Starting phenix.real_space_refine on Fri Aug 7 23:03:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gaf_29896/08_2026/8gaf_29896.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gaf_29896/08_2026/8gaf_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_2026/8gaf_29896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gaf_29896/08_2026/8gaf_29896.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gaf_29896/08_2026/8gaf_29896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gaf_29896/08_2026/8gaf_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/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: 4.74, per 1000 atoms: 0.19 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: 1.87 Conformation dependent library (CDL) restraints added in 946.0 milliseconds 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: 2.00 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: 3.25 Time building geometry restraints manager: 2.54 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=" N9 A K 15 " pdb=" C4 A K 15 " ideal model delta sigma weight residual 1.374 1.388 -0.014 6.00e-03 2.78e+04 5.37e+00 bond pdb=" C3' G K 4 " pdb=" O3' G K 4 " ideal model delta sigma weight residual 1.427 1.446 -0.019 1.20e-02 6.94e+03 2.46e+00 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=" 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 ... (remaining 25143 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 33634 1.63 - 3.26: 421 3.26 - 4.89: 41 4.89 - 6.52: 8 6.52 - 8.15: 1 Bond angle restraints: 34105 Sorted by residual: angle pdb=" C3' G K 4 " pdb=" O3' G K 4 " pdb=" P A K 5 " ideal model delta sigma weight residual 119.70 125.64 -5.94 1.20e+00 6.94e-01 2.45e+01 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' A K 9 " pdb=" O3' A K 9 " pdb=" P G K 10 " ideal model delta sigma weight residual 119.70 124.85 -5.15 1.20e+00 6.94e-01 1.85e+01 angle pdb=" O5' U K 19 " pdb=" C5' U K 19 " pdb=" C4' U K 19 " ideal model delta sigma weight residual 109.40 112.47 -3.07 8.00e-01 1.56e+00 1.47e+01 ... (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: 2939 0.041 - 0.083: 538 0.083 - 0.124: 201 0.124 - 0.166: 22 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=" C2' G K 41 " pdb=" C3' G K 41 " pdb=" O2' G K 41 " pdb=" C1' G K 41 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 4.91e-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: 1.210 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.230 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: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5176 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= 0.103 Angle : 0.452 8.150 34105 Z= 0.305 Chirality : 0.038 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 are 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/Z covalent geometry : bond 0.00164 / 0.10 (25148) covalent geometry : angle 0.45228 / 0.31 (34105) hydrogen bonds : bond 0.14218 / 9.31 ( 821) hydrogen bonds : angle 5.06101 / 3.61 ( 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 : 0.870 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: symmetry clash REVERT: A 16 GLN cc_start: 0.6790 (mp10) cc_final: 0.6562 (mp10) REVERT: A 139 PRO cc_start: 0.6322 (Cg_exo) cc_final: 0.5965 (Cg_endo) REVERT: A 178 TYR cc_start: 0.5794 (m-80) cc_final: 0.5403 (m-80) REVERT: A 227 TYR cc_start: 0.4953 (m-80) cc_final: 0.4364 (m-80) REVERT: B 209 MET cc_start: 0.5155 (ptt) cc_final: 0.4951 (ptt) REVERT: B 228 VAL cc_start: 0.5579 (t) cc_final: 0.4855 (t) REVERT: C 108 ASP cc_start: 0.7324 (t0) cc_final: 0.6668 (m-30) REVERT: D 141 MET cc_start: 0.4158 (mmm) cc_final: 0.3825 (mpp) REVERT: D 220 GLN cc_start: 0.7342 (tt0) cc_final: 0.7038 (tt0) REVERT: E 52 ASN cc_start: 0.8214 (m-40) cc_final: 0.7767 (m-40) REVERT: E 150 MET cc_start: 0.4544 (mtm) cc_final: 0.3634 (mtm) REVERT: E 183 PHE cc_start: 0.6464 (m-80) cc_final: 0.4856 (m-80) REVERT: E 184 ILE cc_start: 0.7703 (mt) cc_final: 0.7027 (tt) REVERT: E 221 MET cc_start: 0.6261 (mtp) cc_final: 0.5267 (mtt) REVERT: E 222 ASN cc_start: 0.7024 (m-40) cc_final: 0.6627 (m110) REVERT: E 277 LYS cc_start: 0.5641 (mppt) cc_final: 0.5064 (ttmt) REVERT: F 7 TYR cc_start: 0.7983 (m-80) cc_final: 0.7624 (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: 0.4708 (mm-30) REVERT: F 129 VAL cc_start: 0.7480 (t) cc_final: 0.7174 (t) REVERT: F 135 ARG cc_start: 0.8980 (ptp-110) cc_final: 0.8277 (mtp180) REVERT: F 227 TYR cc_start: 0.2818 (m-80) cc_final: 0.2197 (m-10) REVERT: F 265 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6471 (mt) REVERT: H 515 LEU cc_start: 0.4500 (OUTLIER) cc_final: 0.4234 (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: 0.6486 (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: 0.6992 (tm-30) REVERT: I 122 PHE cc_start: 0.6787 (t80) cc_final: 0.6462 (t80) REVERT: J 123 ASN cc_start: 0.7724 (m-40) cc_final: 0.7339 (m-40) REVERT: N 43 TRP cc_start: 0.3262 (t60) cc_final: 0.2772 (t60) REVERT: N 50 LYS cc_start: 0.4242 (tptt) cc_final: 0.3747 (tptt) outliers start: 74 outliers final: 11 residues processed: 813 average time/residue: 0.1804 time to fit residues: 218.4015 