Starting phenix.real_space_refine on Thu Mar 5 09:07:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tqu_26072/03_2026/7tqu_26072.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tqu_26072/03_2026/7tqu_26072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tqu_26072/03_2026/7tqu_26072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tqu_26072/03_2026/7tqu_26072.map" model { file = "/net/cci-nas-00/data/ceres_data/7tqu_26072/03_2026/7tqu_26072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tqu_26072/03_2026/7tqu_26072.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 127 5.16 5 C 13211 2.51 5 N 3554 2.21 5 O 3999 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20891 Number of models: 1 Model: "" Number of chains: 17 Chain: "H" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 560 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 112} Link IDs: {'TRANS': 111} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 112 Planarities with less than four sites: {'UNK:plan-1': 112} Unresolved non-hydrogen planarities: 112 Chain: "L" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 510 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'TRANS': 101} Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 306 Unresolved non-hydrogen dihedrals: 102 Planarities with less than four sites: {'UNK:plan-1': 102} Unresolved non-hydrogen planarities: 102 Chain: "a" 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: "b" Number of atoms: 2043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2043 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 16, 'TRANS': 246} Chain breaks: 1 Chain: "c" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1801 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 20, 'TRANS': 212} Chain: "d" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "e" Number of atoms: 2219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2219 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 20, 'TRANS': 261} Chain: "f" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2057 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 16, 'TRANS': 248} Chain: "g" Number of atoms: 1810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1810 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 20, 'TRANS': 213} Chain: "h" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "i" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2226 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 20, 'TRANS': 262} Chain: "j" Number of atoms: 2029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2029 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 16, 'TRANS': 244} Chain breaks: 1 Chain: "k" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1826 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 20, 'TRANS': 215} 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: "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} Time building chain proxies: 4.93, per 1000 atoms: 0.24 Number of scatterers: 20891 At special positions: 0 Unit cell: (166.155, 166.155, 165.11, 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 127 16.00 O 3999 8.00 N 3554 7.00 C 13211 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: 1.61 Conformation dependent library (CDL) restraints added in 890.4 milliseconds 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5204 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 42 sheets defined 14.9% alpha, 35.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'H' and resid 51 through 54 Processing helix chain 'L' and resid 26 through 28 No H-bonds generated for 'chain 'L' and resid 26 through 28' Processing helix chain 'a' and resid 51 through 55 Processing helix chain 'a' and resid 71 through 77 Processing helix chain 'a' and resid 92 through 98 removed outlier: 5.072A pdb=" N LYS a 97 " --> pdb=" O GLY a 94 " (cutoff:3.500A) 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 removed outlier: 4.307A pdb=" N ILE a 286 " --> pdb=" O SER a 283 " (cutoff:3.500A) Processing helix chain 'b' and resid 35 through 37 No H-bonds generated for 'chain 'b' and resid 35 through 37' Processing helix chain 'b' and resid 82 through 86 Processing helix chain 'b' and resid 89 through 98 Processing helix chain 'b' and resid 150 through 154 removed outlier: 4.132A pdb=" N ARG b 153 " --> pdb=" O PRO b 150 " (cutoff:3.500A) Processing helix chain 'b' and resid 186 through 193 removed outlier: 4.295A 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 Processing helix chain 'c' and resid 97 through 104 Processing helix chain 'c' and resid 143 through 149 Processing helix chain 'c' and resid 181 through 185 removed outlier: 4.021A pdb=" N GLU c 185 " --> pdb=" O ASP c 182 " (cutoff:3.500A) Processing helix chain 'd' and resid 35 through 39 Processing helix chain 'd' and resid 50 through 55 Processing helix chain 'e' and resid 41 through 45 Processing helix chain 'e' and resid 51 through 55 Processing helix chain 'e' and resid 71 through 76 Processing helix chain 'e' and resid 92 through 98 removed outlier: 4.649A 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 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 82 through 86 removed outlier: 3.733A 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 89 through 98 Processing helix chain 'f' and resid 144 through 149 Processing helix chain 'f' and resid 150 through 154 removed outlier: 4.294A pdb=" N ARG f 153 " --> pdb=" O PRO f 150 " (cutoff:3.500A) Processing helix chain 'f' and resid 167 through 172 removed outlier: 3.601A pdb=" N ARG f 172 " --> pdb=" O ALA f 168 " (cutoff:3.500A) Processing helix chain 'f' and resid 186 through 193 removed outlier: 4.397A pdb=" N PHE f 191 " --> pdb=" O GLY f 188 " (cutoff:3.500A) Processing helix chain 'g' and resid 43 through 48 Processing helix chain 'g' and resid 64 through 69 Processing helix chain 'g' and resid 97 through 104 Processing helix chain 'g' and resid 143 through 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 71 through 76 Processing helix chain 'i' and resid 92 through 98 removed outlier: 4.763A pdb=" N LYS i 97 " --> pdb=" O GLY i 94 " (cutoff:3.500A) Processing helix chain 'i' and resid 111 through 118 removed outlier: 3.887A pdb=" N LYS i 116 " --> pdb=" O GLN i 112 " (cutoff:3.500A) Processing helix chain 'i' and resid 167 through 172 Processing helix chain 'i' and resid 225 through 229 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 removed outlier: 3.869A pdb=" N ALA j 47 " --> pdb=" O ASP j 44 " (cutoff:3.500A) Processing helix chain 'j' and resid 56 through 60 Processing helix chain 'j' and resid 82 through 86 Processing helix chain 'j' and resid 89 through 99 Processing helix chain 'j' and resid 150 through 154 removed outlier: 4.087A pdb=" N ARG j 153 " --> pdb=" O PRO j 150 " (cutoff:3.500A) Processing helix chain 'j' and resid 186 through 193 removed outlier: 4.244A pdb=" N PHE j 191 " --> pdb=" O GLY j 188 " (cutoff:3.500A) Processing helix chain 'k' and resid 42 through 47 removed outlier: 4.196A pdb=" N LEU k 46 " --> pdb=" O ASN k 42 " (cutoff:3.500A) 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 148 Processing helix chain 'l' and resid 35 through 39 Processing helix chain 'l' and resid 50 through 55 Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.538A pdb=" N UNK H 10 " --> pdb=" O UNK H 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'H' and resid 33 through 35 removed outlier: 3.514A pdb=" N UNK H 106 " --> pdb=" O UNK H 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 47 through 49 Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 11 Processing sheet with id=AA7, first strand: chain 'L' and resid 18 through 21 Processing sheet with id=AA8, first strand: chain 'L' and resid 43 through 45 Processing sheet with id=AA9, first strand: chain 'L' and resid 47 through 49 removed outlier: 6.777A pdb=" N UNK L 52 " --> pdb=" O UNK L 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'a' and resid 39 through 40 Processing sheet with id=AB2, first strand: chain 'a' and resid 39 through 40 Processing sheet with id=AB3, first strand: chain 'a' and resid 80 through 89 removed outlier: 6.687A pdb=" N VAL a 254 " --> pdb=" O VAL a 82 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE a 84 " --> pdb=" O VAL a 252 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL a 252 " --> pdb=" O ILE a 84 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER a 86 " --> pdb=" O THR a 250 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THR a 250 " --> pdb=" O SER a 86 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N THR a 88 " --> pdb=" O ILE a 248 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE a 248 " --> pdb=" O THR a 88 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE a 261 " --> pdb=" O ARG a 124 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ARG a 124 " --> pdb=" O ILE a 261 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N CYS a 263 " --> pdb=" O TYR a 122 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TYR a 122 " --> pdb=" O CYS a 263 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N CYS a 265 " --> pdb=" O PHE a 120 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N PHE a 120 " --> pdb=" O CYS a 265 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'a' and resid 188 through 191 removed outlier: 5.022A pdb=" N PHE a 120 " --> pdb=" O CYS a 265 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N CYS a 265 " --> pdb=" O PHE a 120 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TYR a 122 " --> pdb=" O CYS a 263 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N CYS a 263 " --> pdb=" O TYR a 122 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ARG a 124 " --> pdb=" O ILE a 261 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE a 261 " --> pdb=" O ARG a 124 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N CYS a 263 " --> pdb=" O VAL c 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'a' and resid 100 through 104 Processing sheet with id=AB6, first strand: chain 'i' and resid 31 through 33 removed outlier: 3.889A pdb=" N SER i 33 " --> pdb=" O GLN b 15 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP k 156 " --> pdb=" O THR b 24 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE k 82 " --> pdb=" O CYS k 191 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'b' and resid 32 through 33 removed outlier: 6.708A pdb=" N ILE b 32 " --> pdb=" O VAL b 209 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N HIS b 99 " --> pdb=" O GLY b 262 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLY b 262 " --> pdb=" O HIS b 99 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU b 101 " --> pdb=" O PHE b 260 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N PHE b 260 " --> pdb=" O LEU b 101 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ARG b 103 " --> pdb=" O THR b 258 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N THR b 258 " --> pdb=" O ARG b 103 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'b' and resid 32 through 33 removed outlier: 6.708A pdb=" N ILE b 32 " --> pdb=" O VAL b 209 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N HIS b 99 " --> pdb=" O GLY b 262 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLY b 262 " --> pdb=" O HIS b 99 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU b 101 " --> pdb=" O PHE b 260 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N PHE b 260 " --> pdb=" O LEU b 101 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ARG b 103 " --> pdb=" O THR b 258 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N THR b 258 " --> pdb=" O ARG b 103 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'b' and resid 155 through 156 removed outlier: 6.263A pdb=" N ALA b 121 " --> pdb=" O LEU b 234 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N GLN b 119 " --> pdb=" O PRO b 236 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'c' and resid 82 through 85 removed outlier: 3.579A pdb=" N PHE c 82 " --> pdb=" O CYS c 191 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LYS c 128 " --> pdb=" O GLN c 194 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ARG c 196 " --> pdb=" O THR c 126 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N THR c 126 " --> pdb=" O ARG c 196 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP c 156 " --> pdb=" O THR f 24 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'c' and resid 176 through 177 Processing sheet with id=AC3, first strand: chain 'd' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'e' and resid 31 through 33 removed outlier: 6.483A pdb=" N HIS g 152 " --> pdb=" O THR j 22 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N THR j 24 " --> pdb=" O HIS g 152 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE g 154 " --> pdb=" O THR j 24 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLY g 127 " --> pdb=" O LEU g 157 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS g 191 " --> pdb=" O PHE g 82 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHE g 82 " --> pdb=" O CYS g 191 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'e' and resid 39 through 40 Processing sheet with id=AC6, first strand: chain 'e' and resid 39 through 40 Processing sheet with id=AC7, first strand: chain 'e' and resid 80 through 89 removed outlier: 6.679A pdb=" N VAL e 254 " --> pdb=" O VAL e 82 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE e 84 " --> pdb=" O VAL e 252 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N VAL e 252 " --> pdb=" O ILE e 84 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N SER e 86 " --> pdb=" O THR e 250 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR