Starting phenix.real_space_refine on Mon Aug 25 02:00:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gaf_29896/08_2025/8gaf_29896.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gaf_29896/08_2025/8gaf_29896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gaf_29896/08_2025/8gaf_29896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gaf_29896/08_2025/8gaf_29896.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gaf_29896/08_2025/8gaf_29896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gaf_29896/08_2025/8gaf_29896.map" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.035 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: 5 Type Number sf(0) Gaussians P 43 5.49 5 S 109 5.16 5 C 15275 2.51 5 N 4383 2.21 5 O 4772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 234 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24582 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2261 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain: "B" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2261 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain: "C" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2261 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain: "D" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2261 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain: "E" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2261 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain: "F" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2173 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain breaks: 1 Chain: "G" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2523 Classifications: {'peptide': 325} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 314} Chain breaks: 1 Chain: "H" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1867 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain: "I" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1007 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "J" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1007 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "K" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 916 Classifications: {'RNA': 43} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 16, 'rna3p_pur': 12, 'rna3p_pyr': 6} Link IDs: {'rna2p': 24, 'rna3p': 18} Chain: "M" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2110 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 8, 'TRANS': 255} Chain breaks: 1 Chain: "N" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1674 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 11, 'TRANS': 193} Time building chain proxies: 4.96, per 1000 atoms: 0.20 Number of scatterers: 24582 At special positions: 0 Unit cell: (141.976, 104.022, 198.204, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 109 16.00 P 43 15.00 O 4772 8.00 N 4383 7.00 C 15275 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: 1.99 Conformation dependent library (CDL) restraints added in 865.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5474 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 32 sheets defined 34.2% alpha, 12.9% beta 0 base pairs and 6 stacking pairs defined. Time for finding SS restraints: 2.70 Creating SS restraints... Processing helix chain 'A' and resid 42 through 58 removed outlier: 3.960A pdb=" N LEU A 46 " --> pdb=" O THR A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 78 Processing helix chain 'A' and resid 90 through 106 removed outlier: 4.001A pdb=" N GLU A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 112 Processing helix chain 'A' and resid 186 through 193 removed outlier: 3.703A pdb=" N LYS A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 208 Processing helix chain 'A' and resid 239 through 245 removed outlier: 3.664A pdb=" N LEU A 243 " --> pdb=" O PRO A 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 58 removed outlier: 3.740A pdb=" N LEU B 46 " --> pdb=" O THR B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 removed outlier: 4.010A pdb=" N LEU B 76 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS B 81 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU B 82 " --> pdb=" O ASP B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 106 Processing helix chain 'B' and resid 107 through 112 Processing helix chain 'B' and resid 186 through 193 Processing helix chain 'B' and resid 195 through 208 Processing helix chain 'B' and resid 239 through 245 Processing helix chain 'B' and resid 260 through 262 No H-bonds generated for 'chain 'B' and resid 260 through 262' Processing helix chain 'C' and resid 42 through 58 removed outlier: 3.741A pdb=" N LEU C 46 " --> pdb=" O THR C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 82 removed outlier: 3.637A pdb=" N LEU C 76 " --> pdb=" O ILE C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 106 removed outlier: 4.540A pdb=" N GLU C 96 " --> pdb=" O GLY C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 112 Processing helix chain 'C' and resid 186 through 193 Processing helix chain 'C' and resid 195 through 208 Processing helix chain 'C' and resid 240 through 245 removed outlier: 3.546A pdb=" N LYS C 245 " --> pdb=" O ASP C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 57 removed outlier: 3.923A pdb=" N LEU D 46 " --> pdb=" O THR D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 82 Processing helix chain 'D' and resid 93 through 106 Processing helix chain 'D' and resid 107 through 112 Processing helix chain 'D' and resid 188 through 193 Processing helix chain 'D' and resid 195 through 209 Processing helix chain 'D' and resid 239 through 245 Processing helix chain 'D' and resid 260 through 262 No H-bonds generated for 'chain 'D' and resid 260 through 262' Processing helix chain 'E' and resid 23 through 27 Processing helix chain 'E' and resid 42 through 58 removed outlier: 4.213A pdb=" N LEU E 46 " --> pdb=" O THR E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 82 removed outlier: 3.501A pdb=" N GLU E 82 " --> pdb=" O ASP E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 106 removed outlier: 4.435A pdb=" N GLU E 96 " --> pdb=" O GLY E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 112 Processing helix chain 'E' and resid 186 through 191 removed outlier: 3.658A pdb=" N LYS E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN E 191 " --> pdb=" O HIS E 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 186 through 191' Processing helix chain 'E' and resid 195 through 208 Processing helix chain 'E' and resid 239 through 245 Processing helix chain 'E' and resid 260 through 262 No H-bonds generated for 'chain 'E' and resid 260 through 262' Processing helix chain 'F' and resid 42 through 57 removed outlier: 4.256A pdb=" N LEU F 46 " --> pdb=" O THR F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 81 Processing helix chain 'F' and resid 90 through 106 removed outlier: 4.167A pdb=" N GLU F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 112 Processing helix chain 'F' and resid 186 through 191 removed outlier: 3.786A pdb=" N GLN F 191 " --> pdb=" O HIS F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 208 Processing helix chain 'F' and resid 239 through 247 removed outlier: 3.561A pdb=" N LEU F 243 " --> pdb=" O PRO F 239 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE F 247 " --> pdb=" O LEU F 243 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 15 Processing helix chain 'G' and resid 84 through 88 removed outlier: 4.120A pdb=" N VAL G 88 " --> pdb=" O TYR G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 118 removed outlier: 3.547A pdb=" N LYS G 102 " --> pdb=" O GLU G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 134 removed outlier: 3.574A pdb=" N VAL G 127 " --> pdb=" O GLY G 123 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU G 131 " --> pdb=" O VAL G 127 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER G 132 " --> pdb=" O ALA G 128 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ALA G 134 " --> pdb=" O PHE G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 142 removed outlier: 3.562A pdb=" N MET G 141 " --> pdb=" O LYS G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 149 removed outlier: 3.722A pdb=" N GLU G 148 " --> pdb=" O ASN G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 184 removed outlier: 4.224A pdb=" N TYR G 178 " --> pdb=" O ALA G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 189 removed outlier: 3.592A pdb=" N ASP G 188 " --> pdb=" O THR G 185 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASN G 189 " --> pdb=" O GLN G 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 185 through 189' Processing helix chain 'G' and resid 243 through 257 Processing helix chain 'H' and resid 351 through 359 Processing helix chain 'H' and resid 376 through 383 Processing helix chain 'H' and resid 400 through 406 Processing helix chain 'H' and resid 412 through 427 removed outlier: 4.006A pdb=" N LEU H 416 " --> pdb=" O PRO H 412 " (cutoff:3.500A) Processing helix chain 'H' and resid 433 through 438 removed outlier: 3.626A pdb=" N LEU H 437 " --> pdb=" O ARG H 433 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS H 438 " --> pdb=" O ALA H 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 433 through 438' Processing helix chain 'H' and resid 441 through 446 Processing helix chain 'H' and resid 467 through 486 Processing helix chain 'H' and resid 493 through 502 removed outlier: 6.166A pdb=" N GLY H 499 " --> pdb=" O ASP H 495 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N SER H 500 " --> pdb=" O ARG H 496 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N SER H 502 " --> pdb=" O PHE H 498 " (cutoff:3.500A) Processing helix chain 'H' and resid 505 through 513 removed outlier: 5.357A pdb=" N THR H 511 " --> pdb=" O ALA H 507 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET H 513 " --> pdb=" O PHE H 509 " (cutoff:3.500A) Processing helix chain 'H' and resid 515 through 522 Processing helix chain 'H' and resid 525 through 542 removed outlier: 4.128A pdb=" N HIS H 542 " --> pdb=" O GLN H 538 " (cutoff:3.500A) Processing helix chain 'H' and resid 554 through 570 Processing helix chain 'H' and resid 573 through 581 removed outlier: 3.926A pdb=" N GLU H 581 " --> pdb=" O ASN H 577 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 29 removed outlier: 4.124A pdb=" N ASN I 29 " --> pdb=" O GLN I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 39 Processing helix chain 'I' and resid 40 through 47 Processing helix chain 'I' and resid 48 through 50 No H-bonds generated for 'chain 'I' and resid 48 through 50' Processing helix chain 'I' and resid 51 through 65 Proline residue: I 60 - end of helix Processing helix chain 'I' and resid 68 through 84 removed outlier: 3.663A pdb=" N ALA I 72 " --> pdb=" O PHE I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 113 Processing helix chain 'I' and resid 117 through 124 removed outlier: 3.769A pdb=" N GLU I 124 " --> pdb=" O ASN I 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 29 removed outlier: 4.086A pdb=" N ASN J 29 " --> pdb=" O GLN J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 41 removed outlier: 3.512A pdb=" N PHE J 41 " --> pdb=" O ALA J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 50 Processing helix chain 'J' and resid 51 through 65 Proline residue: J 60 - end of helix Processing helix chain 'J' and resid 68 through 84 removed outlier: 3.835A pdb=" N ALA