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 : 0.815 ------------------------------------------------------------------------------- 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... A 21 ASN A 74 ASN A 81 HIS ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 GLN A 204 GLN A 208 ASN ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN B 62 HIS B 81 HIS B 164 ASN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 C 248 GLN D 59 ASN ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 HIS D 231 HIS ** 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 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 79 ASN G 315 GLN H 368 ASN H 465 GLN ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 538 GLN H 567 GLN I 62 HIS I 74 GLN I 76 GLN I 85 HIS ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 91 ASN J 94 ASN M 181 HIS 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 133 GLN ** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.147434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.132049 restraints weight = 102735.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.134699 restraints weight = 62939.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.136527 restraints weight = 42681.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.137630 restraints weight = 31433.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.138379 restraints weight = 25053.320| |-----------------------------------------------------------------------------| r_work (final): 0.4738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5832 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 25148 Z= 0.195 Angle : 0.741 12.369 34105 Z= 0.387 Chirality : 0.046 0.365 3701 Planarity : 0.006 0.130 4355 Dihedral : 13.652 179.956 3939 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 20.82 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.99 % Favored : 88.54 % Rotamer: Outliers : 5.05 % Allowed : 23.78 % Favored : 71.18 % 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 are not related in a simple way. whole: -3.01 (0.14), residues: 2931 helix: -0.43 (0.16), residues: 945 sheet: -1.47 (0.23), residues: 487 loop : -3.37 (0.13), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 224 TYR 0.019 0.002 TYR B 107 PHE 0.031 0.002 PHE E 261 TRP 0.026 0.003 TRP H 534 HIS 0.019 0.002 HIS B 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.20 (25148) covalent geometry : angle 0.74065 / 0.39 (34105) hydrogen bonds : bond 0.03953 / 2.59 ( 821) hydrogen bonds : angle 4.62101 / 3.28 ( 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 534 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 406 time to evaluate : 0.863 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: A 178 TYR cc_start: 0.6271 (m-80) cc_final: 0.6021 (m-80) REVERT: A 221 MET cc_start: 0.5168 (mtt) cc_final: 0.4773 (mtt) REVERT: A 227 TYR cc_start: 0.5469 (m-80) cc_final: 0.4728 (m-80) REVERT: B 33 ASP cc_start: 0.6264 (OUTLIER) cc_final: 0.5947 (t0) REVERT: C 108 ASP cc_start: 0.7669 (t0) cc_final: 0.6862 (m-30) REVERT: D 8 ASP cc_start: 0.5066 (m-30) cc_final: 0.4806 (t0) REVERT: D 141 MET cc_start: 0.4499 (mmm) cc_final: 0.4064 (mpp) REVERT: D 147 ILE cc_start: 0.7340 (pt) cc_final: 0.7130 (pt) REVERT: D 183 PHE cc_start: 0.6358 (m-80) cc_final: 0.6143 (m-80) REVERT: D 214 HIS cc_start: 0.5704 (m-70) cc_final: 0.5382 (m170) REVERT: D 220 GLN cc_start: 0.7474 (tt0) cc_final: 0.7120 (tt0) REVERT: D 264 TYR cc_start: 0.2463 (OUTLIER) cc_final: 0.1496 (m-10) REVERT: E 52 ASN cc_start: 0.8717 (m-40) cc_final: 0.8248 (m-40) REVERT: E 102 MET cc_start: 0.6791 (mpp) cc_final: 0.6201 (tpp) REVERT: E 150 MET cc_start: 0.5184 (mtm) cc_final: 0.3061 (mmp) REVERT: E 209 MET cc_start: 0.7455 (tpt) cc_final: 0.7083 (tpt) REVERT: E 221 MET cc_start: 0.5106 (mtp) cc_final: 0.4781 (mtt) REVERT: F 4 GLU cc_start: 0.7114 (mp0) cc_final: 0.6415 (tp30) REVERT: F 7 TYR cc_start: 0.8201 (m-80) cc_final: 0.7792 (m-80) REVERT: F 41 VAL cc_start: 0.6892 (t) cc_final: 0.6375 (t) REVERT: F 135 ARG cc_start: 0.9076 (ptp-110) cc_final: 0.8314 (mtp180) REVERT: F 213 ASP cc_start: 0.2556 (t70) cc_final: 0.1634 (m-30) REVERT: F 227 TYR cc_start: 0.2846 (m-80) cc_final: 0.2189 (m-10) REVERT: G 85 TYR cc_start: 0.5900 (p90) cc_final: 0.5189 (p90) REVERT: G 240 PHE cc_start: 0.6760 (OUTLIER) cc_final: 0.6290 (m-80) REVERT: G 247 MET cc_start: 0.6823 (tmm) cc_final: 0.6492 (tmm) REVERT: G 263 ARG cc_start: 0.6401 (OUTLIER) cc_final: 0.6019 (tmt-80) REVERT: H 497 TYR cc_start: 0.6471 (m-80) cc_final: 0.6200 (m-80) REVERT: H 539 ILE cc_start: 0.6771 (mt) cc_final: 0.6511 (mt) REVERT: I 23 LYS cc_start: 0.7938 (tptm) cc_final: 0.7539 (tttt) REVERT: I 25 GLN cc_start: 0.7905 (tm-30) cc_final: 0.6873 (tm-30) REVERT: I 63 LEU cc_start: 0.8893 (mt) cc_final: 0.8682 (pp) REVERT: I 122 PHE cc_start: 0.7029 (t80) cc_final: 0.6538 (t80) REVERT: J 123 ASN cc_start: 0.7921 (m-40) cc_final: 0.7207 (m110) REVERT: M 120 LYS cc_start: 0.6440 (OUTLIER) cc_final: 0.6194 (ptmt) REVERT: M 141 MET cc_start: 0.3292 (ptm) cc_final: 0.2956 (ptm) REVERT: M 167 MET cc_start: 0.3123 (mpp) cc_final: 