e 250 " --> pdb=" O SER e 86 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N THR e 88 " --> pdb=" O ILE e 248 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE e 248 " --> pdb=" O THR e 88 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE e 261 " --> pdb=" O ARG e 124 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARG e 124 " --> pdb=" O ILE e 261 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N CYS e 263 " --> pdb=" O TYR e 122 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N TYR e 122 " --> pdb=" O CYS e 263 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'e' and resid 80 through 89 removed outlier: 6.679A pdb=" N VAL e 254 " --> pdb=" O VAL e 82 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE e 84 " --> pdb=" O VAL e 252 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N VAL e 252 " --> pdb=" O ILE e 84 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N SER e 86 " --> pdb=" O THR e 250 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR e 250 " --> pdb=" O SER e 86 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N THR e 88 " --> pdb=" O ILE e 248 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE e 248 " --> pdb=" O THR e 88 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE e 261 " --> pdb=" O ARG e 124 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARG e 124 " --> pdb=" O ILE e 261 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N CYS e 263 " --> pdb=" O TYR e 122 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N TYR e 122 " --> pdb=" O CYS e 263 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'e' and resid 100 through 104 Processing sheet with id=AD1, first strand: chain 'f' and resid 32 through 33 removed outlier: 6.585A pdb=" N ILE f 32 " --> pdb=" O VAL f 209 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N HIS f 99 " --> pdb=" O GLY f 262 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY f 262 " --> pdb=" O HIS f 99 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU f 101 " --> pdb=" O PHE f 260 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N PHE f 260 " --> pdb=" O LEU f 101 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG f 103 " --> pdb=" O THR f 258 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR f 258 " --> pdb=" O ARG f 103 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'f' and resid 32 through 33 removed outlier: 6.585A pdb=" N ILE f 32 " --> pdb=" O VAL f 209 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N HIS f 99 " --> pdb=" O GLY f 262 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY f 262 " --> pdb=" O HIS f 99 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU f 101 " --> pdb=" O PHE f 260 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N PHE f 260 " --> pdb=" O LEU f 101 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG f 103 " --> pdb=" O THR f 258 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR f 258 " --> pdb=" O ARG f 103 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'f' and resid 155 through 156 removed outlier: 6.163A pdb=" N ALA f 121 " --> pdb=" O LEU f 234 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N GLN f 119 " --> pdb=" O PRO f 236 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'g' and resid 176 through 177 Processing sheet with id=AD5, first strand: chain 'h' and resid 4 through 7 Processing sheet with id=AD6, first strand: chain 'i' and resid 39 through 40 Processing sheet with id=AD7, first strand: chain 'i' and resid 39 through 40 Processing sheet with id=AD8, first strand: chain 'i' and resid 80 through 89 removed outlier: 6.708A pdb=" N VAL i 254 " --> pdb=" O VAL i 82 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE i 84 " --> pdb=" O VAL i 252 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL i 252 " --> pdb=" O ILE i 84 " (cutoff:3.500A) removed outlier: 4.378A 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: 4.497A pdb=" N THR i 88 " --> pdb=" O ILE i 248 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE i 248 " --> pdb=" O THR i 88 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE i 261 " --> pdb=" O ARG i 124 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG i 124 " --> pdb=" O ILE i 261 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N CYS i 263 " --> pdb=" O TYR i 122 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N TYR i 122 " --> pdb=" O CYS i 263 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'i' and resid 80 through 89 removed outlier: 6.708A pdb=" N VAL i 254 " --> pdb=" O VAL i 82 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE i 84 " --> pdb=" O VAL i 252 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL i 252 " --> pdb=" O ILE i 84 " (cutoff:3.500A) removed outlier: 4.378A 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: 4.497A pdb=" N THR i 88 " --> pdb=" O ILE i 248 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE i 248 " --> pdb=" O THR i 88 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE i 261 " --> pdb=" O ARG i 124 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG i 124 " --> pdb=" O ILE i 261 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N CYS i 263 " --> pdb=" O TYR i 122 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N TYR i 122 " --> pdb=" O CYS i 263 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'i' and resid 100 through 104 Processing sheet with id=AE2, first strand: chain 'j' and resid 32 through 33 removed outlier: 6.402A pdb=" N ILE j 32 " --> pdb=" O VAL j 209 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU j 101 " --> pdb=" O PHE j 260 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N PHE j 260 " --> pdb=" O LEU j 101 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG j 103 " --> pdb=" O THR j 258 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR j 258 " --> pdb=" O ARG j 103 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'j' and resid 32 through 33 removed outlier: 6.402A pdb=" N ILE j 32 " --> pdb=" O VAL j 209 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU j 101 " --> pdb=" O PHE j 260 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N PHE j 260 " --> pdb=" O LEU j 101 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG j 103 " --> pdb=" O THR j 258 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR j 258 " --> pdb=" O ARG j 103 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'j' and resid 155 through 156 removed outlier: 6.157A pdb=" N ALA j 121 " --> pdb=" O LEU j 234 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N GLN j 119 " --> pdb=" O PRO j 236 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'k' and resid 108 through 109 Processing sheet with id=AE6, first strand: chain 'l' and resid 4 through 7 687 hydrogen bonds defined for protein. 1635 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: 3.90 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4147 1.31 - 1.45: 7272 1.45 - 1.59: 9767 1.59 - 1.73: 23 1.73 - 1.87: 200 Bond restraints: 21409 Sorted by residual: bond pdb=" CB ILE k 236 " pdb=" CG1 ILE k 236 " ideal model delta sigma weight residual 1.530 1.676 -0.146 2.00e-02 2.50e+03 5.35e+01 bond pdb=" CA PRO i 268 " pdb=" CB PRO i 268 " ideal model delta sigma weight residual 1.539 1.483 0.057 9.30e-03 1.16e+04 3.72e+01 bond pdb=" CB HIS f 224 " pdb=" CG HIS f 224 " ideal model delta sigma weight residual 1.497 1.413 0.084 1.40e-02 5.10e+03 3.58e+01 bond pdb=" CA VAL k 221 " pdb=" C VAL k 221 " ideal model delta sigma weight residual 1.520 1.580 -0.060 1.00e-02 1.00e+04 3.56e+01 bond pdb=" CB HIS b 224 " pdb=" CG HIS b 224 " ideal model delta sigma weight residual 1.497 1.417 0.080 1.40e-02 5.10e+03 3.27e+01 ... (remaining 21404 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 26102 2.85 - 5.70: 2815 5.70 - 8.55: 269 8.55 - 11.40: 34 11.40 - 14.25: 3 Bond angle restraints: 29223 Sorted by residual: angle pdb=" N VAL k 221 " pdb=" CA VAL k 221 " pdb=" C VAL k 221 " ideal model delta sigma weight residual 113.20 124.52 -11.32 9.60e-01 1.09e+00 1.39e+02 angle pdb=" C PRO k 135 " pdb=" N PRO k 136 " pdb=" CA PRO k 136 " ideal model delta sigma weight residual 120.21 129.27 -9.06 9.60e-01 1.09e+00 8.90e+01 angle pdb=" N TRP e 264 " pdb=" CA TRP e 264 " pdb=" C TRP e 264 " ideal model delta sigma weight residual 112.59 123.35 -10.76 1.22e+00 6.72e-01 7.77e+01 angle pdb=" C ARG k 222 " pdb=" CA ARG k 222 " pdb=" CB ARG k 222 " ideal model delta sigma weight residual 116.54 106.57 9.97 1.15e+00 7.56e-01 7.52e+01 angle pdb=" N LEU b 234 " pdb=" CA LEU b 234 " pdb=" C LEU b 234 " ideal model delta sigma weight residual 113.88 103.35 10.53 1.23e+00 6.61e-01 7.33e+01 ... (remaining 29218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 12371 17.81 - 35.63: 288 35.63 - 53.44: 67 53.44 - 71.26: 26 71.26 - 89.07: 10 Dihedral angle restraints: 12762 sinusoidal: 4702 harmonic: 8060 Sorted by residual: dihedral pdb=" C LEU f 82 " pdb=" N LEU f 82 " pdb=" CA LEU f 82 " pdb=" CB LEU f 82 " ideal model delta harmonic sigma weight residual -122.60 -132.84 10.24 0 2.50e+00 1.60e-01 1.68e+01 dihedral pdb=" C LEU b 82 " pdb=" N LEU b 82 " pdb=" CA LEU b 82 " pdb=" CB LEU b 82 " ideal model delta harmonic sigma weight residual -122.60 -132.15 9.55 0 2.50e+00 1.60e-01 1.46e+01 dihedral pdb=" CA ALA g 138 " pdb=" C ALA g 138 " pdb=" N LYS g 139 " pdb=" CA LYS g 139 " ideal model delta harmonic sigma weight residual 180.00 162.65 17.35 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 12759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 2446 0.102 - 0.204: 720 0.204 - 0.306: 117 0.306 - 0.408: 11 0.408 - 0.510: 6 Chirality restraints: 3300 Sorted by residual: chirality pdb=" CA TRP e 264 " pdb=" N TRP e 264 " pdb=" C TRP e 264 " pdb=" CB TRP e 264 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.50e+00 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 -3.12 0.49 2.00e-01 2.50e+01 6.01e+00 chirality pdb=" CA LEU f 82 " pdb=" N LEU f 82 " pdb=" C LEU f 82 " pdb=" CB LEU f 82 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.00e+00 ... (remaining 3297 not shown) Planarity restraints: 3804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP b 79 " 0.079 2.00e-02 2.50e+03 3.85e-02 3.71e+01 pdb=" CG TRP b 79 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP b 79 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP b 79 " -0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP b 79 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP b 79 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP b 79 " -0.051 2.00e-02 2.50e+03 pdb=" CZ2 TRP b 79 " 0.042 2.00e-02 2.50e+03 pdb=" CZ3 TRP b 79 " -0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP b 79 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR b 142 " -0.068 2.00e-02 2.50e+03 3.59e-02 2.57e+01 pdb=" CG TYR b 142 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR b 142 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR b 142 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR b 142 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR b 142 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR b 142 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR b 142 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR a 137 " -0.049 2.00e-02 2.50e+03 2.64e-02 1.39e+01 pdb=" CG TYR a 137 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR a 137 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR a 137 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR a 137 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR a 137 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR a 137 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR a 137 " -0.041 2.00e-02 2.50e+03 ... (remaining 3801 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 8320 2.88 - 3.39: 19172 3.39 - 3.89: 35913 3.89 - 4.40: 42902 4.40 - 4.90: 68609 Nonbonded interactions: 174916 Sorted by model distance: nonbonded pdb=" N VAL i 42 " pdb=" N GLU i 43 " model vdw 2.375 2.560 nonbonded pdb=" N VAL a 42 " pdb=" N GLU a 43 " model vdw 2.384 2.560 nonbonded pdb=" N GLN c 194 " pdb=" O GLN c 194 " model vdw 2.401 2.496 nonbonded pdb=" NZ LYS c 139 " pdb=" OD2 ASP c 146 " model vdw 2.418 3.120 nonbonded pdb=" N LEU b 234 " pdb=" N ALA b 235 " model vdw 2.418 2.560 ... (remaining 174911 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 114) selection = chain 'L' } ncs_group { reference = (chain 'a' and resid 17 through 300) selection = chain 'e' selection = (chain 'i' and resid 17 through 300) } ncs_group { reference = (chain 'b' and (resid 8 through 164 or resid 169 through 272)) selection = (chain 'f' and (resid 8 through 164 or resid 169 through 272)) selection = chain 'j' } ncs_group { reference = chain 'c' selection = (chain 'g' and resid 1 through 233) selection = (chain 'k' and resid 1 through 233) } ncs_group { reference = chain 'd' selection = chain 'h' selection = chain 'l' } 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: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.290 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 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 0.147 21409 Z= 1.117 Angle : 1.812 14.251 29223 Z= 1.226 Chirality : 0.096 0.510 3300 Planarity : 0.009 0.058 3804 Dihedral : 9.740 89.070 7558 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.16), residues: 2516 helix: -2.76 (0.27), residues: 210 sheet: 1.53 (0.20), residues: 608 loop : 0.62 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG c 93 TYR 0.068 0.007 TYR b 142 PHE 0.042 0.006 PHE j 117 TRP 0.079 0.009 TRP b 79 HIS 0.012 0.002 HIS j 118 Details of bonding type rmsd covalent geometry : bond 0.02057 (21409) covalent geometry : angle 