J 72 " --> pdb=" O PHE J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 113 Processing helix chain 'J' and resid 117 through 124 removed outlier: 3.904A pdb=" N GLU J 124 " --> pdb=" O ASN J 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 59 removed outlier: 4.333A pdb=" N LEU M 46 " --> pdb=" O THR M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 95 through 106 Processing helix chain 'M' and resid 106 through 112 removed outlier: 3.990A pdb=" N ARG M 110 " --> pdb=" O TYR M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 193 removed outlier: 4.143A pdb=" N GLN M 191 " --> pdb=" O HIS M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 213 removed outlier: 5.731A pdb=" N PHE M 210 " --> pdb=" O LEU M 206 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ASP M 211 " --> pdb=" O VAL M 207 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP M 213 " --> pdb=" O MET M 209 " (cutoff:3.500A) Processing helix chain 'M' and resid 239 through 247 removed outlier: 3.628A pdb=" N LEU M 243 " --> pdb=" O PRO M 239 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE M 247 " --> pdb=" O LEU M 243 " (cutoff:3.500A) Processing helix chain 'M' and resid 260 through 262 No H-bonds generated for 'chain 'M' and resid 260 through 262' Processing helix chain 'N' and resid 30 through 42 Processing helix chain 'N' and resid 118 through 132 Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 131 removed outlier: 6.263A pdb=" N ASP A 14 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ALA A 223 " --> pdb=" O ASP A 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 41 Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 251 Processing sheet with id=AA4, first strand: chain 'B' and resid 130 through 131 Processing sheet with id=AA5, first strand: chain 'B' and resid 130 through 131 removed outlier: 6.927A pdb=" N TYR B 7 " --> pdb=" O GLU B 230 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLU B 230 " --> pdb=" O TYR B 7 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE B 9 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL B 228 " --> pdb=" O PHE B 9 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE B 11 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU B 226 " --> pdb=" O PHE B 11 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N PHE B 13 " --> pdb=" O ARG B 224 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ARG B 224 " --> pdb=" O PHE B 13 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N VAL B 15 " --> pdb=" O ASN B 222 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ASN B 222 " --> pdb=" O VAL B 15 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 22 through 23 removed outlier: 4.099A pdb=" N LEU B 29 " --> pdb=" O ASP B 23 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 149 removed outlier: 3.630A pdb=" N THR B 166 " --> pdb=" O ARG B 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 248 through 251 Processing sheet with id=AA9, first strand: chain 'C' and resid 40 through 41 Processing sheet with id=AB1, first strand: chain 'C' and resid 40 through 41 removed outlier: 5.840A pdb=" N ASP C 14 " --> pdb=" O ALA C 223 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ALA C 223 " --> pdb=" O ASP C 14 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 247 through 251 Processing sheet with id=AB3, first strand: chain 'D' and resid 129 through 130 removed outlier: 6.169A pdb=" N ASP D 14 " --> pdb=" O ALA D 223 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ALA D 223 " --> pdb=" O ASP D 14 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 40 through 41 Processing sheet with id=AB5, first strand: chain 'D' and resid 248 through 251 Processing sheet with id=AB6, first strand: chain 'E' and resid 135 through 136 removed outlier: 6.457A pdb=" N ASP E 14 " --> pdb=" O ALA E 223 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ALA E 223 " --> pdb=" O ASP E 14 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 129 through 130 Processing sheet with id=AB8, first strand: chain 'E' and resid 248 through 251 Processing sheet with id=AB9, first strand: chain 'F' and resid 40 through 41 Processing sheet with id=AC1, first strand: chain 'F' and resid 40 through 41 removed outlier: 3.764A pdb=" N TYR F 7 " --> pdb=" O ILE F 184 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 248 through 251 Processing sheet with id=AC3, first strand: chain 'G' and resid 26 through 30 removed outlier: 3.737A pdb=" N ARG G 59 " --> pdb=" O ILE G 30 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 42 through 47 removed outlier: 3.907A pdb=" N SER G 158 " --> pdb=" O PHE G 32 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 210 through 211 Processing sheet with id=AC6, first strand: chain 'G' and resid 263 through 265 removed outlier: 3.816A pdb=" N PHE G 264 " --> pdb=" O THR G 271 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR G 271 " --> pdb=" O PHE G 264 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'G' and resid 329 through 332 removed outlier: 6.418A pdb=" N GLY G 329 " --> pdb=" O ARG G 340 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 40 through 41 removed outlier: 3.744A pdb=" N ARG M 135 " --> pdb=" O ARG M 179 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG M 179 " --> pdb=" O ARG M 135 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG M 6 " --> pdb=" O GLU M 230 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU M 230 " --> pdb=" O ARG M 6 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASP M 8 " --> pdb=" O VAL M 228 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL M 228 " --> pdb=" O ASP M 8 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N VAL M 10 " --> pdb=" O LEU M 226 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU M 226 " --> pdb=" O VAL M 10 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU M 12 " --> pdb=" O ARG M 224 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 143 through 145 Processing sheet with id=AD1, first strand: chain 'M' and resid 248 through 251 Processing sheet with id=AD2, first strand: chain 'N' and resid 151 through 152 removed outlier: 4.435A pdb=" N ILE N 4 " --> pdb=" O LEU N 152 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY N 9 " --> pdb=" O VAL N 98 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL N 98 " --> pdb=" O GLY N 9 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG N 101 " --> pdb=" O GLU N 55 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLU N 55 " --> pdb=" O ARG N 101 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ASP N 105 " --> pdb=" O VAL N 51 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N VAL N 51 " --> pdb=" O ASP N 105 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 62 through 63 Processing sheet with id=AD4, first strand: chain 'N' and resid 66 through 70 Processing sheet with id=AD5, first strand: chain 'N' and resid 170 through 172 831 hydrogen bonds defined for protein. 2352 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 6 stacking parallelities Total time for adding SS restraints: 4.18 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8056 1.34 - 1.45: 3463 1.45 - 1.57: 13360 1.57 - 1.69: 85 1.69 - 1.81: 184 Bond restraints: 25148 Sorted by residual: bond pdb=" CA ASN H 392 " pdb=" CB ASN H 392 " ideal model delta sigma weight residual 1.542 1.530 0.012 8.90e-03 1.26e+04 1.79e+00 bond pdb=" C3' G K 4 " pdb=" O3' G K 4 " ideal model delta sigma weight residual 1.427 1.446 -0.019 1.50e-02 4.44e+03 1.57e+00 bond pdb=" CA GLY N 113 " pdb=" C GLY N 113 " ideal model delta sigma weight residual 1.514 1.531 -0.017 1.41e-02 5.03e+03 1.45e+00 bond pdb=" N ILE M 67 " pdb=" CA ILE M 67 " ideal model delta sigma weight residual 1.459 1.473 -0.014 1.25e-02 6.40e+03 1.23e+00 bond pdb=" N ILE C 247 " pdb=" CA ILE C 247 " ideal model delta sigma weight residual 1.459 1.473 -0.014 1.25e-02 6.40e+03 1.22e+00 ... (remaining 25143 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 33716 1.63 - 3.26: 339 3.26 - 4.89: 42 4.89 - 6.52: 7 6.52 - 8.15: 1 Bond angle restraints: 34105 Sorted by residual: angle pdb=" N VAL N 198 " pdb=" CA VAL N 198 " pdb=" C VAL N 198 " ideal model delta sigma weight residual 113.43 108.53 4.90 1.09e+00 8.42e-01 2.02e+01 angle pdb=" CA ARG B 68 " pdb=" C ARG B 68 " pdb=" N GLU B 69 " ideal model delta sigma weight residual 119.46 116.76 2.70 6.10e-01 2.69e+00 1.96e+01 angle pdb=" C3' G K 4 " pdb=" O3' G K 4 " pdb=" P A K 5 " ideal model delta sigma weight residual 120.20 125.64 -5.44 1.50e+00 4.44e-01 1.31e+01 angle pdb=" C LEU A 235 " pdb=" CA LEU A 235 " pdb=" CB LEU A 235 " ideal model delta sigma weight residual 114.40 110.34 4.06 1.25e+00 6.40e-01 1.05e+01 angle pdb=" C3' A K 9 " pdb=" O3' A K 9 " pdb=" P G K 10 " ideal model delta sigma weight residual 120.20 124.85 -4.65 1.50e+00 4.44e-01 9.63e+00 ... (remaining 34100 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 14539 35.93 - 71.86: 620 71.86 - 107.79: 42 107.79 - 143.72: 2 143.72 - 179.64: 2 Dihedral angle restraints: 15205 sinusoidal: 6691 harmonic: 8514 Sorted by residual: dihedral pdb=" O4' C K 14 " pdb=" C1' C K 14 " pdb=" N1 C K 14 " pdb=" C2 C K 14 " ideal model delta sinusoidal sigma weight residual -128.00 51.64 -179.64 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U K 39 " pdb=" C1' U K 39 " pdb=" N1 U K 39 " pdb=" C2 U K 39 " ideal model delta sinusoidal sigma weight residual -128.00 -34.78 -93.22 1 1.70e+01 3.46e-03 3.51e+01 dihedral pdb=" O4' U K 33 " pdb=" C1' U K 33 " pdb=" N1 U K 33 " pdb=" C2 U K 33 " ideal model delta sinusoidal sigma weight residual -128.00 -42.20 -85.80 1 1.70e+01 3.46e-03 3.08e+01 ... (remaining 15202 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2983 0.041 - 0.083: 525 0.083 - 0.124: 186 0.124 - 0.166: 6 0.166 - 0.207: 1 Chirality restraints: 3701 Sorted by residual: chirality pdb=" C3' G K 4 " pdb=" C4' G K 4 " pdb=" O3' G K 4 " pdb=" C2' G K 4 " both_signs ideal model delta sigma weight residual False -2.74 -2.54 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" P G K 10 " pdb=" OP1 G K 10 " pdb=" OP2 G K 10 " pdb=" O5' G K 10 " both_signs ideal model delta sigma weight residual True 2.41 -2.55 -0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" C3' A K 9 " pdb=" C4' A K 9 " pdb=" O3' A K 9 " pdb=" C2' A K 9 " both_signs ideal model delta sigma weight residual False -2.74 -2.61 -0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 3698 not shown) Planarity restraints: 4355 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU J 59 " -0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO J 60 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO J 60 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO J 60 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 377 " -0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO H 378 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO H 378 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO H 378 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP M 33 " -0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO M 34 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO M 34 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO M 34 " -0.017 5.00e-02 4.00e+02 ... (remaining 4352 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 607 2.69 - 3.24: 22712 3.24 - 3.79: 41141 3.79 - 4.35: 54255 4.35 - 4.90: 87429 Nonbonded interactions: 206144 Sorted by model distance: nonbonded