0.2797 (mpp) REVERT: M 237 ASP cc_start: 0.5903 (p0) cc_final: 0.5510 (t70) REVERT: N 50 LYS cc_start: 0.3624 (tptt) cc_final: 0.3269 (tptt) outliers start: 128 outliers final: 52 residues processed: 507 average time/residue: 0.1837 time to fit residues: 145.6209 Evaluate side-chains 373 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 316 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 5 LYS 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 155 GLU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 227 TYR Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 150 MET 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 264 TYR Chi-restraints excluded: chain E residue 62 HIS 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 G residue 1 MET Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 263 ARG 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 435 SER Chi-restraints excluded: chain H residue 474 LEU Chi-restraints excluded: chain H residue 489 LEU Chi-restraints excluded: chain H residue 493 ILE Chi-restraints excluded: chain H residue 515 LEU Chi-restraints excluded: chain H residue 534 TRP Chi-restraints excluded: chain I residue 4 ASP Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain J residue 32 LEU 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 50 VAL Chi-restraints excluded: chain M residue 56 MET Chi-restraints excluded: chain M residue 120 LYS 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 21 VAL 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: 0.0270 chunk 140 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 249 optimal weight: 20.0000 chunk 276 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 151 optimal weight: 7.9990 chunk 268 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 overall best weight: 0.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 HIS ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 HIS ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 GLN B 81 HIS ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 HIS C 212 HIS C 220 GLN C 248 GLN ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 HIS ** E 62 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** ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 ASN F 214 HIS ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 538 GLN H 577 ASN ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN M 21 ASN ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4839 r_free = 0.4839 target = 0.146402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.131430 restraints weight = 104399.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.134341 restraints weight = 62556.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.136139 restraints weight = 41608.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.137413 restraints weight = 30301.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.138150 restraints weight = 23871.913| |-----------------------------------------------------------------------------| r_work (final): 0.4713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5834 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 25148 Z= 0.153 Angle : 0.667 10.740 34105 Z= 0.342 Chirality : 0.044 0.384 3701 Planarity : 0.005 0.119 4355 Dihedral : 13.593 177.939 3931 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.38 % Allowed : 12.21 % Favored : 87.41 % Rotamer: Outliers : 3.79 % Allowed : 24.84 % Favored : 71.37 % 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 are not related in a simple way. whole: -2.73 (0.14), residues: 2931 helix: -0.15 (0.17), residues: 944 sheet: -1.26 (0.24), residues: 480 loop : -3.25 (0.13), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 218 TYR 0.026 0.002 TYR F 101 PHE 0.027 0.002 PHE B 183 TRP 0.038 0.003 TRP G 82 HIS 0.023 0.002 HIS E 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (25148) covalent geometry : angle 0.66700 / 0.34 (34105) hydrogen bonds : bond 0.03294 / 2.19 ( 821) hydrogen bonds : angle 4.57615 / 3.25 ( 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 467 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 371 time to evaluate : 0.918 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 56 MET cc_start: 0.6632 (ptm) cc_final: 0.6213 (ptm) REVERT: A 102 MET cc_start: 0.8196 (tpp) cc_final: 0.7899 (tpp) REVERT: A 109 ILE cc_start: 0.6254 (mm) cc_final: 0.6026 (mm) REVERT: A 115 VAL cc_start: 0.6798 (p) cc_final: 0.6569 (p) REVERT: A 178 TYR cc_start: 0.6293 (m-80) cc_final: 0.6060 (m-80) REVERT: A 184 ILE cc_start: 0.6796 (mt) cc_final: 0.6562 (mt) REVERT: A 221 MET cc_start: 0.5303 (OUTLIER) cc_final: 0.4579 (mtm) REVERT: A 227 TYR cc_start: 0.5473 (m-80) cc_final: 0.4809 (m-80) REVERT: B 32 ILE cc_start: 0.8265 (tp) cc_final: 0.7639 (mt) REVERT: B 44 VAL cc_start: 0.6219 (m) cc_final: 0.5989 (p) REVERT: C 108 ASP cc_start: 0.7755 (t0) cc_final: 0.6898 (m-30) REVERT: C 203 TRP cc_start: 0.5734 (m100) cc_final: 0.4970 (m100) REVERT: D 8 ASP cc_start: 0.4928 (m-30) cc_final: 0.4593 (t0) REVERT: D 141 MET cc_start: 0.4492 (mmm) cc_final: 0.4020 (mpp) REVERT: D 147 ILE cc_start: 0.7503 (pt) cc_final: 