVERT: f 23 ILE cc_start: 0.9410 (mt) cc_final: 0.9086 (mm) REVERT: f 27 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7832 (mt-10) REVERT: f 30 ASN cc_start: 0.8441 (t0) cc_final: 0.8177 (t0) REVERT: f 41 TYR cc_start: 0.8659 (m-80) cc_final: 0.8431 (m-10) REVERT: f 55 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8766 (mt-10) REVERT: f 116 LYS cc_start: 0.9157 (mttt) cc_final: 0.8677 (mttp) REVERT: f 173 LYS cc_start: 0.8916 (mptt) cc_final: 0.8233 (mptt) REVERT: f 196 GLN cc_start: 0.8927 (tt0) cc_final: 0.8287 (tp40) REVERT: f 250 THR cc_start: 0.8657 (m) cc_final: 0.8376 (p) REVERT: f 259 GLU cc_start: 0.8613 (tt0) cc_final: 0.8317 (tt0) REVERT: g 55 MET cc_start: 0.8750 (mmm) cc_final: 0.8391 (tpp) REVERT: g 91 ASP cc_start: 0.8494 (t0) cc_final: 0.8171 (t0) REVERT: g 98 MET cc_start: 0.9516 (tpt) cc_final: 0.9216 (tpt) REVERT: g 106 TYR cc_start: 0.9580 (m-80) cc_final: 0.9087 (m-80) REVERT: g 154 ILE cc_start: 0.9324 (mm) cc_final: 0.8975 (mm) REVERT: g 156 ASP cc_start: 0.8398 (t0) cc_final: 0.7760 (p0) REVERT: g 194 GLN cc_start: 0.9198 (tp40) cc_final: 0.8913 (tp-100) REVERT: g 216 CYS cc_start: 0.8715 (m) cc_final: 0.7981 (m) REVERT: i 25 THR cc_start: 0.9143 (m) cc_final: 0.8866 (t) REVERT: i 78 ARG cc_start: 0.8863 (mmt90) cc_final: 0.8586 (mmt90) REVERT: i 98 LYS cc_start: 0.9008 (mttt) cc_final: 0.8478 (mtpp) REVERT: i 122 TYR cc_start: 0.9347 (m-80) cc_final: 0.8813 (m-80) REVERT: i 130 THR cc_start: 0.9374 (m) cc_final: 0.9046 (p) REVERT: i 154 TYR cc_start: 0.8784 (t80) cc_final: 0.8320 (t80) REVERT: i 188 ARG cc_start: 0.8819 (ttm170) cc_final: 0.8201 (ttm170) REVERT: i 204 TYR cc_start: 0.8781 (t80) cc_final: 0.8094 (t80) REVERT: j 84 ASP cc_start: 0.8386 (t70) cc_final: 0.8130 (t70) REVERT: j 87 LYS cc_start: 0.8351 (ptpp) cc_final: 0.8150 (ptpp) REVERT: j 91 MET cc_start: 0.8624 (mmm) cc_final: 0.8157 (mmt) REVERT: j 110 VAL cc_start: 0.9664 (t) cc_final: 0.9326 (p) REVERT: j 111 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7920 (tt0) REVERT: j 137 GLU cc_start: 0.7316 (pm20) cc_final: 0.6880 (pm20) REVERT: j 199 ASN cc_start: 0.9176 (t0) cc_final: 0.8725 (t0) REVERT: j 223 LYS cc_start: 0.9187 (mtmt) cc_final: 0.8269 (mtmm) REVERT: j 227 TRP cc_start: 0.9135 (m100) cc_final: 0.8863 (m100) REVERT: j 265 ASN cc_start: 0.8501 (OUTLIER) cc_final: 0.8084 (m-40) REVERT: j 266 ILE cc_start: 0.9299 (tp) cc_final: 0.8851 (tt) REVERT: k 55 MET cc_start: 0.9305 (tpp) cc_final: 0.8939 (tpt) REVERT: k 87 SER cc_start: 0.9256 (t) cc_final: 0.8824 (p) REVERT: k 92 LYS cc_start: 0.9054 (mmtm) cc_final: 0.8662 (mtpp) REVERT: k 93 ARG cc_start: 0.8776 (mtm180) cc_final: 0.8557 (mtt180) REVERT: k 155 TRP cc_start: 0.8516 (t60) cc_final: 0.7656 (t60) REVERT: k 164 SER cc_start: 0.9429 (m) cc_final: 0.8776 (t) REVERT: k 177 ARG cc_start: 0.8969 (ttm110) cc_final: 0.8093 (mtm-85) REVERT: k 178 CYS cc_start: 0.8482 (m) cc_final: 0.7595 (m) REVERT: k 216 CYS cc_start: 0.8577 (m) cc_final: 0.8176 (m) REVERT: l 53 PHE cc_start: 0.9309 (m-80) cc_final: 0.9033 (m-80) REVERT: m 111 VAL cc_start: 0.8745 (m) cc_final: 0.8489 (p) REVERT: m 122 TYR cc_start: 0.9170 (m-80) cc_final: 0.8876 (m-80) REVERT: m 165 TRP cc_start: 0.8887 (p-90) cc_final: 0.8637 (p-90) REVERT: m 166 ASP cc_start: 0.8567 (p0) cc_final: 0.7842 (p0) REVERT: m 216 ASN cc_start: 0.7804 (t0) cc_final: 0.7077 (m-40) REVERT: m 218 ASP cc_start: 0.8265 (m-30) cc_final: 0.7596 (m-30) REVERT: m 240 VAL cc_start: 0.9573 (OUTLIER) cc_final: 0.9288 (t) REVERT: n 13 VAL cc_start: 0.9468 (t) cc_final: 0.9203 (p) REVERT: n 60 SER cc_start: 0.9567 (m) cc_final: 0.9121 (p) REVERT: n 71 TRP cc_start: 0.8832 (t60) cc_final: 0.8543 (t60) REVERT: n 216 LEU cc_start: 0.9389 (mt) cc_final: 0.9011 (mt) REVERT: n 249 ILE cc_start: 0.9432 (mt) cc_final: 0.9182 (mt) REVERT: o 87 SER cc_start: 0.9196 (m) cc_final: 0.8014 (p) REVERT: o 157 LEU cc_start: 0.8401 (mt) cc_final: 0.8085 (mt) REVERT: o 207 MET cc_start: 0.8764 (ptp) cc_final: 0.8237 (ptp) REVERT: p 4 GLN cc_start: 0.7791 (mt0) cc_final: 0.7545 (mp10) REVERT: p 40 SER cc_start: 0.8915 (p) cc_final: 0.8706 (t) REVERT: q 47 SER cc_start: 0.8990 (m) cc_final: 0.8677 (p) REVERT: q 61 VAL cc_start: 0.9504 (t) cc_final: 0.9283 (p) REVERT: q 126 ASP cc_start: 0.8286 (m-30) cc_final: 0.8072 (m-30) REVERT: q 154 TYR cc_start: 0.9358 (t80) cc_final: 0.9068 (t80) REVERT: q 167 ASP cc_start: 0.9079 (t0) cc_final: 0.8846 (t0) REVERT: q 173 SER cc_start: 0.9327 (m) cc_final: 0.9107 (p) REVERT: q 190 SER cc_start: 0.9418 (m) cc_final: 0.9193 (m) REVERT: q 231 ASP cc_start: 0.7786 (t0) cc_final: 0.7537 (t0) REVERT: r 26 GLN cc_start: 0.7445 (mt0) cc_final: 0.7062 (mt0) REVERT: r 41 TYR cc_start: 0.8926 (m-80) cc_final: 0.8225 (m-10) REVERT: r 50 VAL cc_start: 0.9420 (m) cc_final: 0.9198 (p) REVERT: r 112 CYS cc_start: 0.8122 (t) cc_final: 0.7895 (t) REVERT: r 116 LYS cc_start: 0.8836 (mttt) cc_final: 0.8404 (mtmt) REVERT: r 210 VAL cc_start: 0.9560 (t) cc_final: 0.9358 (p) REVERT: r 249 ILE cc_start: 0.9596 (mt) cc_final: 0.9325 (mm) REVERT: s 50 ASP cc_start: 0.8916 (m-30) cc_final: 0.8630 (m-30) REVERT: s 74 ASP cc_start: 0.8009 (p0) cc_final: 0.7685 (p0) REVERT: s 144 ARG cc_start: 0.9286 (tmm-80) cc_final: 0.8955 (ttm-80) REVERT: s 154 ILE cc_start: 0.9007 (mt) cc_final: 0.8638 (pt) REVERT: s 175 TYR cc_start: 0.8541 (m-80) cc_final: 0.8294 (m-80) REVERT: s 234 LYS cc_start: 0.8740 (mtmt) cc_final: 0.8185 (mttp) outliers start: 224 outliers final: 163 residues processed: 1287 average time/residue: 0.4788 time to fit residues: 1009.5423 Evaluate side-chains 1252 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 1083 time to evaluate : 3.580 ------------------------------------------------------------------------------- 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 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 10 SER Chi-restraints excluded: chain c residue 17 ASP Chi-restraints excluded: chain c residue 30 VAL 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 213 VAL Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 60 LEU Chi-restraints excluded: chain d residue 61 MET 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 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 58 VAL 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 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 67 MET Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 107 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 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 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 j residue 265 ASN 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 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 106 THR 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 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 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 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 190 THR Chi-restraints excluded: chain o residue 198 VAL Chi-restraints excluded: chain o residue 199 VAL Chi-restraints excluded: chain o residue 227 THR 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 22 THR Chi-restraints excluded: chain q residue 68 SER 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 40 THR 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 r residue 267 THR Chi-restraints excluded: chain r residue 268 VAL 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 Chi-restraints excluded: chain t residue 28 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 197 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 323 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 326 optimal weight: 0.9990 chunk 290 optimal weight: 10.0000 chunk 345 optimal weight: 9.9990 chunk 376 optimal weight: 0.5980 chunk 102 optimal weight: 0.5980 chunk 364 optimal weight: 6.9990 chunk 302 optimal weight: 5.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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** ** 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 151 GLN ** e 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 135 ASN h 15 ASN h 21 ASN ** i 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 30 ASN j 195 HIS ** k 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 194 GLN ** 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 26 ASN l 39 ASN m 18 GLN ** m 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 202 HIS ** 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 27 ASN ** o 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 26 ASN ** r 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 6 ASN s 69 GLN ** s 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 4 GLN t 44 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.113720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.101220 restraints weight = 65763.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.104202 restraints weight = 30962.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.106141 restraints weight = 17837.517| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34975 Z= 0.128 Angle : 0.630 11.326 47711 Z= 0.321 Chirality : 0.046 0.268 5363 Planarity : 0.004 0.047 6193 Dihedral : 5.739 57.708 4860 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.50 % Allowed : 20.25 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.12), residues: 4201 helix: -2.29 (0.22), residues: 420 sheet: 0.79 (0.15), residues: 1039 loop : -0.35 (0.11), residues: 2742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP f 227 HIS 0.009 0.001 HIS j 224 PHE 0.023 0.002 PHE f 191 TYR 0.034 0.002 TYR o 175 ARG 0.006 0.001 ARG j 264 Details of bonding type rmsd hydrogen bonds : bond 0.03527 ( 924) hydrogen bonds : angle 5.69383 ( 2631) covalent geometry : bond 0.00289 (34975) covalent geometry : angle 0.62988 (47711) *********************** 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 1362 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 1233 time to evaluate : 3.670 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. 