pdb=" O VAL C 125 " pdb=" O2' C K 17 " model vdw 2.133 3.040 nonbonded pdb=" O VAL B 125 " pdb=" O2' G K 11 " model vdw 2.191 3.040 nonbonded pdb=" OD1 ASP A 17 " pdb=" OG1 THR A 172 " model vdw 2.212 3.040 nonbonded pdb=" OG1 THR M 117 " pdb=" OG SER N 75 " model vdw 2.249 3.040 nonbonded pdb=" OD2 ASP D 23 " pdb=" OH TYR I 40 " model vdw 2.251 3.040 ... (remaining 206139 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 'A' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'B' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'C' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'D' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'E' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'F' and (resid 2 through 74 or resid 94 through 284)) selection = (chain 'M' and (resid 2 through 152 or resid 165 through 284)) } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 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: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 21.810 Find NCS groups from input model: 0.300 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: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5215 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 : 0.002 0.038 25148 Z= 0.098 Angle : 0.434 8.150 34105 Z= 0.272 Chirality : 0.036 0.207 3701 Planarity : 0.002 0.043 4355 Dihedral : 18.188 179.645 9731 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 2.35 % Allowed : 15.42 % Favored : 82.22 % Rotamer: Outliers : 2.92 % Allowed : 20.27 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 aren not related in a simple way. whole: -3.53 (0.13), residues: 2931 helix: -0.84 (0.16), residues: 908 sheet: -1.92 (0.21), residues: 541 loop : -3.62 (0.12), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 59 TYR 0.008 0.001 TYR G 9 PHE 0.011 0.001 PHE D 9 TRP 0.005 0.001 TRP E 203 HIS 0.002 0.000 HIS H 549 Details of bonding type rmsd covalent geometry : bond 0.00162 (25148) covalent geometry : angle 0.43390 (34105) hydrogen bonds : bond 0.14218 ( 821) hydrogen bonds : angle 5.06101 ( 2352) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 758 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.6790 (mp10) cc_final: 0.6559 (mp10) REVERT: A 139 PRO cc_start: 0.6321 (Cg_exo) cc_final: 0.5965 (Cg_endo) REVERT: A 178 TYR cc_start: 0.5794 (m-80) cc_final: 0.5405 (m-80) REVERT: A 227 TYR cc_start: 0.4952 (m-80) cc_final: 0.4364 (m-80) REVERT: B 209 MET cc_start: 0.5156 (ptt) cc_final: 0.4950 (ptt) REVERT: B 228 VAL cc_start: 0.5579 (t) cc_final: 0.4852 (t) REVERT: C 108 ASP cc_start: 0.7324 (t0) cc_final: 0.6667 (m-30) REVERT: D 141 MET cc_start: 0.4158 (mmm) cc_final: 0.3823 (mpp) REVERT: D 220 GLN cc_start: 0.7342 (tt0) cc_final: 0.7043 (tt0) REVERT: E 52 ASN cc_start: 0.8214 (m-40) cc_final: 0.7766 (m-40) REVERT: E 150 MET cc_start: 0.4544 (mtm) cc_final: 0.3633 (mtm) REVERT: E 183 PHE cc_start: 0.6465 (m-80) cc_final: 0.4854 (m-80) REVERT: E 184 ILE cc_start: 0.7703 (mt) cc_final: 0.7025 (tt) REVERT: E 221 MET cc_start: 0.6261 (mtp) cc_final: 0.5237 (mtt) REVERT: E 222 ASN cc_start: 0.7024 (m-40) cc_final: 0.6632 (m110) REVERT: E 277 LYS cc_start: 0.5641 (mppt) cc_final: 0.5063 (ttmt) REVERT: F 7 TYR cc_start: 0.7983 (m-80) cc_final: 0.7623 (m-80) REVERT: F 16 GLN cc_start: 0.7555 (mm110) cc_final: 0.7298 (mm110) REVERT: F 69 GLU cc_start: 0.5254 (mm-30) cc_final: 0.4707 (mm-30) REVERT: F 129 VAL cc_start: 0.7480 (t) cc_final: 0.7237 (t) REVERT: F 135 ARG cc_start: 0.8980 (ptp-110) cc_final: 0.8278 (mtp180) REVERT: F 227 TYR cc_start: 0.2818 (m-80) cc_final: 0.2196 (m-10) REVERT: F 265 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6474 (mt) REVERT: H 515 LEU cc_start: 0.4500 (OUTLIER) cc_final: 0.4230 (mt) REVERT: H 539 ILE cc_start: 0.6047 (mt) cc_final: 0.5772 (mt) REVERT: I 21 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6485 (mp) REVERT: I 23 LYS cc_start: 0.8071 (tptm) cc_final: 0.7683 (tppp) REVERT: I 25 GLN cc_start: 0.8025 (tm-30) cc_final: 0.6989 (tm-30) REVERT: I 122 PHE cc_start: 0.6787 (t80) cc_final: 0.6463 (t80) REVERT: J 123 ASN cc_start: 0.7724 (m-40) cc_final: 0.7339 (m-40) REVERT: M 126 ARG cc_start: 0.5631 (mtm180) cc_final: 0.5046 (mmp80) REVERT: N 43 TRP cc_start: 0.3262 (t60) cc_final: 0.2773 (t60) REVERT: N 50 LYS cc_start: 0.4242 (tptt) cc_final: 0.3749 (tptt) outliers start: 74 outliers final: 11 residues processed: 813 average time/residue: 0.1791 time to fit residues: 215.5184 Evaluate side-chains 414 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 400 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 68 ARG Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 515 LEU Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 249 VAL Chi-restraints excluded: chain N residue 30 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.2980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN A 81 HIS ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 GLN ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN A 222 ASN B 62 HIS ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 HIS ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 HIS C 85 ASN C 124 GLN ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN D 59 ASN D 212 HIS ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN E 62 HIS E 81 HIS ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 GLN ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 HIS ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 ASN F 52 ASN ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 214 HIS F 234 ASN G 44 GLN G 315 GLN H 368 ASN H 465 GLN H 490 ASN ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 HIS I 76 GLN I 85 HIS I 91 ASN ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 91 ASN J 94 ASN J 110 GLN M 191 GLN ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 64 ASN N 68 ASN ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 88 GLN ** N 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 133 GLN ** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.145382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.129479 restraints weight = 102249.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.132048 restraints weight = 62097.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.133926 restraints weight = 42182.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.135194 restraints weight = 31218.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.135998 restraints weight = 24826.221| |-----------------------------------------------------------------------------| r_work (final): 0.4705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5977 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 25148 Z= 0.179 Angle : 0.705 9.642 34105 Z= 0.366 Chirality : 0.045 0.362 3701 Planarity : 0.005 0.100 4355 Dihedral : 13.695 178.452 3939 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.55 % Allowed : 10.58 % Favored : 88.88 % Rotamer: Outliers : 4.42 % Allowed : 24.37 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 aren not related in a simple way. whole: -2.81 (0.14), residues: 2931 helix: -0.21 (0.16), residues: 952 sheet: -1.37 (0.23), residues: 492 loop : -3.30 (0.13), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 7 TYR 0.026 0.002 TYR H 497 PHE 0.037 0.003 PHE B 183 TRP 0.031 0.004 TRP H 534 HIS 0.025 0.002 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00403 (25148) covalent geometry : angle 0.70535 (34105) hydrogen bonds : bond 0.03508 ( 821) hydrogen bonds : angle 4.54168 ( 2352) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 423 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 VAL cc_start: 0.7017 (p) cc_final: 0.6779 (p) REVERT: A 178 TYR cc_start: 0.6296 (m-80) cc_final: 0.5979 (m-80) REVERT: A 227 TYR cc_start: 0.5480 (m-80) cc_final: 0.4630 (m-80) REVERT: B 3 ILE cc_start: 0.2001 (OUTLIER) cc_final: 0.1444 (mp) REVERT: B 33 ASP cc_start: 0.6207 (OUTLIER) cc_final: 0.5951 (t0) REVERT: C 108 ASP cc_start: 0.7744 (t0) cc_final: 0.7019 (m-30) REVERT: D 141 MET cc_start: 0.4620 (mmm) cc_final: 0.4041 (mpp) REVERT: D 147 ILE cc_start: 0.7466 (pt) cc_final: 0.7265 (pt) REVERT: D 214 HIS cc_start: 0.6016 (m-70) cc_final: 0.5657 (m170) REVERT: D 220 GLN cc_start: 0.7415 (tt0) cc_final: 0.7096 (tt0) REVERT: D 264 TYR cc_start: 0.2475 (OUTLIER) cc_final: 0.1788 (m-10) REVERT: E 52 ASN cc_start: 0.8633 (m-40) cc_final: 0.8081 (m-40) REVERT: E 150 MET cc_start: 0.5641 (mtm) cc_final: 0.4530 (mmp) REVERT: E 188 PHE cc_start: 0.6423 (m-80) cc_final: 0.6101 (m-10) REVERT: E 220 GLN cc_start: 0.5479 (pp30) cc_final: 0.4973 (tm-30) REVERT: E 221 MET cc_start: 0.5037 (mtp) cc_final: 0.3788 (mtt) REVERT: E 259 ARG cc_start: 0.7410 (tmm160) cc_final: 0.7162 (tmm160) REVERT: F 4 GLU cc_start: 0.7182 (mp0) cc_final: 0.6404 (tp30) REVERT: F 7 TYR cc_start: 0.8141 (m-80) cc_final: 0.7749 (m-80) REVERT: F 41 VAL cc_start: 0.6969 (t) cc_final: 0.6418 (t) REVERT: F 112 PHE cc_start: 0.9166 (m-80) cc_final: 0.8959 (m-10) REVERT: F 135 ARG cc_start: 0.9093 (ptp-110) cc_final: 0.8311 (mtp180) REVERT: F 213 ASP cc_start: 0.3391 (t70) cc_final: 0.2664 (m-30) REVERT: F 227 TYR cc_start: 0.2929 (m-80) cc_final: 0.2292 (m-10) REVERT: F 250 VAL cc_start: 0.4671 (OUTLIER) cc_final: 0.4437 (m) REVERT: G 85 TYR cc_start: 0.5993 (p90) cc_final: 0.5335 (p90) REVERT: G 136 GLU cc_start: 0.5070 (mm-30) cc_final: 0.4852 (mt-10) REVERT: H 552 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8078 (pp) REVERT: I 23 LYS cc_start: 0.7955 (tptm) cc_final: 0.7725 (tptt) REVERT: I 25 GLN cc_start: 0.7868 (tm-30) cc_final: 0.6845 (tm-30) REVERT: I 63 LEU cc_start: 0.8988 (mt) cc_final: 0.8718 (pp) REVERT: I 122 PHE cc_start: 0.7332 (t80) cc_final: 0.6710 (t80) REVERT: J 97 GLN cc_start: 0.8829 (mt0) cc_final: 0.8493 (tm-30) REVERT: J 123 ASN cc_start: 0.8160 (m-40) cc_final: 0.7388 (m-40) REVERT: M 12 LEU cc_start: 0.7792 (mm) cc_final: 0.7495 (tp) REVERT: M 29 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7886 (pp) REVERT: M 56 MET cc_start: 0.3190 (OUTLIER) cc_final: 0.2813 (mmm) REVERT: M 120 LYS cc_start: 0.6567 (OUTLIER) cc_final: 0.6362 (ptmt) REVERT: M 244 PHE cc_start: 0.6697 (m-10) cc_final: 0.6465 (m-80) outliers start: 112 outliers final: 45 residues processed: 514 average time/residue: 0.1579 time to fit residues: 125.8493 Evaluate side-chains 380 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 327 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 227 TYR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 264 TYR Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 231 HIS Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 457 THR Chi-restraints excluded: chain H residue 474 LEU Chi-restraints excluded: chain H residue 489 LEU Chi-restraints excluded: chain H residue 515 LEU Chi-restraints excluded: chain H residue 552 LEU Chi-restraints excluded: chain I residue 4 ASP Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain J residue 85 HIS Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 56 MET Chi-restraints excluded: chain M residue 120 LYS Chi-restraints excluded: chain M residue 153 THR Chi-restraints excluded: chain M residue 180 CYS Chi-restraints excluded: chain M residue 249 VAL Chi-restraints excluded: chain N residue 39 MET Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 100 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 291 optimal weight: 0.5980 chunk 140 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 249 optimal weight: 9.9990 chunk 276 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 151 optimal weight: 20.0000 chunk 268 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 51 optimal weight: 0.0030 overall best weight: 2.