0.7264 (pt) REVERT: D 171 PHE cc_start: 0.6973 (m-80) cc_final: 0.6746 (m-80) REVERT: D 220 GLN cc_start: 0.7291 (tt0) cc_final: 0.6889 (tt0) REVERT: D 264 TYR cc_start: 0.2764 (OUTLIER) cc_final: 0.1717 (m-10) REVERT: E 52 ASN cc_start: 0.8699 (m-40) cc_final: 0.8232 (m-40) REVERT: E 209 MET cc_start: 0.7359 (tpt) cc_final: 0.6965 (tpt) REVERT: E 221 MET cc_start: 0.5158 (mtp) cc_final: 0.4944 (mtt) REVERT: F 7 TYR cc_start: 0.8120 (m-80) cc_final: 0.7727 (m-80) REVERT: F 41 VAL cc_start: 0.6739 (t) cc_final: 0.6241 (t) REVERT: F 135 ARG cc_start: 0.9053 (ptp-110) cc_final: 0.8176 (mtp180) REVERT: F 227 TYR cc_start: 0.2953 (m-80) cc_final: 0.2289 (m-10) REVERT: G 1 MET cc_start: 0.5676 (ptt) cc_final: 0.5257 (ptt) REVERT: G 85 TYR cc_start: 0.5837 (p90) cc_final: 0.5083 (p90) REVERT: G 104 HIS cc_start: 0.6122 (t-90) cc_final: 0.5895 (t-90) REVERT: G 247 MET cc_start: 0.6860 (tmm) cc_final: 0.6422 (tmm) REVERT: G 263 ARG cc_start: 0.6479 (OUTLIER) cc_final: 0.6154 (tmt-80) REVERT: H 363 MET cc_start: 0.0910 (mmt) cc_final: -0.0210 (tpt) REVERT: I 23 LYS cc_start: 0.7956 (tptm) cc_final: 0.7546 (tttt) REVERT: I 36 ILE cc_start: 0.8648 (mm) cc_final: 0.8041 (mm) REVERT: I 63 LEU cc_start: 0.8823 (mt) cc_final: 0.8595 (pp) REVERT: I 122 PHE cc_start: 0.7000 (t80) cc_final: 0.6458 (t80) REVERT: J 123 ASN cc_start: 0.7830 (m-40) cc_final: 0.7190 (m-40) REVERT: M 12 LEU cc_start: 0.7609 (mm) cc_final: 0.7401 (tp) REVERT: M 29 LEU cc_start: 0.8007 (pt) cc_final: 0.7647 (pp) REVERT: M 244 PHE cc_start: 0.6169 (m-80) cc_final: 0.5645 (m-80) REVERT: N 50 LYS cc_start: 0.3537 (tptt) cc_final: 0.3074 (tptt) REVERT: N 159 LEU cc_start: 0.3153 (OUTLIER) cc_final: 0.2898 (pp) outliers start: 96 outliers final: 60 residues processed: 445 average time/residue: 0.1711 time to fit residues: 120.2601 Evaluate side-chains 376 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 312 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 227 TYR Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 115 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 81 HIS Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain F residue 42 THR 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 G residue 57 VAL Chi-restraints excluded: chain G residue 263 ARG 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 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 H residue 572 LYS Chi-restraints excluded: chain I residue 4 ASP Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 85 HIS 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 56 MET 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 30 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 100 TYR Chi-restraints excluded: chain N residue 145 PHE Chi-restraints excluded: chain N residue 159 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 268 optimal weight: 7.9990 chunk 241 optimal weight: 0.8980 chunk 205 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 247 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 HIS ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 ASN A 248 GLN ** B 35 GLN ** 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 100 GLN C 191 GLN ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN ** E 21 ASN ** 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 ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 85 ASN ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 486 ASN H 490 ASN H 542 HIS I 97 GLN ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.137394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.121735 restraints weight = 102832.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.124233 restraints weight = 61313.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.126007 restraints weight = 41075.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.127031 restraints weight = 30341.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.127780 restraints weight = 24355.578| |-----------------------------------------------------------------------------| r_work (final): 0.4560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6244 moved from start: 0.5060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.136 25148 Z= 0.246 Angle : 0.760 13.481 34105 Z= 0.396 Chirality : 0.046 0.390 3701 Planarity : 0.006 0.085 4355 Dihedral : 13.651 178.987 3928 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 24.74 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.19 % Favored : 88.50 % Rotamer: Outliers : 5.01 % Allowed : 25.43 % Favored : 69.56 % 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 are not related in a simple way. whole: -2.61 (0.14), residues: 2931 helix: -0.08 (0.17), residues: 955 sheet: -1.29 (0.23), residues: 494 loop : -3.15 (0.14), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 7 TYR 0.024 0.002 TYR A 264 PHE 0.031 0.003 PHE B 183 TRP 0.025 0.003 TRP G 82 HIS 0.039 0.003 HIS E 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.25 (25148) covalent geometry : angle 0.75951 / 0.40 (34105) hydrogen bonds : bond 0.03630 / 2.43 ( 821) hydrogen bonds : angle 4.87585 / 3.47 ( 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 