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: 0.8789 (mp0) cc_final: 0.8486 (mp0) REVERT: a 69 GLU cc_start: 0.7663 (tt0) cc_final: 0.7332 (tt0) REVERT: a 74 SER cc_start: 0.9397 (m) cc_final: 0.9189 (t) REVERT: a 105 ILE cc_start: 0.9450 (mt) cc_final: 0.8679 (tt) REVERT: a 161 ARG cc_start: 0.8483 (ttm170) cc_final: 0.8222 (ttm110) REVERT: a 215 GLU cc_start: 0.8772 (mp0) cc_final: 0.8325 (mp0) REVERT: a 277 GLU cc_start: 0.7706 (mp0) cc_final: 0.7475 (mp0) REVERT: b 87 LYS cc_start: 0.8439 (pttp) cc_final: 0.7857 (ttpt) REVERT: b 97 TYR cc_start: 0.8531 (m-80) cc_final: 0.7873 (m-80) REVERT: b 170 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8317 (mm-30) REVERT: b 173 LYS cc_start: 0.8206 (mttt) cc_final: 0.7918 (ptpt) REVERT: b 183 SER cc_start: 0.9359 (p) cc_final: 0.9132 (t) REVERT: b 237 LEU cc_start: 0.9237 (tp) cc_final: 0.8996 (tp) REVERT: b 246 GLN cc_start: 0.8144 (mt0) cc_final: 0.7693 (mt0) REVERT: c 48 GLU cc_start: 0.9239 (mt-10) cc_final: 0.8768 (mt-10) REVERT: c 56 ASN cc_start: 0.9579 (t0) cc_final: 0.9170 (t0) REVERT: c 91 ASP cc_start: 0.8223 (t0) cc_final: 0.7940 (t0) REVERT: c 112 SER cc_start: 0.9330 (m) cc_final: 0.9023 (p) REVERT: c 131 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8792 (mp) REVERT: c 148 MET cc_start: 0.6897 (ttm) cc_final: 0.6658 (ttt) REVERT: c 156 ASP cc_start: 0.7839 (t0) cc_final: 0.7503 (t0) REVERT: c 225 ARG cc_start: 0.8584 (ptt-90) cc_final: 0.7770 (ptt180) REVERT: d 21 ASN cc_start: 0.7349 (p0) cc_final: 0.6847 (p0) REVERT: e 120 PHE cc_start: 0.9270 (m-80) cc_final: 0.8970 (m-10) REVERT: e 173 SER cc_start: 0.9111 (p) cc_final: 0.8870 (p) REVERT: e 174 SER cc_start: 0.8935 (m) cc_final: 0.8716 (p) REVERT: e 182 TYR cc_start: 0.8876 (t80) cc_final: 0.8390 (t80) REVERT: e 204 TYR cc_start: 0.8783 (t80) cc_final: 0.8118 (t80) REVERT: e 205 ASP cc_start: 0.8951 (t0) cc_final: 0.8479 (t0) REVERT: e 231 ASP cc_start: 0.8327 (t0) cc_final: 0.8045 (t0) REVERT: e 257 LYS cc_start: 0.9035 (ttpp) cc_final: 0.8689 (tttp) REVERT: f 23 ILE cc_start: 0.9356 (mt) cc_final: 0.9053 (mm) REVERT: f 41 TYR cc_start: 0.8588 (m-80) cc_final: 0.8319 (m-10) REVERT: f 55 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8659 (mt-10) REVERT: f 64 TYR cc_start: 0.9143 (m-80) cc_final: 0.8906 (m-80) REVERT: f 116 LYS cc_start: 0.9142 (mttt) cc_final: 0.8676 (mttp) REVERT: f 132 MET cc_start: 0.8720 (mtm) cc_final: 0.8472 (mtp) REVERT: f 193 TYR cc_start: 0.8966 (m-80) cc_final: 0.8300 (m-10) REVERT: f 196 GLN cc_start: 0.8842 (tt0) cc_final: 0.8261 (tp40) REVERT: f 199 ASN cc_start: 0.8989 (t0) cc_final: 0.8713 (t0) REVERT: f 231 ILE cc_start: 0.9517 (mp) cc_final: 0.9303 (mt) REVERT: f 250 THR cc_start: 0.8576 (m) cc_final: 0.8292 (p) REVERT: g 43 MET cc_start: 0.7548 (mtp) cc_final: 0.7305 (mtp) REVERT: g 55 MET cc_start: 0.8612 (mmm) cc_final: 0.8376 (tpp) REVERT: g 91 ASP cc_start: 0.8422 (t0) cc_final: 0.8071 (t0) REVERT: g 99 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9192 (tt) REVERT: g 106 TYR cc_start: 0.9544 (m-80) cc_final: 0.9151 (m-80) REVERT: g 112 SER cc_start: 0.9027 (m) cc_final: 0.8501 (p) REVERT: g 123 MET cc_start: 0.8227 (tpp) cc_final: 0.7997 (tpp) REVERT: g 154 ILE cc_start: 0.9278 (mm) cc_final: 0.8808 (mm) REVERT: g 156 ASP cc_start: 0.8385 (t0) cc_final: 0.7753 (p0) REVERT: g 176 ARG cc_start: 0.9157 (mmm-85) cc_final: 0.8917 (mmm-85) REVERT: g 194 GLN cc_start: 0.9132 (tp40) cc_final: 0.8598 (tp40) REVERT: g 216 CYS cc_start: 0.8536 (m) cc_final: 0.7520 (m) REVERT: g 218 ASP cc_start: 0.8573 (p0) cc_final: 0.8166 (p0) REVERT: i 25 THR cc_start: 0.9089 (m) cc_final: 0.8860 (t) REVERT: i 67 ARG cc_start: 0.8248 (mtt180) cc_final: 0.8006 (mtt180) REVERT: i 98 LYS cc_start: 0.8970 (mttt) cc_final: 0.8578 (mtpp) REVERT: i 200 TYR cc_start: 0.9222 (m-80) cc_final: 0.8998 (m-10) REVERT: i 204 TYR cc_start: 0.8728 (t80) cc_final: 0.8077 (t80) REVERT: i 256 MET cc_start: 0.8487 (mmm) cc_final: 0.8227 (mmm) REVERT: i 257 LYS cc_start: 0.9375 (ttpp) cc_final: 0.9122 (tttp) REVERT: j 71 TRP cc_start: 0.9151 (t60) cc_final: 0.8923 (t60) REVERT: j 91 MET cc_start: 0.8545 (mmm) cc_final: 0.7877 (mmt) REVERT: j 110 VAL cc_start: 0.9643 (t) cc_final: 0.9310 (p) REVERT: j 111 GLN cc_start: 0.8340 (pm20) cc_final: 0.7764 (tt0) REVERT: j 137 GLU cc_start: 0.7350 (pm20) cc_final: 0.6897 (pm20) REVERT: j 193 TYR cc_start: 0.8865 (m-80) cc_final: 0.8600 (m-10) REVERT: j 196 GLN cc_start: 0.9063 (tt0) cc_final: 0.8708 (tt0) REVERT: j 223 LYS cc_start: 0.9004 (mtmt) cc_final: 0.8565 (mttp) REVERT: j 227 TRP cc_start: 0.9092 (m100) cc_final: 0.8847 (m100) REVERT: j 266 ILE cc_start: 0.9290 (tp) cc_final: 0.8883 (tt) REVERT: k 39 GLU cc_start: 0.8229 (tm-30) cc_final: 0.8006 (tm-30) REVERT: k 55 MET cc_start: 0.9232 (tpp) cc_final: 0.8661 (tpt) REVERT: k 67 MET cc_start: 0.9266 (ptm) cc_final: 0.8989 (ptp) REVERT: k 87 SER cc_start: 0.9231 (t) cc_final: 0.8778 (p) REVERT: k 92 LYS cc_start: 0.9012 (mmtm) cc_final: 0.8685 (mtpp) REVERT: k 93 ARG cc_start: 0.8739 (mtm180) cc_final: 0.8526 (mtt180) REVERT: k 144 ARG cc_start: 0.8685 (ttm-80) cc_final: 0.7579 (ttm-80) REVERT: k 155 TRP cc_start: 0.8384 (t60) cc_final: 0.7649 (t60) REVERT: k 178 CYS cc_start: 0.8388 (m) cc_final: 0.7614 (m) REVERT: k 216 CYS cc_start: 0.8539 (m) cc_final: 0.8219 (m) REVERT: l 53 PHE cc_start: 0.9231 (m-80) cc_final: 0.8832 (m-80) REVERT: m 111 VAL cc_start: 0.8627 (m) cc_final: 0.8380 (p) REVERT: m 135 GLU cc_start: 0.8868 (pt0) cc_final: 0.8648 (pt0) REVERT: m 166 ASP cc_start: 0.8594 (p0) cc_final: 0.7803 (p0) REVERT: m 167 ASP cc_start: 0.8637 (t0) cc_final: 0.8212 (t0) REVERT: m 216 ASN cc_start: 0.7713 (t0) cc_final: 0.7100 (m-40) REVERT: m 218 ASP cc_start: 0.8150 (m-30) cc_final: 0.7655 (m-30) REVERT: n 13 VAL cc_start: 0.9501 (t) cc_final: 0.9240 (p) REVERT: n 60 SER cc_start: 0.9510 (m) cc_final: 0.9110 (p) REVERT: n 71 TRP cc_start: 0.8683 (t60) cc_final: 0.8402 (t60) REVERT: n 249 ILE cc_start: 0.9433 (mt) cc_final: 0.9150 (mt) REVERT: n 261 ASN cc_start: 0.7964 (m-40) cc_final: 0.7736 (t0) REVERT: o 74 ASP cc_start: 0.8539 (p0) cc_final: 0.8327 (p0) REVERT: o 86 LEU cc_start: 0.9276 (tp) cc_final: 0.9026 (tp) REVERT: o 87 SER cc_start: 0.9114 (m) cc_final: 0.8030 (p) REVERT: o 99 LEU cc_start: 0.9490 (tp) cc_final: 0.9115 (tt) REVERT: o 144 ARG cc_start: 0.8077 (ttp-170) cc_final: 0.7872 (ttp-170) REVERT: o 177 ARG cc_start: 0.9002 (mtm-85) cc_final: 0.8738 (mtm-85) REVERT: o 194 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8436 (tt0) REVERT: o 205 THR cc_start: 0.8625 (p) cc_final: 0.8363 (m) REVERT: o 207 MET cc_start: 0.8663 (ptp) cc_final: 0.8109 (ptp) REVERT: p 4 GLN cc_start: 0.7795 (mt0) cc_final: 0.7544 (mp10) REVERT: q 47 SER cc_start: 0.9012 (m) cc_final: 0.8353 (p) REVERT: q 105 ILE cc_start: 0.9046 (mt) cc_final: 0.8631 (tt) REVERT: q 126 ASP cc_start: 0.8524 (m-30) cc_final: 0.7930 (m-30) REVERT: q 154 TYR cc_start: 0.9357 (t80) cc_final: 0.9113 (t80) REVERT: q 190 SER cc_start: 0.9369 (m) cc_final: 0.9035 (m) REVERT: r 50 VAL cc_start: 0.9295 (m) cc_final: 0.9068 (p) REVERT: r 116 LYS cc_start: 0.8815 (mttt) cc_final: 0.8313 (mtmt) REVERT: r 249 ILE cc_start: 0.9600 (mt) cc_final: 0.9332 (mm) REVERT: s 50 ASP cc_start: 0.8809 (m-30) cc_final: 0.8530 (m-30) REVERT: s 144 ARG cc_start: 0.9232 (tmm-80) cc_final: 0.8964 (ttm-80) REVERT: s 154 ILE cc_start: 0.9000 (mt) cc_final: 0.8701 (pt) REVERT: s 175 TYR cc_start: 0.8499 (m-80) cc_final: 0.8219 (m-10) REVERT: s 182 ASP cc_start: 0.8375 (t0) cc_final: 0.8148 (t70) REVERT: s 234 LYS cc_start: 0.8587 (mtmt) cc_final: 0.7956 (mttp) REVERT: s 235 LEU cc_start: 0.8011 (tp) cc_final: 0.7652 (tp) outliers start: 129 outliers final: 87 residues processed: 1291 average time/residue: 0.4817 time to fit residues: 1017.7756 Evaluate side-chains 1224 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 1135 time to evaluate : 3.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 61 VAL 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 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 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 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 152 GLU Chi-restraints excluded: chain f residue 263 LEU Chi-restraints excluded: chain g residue 99 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 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 102 ILE Chi-restraints excluded: chain i residue 128 GLU Chi-restraints excluded: chain j residue 25 THR Chi-restraints excluded: chain j residue 38 TRP 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 21 SER Chi-restraints excluded: chain k residue 76 LEU Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 223 LEU Chi-restraints excluded: chain k residue 227 THR Chi-restraints excluded: chain l residue 26 ASN Chi-restraints excluded: chain l residue 44 GLN Chi-restraints excluded: chain m residue 84 ILE Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 196 ILE 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 n residue 226 ASN 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 213 VAL Chi-restraints excluded: chain p residue 25 ILE Chi-restraints excluded: chain p residue 32 TYR 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 100 PHE Chi-restraints excluded: chain q residue 178 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 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 268 VAL 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 203 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 347 optimal weight: 2.9990 chunk 376 optimal weight: 10.0000 chunk 134 optimal weight: 20.0000 chunk 381 optimal weight: 0.0770 chunk 190 optimal weight: 0.9980 chunk 372 optimal weight: 20.0000 chunk 151 optimal weight: 2.9990 chunk 332 optimal weight: 8.9990 chunk 38 optimal weight: 20.0000 chunk 421 optimal weight: 3.9990 chunk 66 optimal weight: 20.0000 overall best weight: 2.