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 HIS ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 GLN ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN D 187 HIS D 197 ASN ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 HIS ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 HIS ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN F 75 ASN ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 ASN F 214 HIS F 234 ASN ** G 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 262 ASN H 486 ASN H 490 ASN H 542 HIS H 567 GLN H 577 ASN I 97 GLN ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 94 ASN M 21 ASN ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 117 ASN ** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.138177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.122206 restraints weight = 102708.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.124708 restraints weight = 61621.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.126467 restraints weight = 41714.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.127604 restraints weight = 31103.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.128407 restraints weight = 25186.072| |-----------------------------------------------------------------------------| r_work (final): 0.4566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 25148 Z= 0.199 Angle : 0.680 10.861 34105 Z= 0.353 Chirality : 0.043 0.220 3701 Planarity : 0.005 0.056 4355 Dihedral : 13.685 178.191 3929 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 21.96 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.25 % Favored : 87.51 % Rotamer: Outliers : 4.69 % Allowed : 25.59 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 aren not related in a simple way. whole: -2.51 (0.15), residues: 2931 helix: 0.05 (0.17), residues: 964 sheet: -0.95 (0.25), residues: 441 loop : -3.19 (0.13), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 263 TYR 0.030 0.002 TYR I 40 PHE 0.046 0.003 PHE B 183 TRP 0.018 0.002 TRP H 534 HIS 0.031 0.002 HIS E 62 Details of bonding type rmsd covalent geometry : bond 0.00438 (25148) covalent geometry : angle 0.67968 (34105) hydrogen bonds : bond 0.03405 ( 821) hydrogen bonds : angle 4.79105 ( 2352) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 376 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 THR cc_start: 0.6800 (OUTLIER) cc_final: 0.6539 (p) REVERT: A 102 MET cc_start: 0.7814 (tpp) cc_final: 0.7353 (tpp) REVERT: A 121 ASN cc_start: 0.3327 (t0) cc_final: 0.2404 (m-40) REVERT: A 138 ASP cc_start: 0.6978 (OUTLIER) cc_final: 0.6581 (m-30) REVERT: A 178 TYR cc_start: 0.6459 (m-80) cc_final: 0.6092 (m-80) REVERT: A 221 MET cc_start: 0.5510 (mtt) cc_final: 0.4191 (mpp) REVERT: A 227 TYR cc_start: 0.6149 (m-80) cc_final: 0.4822 (m-80) REVERT: B 93 GLU cc_start: 0.7375 (pm20) cc_final: 0.6692 (pm20) REVERT: B 183 PHE cc_start: 0.6126 (m-80) cc_final: 0.5790 (m-10) REVERT: B 221 MET cc_start: 0.8100 (ttm) cc_final: 0.7731 (ttm) REVERT: C 56 MET cc_start: 0.4839 (ttp) cc_final: 0.4141 (tpt) REVERT: C 79 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7066 (pp20) REVERT: C 108 ASP cc_start: 0.8084 (t0) cc_final: 0.7429 (m-30) REVERT: D 40 LEU cc_start: 0.8220 (tp) cc_final: 0.7976 (tp) REVERT: D 141 MET cc_start: 0.4974 (mmm) cc_final: 0.4395 (mpp) REVERT: D 147 ILE cc_start: 0.7833 (pt) cc_final: 0.7532 (pt) REVERT: D 171 PHE cc_start: 0.7460 (m-80) cc_final: 0.7228 (m-80) REVERT: D 214 HIS cc_start: 0.6551 (m-70) cc_final: 0.6182 (m170) REVERT: D 220 GLN cc_start: 0.7624 (tt0) cc_final: 0.7285 (tt0) REVERT: D 264 TYR cc_start: 0.3092 (OUTLIER) cc_final: 0.2205 (m-10) REVERT: E 52 ASN cc_start: 0.8862 (m-40) cc_final: 0.8615 (m-40) REVERT: E 134 SER cc_start: 0.7829 (OUTLIER) cc_final: 0.7458 (m) REVERT: E 150 MET cc_start: 0.5548 (mtm) cc_final: 0.3935 (mtm) REVERT: E 209 MET cc_start: 0.5747 (mmm) cc_final: 0.5272 (mmm) REVERT: F 7 TYR cc_start: 0.8035 (m-80) cc_final: 0.7303 (m-80) REVERT: F 41 VAL cc_start: 0.7106 (t) cc_final: 0.6622 (t) REVERT: F 72 ILE cc_start: 0.7149 (mm) cc_final: 0.6827 (mm) REVERT: F 93 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7701 (tm-30) REVERT: F 112 PHE cc_start: 0.9152 (m-80) cc_final: 0.8625 (m-10) REVERT: F 135 ARG cc_start: 0.9099 (ptp-110) cc_final: 0.8192 (mtt180) REVERT: F 227 TYR cc_start: 0.3062 (m-80) cc_final: 0.2418 (m-10) REVERT: F 250 VAL cc_start: 0.4926 (OUTLIER) cc_final: 0.4678 (m) REVERT: G 4 HIS cc_start: 0.5820 (t-90) cc_final: 0.5521 (t-170) REVERT: G 85 TYR cc_start: 0.6308 (p90) cc_final: 0.5710 (p90) REVERT: G 247 MET cc_start: 0.7122 (tmm) cc_final: 0.6600 (tmm) REVERT: I 23 LYS cc_start: 0.7912 (tptm) cc_final: 0.7627 (tttt) REVERT: I 25 GLN cc_start: 0.8057 (tm-30) cc_final: 0.7021 (tm-30) REVERT: I 122 PHE cc_start: 0.7553 (t80) cc_final: 0.7008 (t80) REVERT: J 123 ASN cc_start: 0.7702 (m-40) cc_final: 0.7210 (m-40) REVERT: M 29 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8328 (pp) REVERT: M 56 MET cc_start: 0.3947 (OUTLIER) cc_final: 0.3428 (mmm) REVERT: M 120 LYS cc_start: 0.6665 (OUTLIER) cc_final: 0.6176 (ptmt) REVERT: M 150 MET cc_start: 0.2982 (ptt) cc_final: 0.2651 (ptp) REVERT: N 44 LYS cc_start: 0.7374 (mptt) cc_final: 0.6840 (mmtm) outliers start: 119 outliers final: 69 residues processed: 470 average time/residue: 0.1823 time to fit residues: 132.4512 Evaluate side-chains 406 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 328 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 112 PHE Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain C residue 8 ASP Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 264 TYR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain F residue 62 HIS Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 203 TRP Chi-restraints excluded: chain F residue 231 HIS Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 15 GLU Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 309 LYS Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 457 THR Chi-restraints excluded: chain H residue 515 LEU Chi-restraints excluded: chain H residue 534 TRP Chi-restraints excluded: chain H residue 549 HIS Chi-restraints excluded: chain H residue 550 LEU Chi-restraints excluded: chain H residue 572 LYS Chi-restraints excluded: chain I residue 4 ASP Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 111 PHE Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 56 MET Chi-restraints excluded: chain M residue 120 LYS Chi-restraints excluded: chain M residue 153 THR Chi-restraints excluded: chain M residue 180 CYS Chi-restraints excluded: chain M residue 249 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 13 CYS Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 145 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 268 optimal weight: 2.9990 chunk 241 optimal weight: 0.9980 chunk 205 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 157 optimal weight: 0.8980 chunk 247 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 HIS A 124 GLN ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN C 35 GLN C 55 GLN C 74 ASN ** C 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 GLN C 212 HIS ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 HIS ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 GLN E 208 ASN ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 ASN H 362 GLN H 427 GLN ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 124 GLN ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 133 GLN ** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.134822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.118702 restraints weight = 100913.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.121390 restraints weight = 59814.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.122901 restraints weight = 39942.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.124068 restraints weight = 29475.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.124833 restraints weight = 23707.846| |-----------------------------------------------------------------------------| r_work (final): 0.4514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 moved from start: 0.5974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 25148 Z= 0.181 Angle : 0.660 12.776 34105 Z= 0.339 Chirality : 0.043 0.235 3701 Planarity : 0.004 0.054 4355 Dihedral : 13.788 177.536 3929 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 22.29 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.30 % Favored : 89.49 % Rotamer: Outliers : 4.10 % Allowed : 26.14 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 aren not related in a simple way. whole: -2.46 (0.15), residues: 2931 helix: 0.07 (0.17), residues: 966 sheet: -1.19 (0.24), residues: 494 loop : -3.10 (0.14), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 68 TYR 0.024 0.002 TYR C 107 PHE 0.029 0.002 PHE B 183 TRP 0.023 0.002 TRP N 49 HIS 0.009 0.002 HIS I 61 Details of bonding type rmsd covalent geometry : bond 0.00394 (25148) covalent geometry : angle 0.66038 (34105) hydrogen bonds : bond 0.03224 ( 821) hydrogen bonds : angle 4.92687 ( 2352) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 362 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.8011 (tpp) cc_final: 0.7606 (tpp) REVERT: A 178 TYR cc_start: 0.6391 (m-80) cc_final: 0.6076 (m-80) REVERT: A 221 MET cc_start: 0.5816 (mtt) cc_final: 0.4417 (mtm) REVERT: A 248 GLN cc_start: 0.5809 (tp40) cc_final: 0.5496 (tp40) REVERT: B 183 PHE cc_start: 0.6618 (m-80) cc_final: 0.6023 (m-10) REVERT: C 16 GLN cc_start: 0.6920 (OUTLIER) cc_final: 0.6575 (mp10) REVERT: C 56 MET cc_start: 0.5032 (OUTLIER) cc_final: 0.4359 (tpt) REVERT: C 108 ASP cc_start: 0.8202 (t0) cc_final: 0.7505 (m-30) REVERT: D 141 MET cc_start: 0.4944 (mmm) cc_final: 0.4309 (mpp) REVERT: D 147 ILE cc_start: 0.7883 (pt) cc_final: 0.7671 (pt) REVERT: D 214 HIS cc_start: 0.6371 (m-70) cc_final: 0.6081 (m170) REVERT: D 220 GLN cc_start: 0.7632 (tt0) cc_final: 0.6996 (tt0) REVERT: D 264 TYR cc_start: 0.3059 (OUTLIER) cc_final: 0.2808 (m-10) REVERT: E 52 ASN cc_start: 0.8815 (m-40) cc_final: 0.8564 (m-40) REVERT: E 90 GLU cc_start: 0.6279 (tt0) cc_final: 0.5673 (tp30) REVERT: E 100 GLN cc_start: 0.8337 (mm110) cc_final: 0.8087 (mm110) REVERT: E 116 MET cc_start: 0.5725 (pmm) cc_final: 0.5399 (pmm) REVERT: E 220 GLN cc_start: 0.6869 (OUTLIER) cc_final: 0.5774 (tm-30) REVERT: E 221 MET cc_start: 0.4402 (mtt) cc_final: 0.3856 (mmm) REVERT: F 7 TYR cc_start: 0.8189 (m-80) cc_final: 0.7556 (m-80) REVERT: F 41 VAL cc_start: 0.7259 (t) cc_final: 0.6876 (t) REVERT: F 93 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7447 (tm-30) REVERT: F 112 PHE cc_start: 0.9095 (m-80) cc_final: 0.8709 (m-10) REVERT: F 227 TYR cc_start: 0.3157 (m-80) cc_final: 0.2557 (m-10) REVERT: F 250 VAL cc_start: 0.4886 (OUTLIER) cc_final: 0.4633 (m) REVERT: G 1 MET cc_start: 0.6534 (OUTLIER) cc_final: 0.5871 (ptt) REVERT: G 4 HIS cc_start: 0.6028 (t-90) cc_final: 0.5695 (t-170) REVERT: G 85 TYR cc_start: 0.6491 (p90) cc_final: 0.5992 (p90) REVERT: G 177 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7391 (pm20) REVERT: H 358 TYR cc_start: 0.4661 (OUTLIER) cc_final: 0.3408 (m-80) REVERT: H 503 SER cc_start: 0.8888 (m) cc_final: 0.8450 (p) REVERT: H 552 