1.81172 (29223) hydrogen bonds : bond 0.14883 ( 561) hydrogen bonds : angle 8.14010 ( 1635) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 789 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 64 TYR cc_start: 0.8109 (m-80) cc_final: 0.7825 (m-10) REVERT: a 78 ARG cc_start: 0.8474 (mmt-90) cc_final: 0.6473 (mtm180) REVERT: a 97 LYS cc_start: 0.8917 (pttt) cc_final: 0.8698 (pttt) REVERT: a 109 ASP cc_start: 0.8370 (m-30) cc_final: 0.7890 (m-30) REVERT: a 122 TYR cc_start: 0.9106 (m-80) cc_final: 0.8830 (m-80) REVERT: a 127 LEU cc_start: 0.9449 (tp) cc_final: 0.9231 (tp) REVERT: a 169 THR cc_start: 0.9136 (p) cc_final: 0.8879 (t) REVERT: b 64 TYR cc_start: 0.9398 (m-80) cc_final: 0.8956 (m-80) REVERT: b 74 THR cc_start: 0.8918 (p) cc_final: 0.8716 (p) REVERT: b 193 TYR cc_start: 0.9133 (m-80) cc_final: 0.8928 (m-10) REVERT: b 214 ASN cc_start: 0.8991 (t0) cc_final: 0.8729 (m-40) REVERT: b 256 MET cc_start: 0.8687 (mtp) cc_final: 0.8428 (mtm) REVERT: b 264 ARG cc_start: 0.7204 (ptt180) cc_final: 0.5249 (mmt90) REVERT: c 49 ILE cc_start: 0.8971 (mt) cc_final: 0.8734 (mt) REVERT: c 50 ASP cc_start: 0.7563 (m-30) cc_final: 0.7313 (m-30) REVERT: c 53 ILE cc_start: 0.9627 (mt) cc_final: 0.9336 (mt) REVERT: c 55 MET cc_start: 0.9132 (tpp) cc_final: 0.8897 (tpp) REVERT: c 74 ASP cc_start: 0.8256 (p0) cc_final: 0.7991 (p0) REVERT: c 156 ASP cc_start: 0.8992 (t0) cc_final: 0.8769 (t0) REVERT: d 24 THR cc_start: 0.8742 (p) cc_final: 0.8518 (t) REVERT: d 36 SER cc_start: 0.8096 (p) cc_final: 0.7715 (t) REVERT: d 61 MET cc_start: 0.7445 (ttm) cc_final: 0.7213 (ttp) REVERT: e 31 VAL cc_start: 0.9368 (t) cc_final: 0.8994 (p) REVERT: e 47 SER cc_start: 0.9290 (m) cc_final: 0.9030 (t) REVERT: e 51 ILE cc_start: 0.9324 (pt) cc_final: 0.9063 (pt) REVERT: e 98 LYS cc_start: 0.8817 (mttt) cc_final: 0.8269 (tptt) REVERT: e 105 ILE cc_start: 0.9445 (mt) cc_final: 0.8924 (tt) REVERT: e 146 ARG cc_start: 0.7622 (mmm-85) cc_final: 0.7154 (mpt180) REVERT: e 205 ASP cc_start: 0.8645 (t0) cc_final: 0.8136 (t0) REVERT: e 209 ARG cc_start: 0.8010 (ptm-80) cc_final: 0.7569 (mtt-85) REVERT: e 226 LEU cc_start: 0.9286 (tp) cc_final: 0.8987 (tp) REVERT: e 242 ARG cc_start: 0.7554 (mmm-85) cc_final: 0.6995 (ppt170) REVERT: e 262 ARG cc_start: 0.7903 (mtp180) cc_final: 0.7686 (mtt-85) REVERT: f 13 VAL cc_start: 0.9402 (t) cc_final: 0.9064 (p) REVERT: f 15 GLN cc_start: 0.9182 (tt0) cc_final: 0.8964 (tt0) REVERT: f 91 MET cc_start: 0.8683 (mmm) cc_final: 0.8469 (mmt) REVERT: f 129 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8486 (mm-30) REVERT: f 191 PHE cc_start: 0.9275 (m-80) cc_final: 0.9030 (m-10) REVERT: f 214 ASN cc_start: 0.9025 (t0) cc_final: 0.8817 (t0) REVERT: f 264 ARG cc_start: 0.6357 (ptt180) cc_final: 0.4697 (mtt-85) REVERT: g 10 SER cc_start: 0.9123 (t) cc_final: 0.8834 (p) REVERT: g 77 SER cc_start: 0.9076 (t) cc_final: 0.8643 (m) REVERT: g 91 ASP cc_start: 0.8258 (t0) cc_final: 0.8023 (t0) REVERT: g 178 CYS cc_start: 0.8697 (m) cc_final: 0.8457 (m) REVERT: g 232 GLN cc_start: 0.8894 (tt0) cc_final: 0.6494 (pm20) REVERT: g 234 LYS cc_start: 0.7486 (mmtt) cc_final: 0.6804 (tttm) REVERT: h 24 THR cc_start: 0.9092 (p) cc_final: 0.8864 (t) REVERT: i 47 SER cc_start: 0.9006 (m) cc_final: 0.8593 (p) REVERT: i 55 VAL cc_start: 0.9155 (m) cc_final: 0.8947 (m) REVERT: i 58 THR cc_start: 0.9427 (p) cc_final: 0.9069 (p) REVERT: i 78 ARG cc_start: 0.8326 (mmt-90) cc_final: 0.7368 (mtm180) REVERT: i 90 SER cc_start: 0.8890 (p) cc_final: 0.8564 (m) REVERT: i 146 ARG cc_start: 0.7707 (tpp-160) cc_final: 0.7163 (ptp-170) REVERT: i 172 SER cc_start: 0.8537 (m) cc_final: 0.8158 (p) REVERT: i 264 TRP cc_start: 0.8248 (m100) cc_final: 0.7699 (m100) REVERT: j 26 GLN cc_start: 0.9080 (mt0) cc_final: 0.8817 (mt0) REVERT: j 132 MET cc_start: 0.8697 (mtp) cc_final: 0.8376 (mtm) REVERT: j 145 TYR cc_start: 0.9031 (t80) cc_final: 0.8754 (t80) REVERT: j 214 ASN cc_start: 0.9070 (t0) cc_final: 0.8719 (t0) REVERT: j 256 MET cc_start: 0.8969 (mtp) cc_final: 0.8610 (mtm) REVERT: k 42 ASN cc_start: 0.8153 (t0) cc_final: 0.7837 (t0) REVERT: k 43 MET cc_start: 0.9001 (mmm) cc_final: 0.8397 (mmm) REVERT: k 157 LEU cc_start: 0.9172 (mt) cc_final: 0.8869 (mt) REVERT: k 197 ILE cc_start: 0.9030 (mt) cc_final: 0.8820 (mt) REVERT: k 205 THR cc_start: 0.8721 (p) cc_final: 0.7955 (p) outliers start: 0 outliers final: 0 residues processed: 789 average time/residue: 0.1506 time to fit residues: 180.7454 Evaluate side-chains 512 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 512 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.0970 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 32 ASN ** a 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 112 GLN ** a 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 61 ASN b 111 GLN b 162 ASN b 196 GLN c 75 ASN c 104 ASN d 4 GLN d 21 ASN e 99 HIS ** f 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 162 ASN ** f 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 69 GLN g 73 ASN g 104 ASN i 34 GLN ** i 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 148 GLN i 198 ASN i 230 ASN j 113 ASN j 147 ASN ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 96 HIS k 108 HIS ** k 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 229 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.118447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.106946 restraints weight = 38353.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.109397 restraints weight = 18554.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.110990 restraints weight = 11151.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.112097 restraints weight = 7727.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.112903 restraints weight = 5914.460| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 21409 Z= 0.216 Angle : 0.692 8.930 29223 Z= 0.368 Chirality : 0.047 0.176 3300 Planarity : 0.005 0.049 3804 Dihedral : 5.902 46.058 3000 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.36 % Allowed : 9.92 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.16), residues: 2516 helix: -2.44 (0.29), residues: 217 sheet: 1.01 (0.19), residues: 676 loop : 0.23 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 114 TYR 0.028 0.002 TYR c 68 PHE 0.026 0.002 PHE c 115 TRP 0.019 0.002 TRP b 80 HIS 0.009 0.002 HIS i 99 Details of bonding type rmsd covalent geometry : bond 0.00490 (21409) covalent geometry : angle 0.69235 (29223) hydrogen bonds : bond 0.04440 ( 561) hydrogen bonds : angle 6.32766 ( 1635) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 599 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 78 ARG cc_start: 0.8513 (mmt-90) cc_final: 0.6150 (mtm180) REVERT: a 97 LYS cc_start: 0.8797 (pttt) cc_final: 0.8444 (pptt) REVERT: b 64 TYR cc_start: 0.9278 (m-80) cc_final: 0.8919 (m-80) REVERT: b 145 TYR cc_start: 0.9197 (t80) cc_final: 0.8792 (t80) REVERT: b 193 TYR cc_start: 0.9121 (m-80) cc_final: 0.8858 (m-10) REVERT: b 214 ASN cc_start: 0.8908 (t0) cc_final: 0.8657 (m-40) REVERT: c 48 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8858 (mt-10) REVERT: c 74 ASP cc_start: 0.8124 (p0) cc_final: 0.7880 (t0) REVERT: c 176 ARG cc_start: 0.8963 (mtt-85) cc_final: 0.8633 (mtt-85) REVERT: c 218 ASP cc_start: 0.8928 (p0) cc_final: 0.8707 (p0) REVERT: d 14 GLU cc_start: 0.7190 (tm-30) cc_final: 0.6758 (tm-30) REVERT: d 36 SER cc_start: 0.7931 (p) cc_final: 0.7444 (t) REVERT: d 44 GLN cc_start: 0.7603 (tt0) cc_final: 0.7358 (tt0) REVERT: e 31 VAL cc_start: 0.9205 (t) cc_final: 0.8820 (p) REVERT: e 47 SER cc_start: 0.9119 (m) cc_final: 0.8731 (t) REVERT: e 97 LYS cc_start: 0.8127 (pttm) cc_final: 0.7857 (tptt) REVERT: e 98 LYS cc_start: 0.8664 (mttt) cc_final: 0.8195 (tptt) REVERT: e 146 ARG cc_start: 0.7859 (mmm-85) cc_final: 0.7155 (mpt180) REVERT: e 154 TYR cc_start: 0.8922 (t80) cc_final: 0.8412 (t80) REVERT: e 196 ILE cc_start: 0.7444 (tp) cc_final: 0.7242 (pt) REVERT: e 209 ARG cc_start: 0.7909 (ptm-80) cc_final: 0.7232 (mtt-85) REVERT: e 229 ILE cc_start: 0.8993 (pt) cc_final: 0.8779 (tp) REVERT: e 242 ARG cc_start: 0.7310 (mmm-85) cc_final: 0.6556 (ptt180) REVERT: f 13 VAL cc_start: 0.9224 (t) cc_final: 0.8873 (p) REVERT: f 89 MET cc_start: 0.8872 (mmp) cc_final: 0.8309 (mmt) REVERT: f 91 MET cc_start: 0.8211 (mmm) cc_final: 0.7914 (mmt) REVERT: f 223 LYS cc_start: 0.9156 (mttm) cc_final: 0.8935 (mttm) REVERT: g 10 SER cc_start: 0.9121 (t) cc_final: 0.8765 (p) REVERT: g 61 LYS cc_start: 0.8804 (mmtt) cc_final: 0.8429 (mmtm) REVERT: g 77 SER cc_start: 0.9204 (t) cc_final: 0.8700 (m) REVERT: g 91 ASP cc_start: 0.8413 (t0) cc_final: 0.8166 (t0) REVERT: g 178 CYS cc_start: 0.8543 (m) cc_final: 0.8337 (m) REVERT: g 226 ASP cc_start: 0.6360 (m-30) cc_final: 0.6141 (m-30) REVERT: g 232 GLN cc_start: 0.8839 (tt0) cc_final: 0.6282 (pm20) REVERT: g 234 LYS cc_start: 0.7545 (mmtt) cc_final: 0.7039 (tmtt) REVERT: h 39 ASN cc_start: 0.8668 (m-40) cc_final: 0.8408 (m-40) REVERT: h 59 ASP cc_start: 0.8363 (m-30) cc_final: 0.8123 (m-30) REVERT: i 34 GLN cc_start: 0.8594 (mt0) cc_final: 0.8050 (mt0) REVERT: i 78 ARG cc_start: 0.8338 (mmt-90) cc_final: 0.7325 (mtm180) REVERT: i 90 SER cc_start: 0.8820 (p) cc_final: 0.8531 (t) REVERT: i 146 ARG cc_start: 0.8075 (tpp-160) cc_final: 0.6749 (ptm160) REVERT: i 172 SER cc_start: 0.9050 (m) cc_final: 0.8766 (p) REVERT: i 205 ASP cc_start: 0.8109 (t0) cc_final: 0.7843 (t0) REVERT: i 264 TRP cc_start: 0.8005 (m100) cc_final: 0.7288 (m100) REVERT: j 33 VAL cc_start: 0.9396 (t) cc_final: 0.8934 (m) REVERT: j 141 SER cc_start: 0.8394 (p) cc_final: 0.8170 (p) REVERT: j 183 SER cc_start: 0.9160 (p) cc_final: 0.8930 (p) REVERT: j 232 LEU cc_start: 0.9416 (mt) cc_final: 0.9192 (mt) REVERT: j 252 THR cc_start: 0.9508 (m) cc_final: 0.8913 (p) REVERT: j 256 MET cc_start: 0.8988 (mtp) cc_final: 0.8761 (mtm) REVERT: k 43 MET cc_start: 0.8737 (mmm) cc_final: 0.8491 (tpp) REVERT: k 55 MET cc_start: 0.9228 (tpp) cc_final: 0.8961 (tpp) REVERT: k 59 ASP cc_start: 0.7419 (t0) cc_final: 0.6806 (p0) REVERT: k 61 LYS cc_start: 0.9267 (mmtp) cc_final: 0.8800 (mptt) REVERT: k 75 ASN cc_start: 0.8440 (t0) cc_final: 0.7882 (p0) REVERT: k 112 SER cc_start: 0.9092 (m) cc_final: 0.8766 (p) REVERT: k 145 LYS cc_start: 0.8774 (mttt) cc_final: 0.8305 (tptt) REVERT: k 157 LEU cc_start: 0.9234 (mt) cc_final: 0.9018 (mt) REVERT: k 206 SER cc_start: 0.8922 (t) cc_final: 0.8580 (p) REVERT: k 207 MET cc_start: 0.7983 (mpp) cc_final: 0.7757 (mpp) outliers start: 52 outliers final: 33 residues processed: 626 average time/residue: 0.1403 time to fit residues: 135.8560 Evaluate side-chains 542 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 509 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 88 THR Chi-restraints excluded: chain b residue 79 TRP Chi-restraints excluded: chain b residue 115 SER Chi-restraints excluded: chain b residue 247 VAL Chi-restraints excluded: chain b residue 252 THR Chi-restraints excluded: chain b residue 265 ASN Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 162 SER Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain e residue 29 SER Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 100 PHE Chi-restraints excluded: chain e residue 135 GLU Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 280 ASP Chi-restraints excluded: chain e residue 284 SER Chi-restraints excluded: chain f residue 10 SER Chi-restraints excluded: chain f residue 38 TRP Chi-restraints excluded: chain f residue 74 THR Chi-restraints excluded: chain f residue 115 SER Chi-restraints excluded: chain g residue 7 THR Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 67 MET Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain g residue 148 MET Chi-restraints excluded: chain g residue 227 THR Chi-restraints excluded: chain h residue 51 SER Chi-restraints excluded: chain i residue 51 ILE Chi-restraints excluded: chain i residue 280 ASP Chi-restraints excluded: chain k residue 7 THR Chi-restraints excluded: chain k residue 227 THR Chi-restraints excluded: chain l residue 42 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 81 optimal weight: 0.7980 chunk 234 optimal weight: 10.0000 chunk 127 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 182 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 97 optimal weight: 20.0000 chunk 247 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 overall best weight: 7.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 32 ASN ** a 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 11 ASN c 232 GLN d 4 GLN e 34 GLN e 49 GLN e 99 HIS ** f 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 56 ASN ** g 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 69 GLN i 89 ASN ** i 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 230 ASN j 261 ASN ** l 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.112785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.101204 restraints weight = 39392.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.103613 restraints weight = 19097.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.105146 restraints weight = 11479.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.106205 restraints weight = 8038.