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 99 HIS a 112 GLN ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 11 ASN c 232 GLN ** e 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 249 HIS f 135 ASN h 21 ASN ** i 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 184 ASN ** j 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 194 GLN ** 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 ** m 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 226 ASN n 261 ASN ** n 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 6 ASN p 26 ASN p 48 GLN ** q 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 261 ASN ** 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.114104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.101637 restraints weight = 66010.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.104594 restraints weight = 31160.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.106526 restraints weight = 17962.631| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34975 Z= 0.147 Angle : 0.625 9.176 47711 Z= 0.318 Chirality : 0.046 0.290 5363 Planarity : 0.004 0.053 6193 Dihedral : 5.642 59.165 4860 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.96 % Allowed : 20.49 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.12), residues: 4201 helix: -2.17 (0.22), residues: 422 sheet: 0.78 (0.15), residues: 1035 loop : -0.34 (0.11), residues: 2744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP f 227 HIS 0.010 0.001 HIS k 96 PHE 0.052 0.002 PHE k 19 TYR 0.035 0.002 TYR o 175 ARG 0.010 0.001 ARG f 264 Details of bonding type rmsd hydrogen bonds : bond 0.03422 ( 924) hydrogen bonds : angle 5.55276 ( 2631) covalent geometry : bond 0.00341 (34975) covalent geometry : angle 0.62548 (47711) *********************** 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 1300 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 1154 time to evaluate : 3.641 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: 0.8735 (mp0) cc_final: 0.8265 (mp0) REVERT: a 74 SER cc_start: 0.9401 (m) cc_final: 0.9155 (p) REVERT: a 161 ARG cc_start: 0.8517 (ttm170) cc_final: 0.8294 (ttm110) REVERT: a 205 ASP cc_start: 0.8578 (t0) cc_final: 0.8123 (t70) REVERT: a 277 GLU cc_start: 0.7629 (mp0) cc_final: 0.7276 (mp0) REVERT: b 87 LYS cc_start: 0.8393 (pttp) cc_final: 0.8008 (ttpt) REVERT: b 97 TYR cc_start: 0.8567 (m-80) cc_final: 0.7649 (m-80) REVERT: b 170 GLU cc_start: 0.8516 (mm-30) cc_final: 0.7941 (mm-30) REVERT: b 172 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7367 (mtt90) REVERT: b 173 LYS cc_start: 0.8228 (mttt) cc_final: 0.7998 (mttt) REVERT: b 183 SER cc_start: 0.9330 (p) cc_final: 0.9104 (t) REVERT: b 237 LEU cc_start: 0.9225 (tp) cc_final: 0.8981 (tp) REVERT: b 246 GLN cc_start: 0.8117 (mt0) cc_final: 0.7684 (mt0) REVERT: b 264 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7890 (ptt90) REVERT: c 48 GLU cc_start: 0.9252 (mt-10) cc_final: 0.8813 (mt-10) REVERT: c 95 SER cc_start: 0.8966 (p) cc_final: 0.8690 (t) REVERT: c 112 SER cc_start: 0.9324 (m) cc_final: 0.9018 (p) REVERT: c 148 MET cc_start: 0.7106 (ttm) cc_final: 0.6849 (ttt) REVERT: c 225 ARG cc_start: 0.8641 (ptt-90) cc_final: 0.7835 (ptt180) REVERT: e 69 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8354 (mm-30) REVERT: e 95 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7143 (mm-30) REVERT: e 173 SER cc_start: 0.9139 (p) cc_final: 0.8888 (p) REVERT: e 174 SER cc_start: 0.9055 (m) cc_final: 0.8711 (p) REVERT: e 182 TYR cc_start: 0.8812 (t80) cc_final: 0.8448 (t80) REVERT: e 204 TYR cc_start: 0.8822 (t80) cc_final: 0.8122 (t80) REVERT: e 205 ASP cc_start: 0.8908 (t0) cc_final: 0.8430 (t0) REVERT: e 257 LYS cc_start: 0.9042 (ttpp) cc_final: 0.8684 (tttp) REVERT: e 291 LYS cc_start: 0.8849 (mtpt) cc_final: 0.8556 (mttm) REVERT: f 23 ILE cc_start: 0.9333 (mt) cc_final: 0.9065 (mm) REVERT: f 41 TYR cc_start: 0.8555 (m-80) cc_final: 0.8273 (m-10) REVERT: f 55 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8619 (mt-10) REVERT: f 64 TYR cc_start: 0.9106 (m-80) cc_final: 0.8886 (m-80) REVERT: f 91 MET cc_start: 0.8339 (mmm) cc_final: 0.7891 (tpp) REVERT: f 101 LEU cc_start: 0.9180 (mt) cc_final: 0.8442 (mp) REVERT: f 116 LYS cc_start: 0.9129 (mttt) cc_final: 0.8682 (mttp) REVERT: f 196 GLN cc_start: 0.8838 (tt0) cc_final: 0.8277 (tp40) REVERT: f 225 ASN cc_start: 0.8630 (m-40) cc_final: 0.8244 (m-40) REVERT: f 250 THR cc_start: 0.8565 (m) cc_final: 0.8275 (p) REVERT: f 264 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7505 (ptt-90) REVERT: g 55 MET cc_start: 0.8716 (mmm) cc_final: 0.8284 (tpp) REVERT: g 91 ASP cc_start: 0.8355 (t0) cc_final: 0.8100 (t0) REVERT: g 92 LYS cc_start: 0.8612 (mmmt) cc_final: 0.8412 (mmmt) REVERT: g 99 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9208 (tt) REVERT: g 106 TYR cc_start: 0.9516 (m-80) cc_final: 0.9163 (m-80) REVERT: g 112 SER cc_start: 0.9045 (m) cc_final: 0.8489 (p) REVERT: g 154 ILE cc_start: 0.9289 (mm) cc_final: 0.8800 (mm) REVERT: g 194 GLN cc_start: 0.9120 (tp40) cc_final: 0.8625 (tp40) REVERT: g 216 CYS cc_start: 0.8598 (m) cc_final: 0.7595 (m) REVERT: g 218 ASP cc_start: 0.8494 (p0) cc_final: 0.7951 (p0) REVERT: h 38 SER cc_start: 0.9234 (m) cc_final: 0.8840 (t) REVERT: i 43 GLU cc_start: 0.8380 (mp0) cc_final: 0.7421 (mp0) REVERT: i 98 LYS cc_start: 0.8945 (mttt) cc_final: 0.8523 (mtpp) REVERT: i 154 TYR cc_start: 0.8515 (t80) cc_final: 0.8040 (t80) REVERT: i 168 TYR cc_start: 0.8292 (p90) cc_final: 0.7494 (p90) REVERT: i 171 GLN cc_start: 0.8845 (mp10) cc_final: 0.8465 (mp10) REVERT: i 204 TYR cc_start: 0.8728 (t80) cc_final: 0.8178 (t80) REVERT: j 30 ASN cc_start: 0.8037 (m-40) cc_final: 0.7813 (m110) REVERT: j 84 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7665 (t70) REVERT: j 91 MET cc_start: 0.8557 (mmm) cc_final: 0.7791 (mmt) REVERT: j 110 VAL cc_start: 0.9640 (t) cc_final: 0.9275 (p) REVERT: j 111 GLN cc_start: 0.8384 (pm20) cc_final: 0.7746 (tt0) REVERT: j 137 GLU cc_start: 0.7301 (pm20) cc_final: 0.6839 (pm20) REVERT: j 196 GLN cc_start: 0.9029 (tt0) cc_final: 0.8766 (tt0) REVERT: j 223 LYS cc_start: 0.9030 (mtmt) cc_final: 0.8189 (mtmm) REVERT: j 227 TRP cc_start: 0.9116 (m100) cc_final: 0.8839 (m100) REVERT: j 266 ILE cc_start: 0.9175 (tp) cc_final: 0.8792 (tt) REVERT: k 39 GLU cc_start: 0.8262 (tm-30) cc_final: 0.8021 (tm-30) REVERT: k 67 MET cc_start: 0.9246 (ptm) cc_final: 0.8990 (ptp) REVERT: k 87 SER cc_start: 0.9187 (t) cc_final: 0.8761 (p) REVERT: k 92 LYS cc_start: 0.8998 (mmtm) cc_final: 0.8647 (mtpp) REVERT: k 144 ARG cc_start: 0.8651 (ttm-80) cc_final: 0.7660 (ttm-80) REVERT: k 155 TRP cc_start: 0.8419 (t60) cc_final: 0.7683 (t60) REVERT: k 178 CYS cc_start: 0.8335 (m) cc_final: 0.7543 (m) REVERT: k 216 CYS cc_start: 0.8542 (m) cc_final: 0.8208 (m) REVERT: l 53 PHE cc_start: 0.9300 (m-80) cc_final: 0.8904 (m-80) REVERT: m 111 VAL cc_start: 0.8739 (m) cc_final: 0.8467 (p) REVERT: m 166 ASP cc_start: 0.8637 (p0) cc_final: 0.7766 (p0) REVERT: m 167 ASP cc_start: 0.8611 (t0) cc_final: 0.8337 (t0) REVERT: m 216 ASN cc_start: 0.7694 (t0) cc_final: 0.7074 (m-40) REVERT: m 218 ASP cc_start: 0.8165 (m-30) cc_final: 0.7678 (m-30) REVERT: n 13 VAL cc_start: 0.9494 (t) cc_final: 0.9248 (p) REVERT: n 60 SER cc_start: 0.9514 (m) cc_final: 0.9102 (p) REVERT: n 129 GLU cc_start: 0.8564 (tp30) cc_final: 0.7565 (tp30) REVERT: n 249 ILE cc_start: 0.9437 (mt) cc_final: 0.9111 (mt) REVERT: o 86 LEU cc_start: 0.9268 (tp) cc_final: 0.9008 (tp) REVERT: o 87 SER cc_start: 0.9091 (m) cc_final: 0.8015 (p) REVERT: o 144 ARG cc_start: 0.7813 (ttp-170) cc_final: 0.7572 (ttp-170) REVERT: o 194 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8480 (tt0) REVERT: o 205 THR cc_start: 0.8640 (p) cc_final: 0.8410 (m) REVERT: o 207 MET cc_start: 0.8661 (ptp) cc_final: 0.8107 (ptp) REVERT: o 222 ARG cc_start: 0.8646 (ttm-80) cc_final: 0.8282 (ttm170) REVERT: p 4 GLN cc_start: 0.7850 (mt0) cc_final: 0.7543 (mp10) REVERT: q 126 ASP cc_start: 0.8482 (m-30) cc_final: 0.8193 (m-30) REVERT: q 190 SER cc_start: 0.9189 (m) cc_final: 0.8938 (m) REVERT: q 221 ASP cc_start: 0.7594 (p0) cc_final: 0.7249 (p0) REVERT: r 50 VAL cc_start: 0.9264 (m) cc_final: 0.9038 (p) REVERT: r 116 LYS cc_start: 0.8820 (mttt) cc_final: 0.8316 (mtmt) REVERT: r 153 ARG cc_start: 0.8393 (mmm160) cc_final: 0.8101 (tpt170) REVERT: r 210 VAL cc_start: 0.9564 (p) cc_final: 0.9181 (m) REVERT: r 249 ILE cc_start: 0.9591 (mt) cc_final: 0.9304 (mm) REVERT: s 50 ASP cc_start: 0.8822 (m-30) cc_final: 0.8525 (m-30) REVERT: s 144 ARG cc_start: 0.9241 (tmm-80) cc_final: 0.8931 (ttm-80) REVERT: s 154 ILE cc_start: 0.8950 (mt) cc_final: 0.8615 (pt) REVERT: s 175 TYR cc_start: 0.8534 (m-80) cc_final: 0.8111 (m-10) outliers start: 146 outliers final: 111 residues processed: 1225 average time/residue: 0.4568 time to fit residues: 912.1518 Evaluate side-chains 1210 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 1094 time to evaluate : 3.938 ------------------------------------------------------------------------------- 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 26 GLN Chi-restraints excluded: chain b residue 32 ILE Chi-restraints excluded: chain b residue 172 ARG Chi-restraints excluded: chain b residue 200 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 10 SER Chi-restraints excluded: chain c residue 17 ASP Chi-restraints excluded: chain c residue 76 LEU 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 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 181 MET 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 249 ILE Chi-restraints excluded: chain f residue 263 LEU Chi-restraints excluded: chain f residue 264 ARG Chi-restraints excluded: chain g residue 4 THR Chi-restraints excluded: chain g residue 99 LEU 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 9 LYS 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 102 ILE Chi-restraints excluded: chain i residue 128 GLU 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 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 j residue 265 ASN Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 69 GLN Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain k residue 207 MET 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 l residue 26 ASN