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7994 (pp) REVERT: I 3 LEU cc_start: 0.7863 (tp) cc_final: 0.7604 (tt) REVERT: I 23 LYS cc_start: 0.8009 (tptm) cc_final: 0.7665 (tttt) REVERT: I 25 GLN cc_start: 0.8040 (tm-30) cc_final: 0.7164 (tm-30) REVERT: J 123 ASN cc_start: 0.7570 (m-40) cc_final: 0.7105 (m110) REVERT: M 21 ASN cc_start: 0.6298 (t0) cc_final: 0.5919 (t0) REVERT: M 244 PHE cc_start: 0.7245 (m-10) cc_final: 0.6781 (m-80) REVERT: N 175 MET cc_start: 0.6315 (mtt) cc_final: 0.6011 (mtt) REVERT: N 192 PHE cc_start: 0.4954 (p90) cc_final: 0.2481 (m-80) outliers start: 104 outliers final: 59 residues processed: 448 average time/residue: 0.1600 time to fit residues: 112.8788 Evaluate side-chains 389 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 322 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 112 PHE Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 16 GLN Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 264 TYR Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 81 HIS Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 220 GLN Chi-restraints excluded: chain F residue 62 HIS Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 203 TRP Chi-restraints excluded: chain F residue 231 HIS Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 250 TYR Chi-restraints excluded: chain G residue 263 ARG Chi-restraints excluded: chain G residue 336 ARG Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 358 TYR Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain H residue 515 LEU Chi-restraints excluded: chain H residue 534 TRP Chi-restraints excluded: chain H residue 549 HIS Chi-restraints excluded: chain H residue 550 LEU Chi-restraints excluded: chain H residue 552 LEU Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain J residue 111 PHE Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 59 ASN Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 153 THR Chi-restraints excluded: chain M residue 180 CYS Chi-restraints excluded: chain M residue 249 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 13 CYS Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 140 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 134 optimal weight: 9.9990 chunk 263 optimal weight: 0.0770 chunk 185 optimal weight: 20.0000 chunk 202 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 218 optimal weight: 0.7980 chunk 131 optimal weight: 5.9990 chunk 181 optimal weight: 9.9990 chunk 186 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 187 optimal weight: 0.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS A 121 ASN ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 HIS ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 ASN G 104 HIS ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 124 GLN ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 64 ASN ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.134912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.118906 restraints weight = 100699.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.121271 restraints weight = 60157.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.123028 restraints weight = 40467.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.124209 restraints weight = 29839.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.124974 restraints weight = 23901.496| |-----------------------------------------------------------------------------| r_work (final): 0.4521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 0.6278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 25148 Z= 0.146 Angle : 0.640 10.901 34105 Z= 0.325 Chirality : 0.043 0.274 3701 Planarity : 0.004 0.051 4355 Dihedral : 13.832 179.778 3928 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 21.69 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.12 % Favored : 88.64 % Rotamer: Outliers : 3.94 % Allowed : 26.77 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 aren not related in a simple way. whole: -2.38 (0.15), residues: 2931 helix: 0.11 (0.17), residues: 954 sheet: -1.11 (0.24), residues: 480 loop : -3.01 (0.14), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 68 TYR 0.029 0.002 TYR I 40 PHE 0.021 0.002 PHE B 183 TRP 0.020 0.002 TRP H 534 HIS 0.013 0.001 HIS E 81 Details of bonding type rmsd covalent geometry : bond 0.00331 (25148) covalent geometry : angle 0.64034 (34105) hydrogen bonds : bond 0.03035 ( 821) hydrogen bonds : angle 4.87568 ( 2352) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 346 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.8057 (tpp) cc_final: 0.7647 (tpp) REVERT: A 150 MET cc_start: 0.2963 (ptp) cc_final: 0.2744 (ptp) REVERT: A 178 TYR cc_start: 0.6318 (m-80) cc_final: 0.6012 (m-80) REVERT: A 221 MET cc_start: 0.6035 (mtt) cc_final: 0.4643 (mtm) REVERT: A 248 GLN cc_start: 0.5966 (tp40) cc_final: 0.5684 (tp40) REVERT: B 183 PHE cc_start: 0.6576 (m-80) cc_final: 0.6016 (m-10) REVERT: C 16 GLN cc_start: 0.6800 (OUTLIER) cc_final: 0.6451 (mp10) REVERT: C 78 ASP cc_start: 0.7025 (m-30) cc_final: 0.6773 (m-30) REVERT: D 102 MET cc_start: 0.7843 (mmm) cc_final: 0.7501 (mmt) REVERT: D 141 MET cc_start: 0.4848 (mmm) cc_final: 0.4224 (mpp) REVERT: D 220 GLN cc_start: 0.7607 (tt0) cc_final: 0.7035 (tt0) REVERT: D 264 TYR cc_start: 0.2559 (OUTLIER) cc_final: 0.1766 (m-10) REVERT: E 52 ASN cc_start: 0.8864 (m-40) cc_final: 0.8398 (m110) REVERT: E 90 GLU cc_start: 0.6197 (tt0) cc_final: 0.5641 (tp30) REVERT: E 100 GLN cc_start: 0.8379 (mm110) cc_final: 0.8174 (mm110) REVERT: E 116 MET cc_start: 0.5785 (pmm) cc_final: 0.5546 (pmm) REVERT: E 134 SER cc_start: 0.7649 (OUTLIER) cc_final: 0.6711 (t) REVERT: E 220 GLN cc_start: 0.6995 (OUTLIER) cc_final: 0.5708 (tm-30) REVERT: E 221 MET cc_start: 0.5074 (mtt) cc_final: 0.4322 (mmm) REVERT: F 7 TYR cc_start: 0.8176 (m-80) cc_final: 0.7564 (m-80) REVERT: F 41 VAL cc_start: 0.7130 (OUTLIER) cc_final: 0.6730 (t) REVERT: F 93 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7437 (tm-30) REVERT: F 112 PHE cc_start: 0.8939 (m-80) cc_final: 0.8550 (m-10) REVERT: F 137 ILE cc_start: 0.3804 (OUTLIER) cc_final: 0.3401 (pt) REVERT: F 227 TYR cc_start: 0.2962 (m-80) cc_final: 0.2384 (m-10) REVERT: F 250 VAL cc_start: 0.4892 (OUTLIER) cc_final: 0.4647 (m) REVERT: G 1 MET cc_start: 0.6453 (OUTLIER) cc_final: 0.5749 (ptt) REVERT: G 4 HIS cc_start: 0.5935 (t-90) cc_final: 0.5568 (t-170) REVERT: G 85 TYR cc_start: 0.6490 (p90) cc_final: 0.5975 (p90) REVERT: G 177 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7383 (pm20) REVERT: H 358 TYR cc_start: 0.4744 (OUTLIER) cc_final: 0.3355 (m-80) REVERT: H 540 LEU cc_start: 0.6653 (OUTLIER) cc_final: 0.6446 (tt) REVERT: H 552 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8221 (pt) REVERT: I 3 LEU cc_start: 0.7920 (tp) cc_final: 0.7655 (tt) REVERT: I 23 LYS cc_start: 0.7926 (tptm) cc_final: 0.7649 (tptt) REVERT: I 25 GLN cc_start: 0.8047 (tm-30) cc_final: 0.7571 (tp-100) REVERT: I 56 MET cc_start: 0.5965 (OUTLIER) cc_final: 0.5613 (ppp) REVERT: J 56 MET cc_start: 0.7828 (mmm) cc_final: 0.7499 (mmm) REVERT: J 94 ASN cc_start: 0.7994 (m-40) cc_final: 0.7401 (m-40) REVERT: J 123 ASN cc_start: 0.7514 (m-40) cc_final: 0.7080 (m110) REVERT: M 21 ASN cc_start: 0.6431 (t0) cc_final: 0.6157 (t0) REVERT: M 56 MET cc_start: 0.4972 (mmt) cc_final: 0.4600 (mmm) REVERT: N 175 MET cc_start: 0.6484 (OUTLIER) cc_final: 0.5928 (mtt) outliers start: 100 outliers final: 48 residues processed: 414 average time/residue: 0.1494 time to fit residues: 97.8502 Evaluate side-chains 366 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 305 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 16 GLN Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 264 TYR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 220 GLN Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 62 HIS Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 231 HIS Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 250 TYR Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 358 TYR Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain H residue 515 LEU Chi-restraints excluded: chain H residue 530 VAL Chi-restraints excluded: chain H residue 540 LEU Chi-restraints excluded: chain H residue 549 HIS Chi-restraints excluded: chain H residue 550 LEU Chi-restraints excluded: chain H residue 552 LEU Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 29 ASN Chi-restraints excluded: chain I residue 56 MET Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 111 PHE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 59 ASN Chi-restraints excluded: chain M residue 153 THR Chi-restraints excluded: chain M residue 265 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 13 CYS Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 175 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 212 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 99 optimal weight: 20.0000 chunk 110 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 chunk 111 optimal weight: 0.0970 chunk 105 optimal weight: 7.9990 chunk 203 optimal weight: 0.3980 chunk 201 optimal weight: 0.0000 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 HIS ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 HIS ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 29 ASN ** I 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 ASN ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.135595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.119381 restraints weight = 101510.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.121695 restraints weight = 60315.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.123447 restraints weight = 40638.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.124604 restraints weight = 30107.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.125237 restraints weight = 24295.202| |-----------------------------------------------------------------------------| r_work (final): 0.4538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 0.6453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 25148 Z= 0.130 Angle : 0.636 12.788 34105 Z= 0.321 Chirality : 0.042 0.235 3701 Planarity : 0.004 0.051 4355 Dihedral : 13.893 178.169 3925 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.27 % Favored : 89.53 % Rotamer: Outliers : 3.55 % Allowed : 27.21 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 aren not related in a simple way. whole: -2.25 (0.15), residues: 2931 helix: 0.13 (0.17), residues: 958 sheet: -0.93 (0.24), residues: 460 loop : -2.89 (0.14), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 135 TYR 0.027 0.002 TYR N 173 PHE 0.026 0.002 PHE D 261 TRP 0.017 0.002 TRP H 534 HIS 0.009 0.001 HIS D 214 Details of bonding type rmsd covalent geometry : bond 0.00299 (25148) covalent geometry : angle 0.63627 (34105) hydrogen bonds : bond 0.02915 ( 821) hydrogen bonds : angle 4.85310 ( 2352) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 332 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.7370 (mt) cc_final: 0.7151 (mt) REVERT: A 102 MET cc_start: 0.8074 (tpp) cc_final: 0.7563 (tpp) REVERT: A 116 MET cc_start: 0.5623 (OUTLIER) cc_final: 0.5113 (tmm) REVERT: A 221 MET cc_start: 0.6123 (mtt) cc_final: 0.4833 (mtm) REVERT: A 248 GLN cc_start: 0.6032 (tp40) cc_final: 0.5750 (tp40) REVERT: B 143 LEU cc_start: 0.7720 (mt) cc_final: 0.7147 (tp) REVERT: B 144 GLU cc_start: 0.5989 (OUTLIER) cc_final: 0.5623 (mp0) REVERT: B 150 MET cc_start: 0.5976 (pmm) cc_final: 0.5357 (pmm) REVERT: B 183 PHE cc_start: 0.6503 (m-80) cc_final: 0.5974 (m-10) REVERT: C 16 GLN cc_start: 0.6803 (OUTLIER) cc_final: 0.6509 (mp10) REVERT: C 78 ASP cc_start: 0.7004 (m-30) cc_final: 0.6755 (m-30) REVERT: D 56 MET cc_start: 0.5194 (mmt) cc_final: 0.4873 (mmm) REVERT: D 141 MET cc_start: 0.4891 (mmm) cc_final: 0.4391 (mpp) REVERT: D 220 GLN cc_start: 0.7474 (tt0) cc_final: 0.6915 (tt0) REVERT: D 264 TYR cc_start: 0.2865 (OUTLIER) cc_final: 0.1952 (m-10) REVERT: E 52 ASN cc_start: 0.8831 (m-40) cc_final: 0.8372 (m110) REVERT: E 90 GLU cc_start: 0.6175 (tt0) cc_final: 0.5597 (tp30) REVERT: E 134 SER cc_start: 0.7785 (OUTLIER) cc_final: 0.6962 (t) REVERT: E 184 ILE cc_start: 0.8386 (mp) cc_final: 0.8179 (mp) REVERT: E 220 GLN cc_start: 0.6925 (OUTLIER) cc_final: 0.5577 (tm-30) REVERT: E 221 MET cc_start: 0.4925 (mtt) cc_final: 0.4190 (mmm) REVERT: F 7 TYR cc_start: 0.8257 (m-80) cc_final: 0.7655 (m-80) REVERT: F 41 VAL cc_start: 0.7090 (t) cc_final: 0.6599 (t) REVERT: F 93 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7416 (tm-30) REVERT: F 112 PHE cc_start: 0.8903 (m-80) cc_final: 0.8531 (m-10) REVERT: F 137 ILE cc_start: 0.3746 (OUTLIER) cc_final: 0.3371 (pt) REVERT: F 227 TYR cc_start: 0.2833 (m-80) cc_final: 0.2274 (m-10) REVERT: F 250 VAL cc_start: 0.4714 (OUTLIER) cc_final: 0.4484 (m) REVERT: G 1 MET cc_start: 0.6550 (OUTLIER) cc_final: 0.5866 (ptt) REVERT: G 4 HIS cc_start: 0.5925 (t-90) cc_final: 0.5446 (t-170) REVERT: G 85 TYR cc_start: 0.6373 (p90) cc_final: 0.6059 (p90) REVERT: G 177 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7350 (pm20) REVERT: G 302 ASP cc_start: 0.5434 (m-30) cc_final: 0.4809 (t70) REVERT: H 358 TYR cc_start: 0.4609 (OUTLIER) cc_final: 0.3183 (m-80) REVERT: H 479 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7907 (tm-30) REVERT: H 552 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8190 (pp) REVERT: I 3 LEU cc_start: 0.7921 (tp) cc_final: 0.7654 (tt) REVERT: I 23 LYS cc_start: 0.7955 (tptm) cc_final: 0.7650 (tptt) REVERT: I 25 GLN cc_start: 0.7968 (tm-30) cc_final: 0.7499 (tp-100) REVERT: I 98 GLN cc_start: 0.8267 (tm-30) cc_final: 0.8053 (pp30) REVERT: J 116 ASP cc_start: 0.6648 (m-30) cc_final: 0.6075 (t0) REVERT: J 123 ASN cc_start: 0.7429 (m-40) cc_final: 0.7024 (m110) REVERT: M 21 ASN cc_start: 0.6323 (t0) cc_final: 0.6010 (t0) REVERT: N 130 LYS cc_start: 0.6936 (pptt) cc_final: 0.6604 (pptt) REVERT: N 175 MET cc_start: 0.6172 (OUTLIER) cc_final: 0.5806 (mtt) outliers start: 90 outliers final: 52 residues processed: 397 average time/residue: 0.1514 time to fit residues: 94.6491 Evaluate side-chains 367 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 302 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 16 GLN Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 264 TYR Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 220 GLN Chi-restraints excluded: chain F residue 62 HIS Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 203 TRP Chi-restraints excluded: chain F residue 231 HIS Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 250 TYR Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 358 TYR Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 460 LEU Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain H residue 479 GLU Chi-restraints excluded: chain H residue 493 ILE Chi-restraints excluded: chain H residue 515 LEU Chi-restraints excluded: chain H residue 549 HIS Chi-restraints excluded: chain H residue 552 LEU Chi-restraints excluded: chain I residue 29 ASN Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain J residue 111 PHE Chi-restraints excluded: chain M residue 59 ASN Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 153 THR Chi-restraints excluded: chain M residue 249 VAL Chi-restraints excluded: chain N residue 13 CYS Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 175 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 30 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 185 optimal weight: 20.0000 chunk 249 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 124 GLN ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN E 181 HIS ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN F 63 HIS F 81 HIS ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 490 ASN ** H 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 ASN ** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.129373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.112822 restraints weight = 100065.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.115298 restraints weight = 58701.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.116813 restraints weight = 39548.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.117862 restraints weight = 29394.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.118247 restraints weight = 23926.806| |-----------------------------------------------------------------------------| r_work (final): 0.4420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.7291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 25148 Z= 0.211 Angle : 0.708 10.078 34105 Z= 0.361 Chirality : 0.044 0.284 3701 Planarity : 0.004 0.056 4355 Dihedral : 13.938 178.865 3924 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 25.96 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.40 % Favored : 88.43 % Rotamer: Outliers : 3.94 % Allowed : 27.52 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 aren not related in a simple way. whole: -2.34 (0.15), residues: 2931 helix: -0.03 (0.17), residues: 967 sheet: -1.26 (0.23), residues: 485 loop : -2.81 (0.14), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 68 TYR 0.041 0.002 TYR N 173 PHE 0.040 0.003 PHE N 168 TRP 0.027 0.002 TRP G 82 HIS 0.009 0.002 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00457 (25148) covalent geometry : angle 0.70836 (34105) hydrogen bonds : bond 0.03429 ( 821) hydrogen bonds : angle 5.11551 ( 2352) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 336 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.7254 (mt) cc_final: 0.6909 (mt) REVERT: A 102 MET cc_start: 0.8097 (tpp) cc_final: 0.7686 (tpp) REVERT: A 135 ARG cc_start: 0.8516 (mmm160) cc_final: 0.8086 (mmm-85) REVERT: A 221 MET cc_start: 0.6471 (mtt) cc_final: 0.5065 (mtm) REVERT: A 248 GLN cc_start: 0.6633 (tp40) cc_final: 0.6337 (tp40) REVERT: B 68 ARG cc_start: 0.6398 (OUTLIER) cc_final: 0.5573 (ptp90) REVERT: B 150 MET cc_start: 0.6391 (pmm) cc_final: 0.6089 (pmm) REVERT: B 183 PHE cc_start: 0.6617 (m-80) cc_final: 0.6062 (m-10) REVERT: C 16 GLN cc_start: 0.6756 (OUTLIER) cc_final: 0.6475 (mp10) REVERT: C 78 ASP cc_start: 0.7221 (m-30) cc_final: 0.7007 (m-30) REVERT: C 116 MET cc_start: 0.5701 (pmm) cc_final: 0.5233 (pmm) REVERT: C 141 MET cc_start: 0.6020 (mtm) cc_final: 0.5501 (mtm) REVERT: D 141 MET cc_start: 0.5229 (mmm) cc_final: 0.4625 (mpp) REVERT: D 167 MET cc_start: 0.5664 (mmm) cc_final: 0.5277 (mmm) REVERT: D 169 ARG cc_start: 0.7815 (ptp-170) cc_final: 0.7404 (mtt90) REVERT: D 214 HIS cc_start: 0.6495 (m170) cc_final: 0.6253 (m170) REVERT: D 220 GLN cc_start: 0.7661 (tt0) cc_final: 0.7298 (tm-30) REVERT: D 264 TYR cc_start: 0.2670 (OUTLIER) cc_final: 0.2447 (m-10) REVERT: E 52 ASN cc_start: 0.8881 (m-40) cc_final: 0.8457 (m110) REVERT: E 90 GLU cc_start: 0.6322 (tt0) cc_final: 0.5762 (tp30) REVERT: E 135 ARG cc_start: 0.8093 (mtt-85) cc_final: 0.7893 (mmt180) REVERT: E 220 GLN cc_start: 0.7292 (OUTLIER) cc_final: 0.5974 (tm-30) REVERT: E 221 MET cc_start: 0.5075 (mtt) cc_final: 0.4251 (mmm) REVERT: F 7 TYR cc_start: 0.8165 (m-80) cc_final: 0.7618 (m-80) REVERT: F 41 VAL cc_start: 0.7296 (OUTLIER) cc_final: 0.6916 (t) REVERT: F 93 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7426 (tm-30) REVERT: F 112 PHE cc_start: 0.8776 (m-80) cc_final: 0.8494 (m-10) REVERT: F 170 LYS cc_start: 0.4867 (mmtt) cc_final: 0.4467 (mptt) REVERT: F 227 TYR cc_start: 0.3087 (m-80) cc_final: 0.2494 (m-10) REVERT: F 250 VAL cc_start: 0.4316 (OUTLIER) cc_final: 0.4079 (m) REVERT: G 4 HIS cc_start: 0.6489 (t-90) cc_final: 0.5968 (t-170) REVERT: G 85 TYR cc_start: 0.6483 (p90) cc_final: 0.6113 (p90) REVERT: G 177 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7342 (pm20) REVERT: G 302 ASP cc_start: 0.4882 (m-30) cc_final: 0.4286 (t70) REVERT: G 307 LEU cc_start: 0.2860 (OUTLIER) cc_final: 0.2369 (tp) REVERT: H 358 TYR cc_start: 0.5355 (OUTLIER) cc_final: 0.3544 (m-80) REVERT: H 479 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7891 (tm-30) REVERT: H 550 LEU cc_start: 0.7893 (tp) cc_final: 0.7614 (tt) REVERT: I 25 GLN cc_start: 0.8004 (tm-30) cc_final: 0.7523 (tp-100) REVERT: I 41 PHE cc_start: 0.7882 (t80) cc_final: 0.7468 (t80) REVERT: J 77 TRP cc_start: 0.5754 (OUTLIER) cc_final: 0.4957 (t60) REVERT: J 116 ASP cc_start: 0.6605 (OUTLIER) cc_final: 0.6256 (t0) REVERT: J 120 ASN cc_start: 0.7733 (m-40) cc_final: 0.7393 (m-40) REVERT: J 123 ASN cc_start: 0.7639 (m-40) cc_final: 0.7282 (m110) REVERT: N 43 TRP cc_start: 0.4591 (t60) cc_final: 0.3287 (t60) REVERT: N 74 MET cc_start: 0.3711 (mmm) cc_final: 0.3411 (mmm) REVERT: N 130 LYS cc_start: 0.7401 (pptt) cc_final: 0.7032 (pptt) REVERT: N 175 MET cc_start: 0.6359 (OUTLIER) cc_final: 0.5917 (mtt) outliers start: 100 outliers final: 59 residues processed: 407 average time/residue: 0.1529 time to fit residues: 97.9436 Evaluate side-chains 378 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 307 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 PHE Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 112 PHE Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 16 GLN Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 264 TYR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 220 GLN Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 62 HIS Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 203 TRP Chi-restraints excluded: chain F residue 231 HIS Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 307 LEU Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 358 TYR Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 460 LEU Chi-restraints excluded: chain H residue 479 GLU Chi-restraints excluded: chain H residue 493 ILE Chi-restraints excluded: chain H residue 515 LEU Chi-restraints excluded: chain H residue 530 VAL Chi-restraints excluded: chain I residue 29 ASN Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 77 TRP Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain J residue 111 PHE Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 59 ASN Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 249 VAL Chi-restraints excluded: chain M residue 265 LEU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 145 PHE Chi-restraints excluded: chain N residue 175 MET Chi-restraints excluded: chain N residue 191 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 46 optimal weight: 3.9990 chunk 219 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 83 optimal weight: 0.0270 chunk 95 optimal weight: 1.9990 chunk 226 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 198 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 266 optimal weight: 3.9990 overall best weight: 1.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 HIS ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 HIS G 104 HIS H 542 HIS H 554 GLN I 29 ASN ** I 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 GLN I 98 GLN ** J 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 194 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.129813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.113423 restraints weight = 100211.