482 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 355 time to evaluate : 0.560 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 102 MET cc_start: 0.8027 (tpp) cc_final: 0.7498 (tpp) REVERT: A 178 TYR cc_start: 0.6578 (m-80) cc_final: 0.6118 (m-80) REVERT: A 184 ILE cc_start: 0.7112 (OUTLIER) cc_final: 0.6884 (mt) REVERT: A 221 MET cc_start: 0.6022 (OUTLIER) cc_final: 0.5423 (mtm) REVERT: A 227 TYR cc_start: 0.6063 (m-80) cc_final: 0.5329 (m-80) REVERT: A 248 GLN cc_start: 0.5891 (tp-100) cc_final: 0.5612 (tp40) REVERT: B 6 ARG cc_start: 0.5155 (OUTLIER) cc_final: 0.4945 (ptt180) REVERT: B 32 ILE cc_start: 0.8591 (tp) cc_final: 0.8317 (tp) REVERT: C 56 MET cc_start: 0.4292 (ttp) cc_final: 0.3906 (tpt) REVERT: C 150 MET cc_start: 0.4924 (OUTLIER) cc_final: 0.4460 (ptm) REVERT: C 221 MET cc_start: 0.7070 (mtm) cc_final: 0.6833 (mtm) REVERT: D 8 ASP cc_start: 0.5806 (m-30) cc_final: 0.5545 (t0) REVERT: D 29 LEU cc_start: 0.8841 (mt) cc_final: 0.8638 (mt) REVERT: D 56 MET cc_start: 0.5723 (mmt) cc_final: 0.5521 (mmt) REVERT: D 141 MET cc_start: 0.4695 (mmm) cc_final: 0.4149 (mpp) REVERT: D 147 ILE cc_start: 0.7902 (pt) cc_final: 0.7580 (pt) REVERT: D 169 ARG cc_start: 0.7548 (mpp-170) cc_final: 0.7273 (ptp90) REVERT: D 171 PHE cc_start: 0.7446 (m-80) cc_final: 0.7166 (m-80) REVERT: D 214 HIS cc_start: 0.6452 (m170) cc_final: 0.6216 (m170) REVERT: D 220 GLN cc_start: 0.7820 (tt0) cc_final: 0.7293 (tt0) REVERT: D 221 MET cc_start: 0.7754 (mmm) cc_final: 0.7422 (mmm) REVERT: D 264 TYR cc_start: 0.2914 (OUTLIER) cc_final: 0.2587 (m-10) REVERT: E 52 ASN cc_start: 0.8912 (m-40) cc_final: 0.8665 (m-40) REVERT: E 209 MET cc_start: 0.7177 (tpt) cc_final: 0.6933 (tpt) REVERT: E 259 ARG cc_start: 0.7410 (tmm160) cc_final: 0.7068 (tmm160) REVERT: F 7 TYR cc_start: 0.8098 (m-80) cc_final: 0.7436 (m-80) REVERT: F 41 VAL cc_start: 0.7203 (OUTLIER) cc_final: 0.6788 (t) REVERT: F 135 ARG cc_start: 0.9084 (ptp-110) cc_final: 0.8278 (mtp180) REVERT: F 227 TYR cc_start: 0.2984 (m-80) cc_final: 0.2356 (m-10) REVERT: G 1 MET cc_start: 0.6034 (OUTLIER) cc_final: 0.5561 (ptt) REVERT: G 4 HIS cc_start: 0.5703 (t-90) cc_final: 0.5217 (t-170) REVERT: G 85 TYR cc_start: 0.6267 (p90) cc_final: 0.5594 (p90) REVERT: G 177 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7347 (pm20) REVERT: G 247 MET cc_start: 0.7064 (tmm) cc_final: 0.6598 (tmm) REVERT: H 540 LEU cc_start: 0.6252 (OUTLIER) cc_final: 0.6029 (tt) REVERT: I 23 LYS cc_start: 0.8009 (tptm) cc_final: 0.7626 (tttt) REVERT: I 122 PHE cc_start: 0.7501 (t80) cc_final: 0.6937 (t80) REVERT: J 3 LEU cc_start: 0.6900 (tp) cc_final: 0.6581 (tt) REVERT: J 123 ASN cc_start: 0.7718 (m-40) cc_final: 0.7197 (m-40) REVERT: M 29 LEU cc_start: 0.8424 (pt) cc_final: 0.8138 (pp) REVERT: M 244 PHE cc_start: 0.6882 (m-80) cc_final: 0.6323 (m-80) REVERT: N 38 LEU cc_start: 0.8069 (mp) cc_final: 0.7853 (mp) REVERT: N 44 LYS cc_start: 0.7368 (mptt) cc_final: 0.6822 (mmtm) REVERT: N 159 LEU cc_start: 0.4126 (OUTLIER) cc_final: 0.3755 (pp) outliers start: 127 outliers final: 74 residues processed: 452 average time/residue: 0.1493 time to fit residues: 105.9316 Evaluate side-chains 400 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 317 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 89 LYS 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 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 109 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 115 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 15 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 62 HIS Chi-restraints excluded: chain F residue 85 ASN 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 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 338 VAL Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 435 SER Chi-restraints excluded: chain H residue 474 LEU Chi-restraints excluded: chain H residue 515 LEU Chi-restraints excluded: chain H residue 534 TRP Chi-restraints excluded: chain H residue 540 LEU 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 13 VAL Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 89 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 215 SER 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 69 GLU Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 145 PHE Chi-restraints excluded: chain N residue 159 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: 8.9990 chunk 185 optimal weight: 20.0000 chunk 202 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 218 optimal weight: 4.9990 chunk 131 optimal weight: 0.7980 chunk 181 optimal weight: 20.0000 chunk 186 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 187 optimal weight: 2.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 HIS ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 GLN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 ASN ** E 21 ASN ** 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 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 427 GLN H 490 ASN ** H 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 GLN ** M 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** N 194 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.131897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.115948 restraints weight = 102012.