Chi-restraints excluded: chain l residue 44 GLN Chi-restraints excluded: chain m residue 84 ILE 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 265 CYS 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 n residue 261 ASN Chi-restraints excluded: chain o residue 6 ASN 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 213 VAL Chi-restraints excluded: chain o residue 214 SER 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 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 268 VAL Chi-restraints excluded: chain s residue 53 ILE 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 203 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 388 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 191 optimal weight: 7.9990 chunk 217 optimal weight: 6.9990 chunk 97 optimal weight: 20.0000 chunk 387 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 225 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 259 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 171 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** b 224 HIS b 271 HIS ** 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 147 ASN h 21 ASN ** i 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 265 ASN ** k 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 194 GLN ** 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 l 39 ASN ** m 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 104 ASN ** 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 t 44 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.110768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.098358 restraints weight = 67450.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.101250 restraints weight = 32115.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.103158 restraints weight = 18672.775| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 34975 Z= 0.246 Angle : 0.673 10.845 47711 Z= 0.345 Chirality : 0.047 0.307 5363 Planarity : 0.005 0.046 6193 Dihedral : 5.721 59.529 4860 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.53 % Allowed : 21.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.12), residues: 4201 helix: -2.16 (0.22), residues: 416 sheet: 0.55 (0.15), residues: 1088 loop : -0.44 (0.12), residues: 2697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP f 227 HIS 0.009 0.001 HIS o 229 PHE 0.044 0.002 PHE k 19 TYR 0.035 0.002 TYR o 175 ARG 0.011 0.001 ARG k 222 Details of bonding type rmsd hydrogen bonds : bond 0.03651 ( 924) hydrogen bonds : angle 5.63446 ( 2631) covalent geometry : bond 0.00564 (34975) covalent geometry : angle 0.67328 (47711) *********************** 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 1294 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 1127 time to evaluate : 4.041 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 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: 0.8778 (mp0) cc_final: 0.8280 (mp0) REVERT: a 54 ASP cc_start: 0.8482 (m-30) cc_final: 0.8228 (m-30) REVERT: a 74 SER cc_start: 0.9478 (m) cc_final: 0.9248 (p) REVERT: a 120 PHE cc_start: 0.8815 (m-10) cc_final: 0.8556 (m-10) REVERT: a 161 ARG cc_start: 0.8564 (ttm170) cc_final: 0.8337 (ttm110) REVERT: a 205 ASP cc_start: 0.8518 (t0) cc_final: 0.8032 (t70) REVERT: a 277 GLU cc_start: 0.7710 (mp0) cc_final: 0.7225 (mp0) REVERT: b 84 ASP cc_start: 0.8465 (t0) cc_final: 0.7866 (t0) REVERT: b 87 LYS cc_start: 0.8548 (pttp) cc_final: 0.8193 (ttpt) REVERT: b 97 TYR cc_start: 0.8651 (m-80) cc_final: 0.8029 (m-10) REVERT: b 170 GLU cc_start: 0.8490 (mm-30) cc_final: 0.7727 (mm-30) REVERT: b 172 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.7189 (mtt90) REVERT: b 173 LYS cc_start: 0.8263 (mttt) cc_final: 0.7943 (mttt) REVERT: b 183 SER cc_start: 0.9335 (p) cc_final: 0.9066 (t) REVERT: b 246 GLN cc_start: 0.8145 (mt0) cc_final: 0.7724 (mt0) REVERT: c 48 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8817 (mt-10) REVERT: c 95 SER cc_start: 0.8961 (p) cc_final: 0.8682 (t) REVERT: c 112 SER cc_start: 0.9279 (m) cc_final: 0.8956 (p) REVERT: c 128 LYS cc_start: 0.8529 (mptt) cc_final: 0.8135 (mptt) REVERT: d 21 ASN cc_start: 0.7871 (p0) cc_final: 0.6929 (p0) REVERT: e 95 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7382 (mm-30) REVERT: e 173 SER cc_start: 0.9231 (p) cc_final: 0.8937 (p) REVERT: e 174 SER cc_start: 0.9163 (m) cc_final: 0.8696 (p) REVERT: e 182 TYR cc_start: 0.8925 (t80) cc_final: 0.8513 (t80) REVERT: e 204 TYR cc_start: 0.8872 (t80) cc_final: 0.8286 (t80) REVERT: e 205 ASP cc_start: 0.8858 (t0) cc_final: 0.8290 (t0) REVERT: e 229 ILE cc_start: 0.9152 (tt) cc_final: 0.8912 (tt) REVERT: e 231 ASP cc_start: 0.8361 (t0) cc_final: 0.8124 (t0) REVERT: e 257 LYS cc_start: 0.9015 (ttpp) cc_final: 0.8669 (tttp) REVERT: e 291 LYS cc_start: 0.8896 (mtpt) cc_final: 0.8110 (mttm) REVERT: f 23 ILE cc_start: 0.9342 (mt) cc_final: 0.9085 (mm) REVERT: f 41 TYR cc_start: 0.8561 (m-80) cc_final: 0.8125 (m-10) REVERT: f 44 ASP cc_start: 0.8707 (m-30) cc_final: 0.8449 (m-30) REVERT: f 55 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8687 (mt-10) REVERT: f 116 LYS cc_start: 0.9127 (mttt) cc_final: 0.8680 (mttp) REVERT: f 193 TYR cc_start: 0.8851 (m-80) cc_final: 0.8423 (m-10) REVERT: f 250 THR cc_start: 0.8640 (m) cc_final: 0.8331 (p) REVERT: g 55 MET cc_start: 0.8781 (mmm) cc_final: 0.8358 (tpp) REVERT: g 91 ASP cc_start: 0.8360 (t0) cc_final: 0.8106 (t0) REVERT: g 99 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9135 (tt) REVERT: g 154 ILE cc_start: 0.9320 (mm) cc_final: 0.8940 (mm) REVERT: g 216 CYS cc_start: 0.8726 (m) cc_final: 0.8319 (m) REVERT: i 34 GLN cc_start: 0.8830 (mp10) cc_final: 0.7849 (tt0) REVERT: i 98 LYS cc_start: 0.8980 (mttt) cc_final: 0.8672 (mtpp) REVERT: i 154 TYR cc_start: 0.8603 (t80) cc_final: 0.8136 (t80) REVERT: i 168 TYR cc_start: 0.8389 (p90) cc_final: 0.7615 (p90) REVERT: i 171 GLN cc_start: 0.8841 (mp10) cc_final: 0.8469 (mp10) REVERT: i 204 TYR cc_start: 0.8779 (t80) cc_final: 0.8268 (t80) REVERT: j 44 ASP cc_start: 0.8983 (m-30) cc_final: 0.8707 (m-30) REVERT: j 91 MET cc_start: 0.8614 (mmm) cc_final: 0.7864 (mmt) REVERT: j 110 VAL cc_start: 0.9631 (t) cc_final: 0.9283 (p) REVERT: j 111 GLN cc_start: 0.8425 (pm20) cc_final: 0.7738 (tt0) REVERT: j 137 GLU cc_start: 0.7234 (pm20) cc_final: 0.6737 (pm20) REVERT: j 196 GLN cc_start: 0.9082 (tt0) cc_final: 0.8831 (tt0) REVERT: j 223 LYS cc_start: 0.9042 (mtmt) cc_final: 0.8275 (mttp) REVERT: j 227 TRP cc_start: 0.9167 (m100) cc_final: 0.8878 (m100) REVERT: j 259 GLU cc_start: 0.7975 (pt0) cc_final: 0.7655 (pt0) REVERT: k 39 GLU cc_start: 0.8283 (tm-30) cc_final: 0.8076 (tm-30) REVERT: k 67 MET cc_start: 0.9301 (ptm) cc_final: 0.9039 (ptp) REVERT: k 87 SER cc_start: 0.9201 (t) cc_final: 0.8905 (m) REVERT: k 92 LYS cc_start: 0.8981 (mmtm) cc_final: 0.8571 (mtpp) REVERT: k 144 ARG cc_start: 0.8707 (ttm-80) cc_final: 0.7585 (ttm-80) REVERT: k 155 TRP cc_start: 0.8533 (t60) cc_final: 0.7734 (t60) REVERT: k 178 CYS cc_start: 0.8387 (m) cc_final: 0.7737 (m) REVERT: k 194 GLN cc_start: 0.9192 (mm-40) cc_final: 0.8507 (mm-40) REVERT: k 216 CYS cc_start: 0.8652 (m) cc_final: 0.8316 (m) REVERT: l 53 PHE cc_start: 0.9391 (m-80) cc_final: 0.9039 (m-80) REVERT: l 55 GLU cc_start: 0.8380 (tt0) cc_final: 0.7982 (tt0) REVERT: m 111 VAL cc_start: 0.8804 (m) cc_final: 0.8544 (p) REVERT: m 129 MET cc_start: 0.8894 (mmt) cc_final: 0.8421 (mmt) REVERT: m 166 ASP cc_start: 0.8669 (p0) cc_final: 0.7870 (p0) REVERT: m 209 ARG cc_start: 0.9082 (ttp80) cc_final: 0.8805 (ttp80) REVERT: m 216 ASN cc_start: 0.7741 (t0) cc_final: 0.7117 (m-40) REVERT: m 218 ASP cc_start: 0.8241 (m-30) cc_final: 0.7780 (m-30) REVERT: m 240 VAL cc_start: 0.9605 (OUTLIER) cc_final: 0.9315 (t) REVERT: n 13 VAL cc_start: 0.9492 (t) cc_final: 0.9251 (p) REVERT: n 46 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7665 (mt-10) REVERT: n 60 SER cc_start: 0.9527 (m) cc_final: 0.9111 (p) REVERT: n 249 ILE cc_start: 0.9436 (mt) cc_final: 0.9148 (mt) REVERT: o 65 MET cc_start: 0.8988 (mmm) cc_final: 0.8705 (mmm) REVERT: o 87 SER cc_start: 0.9113 (m) cc_final: 0.7954 (p) REVERT: o 144 ARG cc_start: 0.7772 (ttp-170) cc_final: 0.7465 (ttp-170) REVERT: o 194 GLN cc_start: 0.8762 (mm-40) cc_final: 0.8414 (tt0) REVERT: o 207 MET cc_start: 0.8700 (ptp) cc_final: 0.8049 (ptp) REVERT: o 227 THR cc_start: 0.9205 (OUTLIER) cc_final: 0.9000 (m) REVERT: q 99 HIS cc_start: 0.8447 (OUTLIER) cc_final: 0.8191 (t-90) REVERT: q 126 ASP cc_start: 0.8483 (m-30) cc_final: 0.8204 (m-30) REVERT: q 221 ASP cc_start: 0.7614 (p0) cc_final: 0.7202 (p0) REVERT: r 26 GLN cc_start: 0.7376 (mt0) cc_final: 0.6973 (mt0) REVERT: r 50 VAL cc_start: 0.9334 (m) cc_final: 0.9101 (p) REVERT: r 116 LYS cc_start: 0.8858 (mttt) cc_final: 0.8448 (mtmt) REVERT: r 210 VAL cc_start: 0.9590 (p) cc_final: 0.9216 (m) REVERT: r 249 ILE cc_start: 0.9602 (mt) cc_final: 0.9317 (mm) REVERT: s 44 MET cc_start: 0.8588 (mmm) cc_final: 0.8298 (tpp) REVERT: s 143 ASN cc_start: 0.8420 (t0) cc_final: 0.8188 (t0) REVERT: s 144 ARG cc_start: 0.9294 (tmm-80) cc_final: 0.8973 (ttm-80) REVERT: s 154 ILE cc_start: 0.9049 (mt) cc_final: 0.8704 (pt) outliers start: 167 outliers final: 139 residues processed: 1206 average time/residue: 0.4563 time to fit residues: 898.8448 Evaluate side-chains 1236 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 1092 time to evaluate : 3.649 ------------------------------------------------------------------------------- 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 172 ARG Chi-restraints excluded: chain b residue 200 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 10 SER 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 24 THR 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 135 GLU Chi-restraints excluded: chain e residue 181 MET Chi-restraints excluded: chain e residue 237 VAL Chi-restraints excluded: chain f residue 40 THR Chi-restraints excluded: chain f residue 45 SER Chi-restraints excluded: chain f residue 58 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 249 ILE Chi-restraints excluded: chain f residue 