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.106959 restraints weight = 6187.242| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 21409 Z= 0.339 Angle : 0.740 10.513 29223 Z= 0.389 Chirality : 0.050 0.201 3300 Planarity : 0.006 0.056 3804 Dihedral : 6.155 59.462 3000 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.80 % Allowed : 11.24 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.16), residues: 2516 helix: -2.29 (0.29), residues: 226 sheet: 0.50 (0.19), residues: 656 loop : -0.23 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG a 114 TYR 0.023 0.002 TYR a 154 PHE 0.024 0.003 PHE g 212 TRP 0.022 0.002 TRP j 80 HIS 0.008 0.002 HIS h 13 Details of bonding type rmsd covalent geometry : bond 0.00785 (21409) covalent geometry : angle 0.74002 (29223) hydrogen bonds : bond 0.04298 ( 561) hydrogen bonds : angle 5.97407 ( 1635) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 514 time to evaluate : 0.661 Fit side-chains REVERT: a 34 GLN cc_start: 0.8441 (mt0) cc_final: 0.8193 (mt0) REVERT: a 43 GLU cc_start: 0.8360 (mp0) cc_final: 0.7711 (mp0) REVERT: a 73 GLU cc_start: 0.8683 (tp30) cc_final: 0.8480 (tp30) REVERT: a 78 ARG cc_start: 0.8855 (mmt-90) cc_final: 0.6315 (mtm180) REVERT: a 96 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8169 (tm-30) REVERT: a 97 LYS cc_start: 0.8882 (pttt) cc_final: 0.8429 (pptt) REVERT: a 196 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8551 (pt) REVERT: a 209 ARG cc_start: 0.5356 (mmt-90) cc_final: 0.4804 (ttp-170) REVERT: b 88 ASP cc_start: 0.7155 (p0) cc_final: 0.6906 (p0) REVERT: c 48 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8949 (mt-10) REVERT: c 148 MET cc_start: 0.8861 (tmm) cc_final: 0.8334 (ppp) REVERT: c 176 ARG cc_start: 0.8829 (mtt-85) cc_final: 0.8482 (mtt-85) REVERT: c 218 ASP cc_start: 0.9132 (p0) cc_final: 0.8751 (p0) REVERT: d 14 GLU cc_start: 0.7236 (tm-30) cc_final: 0.6944 (tm-30) REVERT: d 32 TYR cc_start: 0.9150 (m-80) cc_final: 0.8780 (m-80) REVERT: d 36 SER cc_start: 0.7963 (p) cc_final: 0.7477 (t) REVERT: d 44 GLN cc_start: 0.7866 (tt0) cc_final: 0.7402 (tt0) REVERT: e 97 LYS cc_start: 0.8223 (pttm) cc_final: 0.7934 (tptp) REVERT: e 98 LYS cc_start: 0.8803 (mttt) cc_final: 0.8286 (tptt) REVERT: e 105 ILE cc_start: 0.9353 (mt) cc_final: 0.9007 (tt) REVERT: e 135 GLU cc_start: 0.5954 (OUTLIER) cc_final: 0.5403 (tt0) REVERT: e 146 ARG cc_start: 0.7992 (mmm-85) cc_final: 0.7211 (mpt180) REVERT: e 209 ARG cc_start: 0.8196 (ptm-80) cc_final: 0.7303 (mtt-85) REVERT: e 229 ILE cc_start: 0.9114 (pt) cc_final: 0.8900 (tp) REVERT: e 242 ARG cc_start: 0.7630 (mmm-85) cc_final: 0.6493 (ptt180) REVERT: f 13 VAL cc_start: 0.9292 (t) cc_final: 0.8809 (p) REVERT: f 84 ASP cc_start: 0.9026 (OUTLIER) cc_final: 0.8823 (t70) REVERT: f 113 ASN cc_start: 0.8646 (m110) cc_final: 0.8422 (m110) REVERT: f 192 VAL cc_start: 0.9433 (OUTLIER) cc_final: 0.9180 (t) REVERT: f 221 MET cc_start: 0.8900 (mtp) cc_final: 0.8650 (mtp) REVERT: g 10 SER cc_start: 0.9158 (t) cc_final: 0.8794 (p) REVERT: g 48 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8695 (mm-30) REVERT: g 61 LYS cc_start: 0.8966 (mmtt) cc_final: 0.8584 (mmtm) REVERT: g 77 SER cc_start: 0.9199 (t) cc_final: 0.8747 (m) REVERT: g 160 GLN cc_start: 0.9242 (mp10) cc_final: 0.8800 (mp10) REVERT: g 226 ASP cc_start: 0.6582 (m-30) cc_final: 0.6334 (m-30) REVERT: g 232 GLN cc_start: 0.9065 (tt0) cc_final: 0.6657 (pm20) REVERT: g 234 LYS cc_start: 0.7728 (mmtt) cc_final: 0.6945 (tttm) REVERT: i 34 GLN cc_start: 0.8610 (mt0) cc_final: 0.8378 (mt0) REVERT: i 78 ARG cc_start: 0.8521 (mmt-90) cc_final: 0.7414 (mtm180) REVERT: i 90 SER cc_start: 0.8915 (p) cc_final: 0.8698 (t) REVERT: i 95 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8048 (mm-30) REVERT: i 127 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8950 (tt) REVERT: i 146 ARG cc_start: 0.8521 (tpp-160) cc_final: 0.6824 (ptp-170) REVERT: i 172 SER cc_start: 0.9112 (m) cc_final: 0.8793 (p) REVERT: i 205 ASP cc_start: 0.8154 (t0) cc_final: 0.7911 (t0) REVERT: i 264 TRP cc_start: 0.8269 (m100) cc_final: 0.7265 (m100) REVERT: j 44 ASP cc_start: 0.8547 (m-30) cc_final: 0.8329 (m-30) REVERT: j 183 SER cc_start: 0.9276 (p) cc_final: 0.9038 (p) REVERT: j 232 LEU cc_start: 0.9419 (mt) cc_final: 0.9211 (mt) REVERT: k 55 MET cc_start: 0.9311 (tpp) cc_final: 0.8997 (tpp) REVERT: k 75 ASN cc_start: 0.8392 (t0) cc_final: 0.7882 (p0) REVERT: k 145 LYS cc_start: 0.8835 (mttt) cc_final: 0.8443 (tptt) REVERT: l 23 SER cc_start: 0.8943 (p) cc_final: 0.8713 (m) outliers start: 106 outliers final: 73 residues processed: 572 average time/residue: 0.1421 time to fit residues: 124.9092 Evaluate side-chains 543 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 465 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 88 THR Chi-restraints excluded: chain a residue 178 ILE Chi-restraints excluded: chain a residue 181 MET Chi-restraints excluded: chain a residue 196 ILE Chi-restraints excluded: chain a residue 280 ASP Chi-restraints excluded: chain a residue 282 ILE Chi-restraints excluded: chain b residue 79 TRP Chi-restraints excluded: chain b residue 104 SER Chi-restraints excluded: chain b residue 115 SER Chi-restraints excluded: chain b residue 180 LEU Chi-restraints excluded: chain b residue 181 LEU Chi-restraints excluded: chain b residue 247 VAL Chi-restraints excluded: chain b residue 252 THR Chi-restraints excluded: chain b residue 265 ASN Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 58 VAL Chi-restraints excluded: chain c residue 76 LEU Chi-restraints excluded: chain c residue 118 LEU Chi-restraints excluded: chain c residue 162 SER Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain c residue 205 THR Chi-restraints excluded: chain c residue 216 CYS Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 57 VAL Chi-restraints excluded: chain e residue 29 SER Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 83 THR Chi-restraints excluded: chain e residue 100 PHE Chi-restraints excluded: chain e residue 135 GLU Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 251 SER Chi-restraints excluded: chain e residue 284 SER Chi-restraints excluded: chain e residue 295 ILE Chi-restraints excluded: chain f residue 10 SER Chi-restraints excluded: chain f residue 15 GLN Chi-restraints excluded: chain f residue 38 TRP Chi-restraints excluded: chain f residue 58 VAL Chi-restraints excluded: chain f residue 69 VAL Chi-restraints excluded: chain f residue 74 THR Chi-restraints excluded: chain f residue 84 ASP Chi-restraints excluded: chain f residue 115 SER Chi-restraints excluded: chain f residue 160 THR Chi-restraints excluded: chain f residue 192 VAL Chi-restraints excluded: chain f residue 203 ASN Chi-restraints excluded: chain f residue 226 ASN Chi-restraints excluded: chain g residue 7 THR Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 63 ASN Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain g residue 126 THR Chi-restraints excluded: chain g residue 142 THR Chi-restraints excluded: chain g residue 148 MET Chi-restraints excluded: chain g residue 153 ILE Chi-restraints excluded: chain g residue 206 SER Chi-restraints excluded: chain g residue 227 THR Chi-restraints excluded: chain h residue 4 GLN Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 51 SER Chi-restraints excluded: chain i residue 51 ILE Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain i residue 71 CYS Chi-restraints excluded: chain i residue 127 LEU Chi-restraints excluded: chain i residue 252 VAL Chi-restraints excluded: chain i residue 280 ASP Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 84 ASP Chi-restraints excluded: chain j residue 226 ASN Chi-restraints excluded: chain k residue 7 THR Chi-restraints excluded: chain k residue 30 VAL Chi-restraints excluded: chain k residue 132 SER Chi-restraints excluded: chain k residue 163 CYS Chi-restraints excluded: chain k residue 203 THR Chi-restraints excluded: chain k residue 205 THR Chi-restraints excluded: chain k residue 227 THR Chi-restraints excluded: chain l residue 42 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 125 optimal weight: 5.9990 chunk 233 optimal weight: 4.9990 chunk 172 optimal weight: 8.9990 chunk 109 optimal weight: 8.9990 chunk 155 optimal weight: 1.9990 chunk 253 optimal weight: 6.9990 chunk 228 optimal weight: 9.9990 chunk 188 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 205 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 34 GLN ** a 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 198 ASN ** b 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 11 ASN c 232 GLN d 21 ASN d 44 GLN e 34 GLN ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 111 GLN ** f 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 56 ASN ** g 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 69 GLN ** i 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 230 ASN j 15 GLN ** k 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.110654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.099307 restraints weight = 39488.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.101614 restraints weight = 19166.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.103155 restraints weight = 11529.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.104202 restraints weight = 8035.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.104946 restraints weight = 6179.151| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21409 Z= 0.230 Angle : 0.627 8.686 29223 Z= 0.326 Chirality : 0.046 0.169 3300 Planarity : 0.005 0.060 3804 Dihedral : 5.793 53.884 3000 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.85 % Allowed : 13.64 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.16), residues: 2516 helix: -2.05 (0.31), residues: 218 sheet: 0.31 (0.19), residues: 668 loop : -0.31 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG c 196 TYR 0.032 0.002 TYR g 175 PHE 0.019 0.002 PHE g 212 TRP 0.013 0.001 TRP f 80 HIS 0.007 0.001 HIS b 195 Details of bonding type rmsd covalent geometry : bond 0.00537 (21409) covalent geometry : angle 0.62730 (29223) hydrogen bonds : bond 0.03594 ( 561) hydrogen bonds : angle 5.65568 ( 1635) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 503 time to evaluate : 0.674 Fit side-chains REVERT: a 78 ARG cc_start: 0.8872 (mmt-90) cc_final: 0.6256 (mtm180) REVERT: a 97 LYS cc_start: 0.8976 (pttt) cc_final: 0.8495 (pptt) REVERT: a 154 TYR cc_start: 0.8740 (t80) cc_final: 0.8401 (t80) REVERT: a 209 ARG cc_start: 0.5335 (mmt-90) cc_final: 0.3938 (mtt-85) REVERT: a 229 ILE cc_start: 0.8854 (pt) cc_final: 0.8113 (tp) REVERT: c 48 GLU cc_start: 0.9183 (mt-10) cc_final: 0.8861 (mt-10) REVERT: c 55 MET cc_start: 0.9168 (tpp) cc_final: 0.8794 (mmm) REVERT: c 176 ARG cc_start: 0.8832 (mtt-85) cc_final: 0.8563 (mtt-85) REVERT: c 218 ASP cc_start: 0.9090 (p0) cc_final: 0.8686 (p0) REVERT: d 14 GLU cc_start: 0.7177 (tm-30) cc_final: 0.6892 (tm-30) REVERT: d 32 TYR cc_start: 0.9127 (m-80) cc_final: 0.8686 (m-80) REVERT: d 36 SER cc_start: 0.7623 (p) cc_final: 0.7058 (t) REVERT: d 44 GLN cc_start: 0.7742 (tt0) cc_final: 0.7496 (tt0) REVERT: e 97 LYS cc_start: 0.8165 (pttm) cc_final: 0.7894 (tptt) REVERT: e 98 LYS cc_start: 0.8841 (mttt) cc_final: 0.8277 (tptt) REVERT: e 105 ILE cc_start: 0.9320 (mt) cc_final: 0.8929 (tt) REVERT: e 135 GLU cc_start: 0.5750 (OUTLIER) cc_final: 0.5181 (tt0) REVERT: e 146 ARG cc_start: 0.7960 (mmm-85) cc_final: 0.7145 (mpt180) REVERT: e 154 TYR cc_start: 0.9167 (t80) cc_final: 0.8904 (t80) REVERT: f 13 VAL cc_start: 0.9196 (t) cc_final: 0.8744 (p) REVERT: f 42 ILE cc_start: 0.9379 (mt) cc_final: 0.9061 (tt) REVERT: f 70 SER cc_start: 0.8928 (m) cc_final: 0.8697 (p) REVERT: f 89 MET cc_start: 0.9179 (mmt) cc_final: 0.8910 (mmm) REVERT: f 172 ARG cc_start: 0.7745 (mtm-85) cc_final: 0.7043 (mtt90) REVERT: f 192 VAL cc_start: 0.9415 (OUTLIER) cc_final: 0.9160 (t) REVERT: g 10 SER cc_start: 0.9181 (t) cc_final: 0.8799 (p) REVERT: g 61 LYS cc_start: 0.8963 (mmtt) cc_final: 0.8570 (mmtm) REVERT: g 77 SER cc_start: 0.9076 (t) cc_final: 0.8616 (m) REVERT: g 123 MET cc_start: 0.8095 (tmm) cc_final: 0.7815 (tpp) REVERT: g 160 GLN cc_start: 0.9183 (mp10) cc_final: 0.8798 (mp10) REVERT: g 175 TYR cc_start: 0.9058 (m-80) cc_final: 0.8730 (m-10) REVERT: g 226 ASP cc_start: 0.6596 (m-30) cc_final: 0.6317 (m-30) REVERT: g 232 GLN cc_start: 0.9019 (tt0) cc_final: 0.6645 (pm20) REVERT: g 234 LYS cc_start: 0.7667 (mmtt) cc_final: 0.6914 (tttm) REVERT: i 32 ASN cc_start: 0.8644 (t0) cc_final: 0.7842 (t0) REVERT: i 34 GLN cc_start: 0.8591 (mt0) cc_final: 0.8385 (mt0) REVERT: i 78 ARG cc_start: 0.8527 (mmt-90) cc_final: 0.7317 (mtm180) REVERT: i 90 SER cc_start: 0.8932 (p) cc_final: 0.8593 (t) REVERT: i 146 ARG cc_start: 0.8316 (tpp-160) cc_final: 0.6657 (ptp-170) REVERT: i 205 ASP cc_start: 0.8149 (t0) cc_final: 0.7850 (t0) REVERT: i 264 TRP cc_start: 0.8199 (m100) cc_final: 0.7217 (m100) REVERT: j 44 ASP cc_start: 0.8553 (m-30) cc_final: 0.8336 (m-30) REVERT: j 89 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8219 (mtp) REVERT: j 183 SER cc_start: 0.9206 (p) cc_final: 0.8975 (p) REVERT: k 61 LYS cc_start: 0.9338 (mmtp) cc_final: 0.8863 (mptt) REVERT: k 75 ASN cc_start: 0.8306 (t0) cc_final: 0.7987 (p0) REVERT: k 216 CYS cc_start: 0.8946 (m) cc_final: 0.8612 (m) REVERT: l 23 SER cc_start: 0.8911 (p) cc_final: 0.8658 (m) outliers start: 107 outliers final: 73 residues processed: 555 average time/residue: 0.1396 time to fit residues: 119.4822 Evaluate side-chains 549 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 473 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 88 THR Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 178 ILE Chi-restraints excluded: chain a residue 181 MET Chi-restraints excluded: chain a residue 280 ASP Chi-restraints excluded: chain a residue 282 ILE Chi-restraints excluded: chain b residue 79 TRP Chi-restraints excluded: chain b residue 104 SER Chi-restraints excluded: chain b residue 115 SER Chi-restraints excluded: chain b residue 180 LEU Chi-restraints excluded: chain b residue 181 LEU Chi-restraints excluded: chain b residue 247 VAL Chi-restraints excluded: chain b residue 252 THR Chi-restraints excluded: chain b residue 