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.118263 restraints weight = 59968.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.119931 restraints weight = 40429.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.121082 restraints weight = 30108.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.121815 restraints weight = 24232.293| |-----------------------------------------------------------------------------| r_work (final): 0.4464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 moved from start: 0.6077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.171 25148 Z= 0.278 Angle : 0.783 11.221 34105 Z= 0.409 Chirality : 0.047 0.402 3701 Planarity : 0.006 0.079 4355 Dihedral : 13.772 179.202 3928 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 27.74 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.59 % Favored : 87.17 % Rotamer: Outliers : 5.68 % Allowed : 26.38 % Favored : 67.94 % 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 are not related in a simple way. whole: -2.66 (0.14), residues: 2931 helix: -0.17 (0.17), residues: 959 sheet: -1.46 (0.23), residues: 494 loop : -3.09 (0.14), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 246 TYR 0.022 0.003 TYR D 178 PHE 0.034 0.003 PHE B 183 TRP 0.020 0.003 TRP J 77 HIS 0.011 0.002 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.28 (25148) covalent geometry : angle 0.78331 / 0.41 (34105) hydrogen bonds : bond 0.04056 / 2.72 ( 821) hydrogen bonds : angle 5.26296 / 3.74 ( 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 497 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 353 time to evaluate : 0.920 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: A 56 MET cc_start: 0.7729 (ptm) cc_final: 0.7391 (ptm) REVERT: A 102 MET cc_start: 0.7757 (tpp) cc_final: 0.7316 (tpp) REVERT: A 141 MET cc_start: 0.5652 (ptp) cc_final: 0.5352 (ptp) REVERT: A 178 TYR cc_start: 0.6684 (m-80) cc_final: 0.6244 (m-80) REVERT: A 229 PHE cc_start: 0.6795 (m-80) cc_final: 0.6586 (m-80) REVERT: A 251 LYS cc_start: 0.4579 (OUTLIER) cc_final: 0.4321 (mmtp) REVERT: B 32 ILE cc_start: 0.8649 (tp) cc_final: 0.8389 (tp) REVERT: B 68 ARG cc_start: 0.6835 (OUTLIER) cc_final: 0.6136 (ptp90) REVERT: B 108 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7475 (t0) REVERT: B 144 GLU cc_start: 0.6125 (mt-10) cc_final: 0.5891 (mp0) REVERT: B 183 PHE cc_start: 0.6917 (m-80) cc_final: 0.6525 (m-80) REVERT: B 218 ARG cc_start: 0.6528 (OUTLIER) cc_final: 0.5895 (mtm-85) REVERT: B 221 MET cc_start: 0.7472 (ttm) cc_final: 0.7156 (ttm) REVERT: C 150 MET cc_start: 0.4971 (OUTLIER) cc_final: 0.4573 (ptm) REVERT: C 218 ARG cc_start: 0.6666 (OUTLIER) cc_final: 0.6162 (mmt-90) REVERT: D 116 MET cc_start: 0.5710 (pmm) cc_final: 0.4778 (pmm) REVERT: D 141 MET cc_start: 0.4925 (mmm) cc_final: 0.4342 (mpp) REVERT: D 147 ILE cc_start: 0.8152 (pt) cc_final: 0.7863 (pt) REVERT: D 169 ARG cc_start: 0.7727 (mpp-170) cc_final: 0.7513 (ptp90) REVERT: D 171 PHE cc_start: 0.7549 (m-80) cc_final: 0.7145 (m-80) REVERT: D 220 GLN cc_start: 0.7938 (tt0) cc_final: 0.7019 (tt0) REVERT: D 264 TYR cc_start: 0.2521 (OUTLIER) cc_final: 0.1794 (m-10) REVERT: E 52 ASN cc_start: 0.8961 (m-40) cc_final: 0.8697 (m-40) REVERT: E 90 GLU cc_start: 0.6203 (tt0) cc_final: 0.5600 (tp30) REVERT: F 7 TYR cc_start: 0.8191 (m-80) cc_final: 0.7597 (m-80) REVERT: F 41 VAL cc_start: 0.7244 (OUTLIER) cc_final: 0.6964 (t) REVERT: F 187 HIS cc_start: 0.7299 (t-170) cc_final: 0.7037 (t-90) REVERT: G 4 HIS cc_start: 0.5919 (t-90) cc_final: 0.5541 (t-170) REVERT: G 85 TYR cc_start: 0.6384 (p90) cc_final: 0.5722 (p90) REVERT: G 177 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7416 (pm20) REVERT: G 247 MET cc_start: 0.7225 (tmm) cc_final: 0.6684 (tmm) REVERT: H 358 TYR cc_start: 0.4655 (OUTLIER) cc_final: 0.3206 (m-80) REVERT: H 496 ARG cc_start: 0.5539 (OUTLIER) cc_final: 0.4415 (ttp80) REVERT: H 497 TYR cc_start: 0.6797 (m-80) cc_final: 0.5101 (m-10) REVERT: I 23 LYS cc_start: 0.8142 (tptm) cc_final: 0.7784 (tttt) REVERT: J 3 LEU cc_start: 0.7505 (tp) cc_final: 0.7147 (tt) REVERT: J 56 MET cc_start: 0.7972 (mmm) cc_final: 0.7745 (mmm) REVERT: J 123 ASN cc_start: 0.7614 (m-40) cc_final: 0.7204 (m-40) REVERT: M 244 PHE cc_start: 0.7308 (m-80) cc_final: 0.6635 (m-80) REVERT: N 44 LYS cc_start: 0.7214 (mptt) cc_final: 0.6658 (mmtm) REVERT: N 159 LEU cc_start: 0.4524 (OUTLIER) cc_final: 0.4125 (pp) REVERT: N 171 MET cc_start: 0.5003 (ttm) cc_final: 0.4496 (mtt) REVERT: N 192 PHE cc_start: 0.4698 (p90) cc_final: 0.2462 (m-80) outliers start: 144 outliers final: 85 residues processed: 464 average time/residue: 0.1550 time to fit residues: 114.0703 Evaluate side-chains 415 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 319 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 153 THR 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 A residue 251 LYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 112 PHE Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 