263 LEU Chi-restraints excluded: chain g residue 4 THR Chi-restraints excluded: chain g residue 99 LEU Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain g residue 132 SER 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 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 102 ILE 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 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 207 THR Chi-restraints excluded: chain j residue 246 GLN Chi-restraints excluded: chain j residue 247 VAL Chi-restraints excluded: chain j residue 265 ASN 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 69 GLN 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 207 MET Chi-restraints excluded: chain k residue 223 LEU Chi-restraints excluded: chain k residue 226 ASP 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 84 ILE 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 240 VAL Chi-restraints excluded: chain m residue 265 CYS 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 181 LEU Chi-restraints excluded: chain n residue 183 SER 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 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 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 99 HIS 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 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 53 ILE Chi-restraints excluded: chain s residue 76 LEU Chi-restraints excluded: chain s residue 81 ILE 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 t residue 7 THR Chi-restraints excluded: chain t residue 28 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 3 optimal weight: 50.0000 chunk 259 optimal weight: 10.0000 chunk 378 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 270 optimal weight: 8.9990 chunk 292 optimal weight: 6.9990 chunk 180 optimal weight: 10.0000 chunk 311 optimal weight: 20.0000 chunk 427 optimal weight: 20.0000 chunk 328 optimal weight: 9.9990 chunk 383 optimal weight: 0.0170 overall best weight: 5.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 112 GLN ** a 171 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** b 196 GLN b 271 HIS ** 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 265 ASN ** k 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 194 GLN ** 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 l 39 ASN m 202 HIS ** n 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 261 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 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.110510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.098229 restraints weight = 67106.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.101087 restraints weight = 31975.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.102973 restraints weight = 18546.229| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.5009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 34975 Z= 0.249 Angle : 0.689 12.230 47711 Z= 0.351 Chirality : 0.048 0.323 5363 Planarity : 0.005 0.050 6193 Dihedral : 5.808 55.303 4860 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.75 % Allowed : 21.31 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.12), residues: 4201 helix: -2.09 (0.23), residues: 388 sheet: 0.49 (0.15), residues: 1080 loop : -0.53 (0.11), residues: 2733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP f 227 HIS 0.009 0.002 HIS o 229 PHE 0.042 0.002 PHE k 19 TYR 0.031 0.002 TYR n 179 ARG 0.009 0.001 ARG k 222 Details of bonding type rmsd hydrogen bonds : bond 0.03649 ( 924) hydrogen bonds : angle 5.67375 ( 2631) covalent geometry : bond 0.00571 (34975) covalent geometry : angle 0.68942 (47711) *********************** 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 1296 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 1121 time to evaluate : 3.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 0.8781 (mp0) cc_final: 0.8322 (mp0) REVERT: a 69 GLU cc_start: 0.7807 (tt0) cc_final: 0.7564 (tt0) REVERT: a 74 SER cc_start: 0.9480 (m) cc_final: 0.9238 (p) REVERT: a 120 PHE cc_start: 0.8829 (m-10) cc_final: 0.8568 (m-10) REVERT: a 161 ARG cc_start: 0.8563 (ttm170) cc_final: 0.8252 (ttm110) REVERT: a 205 ASP cc_start: 0.8428 (t0) cc_final: 0.7974 (t70) REVERT: a 277 GLU cc_start: 0.7703 (mp0) cc_final: 0.7265 (mp0) REVERT: b 87 LYS cc_start: 0.8625 (pttp) cc_final: 0.8322 (ttpt) REVERT: b 97 TYR cc_start: 0.8678 (m-80) cc_final: 0.7880 (m-80) REVERT: b 149 ASN cc_start: 0.8463 (m-40) cc_final: 0.8136 (t0) REVERT: b 170 GLU cc_start: 0.8507 (mm-30) cc_final: 0.7645 (mm-30) REVERT: b 173 LYS cc_start: 0.8235 (mttt) cc_final: 0.7878 (mttt) REVERT: b 183 SER cc_start: 0.9375 (p) cc_final: 0.9075 (t) REVERT: b 246 GLN cc_start: 0.8207 (mt0) cc_final: 0.7781 (mt0) REVERT: c 48 GLU cc_start: 0.9201 (mt-10) cc_final: 0.8768 (mt-10) REVERT: c 95 SER cc_start: 0.8918 (p) cc_final: 0.8693 (t) REVERT: c 112 SER cc_start: 0.9240 (m) cc_final: 0.8918 (p) REVERT: c 128 LYS cc_start: 0.8774 (mptt) cc_final: 0.8404 (mptt) REVERT: c 225 ARG cc_start: 0.8822 (ptt180) cc_final: 0.8188 (ptt180) REVERT: d 21 ASN cc_start: 0.7969 (p0) cc_final: 0.7022 (p0) REVERT: e 95 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7426 (mm-30) REVERT: e 173 SER cc_start: 0.9281 (p) cc_final: 0.8974 (p) REVERT: e 174 SER cc_start: 0.9142 (m) cc_final: 0.8695 (p) REVERT: e 182 TYR cc_start: 0.8984 (t80) cc_final: 0.8555 (t80) REVERT: e 204 TYR cc_start: 0.8874 (t80) cc_final: 0.8358 (t80) REVERT: e 205 ASP cc_start: 0.8795 (t0) cc_final: 0.8288 (t70) REVERT: e 229 ILE cc_start: 0.9161 (tt) cc_final: 0.8929 (tt) REVERT: e 231 ASP cc_start: 0.8427 (t0) cc_final: 0.8159 (t0) REVERT: e 257 LYS cc_start: 0.9024 (ttpp) cc_final: 0.8687 (tttp) REVERT: e 291 LYS cc_start: 0.8665 (mtpt) cc_final: 0.8337 (mttm) REVERT: f 23 ILE cc_start: 0.9335 (mt) cc_final: 0.9086 (mm) REVERT: f 32 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.9095 (mp) REVERT: f 44 ASP cc_start: 0.8687 (m-30) cc_final: 0.8456 (m-30) REVERT: f 116 LYS cc_start: 0.9113 (mttt) cc_final: 0.8594 (mttp) REVERT: f 250 THR cc_start: 0.8639 (m) cc_final: 0.8323 (p) REVERT: f 264 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7453 (ptt-90) REVERT: g 55 MET cc_start: 0.8738 (mmm) cc_final: 0.8411 (tpp) REVERT: g 91 ASP cc_start: 0.8394 (t0) cc_final: 0.8143 (t0) REVERT: g 99 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9127 (tt) REVERT: g 154 ILE cc_start: 0.9326 (mm) cc_final: 0.8950 (mm) REVERT: g 216 CYS cc_start: 0.8848 (m) cc_final: 0.8388 (m) REVERT: g 218 ASP cc_start: 0.8534 (p0) cc_final: 0.8248 (p0) REVERT: i 23 GLN cc_start: 0.9018 (tt0) cc_final: 0.8591 (tt0) REVERT: i 34 GLN cc_start: 0.8837 (mp10) cc_final: 0.7822 (tt0) REVERT: i 98 LYS cc_start: 0.8909 (mttt) cc_final: 0.8535 (mtpp) REVERT: i 154 TYR cc_start: 0.8658 (t80) cc_final: 0.8140 (t80) REVERT: i 168 TYR cc_start: 0.8483 (p90) cc_final: 0.7663 (p90) REVERT: i 171 GLN cc_start: 0.8811 (mp10) cc_final: 0.8447 (mp10) REVERT: i 204 TYR cc_start: 0.8743 (t80) cc_final: 0.8178 (t80) REVERT: j 44 ASP cc_start: 0.9016 (m-30) cc_final: 0.8505 (m-30) REVERT: j 91 MET cc_start: 0.8566 (mmm) cc_final: 0.7866 (mmt) REVERT: j 111 GLN cc_start: 0.8411 (pm20) cc_final: 0.7744 (tt0) REVERT: j 137 GLU cc_start: 0.7397 (pm20) cc_final: 0.6923 (pm20) REVERT: j 196 GLN cc_start: 0.9053 (tt0) cc_final: 0.8813 (tt0) REVERT: j 223 LYS cc_start: 0.9085 (mtmt) cc_final: 0.8332 (mttp) REVERT: j 227 TRP cc_start: 0.9166 (m100) cc_final: 0.8895 (m100) REVERT: k 18 ASP cc_start: 0.8099 (t70) cc_final: 0.7809 (t70) REVERT: k 39 GLU cc_start: 0.8342 (tm-30) cc_final: 0.8036 (tm-30) REVERT: k 67 MET cc_start: 0.9299 (ptm) cc_final: 0.9015 (ptp) REVERT: k 87 SER cc_start: 0.9191 (t) cc_final: 0.8940 (m) REVERT: k 92 LYS cc_start: 0.8956 (mmtm) cc_final: 0.8537 (mtpp) REVERT: k 144 ARG cc_start: 0.8658 (ttm-80) cc_final: 0.7541 (ttm-80) REVERT: k 155 TRP cc_start: 0.8500 (t60) cc_final: 0.7668 (t60) REVERT: k 178 CYS cc_start: 0.8380 (m) cc_final: 0.7648 (m) REVERT: k 194 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8388 (mm-40) REVERT: k 216 CYS cc_start: 0.8655 (m) cc_final: 0.8319 (m) REVERT: l 53 PHE cc_start: 0.9405 (m-80) cc_final: 0.9074 (m-80) REVERT: l 55 GLU cc_start: 0.8447 (tt0) cc_final: 0.8060 (tt0) REVERT: m 111 VAL cc_start: 0.8763 (m) cc_final: 0.8493 (p) REVERT: m 119 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8409 (t80) REVERT: m 166 ASP cc_start: 0.8630 (p0) cc_final: 0.7847 (p0) REVERT: m 209 ARG cc_start: 0.9024 (ttp80) cc_final: 0.8624 (ttp80) REVERT: m 216 ASN cc_start: 0.7723 (t0) cc_final: 0.7069 (m-40) REVERT: m 218 ASP cc_start: 0.8293 (m-30) cc_final: 0.7831 (m-30) REVERT: m 240 VAL cc_start: 0.9592 (OUTLIER) cc_final: 0.9268 (t) REVERT: n 13 VAL cc_start: 0.9489 (t) cc_final: 0.9255 (p) REVERT: n 46 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7639 (mt-10) REVERT: n 60 SER cc_start: 0.9512 (m) cc_final: 0.9119 (p) REVERT: n 71 TRP cc_start: 0.8640 (t60) cc_final: 0.8383 (t60) REVERT: n 129 GLU cc_start: 0.8667 (tp30) cc_final: 0.7841 (tp30) REVERT: n 249 ILE cc_start: 0.9431 (mt) cc_final: 0.9129 (mt) REVERT: o 65 MET cc_start: 0.8975 (mmm) cc_final: 0.8571 (mmm) REVERT: o 74 ASP cc_start: 0.8524 (p0) cc_final: 0.8258 (p0) REVERT: o 87 SER cc_start: 0.9109 (m) cc_final: 0.7915 (p) REVERT: o 148 MET cc_start: 0.6004 (ttm) cc_final: 0.5644 (ttt) REVERT: o 194 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8477 (tt0) REVERT: o 205 THR cc_start: 0.8688 (p) cc_final: 0.8449 (t) REVERT: o 207 MET cc_start: 0.8707 (ptp) cc_final: 0.8065 (ptp) REVERT: p 4 GLN cc_start: 0.7642 (mp10) cc_final: 0.7272 (mp10) REVERT: q 99 HIS cc_start: 0.8468 (OUTLIER) cc_final: 0.8178 (t-90) REVERT: q 126 ASP cc_start: 0.8499 (m-30) cc_final: 0.8214 (m-30) REVERT: q 221 ASP cc_start: 0.7605 (p0) cc_final: 0.7155 (p0) REVERT: r 26 GLN cc_start: 0.7371 (mt0) cc_final: 0.6938 (mt0) REVERT: r 50 VAL cc_start: 0.9354 (m) cc_final: 0.9122 (p) REVERT: r 116 LYS cc_start: 0.8894 (mttt) cc_final: 0.8510 (mtmt) REVERT: r 249 ILE cc_start: 0.9600 (mt) cc_final: 0.9301 (mm) REVERT: s 44 MET