265 ASN Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 58 VAL Chi-restraints excluded: chain c residue 118 LEU Chi-restraints excluded: chain c residue 162 SER Chi-restraints excluded: chain c residue 216 CYS Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 57 VAL Chi-restraints excluded: chain e residue 29 SER Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 68 SER Chi-restraints excluded: chain e residue 100 PHE Chi-restraints excluded: chain e residue 135 GLU Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 281 MET Chi-restraints excluded: chain e residue 284 SER Chi-restraints excluded: chain e residue 292 VAL Chi-restraints excluded: chain f residue 10 SER Chi-restraints excluded: chain f residue 15 GLN Chi-restraints excluded: chain f residue 58 VAL Chi-restraints excluded: chain f residue 74 THR Chi-restraints excluded: chain f residue 84 ASP Chi-restraints excluded: chain f residue 111 GLN Chi-restraints excluded: chain f residue 115 SER Chi-restraints excluded: chain f residue 143 VAL Chi-restraints excluded: chain f residue 183 SER Chi-restraints excluded: chain f residue 192 VAL Chi-restraints excluded: chain f residue 226 ASN Chi-restraints excluded: chain g residue 7 THR Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 56 ASN Chi-restraints excluded: chain g residue 58 VAL Chi-restraints excluded: chain g residue 63 ASN Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain g residue 126 THR Chi-restraints excluded: chain g residue 142 THR Chi-restraints excluded: chain g residue 148 MET Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 227 THR Chi-restraints excluded: chain h residue 4 GLN Chi-restraints excluded: chain h residue 51 SER Chi-restraints excluded: chain i residue 51 ILE Chi-restraints excluded: chain i residue 71 CYS Chi-restraints excluded: chain i residue 252 VAL Chi-restraints excluded: chain i residue 280 ASP Chi-restraints excluded: chain j residue 15 GLN Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 89 MET Chi-restraints excluded: chain j residue 226 ASN Chi-restraints excluded: chain j residue 252 THR Chi-restraints excluded: chain k residue 7 THR Chi-restraints excluded: chain k residue 30 VAL Chi-restraints excluded: chain k residue 50 ASP Chi-restraints excluded: chain k residue 122 SER Chi-restraints excluded: chain k residue 148 MET Chi-restraints excluded: chain k residue 157 LEU Chi-restraints excluded: chain k residue 199 VAL Chi-restraints excluded: chain k residue 203 THR Chi-restraints excluded: chain l residue 42 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 203 optimal weight: 10.0000 chunk 175 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 chunk 174 optimal weight: 8.9990 chunk 146 optimal weight: 20.0000 chunk 239 optimal weight: 0.8980 chunk 136 optimal weight: 9.9990 chunk 258 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 overall best weight: 6.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 26 GLN ** b 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 232 GLN e 34 GLN ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 69 GLN ** i 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 230 ASN j 149 ASN k 152 HIS ** k 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.108939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.097604 restraints weight = 39808.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.099844 restraints weight = 19544.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.101383 restraints weight = 11859.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.102376 restraints weight = 8313.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.103093 restraints weight = 6447.477| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 21409 Z= 0.301 Angle : 0.669 9.306 29223 Z= 0.347 Chirality : 0.048 0.167 3300 Planarity : 0.005 0.072 3804 Dihedral : 5.924 55.907 3000 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.89 % Allowed : 14.77 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.16), residues: 2516 helix: -2.08 (0.30), residues: 226 sheet: 0.04 (0.19), residues: 667 loop : -0.45 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG i 67 TYR 0.020 0.002 TYR g 175 PHE 0.021 0.002 PHE g 212 TRP 0.014 0.002 TRP f 80 HIS 0.014 0.002 HIS f 109 Details of bonding type rmsd covalent geometry : bond 0.00702 (21409) covalent geometry : angle 0.66939 (29223) hydrogen bonds : bond 0.03754 ( 561) hydrogen bonds : angle 5.73544 ( 1635) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 481 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: a 97 LYS cc_start: 0.8970 (pttt) cc_final: 0.8508 (pptt) REVERT: a 154 TYR cc_start: 0.8908 (t80) cc_final: 0.8502 (t80) REVERT: a 189 MET cc_start: 0.8121 (ptp) cc_final: 0.7667 (ptt) REVERT: a 209 ARG cc_start: 0.5521 (mmt-90) cc_final: 0.3831 (mtt-85) REVERT: a 229 ILE cc_start: 0.8812 (pt) cc_final: 0.8117 (tp) REVERT: b 137 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7290 (mt-10) REVERT: c 48 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8930 (mt-10) REVERT: c 55 MET cc_start: 0.9100 (tpp) cc_final: 0.8631 (tpp) REVERT: c 67 MET cc_start: 0.9201 (ptt) cc_final: 0.9000 (ptt) REVERT: c 123 MET cc_start: 0.8755 (tmm) cc_final: 0.8517 (tpt) REVERT: c 176 ARG cc_start: 0.8852 (mtt-85) cc_final: 0.8358 (mtt-85) REVERT: c 218 ASP cc_start: 0.9172 (p0) cc_final: 0.8691 (p0) REVERT: d 14 GLU cc_start: 0.7252 (tm-30) cc_final: 0.7016 (tm-30) REVERT: d 32 TYR cc_start: 0.9192 (m-80) cc_final: 0.8748 (m-80) REVERT: d 36 SER cc_start: 0.7621 (p) cc_final: 0.7035 (t) REVERT: d 44 GLN cc_start: 0.7714 (tt0) cc_final: 0.7355 (tt0) REVERT: e 97 LYS cc_start: 0.8180 (pttm) cc_final: 0.7919 (tptt) REVERT: e 98 LYS cc_start: 0.8888 (mttt) cc_final: 0.8370 (mmtt) REVERT: e 146 ARG cc_start: 0.8061 (mmm-85) cc_final: 0.7207 (mpt180) REVERT: e 154 TYR cc_start: 0.9180 (t80) cc_final: 0.8718 (t80) REVERT: f 13 VAL cc_start: 0.9254 (t) cc_final: 0.8813 (p) REVERT: f 111 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8718 (mt0) REVERT: f 192 VAL cc_start: 0.9432 (OUTLIER) cc_final: 0.9168 (t) REVERT: g 10 SER cc_start: 0.9162 (t) cc_final: 0.8785 (p) REVERT: g 61 LYS cc_start: 0.8962 (mmtt) cc_final: 0.8599 (mptt) REVERT: g 77 SER cc_start: 0.9049 (t) cc_final: 0.8598 (m) REVERT: g 123 MET cc_start: 0.8175 (tmm) cc_final: 0.7901 (tpp) REVERT: g 160 GLN cc_start: 0.9193 (mp10) cc_final: 0.8770 (mp10) REVERT: g 232 GLN cc_start: 0.9111 (tt0) cc_final: 0.6825 (pm20) REVERT: g 234 LYS cc_start: 0.7473 (mmtt) cc_final: 0.6895 (tttm) REVERT: i 32 ASN cc_start: 0.8713 (t0) cc_final: 0.7968 (t0) REVERT: i 78 ARG cc_start: 0.8573 (mmt-90) cc_final: 0.7383 (mtm180) REVERT: i 83 THR cc_start: 0.9696 (t) cc_final: 0.9400 (m) REVERT: i 90 SER cc_start: 0.8971 (p) cc_final: 0.8596 (t) REVERT: i 146 ARG cc_start: 0.8472 (tpp-160) cc_final: 0.6611 (ptp-170) REVERT: i 205 ASP cc_start: 0.8155 (t0) cc_final: 0.7925 (t0) REVERT: i 264 TRP cc_start: 0.8278 (m100) cc_final: 0.7216 (m100) REVERT: j 48 ASN cc_start: 0.7700 (m-40) cc_final: 0.7347 (m-40) REVERT: j 89 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8267 (mtp) REVERT: j 183 SER cc_start: 0.9270 (p) cc_final: 0.9033 (p) REVERT: k 5 MET cc_start: 0.3734 (tpp) cc_final: 0.2883 (tpp) REVERT: k 75 ASN cc_start: 0.8304 (t0) cc_final: 0.7964 (p0) REVERT: k 216 CYS cc_start: 0.9099 (m) cc_final: 0.8676 (m) REVERT: l 23 SER cc_start: 0.8904 (p) cc_final: 0.8669 (m) outliers start: 108 outliers final: 89 residues processed: 541 average time/residue: 0.1401 time to fit residues: 116.6051 Evaluate side-chains 552 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 459 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 88 THR Chi-restraints excluded: chain a residue 178 ILE Chi-restraints excluded: chain a residue 181 MET Chi-restraints excluded: chain a residue 248 ILE Chi-restraints excluded: chain a residue 280 ASP Chi-restraints excluded: chain a residue 282 ILE Chi-restraints excluded: chain b residue 79 TRP Chi-restraints excluded: chain b residue 104 SER Chi-restraints excluded: chain b residue 115 SER Chi-restraints excluded: chain b residue 137 GLU Chi-restraints excluded: chain b residue 247 VAL Chi-restraints excluded: chain b residue 252 THR Chi-restraints excluded: chain b residue 265 ASN Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 58 VAL Chi-restraints excluded: chain c residue 118 LEU Chi-restraints excluded: chain c residue 162 SER Chi-restraints excluded: chain c residue 205 THR Chi-restraints excluded: chain c residue 216 CYS Chi-restraints excluded: chain c residue 227 THR Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 57 VAL Chi-restraints excluded: chain e residue 29 SER Chi-restraints excluded: chain e residue 36 VAL Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 68 SER Chi-restraints excluded: chain e residue 100 PHE Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 201 SER Chi-restraints excluded: chain e residue 251 SER Chi-restraints excluded: chain e residue 281 MET Chi-restraints excluded: chain e residue 284 SER Chi-restraints excluded: chain f residue 10 SER Chi-restraints excluded: chain f residue 15 GLN Chi-restraints excluded: chain f residue 17 THR Chi-restraints excluded: chain f residue 38 TRP Chi-restraints excluded: chain f residue 58 VAL Chi-restraints excluded: chain f residue 74 THR Chi-restraints excluded: chain f residue 84 ASP Chi-restraints excluded: chain f residue 111 GLN Chi-restraints excluded: chain f residue 115 SER Chi-restraints excluded: chain f residue 143 VAL Chi-restraints excluded: chain f residue 160 THR Chi-restraints excluded: chain f residue 183 SER Chi-restraints excluded: chain f residue 192 VAL Chi-restraints excluded: chain f residue 203 ASN Chi-restraints excluded: chain f residue 226 ASN Chi-restraints excluded: chain g residue 7 THR Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 58 VAL Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain g residue 113 ILE Chi-restraints excluded: chain g residue 126 THR Chi-restraints excluded: chain g residue 142 THR Chi-restraints excluded: chain g residue 148 MET Chi-restraints excluded: chain g residue 153 ILE Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 197 ILE Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 227 THR Chi-restraints excluded: chain h residue 4 GLN Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 42 THR Chi-restraints excluded: chain h residue 51 SER Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain i residue 71 CYS Chi-restraints excluded: chain i residue 190 SER Chi-restraints excluded: chain i residue 252 VAL Chi-restraints excluded: chain i residue 280 ASP Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 89 MET Chi-restraints excluded: chain j residue 213 VAL Chi-restraints excluded: chain j residue 217 VAL Chi-restraints excluded: chain j residue 226 ASN Chi-restraints excluded: chain j residue 252 THR Chi-restraints excluded: chain k residue 7 THR Chi-restraints excluded: chain k residue 30 VAL Chi-restraints excluded: chain k residue 50 ASP Chi-restraints excluded: chain k residue 113 ILE Chi-restraints excluded: chain k residue 122 SER Chi-restraints excluded: chain k residue 148 MET Chi-restraints excluded: chain k residue 157 LEU Chi-restraints excluded: chain k residue 163 CYS Chi-restraints excluded: chain k residue 199 VAL Chi-restraints excluded: chain k residue 203 THR Chi-restraints excluded: chain k residue 205 THR Chi-restraints excluded: chain l residue 42 THR Chi-restraints excluded: chain l residue 57 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 182 optimal weight: 20.0000 chunk 133 optimal weight: 2.9990 chunk 18 optimal weight: 50.0000 chunk 251 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 199 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 232 GLN d 31 ASN e 34 GLN e 89 ASN ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 111 GLN ** f 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 69 GLN ** g 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 198 ASN i 230 ASN ** k 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.113997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.102737 restraints weight = 38979.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.105115 restraints weight = 18702.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.106679 restraints weight = 11169.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.107730 restraints weight = 7715.