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.115890 restraints weight = 58593.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.117559 restraints weight = 38908.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.118642 restraints weight = 28776.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.119307 restraints weight = 23249.084| |-----------------------------------------------------------------------------| r_work (final): 0.4440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.7537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 25148 Z= 0.165 Angle : 0.691 13.551 34105 Z= 0.349 Chirality : 0.043 0.232 3701 Planarity : 0.004 0.103 4355 Dihedral : 14.007 176.724 3924 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 24.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.95 % Favored : 88.88 % Rotamer: Outliers : 3.12 % Allowed : 29.46 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 aren not related in a simple way. whole: -2.34 (0.15), residues: 2931 helix: -0.11 (0.17), residues: 968 sheet: -1.17 (0.23), residues: 476 loop : -2.78 (0.14), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 101 TYR 0.055 0.002 TYR N 173 PHE 0.026 0.002 PHE D 261 TRP 0.041 0.002 TRP H 534 HIS 0.008 0.002 HIS N 136 Details of bonding type rmsd covalent geometry : bond 0.00377 (25148) covalent geometry : angle 0.69104 (34105) hydrogen bonds : bond 0.03342 ( 821) hydrogen bonds : angle 5.14732 ( 2352) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 329 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.7272 (mt) cc_final: 0.7072 (mt) REVERT: A 102 MET cc_start: 0.8043 (tpp) cc_final: 0.7647 (tpp) REVERT: A 135 ARG cc_start: 0.8632 (mmm160) cc_final: 0.8268 (mmm-85) REVERT: A 221 MET cc_start: 0.6463 (mtt) cc_final: 0.5053 (mtm) REVERT: A 248 GLN cc_start: 0.6438 (tp40) cc_final: 0.6180 (tp40) REVERT: B 68 ARG cc_start: 0.5883 (OUTLIER) cc_final: 0.5344 (ptp90) REVERT: B 84 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8737 (pm20) REVERT: B 143 LEU cc_start: 0.7753 (mt) cc_final: 0.7261 (tp) REVERT: B 144 GLU cc_start: 0.6313 (OUTLIER) cc_final: 0.6066 (mp0) REVERT: B 150 MET cc_start: 0.6318 (pmm) cc_final: 0.4930 (pmm) REVERT: B 183 PHE cc_start: 0.6778 (m-80) cc_final: 0.6290 (m-10) REVERT: C 16 GLN cc_start: 0.6843 (OUTLIER) cc_final: 0.6492 (mt0) REVERT: C 56 MET cc_start: 0.4206 (tpt) cc_final: 0.3573 (tpt) REVERT: C 78 ASP cc_start: 0.7261 (m-30) cc_final: 0.7039 (m-30) REVERT: C 93 GLU cc_start: 0.7706 (tp30) cc_final: 0.7469 (tm-30) REVERT: D 141 MET cc_start: 0.5307 (mmm) cc_final: 0.4596 (mpp) REVERT: D 150 MET cc_start: 0.5018 (ptp) cc_final: 0.4647 (ptp) REVERT: D 167 MET cc_start: 0.5517 (mmm) cc_final: 0.4970 (mmm) REVERT: D 169 ARG cc_start: 0.7862 (ptp-170) cc_final: 0.7274 (mtt90) REVERT: D 171 PHE cc_start: 0.7652 (m-80) cc_final: 0.7413 (m-80) REVERT: D 220 GLN cc_start: 0.7592 (tt0) cc_final: 0.6949 (tt0) REVERT: D 239 PRO cc_start: 0.7747 (Cg_exo) cc_final: 0.7512 (Cg_endo) REVERT: D 264 TYR cc_start: 0.2184 (OUTLIER) cc_final: 0.1824 (m-10) REVERT: E 52 ASN cc_start: 0.9009 (m-40) cc_final: 0.8578 (m110) REVERT: E 90 GLU cc_start: 0.6391 (tt0) cc_final: 0.5869 (tp30) REVERT: E 100 GLN cc_start: 0.8589 (mm-40) cc_final: 0.8349 (mm110) REVERT: E 209 MET cc_start: 0.4913 (mmm) cc_final: 0.4671 (mmm) REVERT: E 220 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.6093 (tm-30) REVERT: F 7 TYR cc_start: 0.8154 (m-80) cc_final: 0.7614 (m-80) REVERT: F 40 LEU cc_start: 0.7725 (mt) cc_final: 0.7443 (mt) REVERT: F 41 VAL cc_start: 0.7271 (OUTLIER) cc_final: 0.7010 (t) REVERT: F 93 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7413 (tm-30) REVERT: F 112 PHE cc_start: 0.8763 (m-80) cc_final: 0.8502 (m-10) REVERT: F 170 LYS cc_start: 0.4978 (mmtt) cc_final: 0.4585 (mptt) REVERT: F 227 TYR cc_start: 0.3021 (m-80) cc_final: 0.2441 (m-10) REVERT: F 250 VAL cc_start: 0.4241 (OUTLIER) cc_final: 0.4020 (m) REVERT: G 1 MET cc_start: 0.6533 (OUTLIER) cc_final: 0.6158 (ptt) REVERT: G 4 HIS cc_start: 0.6451 (t-90) cc_final: 0.5975 (t-170) REVERT: G 85 TYR cc_start: 0.6427 (p90) cc_final: 0.5960 (p90) REVERT: G 177 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7320 (pm20) REVERT: G 302 ASP cc_start: 0.4025 (m-30) cc_final: 0.3650 (t70) REVERT: H 358 TYR cc_start: 0.5774 (OUTLIER) cc_final: 0.3968 (m-80) REVERT: H 454 LYS cc_start: 0.5934 (pttm) cc_final: 0.5672 (pttt) REVERT: H 479 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7888 (tm-30) REVERT: I 3 LEU cc_start: 0.8067 (tp) cc_final: 0.7856 (tt) REVERT: I 25 GLN cc_start: 0.8114 (tm-30) cc_final: 0.7613 (tp-100) REVERT: I 39 ARG cc_start: 0.8220 (mtm180) cc_final: 0.7997 (mtm180) REVERT: I 41 PHE cc_start: 0.8045 (t80) cc_final: 0.7761 (t80) REVERT: J 56 MET cc_start: 0.7905 (mmm) cc_final: 0.7560 (mmm) REVERT: J 77 TRP cc_start: 0.5713 (OUTLIER) cc_final: 0.4987 (t60) REVERT: J 116 ASP cc_start: 0.6806 (m-30) cc_final: 0.6331 (t0) REVERT: J 120 ASN cc_start: 0.7717 (m-40) cc_final: 0.7386 (m-40) REVERT: J 123 ASN cc_start: 0.7692 (m-40) cc_final: 0.7322 (m110) REVERT: N 43 TRP cc_start: 0.5028 (t60) cc_final: 0.3893 (t60) REVERT: N 175 MET cc_start: 0.6352 (OUTLIER) cc_final: 0.5987 (mtt) outliers start: 79 outliers final: 56 residues processed: 386 average time/residue: 0.1561 time to fit residues: 94.5305 Evaluate side-chains 370 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 301 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 16 GLN Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 264 TYR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 220 GLN Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 62 HIS Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 203 TRP Chi-restraints excluded: chain F residue 231 HIS Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 358 TYR Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 460 LEU Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain H residue 479 GLU Chi-restraints excluded: chain H residue 493 ILE Chi-restraints excluded: chain H residue 572 LYS Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 77 TRP Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain J residue 111 PHE Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 59 ASN Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 152 VAL Chi-restraints excluded: chain M residue 249 VAL Chi-restraints excluded: chain M residue 265 LEU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 175 MET Chi-restraints excluded: chain N residue 191 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 239 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 chunk 280 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 188 optimal weight: 8.9990 chunk 112 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 GLN ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 HIS ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 ASN ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN I 98 GLN ** J 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 117 ASN ** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.124194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.107676 restraints weight = 99314.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.110017 restraints weight = 56953.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.111698 restraints weight = 37602.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.112705 restraints weight = 27651.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 66)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.113271 restraints weight = 22518.010| |-----------------------------------------------------------------------------| r_work (final): 0.4347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.8420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.121 25148 Z= 0.233 Angle : 0.782 19.368 34105 Z= 0.398 Chirality : 0.046 0.253 3701 Planarity : 0.005 0.057 4355 Dihedral : 14.110 176.130 3922 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 30.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.04 % Favored : 87.79 % Rotamer: Outliers : 3.27 % Allowed : 29.69 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -2.47 (0.15), residues: 2931 helix: -0.23 (0.17), residues: 946 sheet: -1.47 (0.23), residues: 482 loop : -2.72 (0.14), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG J 39 TYR 0.056 0.003 TYR N 173 PHE 0.026 0.003 PHE D 13 TRP 0.033 0.003 TRP H 534 HIS 0.013 0.002 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00515 (25148) covalent geometry : angle 0.78200 (34105) hydrogen bonds : bond 0.03854 ( 821) hydrogen bonds : angle 5.49595 ( 2352) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 329 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ARG cc_start: 0.7622 (ttt180) cc_final: 0.7406 (ttt180) REVERT: A 102 MET cc_start: 0.8100 (tpp) cc_final: 0.7717 (tpp) REVERT: A 135 ARG cc_start: 0.8782 (mmm160) cc_final: 0.8255 (mmm-85) REVERT: A 221 MET cc_start: 0.6343 (mtt) cc_final: 0.5891 (mtt) REVERT: A 235 LEU cc_start: 0.8347 (tp) cc_final: 0.8138 (tp) REVERT: B 68 ARG cc_start: 0.6350 (OUTLIER) cc_final: 0.6113 (ptp90) REVERT: B 108 ASP cc_start: 0.6968 (t70) cc_final: 0.6508 (t0) REVERT: B 183 PHE cc_start: 0.6964 (m-80) cc_final: 0.6572 (m-80) REVERT: C 16 GLN cc_start: 0.6802 (OUTLIER) cc_final: 0.6134 (mt0) REVERT: C 17 ASP cc_start: 0.6667 (OUTLIER) cc_final: 0.6315 (m-30) REVERT: C 141 MET cc_start: 0.6177 (mtm) cc_final: 0.5558 (mtm) REVERT: D 116 MET cc_start: 0.6166 (pmm) cc_final: 0.5728 (pmm) REVERT: D 141 MET cc_start: 0.5455 (mmm) cc_final: 0.4995 (mpp) REVERT: D 150 MET cc_start: 0.5556 (ptp) cc_final: 0.5242 (ptp) REVERT: D 167 MET cc_start: 0.5759 (mmm) cc_final: 0.5314 (mmm) REVERT: D 220 GLN cc_start: 0.7984 (tt0) cc_final: 0.7216 (tt0) REVERT: D 239 PRO cc_start: 0.7707 (Cg_exo) cc_final: 0.7402 (Cg_endo) REVERT: D 264 TYR cc_start: 0.2342 (OUTLIER) cc_final: 0.1915 (m-10) REVERT: E 52 ASN cc_start: 0.8958 (m-40) cc_final: 0.8526 (m110) REVERT: E 90 GLU cc_start: 0.6553 (tt0) cc_final: 0.5961 (tp30) REVERT: E 100 GLN cc_start: 0.8613 (mm-40) cc_final: 0.8314 (mm110) REVERT: E 220 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.6115 (tm-30) REVERT: F 7 TYR cc_start: 0.8140 (m-80) cc_final: 0.7598 (m-80) REVERT: F 41 VAL cc_start: 0.7327 (t) cc_final: 0.7092 (t) REVERT: F 93 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7624 (tm-30) REVERT: F 96 GLU cc_start: 0.8451 (tp30) cc_final: 0.8247 (tp30) REVERT: F 112 PHE cc_start: 0.8687 (m-80) cc_final: 0.8447 (m-10) REVERT: F 169 ARG cc_start: 0.7123 (mmt-90) cc_final: 0.6626 (mmp80) REVERT: F 170 LYS cc_start: 0.5039 (mmtt) cc_final: 0.4654 (mptt) REVERT: F 227 TYR cc_start: 0.3222 (m-80) cc_final: 0.2886 (m-10) REVERT: F 250 VAL cc_start: 0.4216 (OUTLIER) cc_final: 0.3973 (m) REVERT: G 1 MET cc_start: 0.6491 (OUTLIER) cc_final: 0.6279 (ptt) REVERT: G 4 HIS cc_start: 0.6642 (t-90) cc_final: 0.6134 (t-170) REVERT: G 82 TRP cc_start: 0.5814 (p-90) cc_final: 0.5380 (p-90) REVERT: G 85 TYR cc_start: 0.6512 (p90) cc_final: 0.6104 (p90) REVERT: G 177 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7373 (pm20) REVERT: G 247 MET cc_start: 0.7933 (tmm) cc_final: 0.7669 (tmm) REVERT: G 307 LEU cc_start: 0.3593 (OUTLIER) cc_final: 0.3217 (tp) REVERT: H 358 TYR cc_start: 0.6280 (OUTLIER) cc_final: 0.4490 (m-80) REVERT: H 479 