cc_start: 0.8562 (mmm) cc_final: 0.8326 (tpp) REVERT: s 55 MET cc_start: 0.8923 (tpp) cc_final: 0.8508 (ttm) REVERT: s 143 ASN cc_start: 0.8498 (t0) cc_final: 0.8268 (t0) REVERT: s 144 ARG cc_start: 0.9284 (tmm-80) cc_final: 0.8935 (ttm-80) REVERT: s 154 ILE cc_start: 0.9135 (mt) cc_final: 0.8851 (pt) REVERT: s 175 TYR cc_start: 0.8635 (m-80) cc_final: 0.8349 (m-10) REVERT: s 191 CYS cc_start: 0.9147 (t) cc_final: 0.8729 (t) REVERT: s 193 TYR cc_start: 0.8762 (m-10) cc_final: 0.8545 (m-10) REVERT: t 32 TYR cc_start: 0.8644 (m-10) cc_final: 0.8336 (m-10) outliers start: 175 outliers final: 151 residues processed: 1211 average time/residue: 0.4744 time to fit residues: 941.7335 Evaluate side-chains 1243 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 1086 time to evaluate : 3.877 ------------------------------------------------------------------------------- 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 209 VAL 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 10 SER 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 24 THR 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 135 GLU Chi-restraints excluded: chain e residue 196 ILE 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 45 SER Chi-restraints excluded: chain f residue 58 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 g residue 2 LEU Chi-restraints excluded: chain g residue 4 THR Chi-restraints excluded: chain g residue 99 LEU Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain g residue 132 SER 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 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 102 ILE Chi-restraints excluded: chain i residue 132 VAL Chi-restraints excluded: chain i residue 190 SER 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 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 207 THR Chi-restraints excluded: chain j residue 246 GLN Chi-restraints excluded: chain j residue 247 VAL Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 69 GLN 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 207 MET 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 119 PHE Chi-restraints excluded: chain m residue 130 THR Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 196 ILE Chi-restraints excluded: chain m residue 212 LEU 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 69 VAL Chi-restraints excluded: chain n residue 84 ASP Chi-restraints excluded: chain n residue 152 GLU Chi-restraints excluded: chain n residue 181 LEU Chi-restraints excluded: chain n residue 183 SER 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 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 214 SER Chi-restraints excluded: chain o residue 226 ASP 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 51 ILE 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 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 226 ASN Chi-restraints excluded: chain r residue 268 VAL Chi-restraints excluded: chain s residue 53 ILE Chi-restraints excluded: chain s residue 76 LEU Chi-restraints excluded: chain s residue 81 ILE 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 28 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 414 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 273 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 chunk 337 optimal weight: 20.0000 chunk 189 optimal weight: 0.9980 chunk 351 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 224 optimal weight: 7.9990 chunk 167 optimal weight: 8.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 112 GLN ** a 171 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** b 196 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** e 230 ASN f 135 ASN ** i 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 30 ASN j 196 GLN ** k 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 194 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 l 39 ASN ** n 119 GLN ** 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 q 18 GLN ** r 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 261 ASN ** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.111336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.099040 restraints weight = 67186.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.101926 restraints weight = 32005.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.103826 restraints weight = 18570.099| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 34975 Z= 0.202 Angle : 0.679 11.316 47711 Z= 0.345 Chirality : 0.047 0.340 5363 Planarity : 0.005 0.054 6193 Dihedral : 5.806 52.885 4860 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.42 % Allowed : 22.04 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.12), residues: 4201 helix: -1.92 (0.24), residues: 357 sheet: 0.51 (0.15), residues: 1077 loop : -0.56 (0.11), residues: 2767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP f 227 HIS 0.008 0.001 HIS j 224 PHE 0.041 0.002 PHE k 19 TYR 0.030 0.002 TYR o 105 ARG 0.012 0.001 ARG i 67 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 924) hydrogen bonds : angle 5.63647 ( 2631) covalent geometry : bond 0.00469 (34975) covalent geometry : angle 0.67893 (47711) *********************** 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 1293 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 1130 time to evaluate : 3.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN 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: 0.8841 (mp0) cc_final: 0.8289 (mp0) REVERT: a 54 ASP cc_start: 0.8686 (m-30) cc_final: 0.8403 (m-30) REVERT: a 74 SER cc_start: 0.9460 (m) cc_final: 0.9234 (p) REVERT: a 120 PHE cc_start: 0.8776 (m-10) cc_final: 0.8519 (m-10) REVERT: a 161 ARG cc_start: 0.8550 (ttm170) cc_final: 0.8251 (ttm110) REVERT: a 205 ASP cc_start: 0.8311 (t0) cc_final: 0.7662 (t70) REVERT: a 277 GLU cc_start: 0.7694 (mp0) cc_final: 0.7339 (mp0) REVERT: b 87 LYS cc_start: 0.8627 (pttp) cc_final: 0.8357 (ttpt) REVERT: b 97 TYR cc_start: 0.8645 (m-80) cc_final: 0.7700 (m-80) REVERT: b 173 LYS cc_start: 0.8263 (mttt) cc_final: 0.8016 (mttt) REVERT: b 183 SER cc_start: 0.9339 (p) cc_final: 0.9032 (t) REVERT: b 246 GLN cc_start: 0.8224 (mt0) cc_final: 0.7816 (mt0) REVERT: c 48 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8688 (mt-10) REVERT: c 56 ASN cc_start: 0.9536 (t0) cc_final: 0.9159 (t0) REVERT: c 61 LYS cc_start: 0.9303 (mmtm) cc_final: 0.9077 (mmtm) REVERT: c 91 ASP cc_start: 0.8261 (t0) cc_final: 0.8054 (t0) REVERT: c 95 SER cc_start: 0.8953 (p) cc_final: 0.8748 (t) REVERT: c 103 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9071 (mp) REVERT: c 104 ASN cc_start: 0.8874 (m-40) cc_final: 0.8643 (m-40) REVERT: c 112 SER cc_start: 0.9220 (m) cc_final: 0.8940 (p) REVERT: c 225 ARG cc_start: 0.8839 (ptt180) cc_final: 0.8212 (ptt180) REVERT: d 21 ASN cc_start: 0.7940 (p0) cc_final: 0.6999 (p0) REVERT: d 63 LYS cc_start: 0.8761 (ttpp) cc_final: 0.8481 (ttpp) REVERT: e 95 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7418 (mm-30) REVERT: e 173 SER cc_start: 0.9272 (p) cc_final: 0.8961 (p) REVERT: e 174 SER cc_start: 0.9018 (m) cc_final: 0.8664 (p) REVERT: e 182 TYR cc_start: 0.8983 (t80) cc_final: 0.8498 (t80) REVERT: e 204 TYR cc_start: 0.8857 (t80) cc_final: 0.8337 (t80) REVERT: e 205 ASP cc_start: 0.8784 (t0) cc_final: 0.8285 (t70) REVERT: e 229 ILE cc_start: 0.9138 (tt) cc_final: 0.8874 (tt) REVERT: e 231 ASP cc_start: 0.8435 (t0) cc_final: 0.8175 (t0) REVERT: e 257 LYS cc_start: 0.9024 (ttpp) cc_final: 0.8663 (tttp) REVERT: e 291 LYS cc_start: 0.8671 (mtpt) cc_final: 0.8392 (mttm) REVERT: f 23 ILE cc_start: 0.9325 (mt) cc_final: 0.9087 (mm) REVERT: f 30 ASN cc_start: 0.8366 (t0) cc_final: 0.7954 (t0) REVERT: f 32 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.9115 (mp) REVERT: f 44 ASP cc_start: 0.8700 (m-30) cc_final: 0.8475 (m-30) REVERT: f 55 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8647 (mt-10) REVERT: f 87 LYS cc_start: 0.9044 (ptmm) cc_final: 0.8521 (ptpp) REVERT: f 91 MET cc_start: 0.8209 (mmm) cc_final: 0.7827 (tpp) REVERT: f 116 LYS cc_start: 0.9143 (mttt) cc_final: 0.8633 (mttp) REVERT: f 225 ASN cc_start: 0.8586 (m-40) cc_final: 0.8162 (m-40) REVERT: f 250 THR cc_start: 0.8600 (m) cc_final: 0.8285 (p) REVERT: f 264 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7184 (ptt-90) REVERT: g 91 ASP cc_start: 0.8350 (t0) cc_final: 0.8091 (t0) REVERT: g 99 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9157 (tt) REVERT: g 123 MET cc_start: 0.8197 (tpp) cc_final: 0.7907 (tpt) REVERT: g 216 CYS cc_start: 0.8825 (m) cc_final: 0.8344 (m) REVERT: g 218 ASP cc_start: 0.8467 (p0) cc_final: 0.8166 (p0) REVERT: i 34 GLN cc_start: 0.8819 (mp10) cc_final: 0.7825 (tt0) REVERT: i 96 GLU cc_start: 0.8346 (tm-30) cc_final: 0.8081 (tt0) REVERT: i 98 LYS cc_start: 0.8934 (mttt) cc_final: 0.8524 (mtpp) REVERT: i 154 TYR cc_start: 0.8602 (t80) cc_final: 0.8177 (t80) REVERT: i 168 TYR cc_start: 0.8491 (p90) cc_final: 0.7623 (p90) REVERT: i 171 GLN cc_start: 0.8862 (mp10) cc_final: 0.8483 (mp10) REVERT: i 204 TYR cc_start: 0.8783 (t80) cc_final: 0.8172 (t80) REVERT: j 44 ASP cc_start: 0.9009 (m-30) cc_final: 0.8505 (m-30) REVERT: j 91 MET cc_start: 0.8580 (mmm) cc_final: 0.8125 (mmp) REVERT: j 110 VAL cc_start: 0.9609 (t) cc_final: 0.9332 (p) REVERT: j 111 GLN cc_start: 0.8436 (pm20) cc_final: 0.7698 (tt0) REVERT: j 137 GLU cc_start: 0.7378 (pm20) cc_final: 0.6896 (pm20) REVERT: j 196 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8812 (tt0) REVERT: j 223 LYS cc_start: 0.9052 (mtmt) cc_final: 0.8352 (mttp) REVERT: j 227 TRP cc_start: 0.9181 (m100) cc_final: 0.8900 (m100) REVERT: j 265 ASN cc_start: 0.7784 (OUTLIER) cc_final: 0.7490 (m110) REVERT: k 18 ASP cc_start: 0.8124 (t70) cc_final: 0.7910 (t70) REVERT: k 39 GLU cc_start: 0.8355 (tm-30) cc_final: 0.7998 (tm-30) REVERT: k 55 MET cc_start: 0.9203 (tpt) cc_final: 0.8651 (tpt) REVERT: k 67 MET cc_start: 0.9268 (ptm) cc_final: 0.8974 (ptp) REVERT: k 87 SER cc_start: 0.9158 (t) cc_final: 0.8923 (m) REVERT: k 92 LYS cc_start: 0.8974 (mmtm) cc_final: 0.8623 (mtpp) REVERT: k 144 