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.108527 restraints weight = 5896.247| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21409 Z= 0.186 Angle : 0.595 9.513 29223 Z= 0.306 Chirality : 0.045 0.166 3300 Planarity : 0.004 0.071 3804 Dihedral : 5.626 54.629 3000 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.53 % Allowed : 16.49 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.16), residues: 2516 helix: -2.03 (0.31), residues: 225 sheet: 0.10 (0.19), residues: 651 loop : -0.43 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 76 TYR 0.018 0.001 TYR g 68 PHE 0.019 0.002 PHE g 212 TRP 0.013 0.001 TRP f 80 HIS 0.008 0.001 HIS f 224 Details of bonding type rmsd covalent geometry : bond 0.00436 (21409) covalent geometry : angle 0.59539 (29223) hydrogen bonds : bond 0.03296 ( 561) hydrogen bonds : angle 5.54252 ( 1635) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 498 time to evaluate : 0.765 Fit side-chains REVERT: a 97 LYS cc_start: 0.8925 (pttt) cc_final: 0.8491 (pptt) REVERT: a 154 TYR cc_start: 0.8926 (t80) cc_final: 0.8528 (t80) REVERT: a 209 ARG cc_start: 0.5463 (mmt-90) cc_final: 0.3766 (mtt-85) REVERT: a 229 ILE cc_start: 0.8769 (pt) cc_final: 0.8087 (tp) REVERT: b 11 ASP cc_start: 0.7152 (p0) cc_final: 0.6849 (p0) REVERT: b 137 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7234 (mt-10) REVERT: c 48 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8912 (mt-10) REVERT: c 55 MET cc_start: 0.9100 (tpp) cc_final: 0.8696 (tpp) REVERT: c 176 ARG cc_start: 0.8821 (mtt-85) cc_final: 0.8424 (mtt-85) REVERT: c 218 ASP cc_start: 0.9148 (p0) cc_final: 0.8659 (p0) REVERT: d 14 GLU cc_start: 0.7315 (tm-30) cc_final: 0.7110 (tm-30) REVERT: d 32 TYR cc_start: 0.9159 (m-80) cc_final: 0.8778 (m-80) REVERT: e 97 LYS cc_start: 0.8129 (pttm) cc_final: 0.7843 (tptt) REVERT: e 98 LYS cc_start: 0.8911 (mttt) cc_final: 0.8355 (mmtt) REVERT: e 146 ARG cc_start: 0.7965 (mmm-85) cc_final: 0.7125 (mpt180) REVERT: e 154 TYR cc_start: 0.9154 (t80) cc_final: 0.8917 (t80) REVERT: e 188 ARG cc_start: 0.6091 (ptt180) cc_final: 0.5655 (ptt180) REVERT: f 13 VAL cc_start: 0.9217 (t) cc_final: 0.8795 (p) REVERT: f 42 ILE cc_start: 0.9382 (mt) cc_final: 0.9108 (tt) REVERT: f 191 PHE cc_start: 0.9423 (m-80) cc_final: 0.9211 (m-10) REVERT: f 192 VAL cc_start: 0.9434 (OUTLIER) cc_final: 0.9146 (t) REVERT: f 259 GLU cc_start: 0.8719 (pt0) cc_final: 0.8482 (pt0) REVERT: g 10 SER cc_start: 0.9175 (t) cc_final: 0.8778 (p) REVERT: g 61 LYS cc_start: 0.8941 (mmtt) cc_final: 0.8600 (mptt) REVERT: g 77 SER cc_start: 0.8993 (t) cc_final: 0.8563 (m) REVERT: g 123 MET cc_start: 0.8093 (tmm) cc_final: 0.7844 (tpp) REVERT: g 160 GLN cc_start: 0.9200 (mp10) cc_final: 0.8839 (mp10) REVERT: g 232 GLN cc_start: 0.9084 (tt0) cc_final: 0.6816 (pm20) REVERT: g 234 LYS cc_start: 0.7348 (mmtt) cc_final: 0.6828 (tttm) REVERT: i 32 ASN cc_start: 0.8700 (t0) cc_final: 0.8209 (t0) REVERT: i 34 GLN cc_start: 0.8509 (mt0) cc_final: 0.8025 (mt0) REVERT: i 62 VAL cc_start: 0.9095 (t) cc_final: 0.8791 (m) REVERT: i 78 ARG cc_start: 0.8547 (mmt-90) cc_final: 0.7292 (mtm180) REVERT: i 146 ARG cc_start: 0.8493 (tpp-160) cc_final: 0.6607 (ptt180) REVERT: i 205 ASP cc_start: 0.8160 (t0) cc_final: 0.7871 (t0) REVERT: i 264 TRP cc_start: 0.8215 (m100) cc_final: 0.7316 (m100) REVERT: j 48 ASN cc_start: 0.7697 (m-40) cc_final: 0.7325 (m-40) REVERT: j 89 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8286 (mtp) REVERT: j 183 SER cc_start: 0.9215 (p) cc_final: 0.8964 (p) REVERT: j 264 ARG cc_start: 0.5360 (mtt180) cc_final: 0.4478 (mtt-85) REVERT: k 5 MET cc_start: 0.3837 (tpp) cc_final: 0.3489 (ptm) REVERT: k 55 MET cc_start: 0.9243 (tpp) cc_final: 0.9000 (tpp) REVERT: k 65 MET cc_start: 0.8019 (tpp) cc_final: 0.7772 (tpp) REVERT: k 75 ASN cc_start: 0.8232 (t0) cc_final: 0.7970 (p0) REVERT: k 112 SER cc_start: 0.9387 (m) cc_final: 0.8427 (p) REVERT: k 123 MET cc_start: 0.7266 (ttp) cc_final: 0.6898 (ttp) REVERT: k 206 SER cc_start: 0.8995 (t) cc_final: 0.8619 (p) REVERT: k 216 CYS cc_start: 0.9111 (m) cc_final: 0.8207 (m) outliers start: 100 outliers final: 79 residues processed: 553 average time/residue: 0.1397 time to fit residues: 118.9728 Evaluate side-chains 560 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 478 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 88 THR Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 178 ILE Chi-restraints excluded: chain a residue 181 MET Chi-restraints excluded: chain a residue 282 ILE Chi-restraints excluded: chain b residue 79 TRP Chi-restraints excluded: chain b residue 104 SER Chi-restraints excluded: chain b residue 112 CYS Chi-restraints excluded: chain b residue 115 SER Chi-restraints excluded: chain b residue 137 GLU Chi-restraints excluded: chain b residue 180 LEU Chi-restraints excluded: chain b residue 181 LEU Chi-restraints excluded: chain b residue 252 THR Chi-restraints excluded: chain b residue 265 ASN Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 58 VAL Chi-restraints excluded: chain c residue 118 LEU Chi-restraints excluded: chain c residue 162 SER Chi-restraints excluded: chain c residue 205 THR Chi-restraints excluded: chain c residue 216 CYS Chi-restraints excluded: chain c residue 227 THR Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 57 VAL Chi-restraints excluded: chain e residue 29 SER Chi-restraints excluded: chain e residue 39 LEU Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 68 SER Chi-restraints excluded: chain e residue 89 ASN Chi-restraints excluded: chain e residue 100 PHE Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 251 SER Chi-restraints excluded: chain e residue 281 MET Chi-restraints excluded: chain e residue 284 SER Chi-restraints excluded: chain f residue 10 SER Chi-restraints excluded: chain f residue 15 GLN Chi-restraints excluded: chain f residue 17 THR Chi-restraints excluded: chain f residue 58 VAL Chi-restraints excluded: chain f residue 69 VAL Chi-restraints excluded: chain f residue 74 THR Chi-restraints excluded: chain f residue 84 ASP Chi-restraints excluded: chain f residue 115 SER Chi-restraints excluded: chain f residue 160 THR Chi-restraints excluded: chain f residue 183 SER Chi-restraints excluded: chain f residue 192 VAL Chi-restraints excluded: chain f residue 203 ASN Chi-restraints excluded: chain f residue 226 ASN Chi-restraints excluded: chain g residue 7 THR Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 58 VAL Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain g residue 113 ILE Chi-restraints excluded: chain g residue 126 THR Chi-restraints excluded: chain g residue 134 SER Chi-restraints excluded: chain g residue 142 THR Chi-restraints excluded: chain g residue 148 MET Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 206 SER Chi-restraints excluded: chain h residue 4 GLN Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain i residue 71 CYS Chi-restraints excluded: chain i residue 252 VAL Chi-restraints excluded: chain i residue 280 ASP Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 84 ASP Chi-restraints excluded: chain j residue 89 MET Chi-restraints excluded: chain j residue 226 ASN Chi-restraints excluded: chain j residue 252 THR Chi-restraints excluded: chain k residue 7 THR Chi-restraints excluded: chain k residue 30 VAL Chi-restraints excluded: chain k residue 50 ASP Chi-restraints excluded: chain k residue 118 LEU Chi-restraints excluded: chain k residue 122 SER Chi-restraints excluded: chain k residue 157 LEU Chi-restraints excluded: chain k residue 199 VAL Chi-restraints excluded: chain l residue 42 THR Chi-restraints excluded: chain l residue 57 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 78 optimal weight: 1.9990 chunk 199 optimal weight: 9.9990 chunk 6 optimal weight: 30.0000 chunk 42 optimal weight: 10.0000 chunk 191 optimal weight: 9.9990 chunk 157 optimal weight: 3.9990 chunk 16 optimal weight: 20.0000 chunk 187 optimal weight: 20.0000 chunk 227 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 239 optimal weight: 0.5980 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 30 ASN c 232 GLN ** d 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 34 GLN ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 230 ASN ** l 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.110218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.098959 restraints weight = 39907.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.101241 restraints weight = 19424.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.102772 restraints weight = 11731.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.103821 restraints weight = 8166.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.104344 restraints weight = 6268.910| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 21409 Z= 0.244 Angle : 0.622 9.733 29223 Z= 0.320 Chirality : 0.046 0.176 3300 Planarity : 0.005 0.070 3804 Dihedral : 5.571 58.851 3000 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 5.12 % Allowed : 16.22 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.16), residues: 2516 helix: -2.11 (0.30), residues: 238 sheet: -0.02 (0.19), residues: 657 loop : -0.47 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG b 76 TYR 0.024 0.002 TYR g 68 PHE 0.019 0.002 PHE g 212 TRP 0.013 0.001 TRP f 80 HIS 0.007 0.001 HIS f 224 Details of bonding type rmsd covalent geometry : bond 0.00573 (21409) covalent geometry : angle 0.62249 (29223) hydrogen bonds : bond 0.03454 ( 561) hydrogen bonds : angle 5.55777 ( 1635) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 486 time to evaluate : 0.757 Fit side-chains REVERT: a 97 LYS cc_start: 0.8957 (pttt) cc_final: 0.8507 (pptt) REVERT: a 154 TYR cc_start: 0.8877 (t80) cc_final: 0.8499 (t80) REVERT: a 209 ARG cc_start: 0.5674 (mmt-90) cc_final: 0.3828 (mtt-85) REVERT: a 229 ILE cc_start: 0.8751 (pt) cc_final: 0.8095 (tp) REVERT: b 11 ASP cc_start: 0.7275 (p0) cc_final: 0.6944 (p0) REVERT: b 137 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7302 (mt-10) REVERT: c 48 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8931 (mt-10) REVERT: c 55 MET cc_start: 0.9092 (tpp) cc_final: 0.8695 (tpp) REVERT: d 9 LYS cc_start: 0.8215 (tppt) cc_final: 0.7923 (tppt) REVERT: d 36 SER cc_start: 0.7485 (p) cc_final: 0.6860 (t) REVERT: e 24 SER cc_start: 0.8487 (m) cc_final: 0.7971 (p) REVERT: e 97 LYS cc_start: 0.8135 (pttm) cc_final: 0.7876 (tptt) REVERT: e 98 LYS cc_start: 0.8904 (mttt) cc_final: 0.8379 (mmtt) REVERT: e 146 ARG cc_start: 0.8059 (mmm-85) cc_final: 0.7186 (mpt180) REVERT: e 154 TYR cc_start: 0.9176 (t80) cc_final: 0.8698 (t80) REVERT: e 188 ARG cc_start: 0.6258 (ptt180) cc_final: 0.5817 (ptt180) REVERT: f 13 VAL cc_start: 0.9223 (t) cc_final: 0.8761 (p) REVERT: f 42 ILE cc_start: 0.9357 (mt) cc_final: 0.9035 (tt) REVERT: f 111 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8405 (mt0) REVERT: f 191 PHE cc_start: 0.9453 (m-80) cc_final: 0.9249 (m-10) REVERT: f 192 VAL cc_start: 0.9408 (OUTLIER) cc_final: 0.9126 (t) REVERT: g 10 SER cc_start: 0.9174 (t) cc_final: 0.8782 (p) REVERT: g 61 LYS cc_start: 0.8946 (mmtt) cc_final: 0.8575 (mptt) REVERT: g 77 SER cc_start: 0.8988 (t) cc_final: 0.8551 (m) REVERT: g 123 MET cc_start: 0.8156 (tmm) cc_final: 0.7667 (tpp) REVERT: g 160 GLN cc_start: 0.9202 (mp10) cc_final: 0.8870 (mp10) REVERT: g 232 GLN cc_start: 0.9093 (tt0) cc_final: 0.6805 (pm20) REVERT: g 234 LYS cc_start: 0.7339 (mmtt) cc_final: 0.6762 (tttm) REVERT: i 32 ASN cc_start: 0.8734 (t0) cc_final: 0.7911 (t0) REVERT: i 34 GLN cc_start: 0.8512 (mt0) cc_final: 0.7918 (mt0) REVERT: i 78 ARG cc_start: 0.8547 (mmt-90) cc_final: 0.7388 (mtm180) REVERT: i 83 THR cc_start: 0.9656 (t) cc_final: 0.9376 (m) REVERT: i 146 ARG cc_start: 0.8599 (tpp-160) cc_final: 0.6599 (ptt180) REVERT: i 189 MET cc_start: 0.7842 (ptm) cc_final: 0.7584 (ptm) REVERT: i 205 ASP cc_start: 0.8146 (t0) cc_final: 0.7887 (t0) REVERT: i 264 TRP cc_start: 0.8230 (m100) cc_final: 0.7321 (m100) REVERT: j 48 ASN cc_start: 0.7682 (m-40) cc_final: 0.7301 (m-40) REVERT: j 89 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8414 (mtp) REVERT: j 210 VAL cc_start: 0.9149 (OUTLIER) cc_final: 0.8936 (p) REVERT: j 264 ARG cc_start: 0.5535 (mtt180) cc_final: 0.3866 (mtp85) REVERT: k 75 ASN cc_start: 0.8289 (t0) cc_final: 0.8030 (p0) REVERT: k 206 SER cc_start: 0.8996 (t) cc_final: 0.8621 (p) REVERT: k 216 CYS cc_start: 0.9148 (m) cc_final: 0.8763 (m) REVERT: l 34 LYS cc_start: 0.8578 (pttt) cc_final: 0.7658 (mmtt) outliers start: 113 outliers final: 94 residues processed: 549 average time/residue: 0.1400 time to fit residues: 118.6279 Evaluate side-chains 577 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 478 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 68 SER Chi-restraints excluded: chain a residue 88 THR Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 178 ILE Chi-restraints excluded: chain a residue 181 MET Chi-restraints excluded: chain a residue 248 ILE Chi-restraints excluded: chain a residue 282 ILE Chi-restraints excluded: chain b residue 79 TRP Chi-restraints excluded: chain b residue 104 SER Chi-restraints excluded: chain b residue 112 CYS Chi-restraints excluded: chain b residue 115 SER Chi-restraints excluded: chain b residue 137 GLU Chi-restraints excluded: chain b residue 180 LEU Chi-restraints excluded: chain b residue 181 LEU Chi-restraints excluded: chain b residue 247 VAL Chi-restraints excluded: chain b residue 252 THR Chi-restraints excluded: chain b residue 265 ASN Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 58 VAL Chi-restraints excluded: chain c residue 118 LEU Chi-restraints excluded: chain c residue 162 SER Chi-restraints excluded: chain c residue 205 THR Chi-restraints excluded: chain c residue 216 CYS Chi-restraints excluded: chain c residue 227 THR Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 57 VAL Chi-restraints excluded: chain e residue 29 SER Chi-restraints excluded: chain e residue 39 LEU Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 68 SER Chi-restraints excluded: chain e residue 100 PHE Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 251 SER Chi-restraints excluded: chain e residue 281 MET Chi-restraints excluded: chain e residue 284 SER Chi-restraints excluded: chain e residue 292 VAL Chi-restraints excluded: chain e residue 295 ILE Chi-restraints excluded: chain f residue 10 SER Chi-restraints excluded: chain f residue 15 GLN Chi-restraints excluded: chain f residue 17 THR Chi-restraints excluded: chain f residue 38 TRP Chi-restraints excluded: chain f residue 58 VAL Chi-restraints excluded: chain f residue 69 VAL Chi-restraints excluded: chain f residue 74 THR Chi-restraints excluded: chain f residue 84 ASP Chi-restraints excluded: chain f residue 111 GLN Chi-restraints excluded: chain f residue 115 SER Chi-restraints excluded: chain f residue 143 VAL Chi-restraints excluded: chain f residue 160 THR Chi-restraints