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8051 (tm-30) REVERT: H 513 MET cc_start: 0.6025 (mmp) cc_final: 0.5595 (mmp) REVERT: I 13 VAL cc_start: 0.8177 (p) cc_final: 0.7774 (m) REVERT: I 25 GLN cc_start: 0.8138 (tm-30) cc_final: 0.7497 (tp-100) REVERT: I 36 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8456 (mm) REVERT: I 39 ARG cc_start: 0.8061 (mtm180) cc_final: 0.7841 (mtm180) REVERT: I 116 ASP cc_start: 0.7824 (t0) cc_final: 0.7415 (t0) REVERT: J 77 TRP cc_start: 0.5690 (OUTLIER) cc_final: 0.5043 (t60) REVERT: J 123 ASN cc_start: 0.7677 (m-40) cc_final: 0.7305 (m110) REVERT: M 29 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8832 (pp) REVERT: N 43 TRP cc_start: 0.4205 (t60) cc_final: 0.3423 (t60) REVERT: N 175 MET cc_start: 0.5972 (OUTLIER) cc_final: 0.5583 (mtt) outliers start: 83 outliers final: 55 residues processed: 393 average time/residue: 0.1585 time to fit residues: 98.6460 Evaluate side-chains 370 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 301 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 PHE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 112 PHE Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 16 GLN Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 264 TYR Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 220 GLN Chi-restraints excluded: chain F residue 62 HIS Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 203 TRP Chi-restraints excluded: chain F residue 231 HIS Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 307 LEU Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 358 TYR Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 460 LEU Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain H residue 479 GLU Chi-restraints excluded: chain H residue 493 ILE Chi-restraints excluded: chain H residue 572 LYS Chi-restraints excluded: chain I residue 29 ASN Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 77 TRP Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain J residue 111 PHE Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 59 ASN Chi-restraints excluded: chain M residue 152 VAL Chi-restraints excluded: chain M residue 249 VAL Chi-restraints excluded: chain M residue 265 LEU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 142 CYS Chi-restraints excluded: chain N residue 175 MET Chi-restraints excluded: chain N residue 191 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 169 optimal weight: 9.9990 chunk 267 optimal weight: 0.7980 chunk 278 optimal weight: 0.6980 chunk 219 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 239 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 ASN ** C 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN C 187 HIS C 197 ASN ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 HIS ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 HIS G 4 HIS ** I 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 GLN I 97 GLN ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 HIS ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.127843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.111620 restraints weight = 98969.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.114045 restraints weight = 56244.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.115701 restraints weight = 36978.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.116734 restraints weight = 27211.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.117428 restraints weight = 21821.725| |-----------------------------------------------------------------------------| r_work (final): 0.4411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.8332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.157 25148 Z= 0.158 Angle : 0.736 16.359 34105 Z= 0.371 Chirality : 0.044 0.227 3701 Planarity : 0.004 0.087 4355 Dihedral : 14.150 174.104 3922 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 25.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.24 % Favored : 89.59 % Rotamer: Outliers : 2.48 % Allowed : 30.76 % Favored : 66.76 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 aren not related in a simple way. whole: -2.49 (0.15), residues: 2931 helix: -0.39 (0.16), residues: 974 sheet: -1.39 (0.23), residues: 492 loop : -2.70 (0.15), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG N 101 TYR 0.068 0.002 TYR N 173 PHE 0.037 0.002 PHE C 112 TRP 0.038 0.002 TRP H 534 HIS 0.008 0.001 HIS I 85 Details of bonding type rmsd covalent geometry : bond 0.00366 (25148) covalent geometry : angle 0.73614 (34105) hydrogen bonds : bond 0.03415 ( 821) hydrogen bonds : angle 5.37691 ( 2352) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 319 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.7794 (tpp) cc_final: 0.7368 (tpp) REVERT: A 209 MET cc_start: 0.4372 (tpp) cc_final: 0.4087 (tpp) REVERT: A 221 MET cc_start: 0.6215 (mtt) cc_final: 0.4980 (mtm) REVERT: B 183 PHE cc_start: 0.6808 (m-80) cc_final: 0.6353 (m-80) REVERT: C 16 GLN cc_start: 0.7145 (OUTLIER) cc_final: 0.6499 (mp10) REVERT: C 72 ILE cc_start: 0.5508 (tp) cc_final: 0.5291 (tt) REVERT: C 141 MET cc_start: 0.5919 (mtm) cc_final: 0.5356 (mtm) REVERT: C 147 ILE cc_start: 0.7717 (pt) cc_final: 0.7481 (pt) REVERT: C 209 MET cc_start: 0.7516 (tpp) cc_final: 0.7092 (tpp) REVERT: D 116 MET cc_start: 0.6041 (pmm) cc_final: 0.5383 (pmm) REVERT: D 141 MET cc_start: 0.5089 (mmm) cc_final: 0.4505 (mpp) REVERT: D 150 MET cc_start: 0.5158 (ptp) cc_final: 0.4816 (ptp) REVERT: D 167 MET cc_start: 0.5484 (mmm) cc_final: 0.5012 (mmm) REVERT: D 220 GLN cc_start: 0.7687 (tt0) cc_final: 0.7128 (tm-30) REVERT: D 239 PRO cc_start: 0.7845 (Cg_exo) cc_final: 0.7600 (Cg_endo) REVERT: D 264 TYR cc_start: 0.2038 (OUTLIER) cc_final: 0.1582 (m-10) REVERT: E 52 ASN cc_start: 0.8921 (m-40) cc_final: 0.8451 (m110) REVERT: E 90 GLU cc_start: 0.6481 (tt0) cc_final: 0.5909 (tp30) REVERT: E 100 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8213 (mm110) REVERT: E 135 ARG cc_start: 0.8111 (mtt-85) cc_final: 0.7820 (mmt90) REVERT: E 209 MET cc_start: 0.4920 (mmm) cc_final: 0.4672 (mmm) REVERT: E 220 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.5898 (tm-30) REVERT: E 221 MET cc_start: 0.5125 (mtt) cc_final: 0.4245 (mmt) REVERT: F 7 TYR cc_start: 0.8147 (m-80) cc_final: 0.7716 (m-80) REVERT: F 41 VAL cc_start: 0.6962 (t) cc_final: 0.6645 (t) REVERT: F 93 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7613 (tm-30) REVERT: F 96 GLU cc_start: 0.8430 (tp30) cc_final: 0.8225 (tp30) REVERT: F 112 PHE cc_start: 0.8950 (m-80) cc_final: 0.8435 (m-10) REVERT: F 170 LYS cc_start: 0.5061 (mmtt) cc_final: 0.4608 (mptt) REVERT: F 227 TYR cc_start: 0.3017 (m-80) cc_final: 0.2610 (m-10) REVERT: G 1 MET cc_start: 0.6740 (OUTLIER) cc_final: 0.6459 (ptt) REVERT: G 4 HIS cc_start: 0.6072 (t70) cc_final: 0.5743 (t-170) REVERT: G 82 TRP cc_start: 0.5806 (p-90) cc_final: 0.5356 (p-90) REVERT: G 85 TYR cc_start: 0.6482 (p90) cc_final: 0.6056 (p90) REVERT: G 177 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7355 (pm20) REVERT: G 247 MET cc_start: 0.7872 (tmm) cc_final: 0.7617 (tmm) REVERT: G 307 LEU cc_start: 0.2891 (OUTLIER) cc_final: 0.2464 (tp) REVERT: H 358 TYR cc_start: 0.6203 (OUTLIER) cc_final: 0.4409 (m-80) REVERT: H 454 LYS cc_start: 0.6347 (pttm) cc_final: 0.6056 (pttt) REVERT: H 479 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7928 (tm-30) REVERT: H 497 TYR cc_start: 0.6920 (m-10) cc_final: 0.6585 (m-10) REVERT: H 513 MET cc_start: 0.5861 (mmp) cc_final: 0.5426 (mmp) REVERT: H 550 LEU cc_start: 0.8133 (tp) cc_final: 0.7496 (tt) REVERT: I 13 VAL cc_start: 0.8077 (p) cc_final: 0.7694 (m) REVERT: I 25 GLN cc_start: 0.8009 (tm-30) cc_final: 0.7352 (tp-100) REVERT: I 36 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8402 (mm) REVERT: J 18 PHE cc_start: 0.7554 (t80) cc_final: 0.7022 (t80) REVERT: J 77 TRP cc_start: 0.5550 (OUTLIER) cc_final: 0.5003 (t60) REVERT: J 123 ASN cc_start: 0.7712 (m-40) cc_final: 0.7326 (m110) REVERT: N 43 TRP cc_start: 0.4774 (t60) cc_final: 0.4080 (t60) REVERT: N 51 VAL cc_start: 0.5359 (OUTLIER) cc_final: 0.5050 (t) REVERT: N 175 MET cc_start: 0.5946 (OUTLIER) cc_final: 0.5526 (mtt) outliers start: 63 outliers final: 37 residues processed: 368 average time/residue: 0.1621 time to fit residues: 94.3426 Evaluate side-chains 348 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 300 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 112 PHE Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 16 GLN Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 264 TYR Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 220 GLN Chi-restraints excluded: chain F residue 62 HIS Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 203 TRP Chi-restraints excluded: chain F residue 231 HIS Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 307 LEU Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 358 TYR Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 460 LEU Chi-restraints excluded: chain H residue 479 GLU Chi-restraints excluded: chain H residue 493 ILE Chi-restraints excluded: chain I residue 29 ASN Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 77 TRP Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain J residue 111 PHE Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 59 ASN Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 152 VAL Chi-restraints excluded: chain M residue 249 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 144 GLU Chi-restraints excluded: chain N residue 175 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 118 optimal weight: 3.9990 chunk 286 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 230 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 ASN C 197 ASN ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 GLN ** J 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 194 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.120055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.103078 restraints weight = 99834.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.105528 restraints weight = 58446.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.107115 restraints weight = 38275.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.108246 restraints weight = 28114.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.108984 restraints weight = 22461.539| |-----------------------------------------------------------------------------| r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.9268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.134 25148 Z= 0.288 Angle : 0.856 15.033 34105 Z= 0.438 Chirality : 0.049 0.264 3701 Planarity : 0.006 0.068 4355 Dihedral : 14.229 174.966 3922 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 34.57 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.56 % Favored : 87.24 % Rotamer: Outliers : 2.88 % Allowed : 30.99 % Favored : 66.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -2.72 (0.14), residues: 2931 helix: -0.62 (0.16), residues: 958 sheet: -1.51 (0.24), residues: 452 loop : -2.77 (0.14), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 48 TYR 0.064 0.003 TYR N 173 PHE 0.056 0.003 PHE C 112 TRP 0.031 0.003 TRP J 77 HIS 0.014 0.002 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00633 (25148) covalent geometry : angle 0.85637 (34105) hydrogen bonds : bond 0.04337 ( 821) hydrogen bonds : angle 5.89029 ( 2352) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5124.83 seconds wall clock time: 89 minutes 14.05 seconds (5354.05 seconds total)