ARG cc_start: 0.8603 (ttm-80) cc_final: 0.7849 (ttm-80) REVERT: k 155 TRP cc_start: 0.8510 (t60) cc_final: 0.7688 (t60) REVERT: k 178 CYS cc_start: 0.8319 (m) cc_final: 0.7674 (m) REVERT: k 216 CYS cc_start: 0.8633 (m) cc_final: 0.8285 (m) REVERT: l 53 PHE cc_start: 0.9409 (m-80) cc_final: 0.9094 (m-80) REVERT: l 55 GLU cc_start: 0.8370 (tt0) cc_final: 0.7982 (tt0) REVERT: m 111 VAL cc_start: 0.8736 (m) cc_final: 0.8480 (p) REVERT: m 119 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8454 (t80) REVERT: m 166 ASP cc_start: 0.8631 (p0) cc_final: 0.7942 (p0) REVERT: m 209 ARG cc_start: 0.8992 (ttp80) cc_final: 0.8485 (ttp80) REVERT: m 216 ASN cc_start: 0.7768 (t0) cc_final: 0.7072 (m-40) REVERT: m 218 ASP cc_start: 0.8258 (m-30) cc_final: 0.7814 (m-30) REVERT: m 240 VAL cc_start: 0.9570 (OUTLIER) cc_final: 0.9230 (t) REVERT: n 13 VAL cc_start: 0.9483 (t) cc_final: 0.9261 (p) REVERT: n 46 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7792 (mt-10) REVERT: n 60 SER cc_start: 0.9483 (m) cc_final: 0.9121 (p) REVERT: n 129 GLU cc_start: 0.8655 (tp30) cc_final: 0.7838 (tp30) REVERT: n 249 ILE cc_start: 0.9429 (mt) cc_final: 0.9129 (mt) REVERT: o 74 ASP cc_start: 0.8526 (p0) cc_final: 0.8300 (p0) REVERT: o 86 LEU cc_start: 0.9319 (tp) cc_final: 0.9054 (tp) REVERT: o 87 SER cc_start: 0.9097 (m) cc_final: 0.7940 (p) REVERT: o 144 ARG cc_start: 0.7812 (ttp-170) cc_final: 0.7471 (ttp-170) REVERT: o 148 MET cc_start: 0.5934 (ttm) cc_final: 0.5625 (ttt) REVERT: o 155 TRP cc_start: 0.8835 (t60) cc_final: 0.7716 (t60) REVERT: o 194 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8461 (tt0) REVERT: o 205 THR cc_start: 0.8739 (p) cc_final: 0.8507 (t) REVERT: o 207 MET cc_start: 0.8679 (ptp) cc_final: 0.8144 (ptp) REVERT: p 4 GLN cc_start: 0.7616 (mp10) cc_final: 0.7356 (mp10) REVERT: q 99 HIS cc_start: 0.8455 (OUTLIER) cc_final: 0.8196 (t-90) REVERT: q 126 ASP cc_start: 0.8512 (m-30) cc_final: 0.8176 (m-30) REVERT: q 221 ASP cc_start: 0.7667 (p0) cc_final: 0.7208 (p0) REVERT: r 26 GLN cc_start: 0.7421 (mt0) cc_final: 0.6884 (mt0) REVERT: r 50 VAL cc_start: 0.9327 (m) cc_final: 0.9110 (p) REVERT: r 210 VAL cc_start: 0.9606 (p) cc_final: 0.9203 (m) REVERT: r 249 ILE cc_start: 0.9589 (mt) cc_final: 0.9293 (mm) REVERT: s 44 MET cc_start: 0.8577 (mmm) cc_final: 0.8336 (tpp) REVERT: s 55 MET cc_start: 0.8906 (tpp) cc_final: 0.8505 (ttm) REVERT: s 92 LYS cc_start: 0.8841 (mtmm) cc_final: 0.8589 (mtmm) REVERT: s 143 ASN cc_start: 0.8518 (t0) cc_final: 0.8289 (t0) REVERT: s 144 ARG cc_start: 0.9274 (tmm-80) cc_final: 0.8927 (ttm-80) REVERT: s 154 ILE cc_start: 0.9141 (mt) cc_final: 0.8865 (pt) REVERT: s 175 TYR cc_start: 0.8653 (m-80) cc_final: 0.8391 (m-10) REVERT: s 193 TYR cc_start: 0.8752 (m-10) cc_final: 0.8547 (m-10) outliers start: 163 outliers final: 138 residues processed: 1211 average time/residue: 0.4557 time to fit residues: 896.1837 Evaluate side-chains 1246 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 1099 time to evaluate : 4.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 61 VAL Chi-restraints excluded: chain a residue 62 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 11 ASP 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 86 LEU Chi-restraints excluded: chain b residue 200 LEU Chi-restraints excluded: chain b residue 268 VAL Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain c residue 50 ASP Chi-restraints excluded: chain c residue 67 MET Chi-restraints excluded: chain c residue 74 ASP Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 103 LEU 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 24 THR Chi-restraints excluded: chain d residue 62 LEU Chi-restraints excluded: chain e residue 51 ILE 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 281 MET Chi-restraints excluded: chain f residue 32 ILE Chi-restraints excluded: chain f residue 40 THR Chi-restraints excluded: chain f residue 58 VAL Chi-restraints excluded: chain f residue 88 ASP Chi-restraints excluded: chain f residue 126 LEU Chi-restraints excluded: chain f residue 132 MET Chi-restraints excluded: chain f residue 146 ILE Chi-restraints excluded: chain f residue 263 LEU Chi-restraints excluded: chain f residue 264 ARG Chi-restraints excluded: chain g residue 4 THR Chi-restraints excluded: chain g residue 99 LEU Chi-restraints excluded: chain g residue 132 SER 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 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 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 126 LEU Chi-restraints excluded: chain j residue 181 LEU Chi-restraints excluded: chain j residue 196 GLN Chi-restraints excluded: chain j residue 207 THR Chi-restraints excluded: chain j residue 246 GLN Chi-restraints excluded: chain j residue 247 VAL Chi-restraints excluded: chain j residue 265 ASN Chi-restraints excluded: chain k residue 10 SER Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 69 GLN 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 174 VAL 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 226 ASP Chi-restraints excluded: chain k residue 227 THR Chi-restraints excluded: chain m residue 61 VAL 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 240 VAL Chi-restraints excluded: chain m residue 265 CYS Chi-restraints excluded: chain n residue 42 ILE 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 107 THR Chi-restraints excluded: chain n residue 152 GLU Chi-restraints excluded: chain n residue 181 LEU 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 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 213 VAL Chi-restraints excluded: chain o residue 214 SER Chi-restraints excluded: chain o residue 226 ASP 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 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 192 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 53 ILE Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 76 LEU Chi-restraints excluded: chain s residue 81 ILE 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 28 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 202 optimal weight: 4.9990 chunk 303 optimal weight: 20.0000 chunk 78 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 372 optimal weight: 20.0000 chunk 168 optimal weight: 9.9990 chunk 374 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 218 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 112 GLN ** a 171 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 6 ASN c 11 ASN ** c 69 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** e 230 ASN f 135 ASN ** g 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 ASN ** i 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 194 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 l 39 ASN ** n 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 196 GLN ** o 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 26 ASN p 31 ASN ** r 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 226 ASN ** 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 44 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.113462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.101245 restraints weight = 66673.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.104145 restraints weight = 31529.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.105989 restraints weight = 18227.400| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.5262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 34975 Z= 0.157 Angle : 0.666 11.625 47711 Z= 0.338 Chirality : 0.047 0.348 5363 Planarity : 0.005 0.075 6193 Dihedral : 5.732 56.285 4860 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.69 % Allowed : 22.72 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.12), residues: 4201 helix: -1.88 (0.24), residues: 369 sheet: 0.58 (0.15), residues: 1048 loop : -0.57 (0.11), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP n 71 HIS 0.026 0.001 HIS j 195 PHE 0.040 0.002 PHE k 19 TYR 0.036 0.002 TYR m 255 ARG 0.010 0.001 ARG i 67 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 924) hydrogen bonds : angle 5.55490 ( 2631) covalent geometry : bond 0.00367 (34975) covalent geometry : angle 0.66601 (47711) ********************** 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 1277 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 1141 time to evaluate : 5.169 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 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: 0.8827 (mp0) cc_final: 0.8278 (mp0) REVERT: a 54 ASP cc_start: 0.8643 (m-30) cc_final: 0.8417 (m-30) REVERT: a 74 SER cc_start: 0.9424 (m) cc_final: 0.9206 (p) REVERT: a 161 ARG cc_start: 0.8539 (ttm170) cc_final: 0.8232 (ttm110) REVERT: a 205 ASP cc_start: 0.7978 (t0) cc_final: 0.7607 (t70) REVERT: b 97 TYR cc_start: 0.8570 (m-80) cc_final: 0.7805 (m-10) REVERT: b 183 SER cc_start: 0.9336 (p) cc_final: 0.9073 (t) REVERT: b 227 TRP cc_start: 0.8679 (m100) cc_final: 0.8387 (m100) REVERT: b 246 GLN cc_start: 0.8219 (mt0) cc_final: 0.7806 (mt0) REVERT: c 48 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8641 (mt-10) REVERT: c 56 ASN cc_start: 0.9540 (t0) cc_final: 0.9074 (t0) REVERT: c 104 ASN cc_start: 0.8826 (m-40) cc_final: 0.8599 (m-40) REVERT: c 112 SER cc_start: 0.9218 (m) cc_final: 0.8957 (p) REVERT: c 148 MET cc_start: 0.5814 (ttt) cc_final: 0.5117 (ttm) REVERT: c 225 ARG cc_start: 0.8819 (ptt180) cc_final: 0.8202 (ptt180) REVERT: d 21 ASN cc_start: 0.7952 (p0) cc_final: 0.7015 (p0) REVERT: d 63 LYS cc_start: 0.8733 (ttpp) cc_final: 0.8486 (ttpp) REVERT: e 95 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7491 (mm-30) REVERT: e 173 SER cc_start: 0.9251 (p) cc_final: 0.8966 (p) REVERT: e 174 SER cc_start: 0.9016 (m) cc_final: 0.8734 (p) REVERT: e 182 TYR cc_start: 0.8898 (t80) cc_final: 0.8458 (t80) REVERT: e 204 TYR cc_start: 0.8847 (t80) cc_final: 0.8421 (t80) REVERT: e 205 ASP cc_start: 0.8743 (t0) cc_final: 0.8153 (t0) REVERT: e 229 ILE cc_start: 0.9132 (tt) cc_final: 0.8873 (tt) REVERT: e 231 ASP cc_start: 0.8441 (t0) cc_final: 0.8207 (t0) REVERT: e 257 LYS cc_start: 0.9024 (ttpp) cc_final: 0.8636 (tttp) REVERT: e 286 ILE cc_start: 0.8881 (pt) cc_final: 0.8595 (mt) REVERT: f 23 ILE cc_start: 0.9303 (mt) cc_final: 0.9053 (mm) REVERT: f 30 ASN cc_start: 0.8342 (t0) cc_final: 0.7862 (t0) REVERT: f 55 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8634 (mt-10) REVERT: f 87 LYS cc_start: 0.9058 (ptmm) cc_final: 0.8535 (ptpp) REVERT: f 91 MET cc_start: 0.8196 (mmm) cc_final: 0.7796 (tpp) REVERT: f 116 LYS cc_start: 0.9159 (mttt) cc_final: 0.8645 (mttp) REVERT: f 207 THR cc_start: 0.9478 (m) cc_final: 0.9164 (t) REVERT: f 225 ASN cc_start: 0.8422 (m-40) cc_final: 0.7807 (m-40) REVERT: f 250 THR cc_start: 0.8509 (m) cc_final: 0.8191 (p) REVERT: f 264 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7015 (ptt-90) REVERT: g 91 ASP cc_start: 0.8383 (t0) cc_final: 0.8134 (t0) REVERT: g 99 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9192 (tt) REVERT: g 112 SER cc_start: 0.9035 (m) cc_final: 0.8359 (p) REVERT: g 123 MET cc_start: 0.8263 (tpp) cc_final: 0.7961 (tpt) REVERT: g 154 ILE cc_start: 0.9306 (mm) cc_final: 0.8903 (mm) REVERT: g 216 CYS cc_start: 0.8814 (m) cc_final: 0.7947 (m) REVERT: g 218 ASP cc_start: 0.8518 (p0) cc_final: 0.8103 (p0) REVERT: g 220 SER cc_start: 0.8432 (p) cc_final: 0.8152 (t) REVERT: h 38 SER cc_start: 0.9278 (m) cc_final: 0.8936 (t) REVERT: i 23 GLN cc_start: 0.8985 (tt0) cc_final: 0.8607 (tt0) REVERT: i 34 GLN cc_start: 0.8773 (mp10) cc_final: 0.7829 (tt0) REVERT: i 96 GLU cc_start: 0.8322 (tm-30) cc_final: 0.8065 (tt0) REVERT: i 98 LYS cc_start: 0.8956 (mttt) cc_final: 0.8562 (mtpp) REVERT: i 154 TYR cc_start: 0.8455 (t80) cc_final: 0.7961 (t80) REVERT: i 168 TYR cc_start: 0.8503 (p90) cc_final: 0.7549 (p90) REVERT: i 171 GLN cc_start: 0.8838 (mp10) cc_final: 0.8471 (mp10) REVERT: i 204 TYR cc_start: 0.8768 (t80) cc_final: 0.8214 (t80) REVERT: i 256 MET cc_start: 0.8486 (mmm) cc_final: 0.8255 (mmm) REVERT: j 44 ASP cc_start: 0.9004 (m-30) cc_final: 0.8502 (m-30) REVERT: j 91 MET cc_start: 0.8514 (mmm) cc_final: 0.8047 (mmp) REVERT: j 110 VAL cc_start: 0.9614 (t) cc_final: 0.9360 (p) REVERT: j 137 GLU cc_start: 0.7352 (pm20) cc_final: 0.6874 (pm20) REVERT: j 223 LYS cc_start: 0.9018 (mtmt) cc_final: 0.8290 (mttp) REVERT: j 227 TRP cc_start: 0.9149 (m100) cc_final: 0.8861 (m100) REVERT: k 17 ASP cc_start: 0.8191 (t70) cc_final: 0.6566 (p0) REVERT: k 18 ASP cc_start: 0.8194 (t70) cc_final: 0.7917 (t70) REVERT: k 39 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7969 (tm-30) REVERT: k 55 MET cc_start: 0.9096 (tpt) cc_final: 0.8619 (tpt) REVERT: k 67 MET cc_start: 0.9235 (ptm) cc_final: 0.9017 (ptp) REVERT: k 87 SER cc_start: 0.9125 (t) cc_final: 0.8891 (m) REVERT: k 92 LYS cc_start: 0.8951 (mmtm) cc_final: 0.8613 (mtpp) REVERT: k 144 ARG cc_start: 0.8506 (ttm-80) cc_final: 0.7729 (ttm-80) REVERT: k 155 TRP cc_start: 0.8466 (t60) cc_final: 0.7664 (t60) REVERT: k 178 CYS cc_start: 0.8264 (m) cc_final: 0.7408 (m) REVERT: k 180 ARG cc_start: 0.7967 (tpp80) cc_final: 0.7417 (tpp-160) REVERT: k 216 CYS cc_start: 0.8603 (m) cc_final: 0.8250 (m) REVERT: l 53 PHE cc_start: 0.9416 (m-80) cc_final: 0.9110 (m-80) REVERT: m 122 TYR cc_start: 0.8793 (m-80) cc_final: 0.8444 (m-80) REVERT: m 166 ASP cc_start: 0.8657 (p0) cc_final: 0.7937 (p0) REVERT: m 209 ARG cc_start: 0.8868 (ttp80) cc_final: 0.8404 (ttp80) REVERT: m 216 ASN cc_start: 0.7734 (t0) cc_final: 0.7125 (m-40) REVERT: m 218 ASP cc_start: 0.8317 (m-30) cc_final: 0.7883 (m-30) REVERT: m 240 VAL cc_start: 0.9535 (OUTLIER) cc_final: 0.9160 (t) REVERT: m 281 MET cc_start: 0.8060 (mmt) cc_final: 0.7602 (mmt) REVERT: n 13 VAL cc_start: 0.9539 (t) cc_final: 0.9319 (p) REVERT: n 60 SER cc_start: 0.9462 (m) cc_final: 0.9110 (p) REVERT: n 129 GLU cc_start: 0.8688 (tp30) cc_final: 0.7898 (tp30) REVERT: n 153 ARG cc_start: 0.7675 (mtm180) cc_final: 0.7467 (ptt180) REVERT: n 249 ILE cc_start: 0.9397 (mt) cc_final: 0.9123 (mt) REVERT: o 86 LEU cc_start: 0.9267 (tp) cc_final: 0.9028 (tp) REVERT: o 87 SER cc_start: 0.9065 (m) cc_final: 0.7945 (p) REVERT: o 105 TYR cc_start: 0.9002 (m-80) cc_final: 0.8733 (m-80) REVERT: o 144 ARG cc_start: 0.7657 (ttp-170) cc_final: 0.7311 (ttp-170) REVERT: o 148 MET cc_start: 0.5839 (ttm) cc_final: 0.5541 (ttt) REVERT: o 155 TRP cc_start: 0.8855 (t60) cc_final: 0.7740 (t60) REVERT: o 194 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8462 (tt0) REVERT: o 207 MET cc_start: 0.8676 (ptp) cc_final: 0.8196 (ptp) REVERT: p 4 GLN cc_start: 0.7607 (mp10) cc_final: 0.7355 (mp10) REVERT: q 126 ASP cc_start: 0.8564 (m-30) cc_final: 0.8191 (m-30) REVERT: q 267 ARG cc_start: 0.9322 (mtp85) cc_final: 0.8969 (ttm110) REVERT: r 50 VAL cc_start: 0.9290 (m) cc_final: 0.9076 (p) REVERT: r 145 TYR cc_start: 0.8656 (t80) cc_final: 0.8376 (t80) REVERT: r 153 ARG cc_start: 0.8381 (mmm160) cc_final: 0.8065 (tpt170) REVERT: r 174 PHE cc_start: 0.8597 (m-80) cc_final: 0.8333 (t80) REVERT: r 249 ILE cc_start: 0.9564 (mt) cc_final: 0.9232 (mm) REVERT: s 44 MET cc_start: 0.8489 (mmm) cc_final: 0.8240 (tpp) REVERT: s 55 MET cc_start: 0.8864 (tpp) cc_final: 0.8518 (ttm) REVERT: s 85 SER cc_start: 0.9539 (OUTLIER) cc_final: 0.9035 (m) REVERT: s 144 ARG cc_start: 0.9246 (tmm-80) cc_final: 0.8891 (ttm-80) REVERT: s 154 ILE cc_start: 0.9115 (mt) cc_final: 0.8851 (pt) REVERT: s 175 TYR cc_start: 0.8648 (m-80) cc_final: 0.8366 (m-10) outliers start: 136 outliers final: 119 residues processed: 1204 average time/residue: 0.6449 time to fit residues: 1281.0169 Evaluate side-chains 1245 residues out of total 3684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 1122 time to evaluate : 4.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 61 VAL Chi-restraints excluded: chain a residue 62 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 268 VAL Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain c residue 50 ASP Chi-restraints excluded: chain c residue 67 MET 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 24 THR Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 134 THR Chi-restraints excluded: chain e residue 135 GLU Chi-restraints excluded: chain e residue 196 ILE Chi-restraints excluded: chain e residue 237 VAL Chi-restraints excluded: chain e residue 281 MET Chi-restraints excluded: chain f residue 88 ASP Chi-restraints excluded: chain f residue 126 LEU Chi-restraints excluded: chain f residue 132 MET Chi-restraints excluded: chain f residue 146 ILE Chi-restraints excluded: chain f residue 263 LEU Chi-restraints excluded: chain f residue 264 ARG 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 227 THR Chi-restraints excluded: chain h residue 7 THR Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 57 VAL 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 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 207 THR Chi-restraints excluded: chain j residue 246 GLN Chi-restraints excluded: chain k residue 69 GLN Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain k residue 174 VAL 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 226 ASP 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 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 42 ILE 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 107 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 6 ASN Chi-restraints excluded: chain o residue 132 SER Chi-restraints excluded: chain o residue 153 ILE 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 32 TYR Chi-restraints excluded: chain p residue 40 SER 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 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 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 53 ILE Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 76 LEU Chi-restraints excluded: chain s residue 81 ILE 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 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 139 optimal weight: 9.9990 chunk 302 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 chunk 387 optimal weight: 10.0000 chunk 344 optimal weight: 8.9990 chunk 397 optimal weight: 5.9990 chunk 354 optimal weight: 5.9990 chunk 406 optimal weight: 0.9990 chunk 236 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 40.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 171 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 69 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** e 230 ASN f 135 ASN ** h 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 ASN ** i 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 194 GLN ** l 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 202 HIS ** n 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 196 GLN p 8 GLN ** p 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 26 ASN ** r 147 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 44 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.112447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.100168 restraints weight = 67007.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.103071 restraints weight = 31757.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.104984 restraints weight = 18413.201| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.5336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 34975 Z= 0.195 Angle : 0.688 17.553 47711 Z= 0.347 Chirality : 0.047 0.344 5363 Planarity : 0.005 0.060 6193 Dihedral : 5.728 57.310 4860 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.96 % Allowed : 22.88 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.12), residues: 4201 helix: -1.90 (0.24), residues: 369 sheet: 0.50 (0.15), residues: 1060 loop : -0.60 (0.11), residues: 2772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP n 71 HIS 0.008 0.001 HIS j 224 PHE 0.039 0.002 PHE k 19 TYR 0.034 0.002 TYR m 255 ARG 0.010 0.001 ARG t 43 Details of bonding type rmsd hydrogen bonds : bond 0.03484 ( 924) hydrogen bonds : angle 5.54960 ( 2631) covalent geometry : bond 0.00456 (34975) covalent geometry : angle 0.68757 (47711) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17338.46 seconds wall clock time: 305 minutes 54.21 seconds (18354.21 seconds total)