excluded: chain f residue 183 SER Chi-restraints excluded: chain f residue 192 VAL Chi-restraints excluded: chain f residue 203 ASN Chi-restraints excluded: chain f residue 217 VAL Chi-restraints excluded: chain f residue 226 ASN Chi-restraints excluded: chain g residue 7 THR Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 58 VAL Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain g residue 113 ILE Chi-restraints excluded: chain g residue 126 THR Chi-restraints excluded: chain g residue 134 SER Chi-restraints excluded: chain g residue 142 THR Chi-restraints excluded: chain g residue 148 MET Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 197 ILE Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 206 SER Chi-restraints excluded: chain h residue 4 GLN Chi-restraints excluded: chain h residue 42 THR Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain i residue 71 CYS Chi-restraints excluded: chain i residue 190 SER Chi-restraints excluded: chain i residue 252 VAL Chi-restraints excluded: chain i residue 280 ASP Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 84 ASP Chi-restraints excluded: chain j residue 89 MET Chi-restraints excluded: chain j residue 210 VAL Chi-restraints excluded: chain j residue 226 ASN Chi-restraints excluded: chain j residue 252 THR Chi-restraints excluded: chain k residue 7 THR Chi-restraints excluded: chain k residue 30 VAL Chi-restraints excluded: chain k residue 50 ASP Chi-restraints excluded: chain k residue 113 ILE Chi-restraints excluded: chain k residue 118 LEU Chi-restraints excluded: chain k residue 122 SER Chi-restraints excluded: chain k residue 148 MET Chi-restraints excluded: chain k residue 157 LEU Chi-restraints excluded: chain k residue 163 CYS Chi-restraints excluded: chain k residue 190 THR Chi-restraints excluded: chain k residue 199 VAL Chi-restraints excluded: chain k residue 203 THR Chi-restraints excluded: chain l residue 42 THR Chi-restraints excluded: chain l residue 57 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 245 optimal weight: 5.9990 chunk 254 optimal weight: 2.9990 chunk 190 optimal weight: 10.0000 chunk 177 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 76 optimal weight: 0.0870 chunk 211 optimal weight: 7.9990 chunk 195 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 197 optimal weight: 0.9990 chunk 224 optimal weight: 10.0000 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 34 GLN a 148 GLN e 148 GLN ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 230 ASN ** k 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.112906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.101800 restraints weight = 39019.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.104118 restraints weight = 18963.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.105580 restraints weight = 11374.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.106650 restraints weight = 7950.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.107418 restraints weight = 6084.888| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21409 Z= 0.143 Angle : 0.574 9.558 29223 Z= 0.294 Chirality : 0.044 0.178 3300 Planarity : 0.004 0.065 3804 Dihedral : 5.365 56.235 3000 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.26 % Allowed : 17.58 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.16), residues: 2516 helix: -2.02 (0.30), residues: 232 sheet: 0.13 (0.20), residues: 633 loop : -0.41 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG k 196 TYR 0.019 0.001 TYR g 68 PHE 0.016 0.001 PHE g 212 TRP 0.013 0.001 TRP f 80 HIS 0.007 0.001 HIS f 224 Details of bonding type rmsd covalent geometry : bond 0.00337 (21409) covalent geometry : angle 0.57438 (29223) hydrogen bonds : bond 0.03085 ( 561) hydrogen bonds : angle 5.35777 ( 1635) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 504 time to evaluate : 0.633 Fit side-chains REVERT: a 97 LYS cc_start: 0.8909 (pttt) cc_final: 0.8459 (pptt) REVERT: a 154 TYR cc_start: 0.8871 (t80) cc_final: 0.8573 (t80) REVERT: a 189 MET cc_start: 0.7799 (ptp) cc_final: 0.7434 (ptt) REVERT: a 209 ARG cc_start: 0.5596 (mmt-90) cc_final: 0.3741 (mtt-85) REVERT: a 229 ILE cc_start: 0.8716 (pt) cc_final: 0.8047 (tp) REVERT: b 11 ASP cc_start: 0.7349 (p0) cc_final: 0.7079 (p0) REVERT: b 137 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7174 (mt-10) REVERT: c 48 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8861 (mt-10) REVERT: c 55 MET cc_start: 0.9064 (tpp) cc_final: 0.8659 (tpp) REVERT: c 148 MET cc_start: 0.8743 (tmm) cc_final: 0.8209 (ppp) REVERT: d 32 TYR cc_start: 0.9150 (m-80) cc_final: 0.8741 (m-80) REVERT: d 36 SER cc_start: 0.7417 (p) cc_final: 0.6791 (t) REVERT: d 44 GLN cc_start: 0.7863 (pt0) cc_final: 0.7647 (pt0) REVERT: e 24 SER cc_start: 0.8425 (m) cc_final: 0.7895 (p) REVERT: e 69 GLU cc_start: 0.8375 (tp30) cc_final: 0.8038 (tt0) REVERT: e 97 LYS cc_start: 0.8087 (pttm) cc_final: 0.7842 (tptt) REVERT: e 98 LYS cc_start: 0.8895 (mttt) cc_final: 0.8362 (mmtt) REVERT: e 146 ARG cc_start: 0.7987 (mmm-85) cc_final: 0.7143 (mpt180) REVERT: e 154 TYR cc_start: 0.9164 (t80) cc_final: 0.8905 (t80) REVERT: e 188 ARG cc_start: 0.6558 (ptt180) cc_final: 0.6165 (ptt180) REVERT: f 42 ILE cc_start: 0.9355 (mt) cc_final: 0.9104 (tt) REVERT: f 111 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8321 (mt0) REVERT: f 192 VAL cc_start: 0.9404 (p) cc_final: 0.9106 (t) REVERT: f 223 LYS cc_start: 0.9311 (mttm) cc_final: 0.9059 (mttm) REVERT: f 266 ILE cc_start: 0.8925 (tp) cc_final: 0.8674 (tp) REVERT: g 10 SER cc_start: 0.9172 (t) cc_final: 0.8777 (p) REVERT: g 18 ASP cc_start: 0.8092 (t0) cc_final: 0.7856 (t0) REVERT: g 77 SER cc_start: 0.8942 (t) cc_final: 0.8530 (m) REVERT: g 123 MET cc_start: 0.8053 (tmm) cc_final: 0.7820 (tpp) REVERT: g 160 GLN cc_start: 0.9191 (mp10) cc_final: 0.8828 (mp10) REVERT: g 232 GLN cc_start: 0.9024 (tt0) cc_final: 0.6791 (pm20) REVERT: g 234 LYS cc_start: 0.7364 (mmtt) cc_final: 0.6788 (tttm) REVERT: i 32 ASN cc_start: 0.8683 (t0) cc_final: 0.8194 (t0) REVERT: i 34 GLN cc_start: 0.8471 (mt0) cc_final: 0.7919 (mt0) REVERT: i 62 VAL cc_start: 0.9074 (t) cc_final: 0.8767 (m) REVERT: i 78 ARG cc_start: 0.8555 (mmt-90) cc_final: 0.7352 (mtm180) REVERT: i 146 ARG cc_start: 0.8589 (tpp-160) cc_final: 0.6584 (ptt180) REVERT: i 189 MET cc_start: 0.7741 (ptm) cc_final: 0.7478 (ptm) REVERT: i 205 ASP cc_start: 0.8158 (t0) cc_final: 0.7890 (t0) REVERT: i 264 TRP cc_start: 0.8172 (m100) cc_final: 0.7397 (m100) REVERT: j 48 ASN cc_start: 0.7637 (m-40) cc_final: 0.7280 (m-40) REVERT: j 196 GLN cc_start: 0.8406 (tt0) cc_final: 0.7929 (tt0) REVERT: j 252 THR cc_start: 0.9511 (OUTLIER) cc_final: 0.8832 (p) REVERT: j 264 ARG cc_start: 0.5652 (mtt180) cc_final: 0.4591 (mtt-85) REVERT: k 112 SER cc_start: 0.9369 (m) cc_final: 0.8474 (p) REVERT: k 206 SER cc_start: 0.8975 (t) cc_final: 0.8580 (p) REVERT: k 216 CYS cc_start: 0.9125 (m) cc_final: 0.8325 (m) REVERT: l 34 LYS cc_start: 0.8586 (pttt) cc_final: 0.7710 (mmtt) outliers start: 94 outliers final: 71 residues processed: 552 average time/residue: 0.1378 time to fit residues: 117.3419 Evaluate side-chains 541 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 467 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 88 THR Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 181 MET Chi-restraints excluded: chain a residue 282 ILE Chi-restraints excluded: chain b residue 79 TRP Chi-restraints excluded: chain b residue 112 CYS Chi-restraints excluded: chain b residue 115 SER Chi-restraints excluded: chain b residue 137 GLU Chi-restraints excluded: chain b residue 180 LEU Chi-restraints excluded: chain b residue 181 LEU Chi-restraints excluded: chain b residue 247 VAL Chi-restraints excluded: chain b residue 252 THR Chi-restraints excluded: chain b residue 265 ASN Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 58 VAL Chi-restraints excluded: chain c residue 118 LEU Chi-restraints excluded: chain c residue 162 SER Chi-restraints excluded: chain c residue 205 THR Chi-restraints excluded: chain c residue 216 CYS Chi-restraints excluded: chain c residue 227 THR Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 57 VAL Chi-restraints excluded: chain e residue 29 SER Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 68 SER Chi-restraints excluded: chain e residue 100 PHE Chi-restraints excluded: chain e residue 135 GLU Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 281 MET Chi-restraints excluded: chain e residue 284 SER Chi-restraints excluded: chain e residue 292 VAL Chi-restraints excluded: chain f residue 15 GLN Chi-restraints excluded: chain f residue 17 THR Chi-restraints excluded: chain f residue 58 VAL Chi-restraints excluded: chain f residue 69 VAL Chi-restraints excluded: chain f residue 74 THR Chi-restraints excluded: chain f residue 84 ASP Chi-restraints excluded: chain f residue 111 GLN Chi-restraints excluded: chain f residue 115 SER Chi-restraints excluded: chain f residue 160 THR Chi-restraints excluded: chain f residue 183 SER Chi-restraints excluded: chain f residue 203 ASN Chi-restraints excluded: chain f residue 226 ASN Chi-restraints excluded: chain g residue 7 THR Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 58 VAL Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain g residue 113 ILE Chi-restraints excluded: chain g residue 148 MET Chi-restraints excluded: chain g residue 197 ILE Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 206 SER Chi-restraints excluded: chain h residue 4 GLN Chi-restraints excluded: chain i residue 252 VAL Chi-restraints excluded: chain i residue 280 ASP Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 84 ASP Chi-restraints excluded: chain j residue 226 ASN Chi-restraints excluded: chain j residue 252 THR Chi-restraints excluded: chain k residue 7 THR Chi-restraints excluded: chain k residue 30 VAL Chi-restraints excluded: chain k residue 50 ASP Chi-restraints excluded: chain k residue 113 ILE Chi-restraints excluded: chain k residue 122 SER Chi-restraints excluded: chain k residue 163 CYS Chi-restraints excluded: chain k residue 190 THR Chi-restraints excluded: chain k residue 203 THR Chi-restraints excluded: chain l residue 42 THR Chi-restraints excluded: chain l residue 57 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 95 optimal weight: 0.0270 chunk 235 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 206 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 130 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 chunk 137 optimal weight: 9.9990 chunk 224 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 chunk 111 optimal weight: 20.0000 overall best weight: 2.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 48 ASN e 34 GLN ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 230 ASN ** j 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 ASN l 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.113049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.101800 restraints weight = 39250.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.104080 restraints weight = 19046.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.105609 restraints weight = 11530.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.106684 restraints weight = 8060.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.107408 restraints weight = 6176.693| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21409 Z= 0.161 Angle : 0.587 10.666 29223 Z= 0.298 Chirality : 0.044 0.180 3300 Planarity : 0.004 0.060 3804 Dihedral : 5.292 50.630 3000 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.58 % Allowed : 18.49 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.16), residues: 2516 helix: -2.01 (0.30), residues: 233 sheet: 0.05 (0.20), residues: 644 loop : -0.37 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG c 176 TYR 0.026 0.001 TYR g 68 PHE 0.019 0.001 PHE f 191 TRP 0.012 0.001 TRP f 80 HIS 0.007 0.001 HIS f 224 Details of bonding type rmsd covalent geometry : bond 0.00380 (21409) covalent geometry : angle 0.58656 (29223) hydrogen bonds : bond 0.03128 ( 561) hydrogen bonds : angle 5.30619 ( 1635) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 476 time to evaluate : 0.615 Fit side-chains REVERT: a 97 LYS cc_start: 0.8895 (pttt) cc_final: 0.8458 (pptt) REVERT: a 154 TYR cc_start: 0.8902 (t80) cc_final: 0.8559 (t80) REVERT: a 189 MET cc_start: 0.7832 (ptp) cc_final: 0.7624 (ptt) REVERT: a 209 ARG cc_start: 0.5665 (mmt-90) cc_final: 0.3797 (mtt-85) REVERT: a 229 ILE cc_start: 0.8701 (pt) cc_final: 0.8041 (tp) REVERT: b 11 ASP cc_start: 0.7383 (p0) cc_final: 0.7060 (p0) REVERT: b 137 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7192 (mt-10) REVERT: c 48 GLU cc_start: 0.9113 (mt-10) cc_final: 0.8853 (mt-10) REVERT: c 55 MET cc_start: 0.9059 (tpp) cc_final: 0.8666 (tpp) REVERT: e 24 SER cc_start: 0.8463 (m) cc_final: 0.7937 (p) REVERT: e 69 GLU cc_start: 0.8376 (tp30) cc_final: 0.8028 (tt0) REVERT: e 97 LYS cc_start: 0.8067 (pttm) cc_final: 0.7844 (tptt) REVERT: e 98 LYS cc_start: 0.8866 (mttt) cc_final: 0.8337 (mmtt) REVERT: e 146 ARG cc_start: 0.7984 (mmm-85) cc_final: 0.7144 (mpt180) REVERT: e 154 TYR cc_start: 0.9181 (t80) cc_final: 0.8932 (t80) REVERT: e 188 ARG cc_start: 0.6444 (ptt180) cc_final: 0.5980 (ptt180) REVERT: f 13 VAL cc_start: 0.9169 (t) cc_final: 0.8871 (p) REVERT: f 24 THR cc_start: 0.9288 (p) cc_final: 0.9054 (t) REVERT: f 42 ILE cc_start: 0.9380 (mt) cc_final: 0.9071 (tt) REVERT: f 192 VAL cc_start: 0.9397 (p) cc_final: 0.9072 (t) REVERT: g 10 SER cc_start: 0.9188 (t) cc_final: 0.8803 (p) REVERT: g 61 LYS cc_start: 0.8967 (mmmt) cc_final: 0.8542 (mmtm) REVERT: g 77 SER cc_start: 0.8907 (t) cc_final: 0.8504 (m) REVERT: g 123 MET cc_start: 0.8023 (tmm) cc_final: 0.7803 (tpp) REVERT: g 160 GLN cc_start: 0.9210 (mp10) cc_final: 0.8838 (mp10) REVERT: g 232 GLN cc_start: 0.9011 (tt0) cc_final: 0.6798 (pm20) REVERT: g 234 LYS cc_start: 0.7372 (mmtt) cc_final: 0.6798 (tttm) REVERT: i 32 ASN cc_start: 0.8688 (t0) cc_final: 0.7815 (t0) REVERT: i 34 GLN cc_start: 0.8441 (mt0) cc_final: 0.7844 (mt0) REVERT: i 78 ARG cc_start: 0.8498 (mmt-90) cc_final: 0.7323 (mtm180) REVERT: i 83 THR cc_start: 0.9624 (t) cc_final: 0.9359 (m) REVERT: i 146 ARG cc_start: 0.8545 (tpp-160) cc_final: 0.6559 (ptt180) REVERT: i 205 ASP cc_start: 0.8157 (t0) cc_final: 0.7918 (t0) REVERT: i 264 TRP cc_start: 0.8144 (m100) cc_final: 0.7382 (m100) REVERT: j 48 ASN cc_start: 0.7601 (m-40) cc_final: 0.7255 (m-40) REVERT: j 196 GLN cc_start: 0.8405 (tt0) cc_final: 0.7868 (tt0) REVERT: j 252 THR cc_start: 0.9500 (OUTLIER) cc_final: 0.8841 (p) REVERT: j 264 ARG cc_start: 0.5728 (mtt180) cc_final: 0.4646 (mtt-85) REVERT: k 69 GLN cc_start: 0.8462 (mt0) cc_final: 0.8035 (mt0) REVERT: k 112 SER cc_start: 0.9374 (m) cc_final: 0.8484 (p) REVERT: k 206 SER cc_start: 0.8955 (t) cc_final: 0.8545 (p) REVERT: k 216 CYS cc_start: 0.9158 (m) cc_final: 0.8341 (m) REVERT: l 34 LYS cc_start: 0.8563 (pttt) cc_final: 0.7724 (mmtt) outliers start: 79 outliers final: 67 residues processed: 521 average time/residue: 0.1417 time to fit residues: 113.0622 Evaluate side-chains 535 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 466 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 88 THR Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 181 MET Chi-restraints excluded: chain a residue 282 ILE Chi-restraints excluded: chain b residue 79 TRP Chi-restraints excluded: chain b residue 115 SER Chi-restraints excluded: chain b residue 137 GLU Chi-restraints excluded: chain b residue 180 LEU Chi-restraints excluded: chain b residue 181 LEU Chi-restraints excluded: chain b residue 252 THR Chi-restraints excluded: chain b residue 265 ASN Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 58 VAL Chi-restraints excluded: chain c residue 162 SER Chi-restraints excluded: chain c residue 205 THR Chi-restraints excluded: chain c residue 216 CYS Chi-restraints excluded: chain c residue 227 THR Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 57 VAL Chi-restraints excluded: chain e residue 29 SER Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 68 SER Chi-restraints excluded: chain e residue 135 GLU Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 281 MET Chi-restraints excluded: chain e residue 284 SER Chi-restraints excluded: chain e residue 292 VAL Chi-restraints excluded: chain f residue 15 GLN Chi-restraints excluded: chain f residue 17 THR Chi-restraints excluded: chain f residue 58 VAL Chi-restraints excluded: chain f residue 69 VAL Chi-restraints excluded: chain f residue 74 THR Chi-restraints excluded: chain f residue 84 ASP Chi-restraints excluded: chain f residue 115 SER Chi-restraints excluded: chain f residue 160 THR Chi-restraints excluded: chain f residue 183 SER Chi-restraints excluded: chain f residue 203 ASN Chi-restraints excluded: chain f residue 226 ASN Chi-restraints excluded: chain g residue 7 THR Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 58 VAL Chi-restraints excluded: chain g residue 94 LEU Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain g residue 113 ILE Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 197 ILE Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain h residue 4 GLN Chi-restraints excluded: chain h residue 42 THR Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain i residue 252 VAL Chi-restraints excluded: chain i residue 280 ASP Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 84 ASP Chi-restraints excluded: chain j residue 226 ASN Chi-restraints excluded: chain j residue 252 THR Chi-restraints excluded: chain k residue 7 THR Chi-restraints excluded: chain k residue 30 VAL Chi-restraints excluded: chain k residue 50 ASP Chi-restraints excluded: chain k residue 113 ILE Chi-restraints excluded: chain k residue 122 SER Chi-restraints excluded: chain k residue 190 THR Chi-restraints excluded: chain k residue 203 THR Chi-restraints excluded: chain l residue 42 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 66 optimal weight: 1.9990 chunk 4 optimal weight: 20.0000 chunk 233 optimal weight: 2.9990 chunk 65 optimal weight: 20.0000 chunk 109 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 37 optimal weight: 0.0980 chunk 227 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 17 ASN ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 230 ASN j 15 GLN j 147 ASN ** k 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.114266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.102739 restraints weight = 39237.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.105110 restraints weight = 19021.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.106713 restraints weight = 11512.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.107720 restraints weight = 7990.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.108531 restraints weight = 6181.946| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21409 Z= 0.118 Angle : 0.566 12.469 29223 Z= 0.288 Chirality : 0.043 0.173 3300 Planarity : 0.004 0.046 3804 Dihedral : 5.088 44.723 3000 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.99 % Allowed : 19.17 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.16), residues: 2516 helix: -2.09 (0.29), residues: 237 sheet: 0.26 (0.20), residues: 627 loop : -0.35 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG c 176 TYR 0.030 0.001 TYR g 68 PHE 0.015 0.001 PHE g 212 TRP 0.012 0.001 TRP f 80 HIS 0.007 0.001 HIS f 224 Details of bonding type rmsd covalent geometry : bond 0.00280 (21409) covalent geometry : angle 0.56593 (29223) hydrogen bonds : bond 0.02893 ( 561) hydrogen bonds : angle 5.17856 ( 1635) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 492 time to evaluate : 0.701 Fit side-chains REVERT: a 97 LYS cc_start: 0.8869 (pttt) cc_final: 0.8445 (pptt) REVERT: a 154 TYR cc_start: 0.8864 (t80) cc_final: 0.8553 (t80) REVERT: a 189 MET cc_start: 0.7829 (ptp) cc_final: 0.7611 (ptt) REVERT: a 209 ARG cc_start: 0.5570 (mmt-90) cc_final: 0.3726 (mtt-85) REVERT: a 229 ILE cc_start: 0.8664 (pt) cc_final: 0.8004 (tp) REVERT: b 11 ASP cc_start: 0.7561 (p0) cc_final: 0.7302 (p0) REVERT: b 137 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7106 (mt-10) REVERT: c 48 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8828 (mt-10) REVERT: c 69 GLN cc_start: 0.8293 (mt0) cc_final: 0.8060 (mp10) REVERT: c 148 MET cc_start: 0.8714 (tmm) cc_final: 0.8237 (ppp) REVERT: d 9 LYS cc_start: 0.8154 (tppt) cc_final: 0.7916 (mmtm) REVERT: e 24 SER cc_start: 0.8435 (m) cc_final: 0.7903 (p) REVERT: e 69 GLU cc_start: 0.8399 (tp30) cc_final: 0.8173 (tt0) REVERT: e 97 LYS cc_start: 0.8029 (pttm) cc_final: 0.7794 (tptt) REVERT: e 98 LYS cc_start: 0.8867 (mttt) cc_final: 0.8315 (mmtt) REVERT: e 146 ARG cc_start: 0.7861 (mmm-85) cc_final: 0.7121 (mpt180) REVERT: e 154 TYR cc_start: 0.9133 (t80) cc_final: 0.8910 (t80) REVERT: e 188 ARG cc_start: 0.6538 (ptt180) cc_final: 0.5989 (ptt180) REVERT: f 13 VAL cc_start: 0.9137 (t) cc_final: 0.8792 (p) REVERT: f 24 THR cc_start: 0.9195 (p) cc_final: 0.8986 (t) REVERT: f 42 ILE cc_start: 0.9349 (mt) cc_final: 0.9069 (tt) REVERT: f 192 VAL cc_start: 0.9353 (p) cc_final: 0.9021 (t) REVERT: f 223 LYS cc_start: 0.9403 (mtmm) cc_final: 0.9111 (mttm) REVERT: f 266 ILE cc_start: 0.8927 (tp) cc_final: 0.8717 (tp) REVERT: g 10 SER cc_start: 0.9199 (t) cc_final: 0.8799 (p) REVERT: g 77 SER cc_start: 0.8856 (t) cc_final: 0.8441 (m) REVERT: g 98 MET cc_start: 0.9344 (tpp) cc_final: 0.9057 (tpt) REVERT: g 123 MET cc_start: 0.7846 (tmm) cc_final: 0.7635 (tpp) REVERT: g 160 GLN cc_start: 0.9210 (mp10) cc_final: 0.8880 (mp10) REVERT: g 232 GLN cc_start: 0.8936 (tt0) cc_final: 0.6734 (pm20) REVERT: g 234 LYS cc_start: 0.7366 (mmtt) cc_final: 0.6782 (tttm) REVERT: i 34 GLN cc_start: 0.8368 (mt0) cc_final: 0.7823 (mt0) REVERT: i 78 ARG cc_start: 0.8418 (mmt-90) cc_final: 0.7202 (mtm180) REVERT: i 146 ARG cc_start: 0.8541 (tpp-160) cc_final: 0.6548 (ptt180) REVERT: i 205 ASP cc_start: 0.8136 (t0) cc_final: 0.7852 (t0) REVERT: i 264 TRP cc_start: 0.8087 (m100) cc_final: 0.7402 (m100) REVERT: j 48 ASN cc_start: 0.7605 (m-40) cc_final: 0.7295 (m-40) REVERT: j 196 GLN cc_start: 0.8289 (tt0) cc_final: 0.7776 (tt0) REVERT: j 252 THR cc_start: 0.9480 (OUTLIER) cc_final: 0.8855 (p) REVERT: j 264 ARG cc_start: 0.5610 (mtt180) cc_final: 0.4503 (mtt-85) REVERT: k 69 GLN cc_start: 0.8410 (mt0) cc_final: 0.7856 (mp10) REVERT: k 112 SER cc_start: 0.9310 (m) cc_final: 0.8366 (p) REVERT: k 165 MET cc_start: 0.8862 (tmm) cc_final: 0.8468 (ttt) REVERT: k 206 SER cc_start: 0.8940 (t) cc_final: 0.8496 (p) REVERT: k 216 CYS cc_start: 0.9176 (m) cc_final: 0.8408 (m) REVERT: l 34 LYS cc_start: 0.8552 (pttt) cc_final: 0.7705 (mmtt) REVERT: l 38 SER cc_start: 0.9152 (m) cc_final: 0.8580 (t) outliers start: 66 outliers final: 59 residues processed: 533 average time/residue: 0.1383 time to fit residues: 113.6067 Evaluate side-chains 542 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 481 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 88 THR Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 181 MET Chi-restraints excluded: chain a residue 282 ILE Chi-restraints excluded: chain b residue 79 TRP Chi-restraints excluded: chain b residue 115 SER Chi-restraints excluded: chain b residue 137 GLU Chi-restraints excluded: chain b residue 180 LEU Chi-restraints excluded: chain b residue 181 LEU Chi-restraints excluded: chain b residue 252 THR Chi-restraints excluded: chain b residue 265 ASN Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 58 VAL Chi-restraints excluded: chain c residue 162 SER Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain c residue 205 THR Chi-restraints excluded: chain c residue 216 CYS Chi-restraints excluded: chain c residue 227 THR Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 57 VAL Chi-restraints excluded: chain e residue 29 SER Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 68 SER Chi-restraints excluded: chain e residue 135 GLU Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 281 MET Chi-restraints excluded: chain e residue 284 SER Chi-restraints excluded: chain e residue 292 VAL Chi-restraints excluded: chain f residue 15 GLN Chi-restraints excluded: chain f residue 17 THR Chi-restraints excluded: chain f residue 58 VAL Chi-restraints excluded: chain f residue 69 VAL Chi-restraints excluded: chain f residue 84 ASP Chi-restraints excluded: chain f residue 115 SER Chi-restraints excluded: chain f residue 143 VAL Chi-restraints excluded: chain f residue 217 VAL Chi-restraints excluded: chain f residue 226 ASN Chi-restraints excluded: chain g residue 7 THR Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 58 VAL Chi-restraints excluded: chain g residue 94 LEU Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain g residue 113 ILE Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain i residue 252 VAL Chi-restraints excluded: chain i residue 280 ASP Chi-restraints excluded: chain j residue 15 GLN Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 84 ASP Chi-restraints excluded: chain j residue 213 VAL Chi-restraints excluded: chain j residue 226 ASN Chi-restraints excluded: chain j residue 252 THR Chi-restraints excluded: chain k residue 7 THR Chi-restraints excluded: chain k residue 50 ASP Chi-restraints excluded: chain k residue 122 SER Chi-restraints excluded: chain k residue 190 THR Chi-restraints excluded: chain k residue 203 THR Chi-restraints excluded: chain l residue 42 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 241 optimal weight: 0.3980 chunk 36 optimal weight: 0.0470 chunk 122 optimal weight: 9.9990 chunk 262 optimal weight: 9.9990 chunk 148 optimal weight: 0.2980 chunk 49 optimal weight: 8.9990 chunk 203 optimal weight: 9.9990 chunk 195 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 overall best weight: 2.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 17 ASN ** d 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 69 GLN g 104 ASN i 230 ASN ** k 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.114762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.103517 restraints weight = 39108.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.105850 restraints weight = 19163.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.107307 restraints weight = 11596.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.108431 restraints weight = 8147.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.109196 restraints weight = 6236.915| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21409 Z= 0.151 Angle : 0.583 12.743 29223 Z= 0.294 Chirality : 0.044 0.168 3300 Planarity : 0.004 0.046 3804 Dihedral : 5.082 41.884 3000 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.13 % Allowed : 19.39 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.16), residues: 2516 helix: -2.01 (0.29), residues: 244 sheet: 0.19 (0.20), residues: 638 loop : -0.34 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG c 176 TYR 0.030 0.001 TYR g 68 PHE 0.016 0.001 PHE g 212 TRP 0.013 0.001 TRP f 80 HIS 0.007 0.001 HIS f 224 Details of bonding type rmsd covalent geometry : bond 0.00360 (21409) covalent geometry : angle 0.58275 (29223) hydrogen bonds : bond 0.02993 ( 561) hydrogen bonds : angle 5.20413 ( 1635) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3549.95 seconds wall clock time: 62 minutes 13.61 seconds (3733.61 seconds total)