203 TRP Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 218 ARG 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 109 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 203 TRP Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 95 THR 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 95 THR Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 62 HIS Chi-restraints excluded: chain F residue 85 ASN 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 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 62 LEU Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 273 CYS Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 354 ILE 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 457 THR Chi-restraints excluded: chain H residue 460 LEU Chi-restraints excluded: chain H residue 474 LEU Chi-restraints excluded: chain H residue 496 ARG 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 21 LEU Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 32 LEU 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 30 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 145 PHE Chi-restraints excluded: chain N residue 159 LEU Chi-restraints excluded: chain N residue 193 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 212 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 110 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 224 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 203 optimal weight: 6.9990 chunk 201 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 HIS ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 GLN ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 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 74 ASN E 63 HIS ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 GLN ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 HIS ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 ASN G 262 ASN ** H 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 222 ASN ** N 64 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.131141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.114963 restraints weight = 101262.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.117340 restraints weight = 59595.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.119031 restraints weight = 40000.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.120197 restraints weight = 29651.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.120809 restraints weight = 23753.447| |-----------------------------------------------------------------------------| r_work (final): 0.4451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.6497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 25148 Z= 0.215 Angle : 0.734 9.788 34105 Z= 0.378 Chirality : 0.047 0.397 3701 Planarity : 0.005 0.067 4355 Dihedral : 13.793 179.492 3927 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 26.85 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.57 % Favored : 88.16 % Rotamer: Outliers : 4.73 % Allowed : 27.52 % Favored : 67.74 % 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 are not related in a simple way. whole: -2.62 (0.14), residues: 2931 helix: -0.20 (0.17), residues: 958 sheet: -1.32 (0.23), residues: 484 loop : -3.05 (0.14), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 224 TYR 0.020 0.002 TYR H 440 PHE 0.028 0.003 PHE B 66 TRP 0.015 0.002 TRP J 77 HIS 0.009 0.002 HIS I 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.22 (25148) covalent geometry : angle 0.73397 / 0.38 (34105) hydrogen bonds : bond 0.03642 / 2.43 ( 821) hydrogen bonds : angle 5.25287 / 3.73 ( 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 473 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 353 time to evaluate : 0.928 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 56 MET cc_start: 0.7729 (ptm) cc_final: 0.7177 (ptm) REVERT: A 102 MET cc_start: 0.7891 (tpp) cc_final: 0.7447 (tpp) REVERT: A 141 MET cc_start: 0.5830 (ptp) cc_final: 0.5542 (ptp) REVERT: A 178 TYR cc_start: 0.6652 (m-80) cc_final: 0.6287 (m-80) REVERT: A 229 PHE cc_start: 0.6894 (m-80) cc_final: 0.6634 (m-80) REVERT: A 251 LYS cc_start: 0.4285 (OUTLIER) cc_final: 0.3558 (mmtm) REVERT: B 32 ILE cc_start: 0.8674 (tp) cc_final: 0.8410 (tp) REVERT: B 68 ARG cc_start: 0.6535 (OUTLIER) cc_final: 0.5914 (ptp90) REVERT: B 144 GLU cc_start: 0.6117 (mt-10) cc_final: 0.5908 (mp0) REVERT: B 183 PHE cc_start: 0.6886 (m-80) cc_final: 0.6441 (m-80) REVERT: B 218 ARG cc_start: 0.6652 (OUTLIER) cc_final: 0.5648 (mtm-85) REVERT: C 141 MET cc_start: 0.5389 (mtm) cc_final: 0.5019 (mtm) REVERT: C 203 TRP cc_start: 0.6600 (OUTLIER) cc_final: 0.5887 (m100) REVERT: D 8 ASP cc_start: 0.5762 (m-30) cc_final: 0.5430 (t0) REVERT: D 141 MET cc_start: 0.5182 (mmm) cc_final: 0.4556 (mpp) REVERT: D 167 MET cc_start: 0.5261 (mmm) cc_final: 0.4826 (mmm) REVERT: D 169 ARG cc_start: 0.7694 (mpp-170) cc_final: 0.7485 (ptp90) REVERT: D 220 GLN cc_start: 0.7890 (tt0) cc_final: 0.7127 (tt0) REVERT: D 264 TYR cc_start: 0.2534 (OUTLIER) cc_final: 0.1887 (m-10) REVERT: E 52 ASN cc_start: 0.8906 (m-40) cc_final: 0.8621 (m-40) REVERT: E 90 GLU cc_start: 0.6208 (tt0) cc_final: 0.5601 (tp30) REVERT: E 116 MET cc_start: 0.6087 (pmm) cc_final: 0.5660 (pmm) REVERT: E 134 SER cc_start: 0.8019 (OUTLIER) cc_final: 0.7219 (t) REVERT: F 7 TYR cc_start: 0.8035 (m-80) cc_final: 0.7397 (m-80) REVERT: F 187 HIS cc_start: 0.7540 (t-170) cc_final: 0.7146 (t-90) REVERT: G 1 MET cc_start: 0.6200 (OUTLIER) cc_final: 0.5562 (ptt) REVERT: G 4 HIS cc_start: 0.5907 (t-90) cc_final: 0.5455 (t-170) REVERT: G 85 TYR cc_start: 0.6555 (p90) cc_final: 0.5975 (p90) REVERT: G 177 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7304 (pm20) REVERT: G 247 MET cc_start: 0.7435 (tmm) cc_final: 0.6940 (tmm) REVERT: H 358 TYR cc_start: 0.4911 (OUTLIER) cc_final: 0.3207 (m-80) REVERT: H 497 TYR cc_start: 0.6685 (m-80) cc_final: 0.6294 (m-10) REVERT: H 540 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6544 (tt) REVERT: I 23 LYS cc_start: 0.8118 (tptm) cc_final: 0.7765 (tttt) REVERT: I 39 ARG cc_start: 0.7771 (mtm180) cc_final: 0.7173 (mtm180) REVERT: J 3 LEU cc_start: 0.7457 (tp) cc_final: 0.7159 (tt) REVERT: J 56 MET cc_start: 0.7870 (mmm) cc_final: 0.7598 (mmm) REVERT: J 123 ASN cc_start: 0.7778 (m-40) cc_final: 0.7280 (m-40) REVERT: M 21 ASN cc_start: 0.6364 (t0) cc_final: 0.6145 (t0) REVERT: M 56 MET cc_start: 0.2466 (mmm) cc_final: 0.2212 (mmm) REVERT: N 44 LYS cc_start: 0.7309 (mptt) cc_final: 0.6739 (mmtm) REVERT: N 74 MET cc_start: 0.4772 (OUTLIER) cc_final: 0.4038 (mmm) REVERT: N 159 LEU cc_start: 0.4273 (OUTLIER) cc_final: 0.3895 (pp) REVERT: N 171 MET cc_start: 0.5152 (ttm) cc_final: 0.4781 (mtt) REVERT: N 175 MET cc_start: 0.6062 (OUTLIER) cc_final: 0.5641 (mmt) REVERT: N 192 PHE cc_start: 0.4857 (p90) cc_final: 0.2212 (m-80) outliers start: 120 outliers final: 82 residues processed: 439 average time/residue: 0.1556 time to fit residues: 109.4488 Evaluate side-chains 412 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 318 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 153 THR 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 251 LYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 112 PHE Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 203 TRP Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 218 ARG 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 25 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 203 TRP Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 229 PHE 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 95 THR Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 180 CYS 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 231 HIS Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 250 TYR Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 354 ILE Chi-restraints excluded: chain H residue 358 TYR Chi-restraints excluded: chain H residue 406 LEU 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 474 LEU Chi-restraints excluded: chain H residue 493 ILE Chi-restraints excluded: chain H residue 511 THR Chi-restraints excluded: chain H residue 514 ARG Chi-restraints excluded: chain H residue 515 LEU Chi-restraints excluded: chain H residue 534 TRP 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 572 LYS Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 58 LEU 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 64 ASP Chi-restraints excluded: chain M residue 144 GLU 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 30 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 145 PHE Chi-restraints excluded: chain N residue 159 LEU Chi-restraints excluded: chain N residue 175 MET Chi-restraints excluded: chain N residue 193 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 30 optimal weight: 0.7980 chunk 69 optimal weight: 0.0980 chunk 223 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 101 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 185 optimal weight: 9.9990 chunk 249 optimal weight: 20.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 HIS ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 ASN C 74 ASN ** C 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** 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 ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 GLN ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 64 ASN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 137 GLN ** 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 = 0.4650 r_free = 0.4650 target = 0.133456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.117569 restraints weight = 100309.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.120087 restraints weight = 59125.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.121861 restraints weight = 39253.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.122975 restraints weight = 28791.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.123649 restraints weight = 23061.986| |-----------------------------------------------------------------------------| r_work (final): 0.4498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6427 moved from start: 0.6547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 25148 Z= 0.154 Angle : 0.687 10.355 34105 Z= 0.353 Chirality : 0.045 0.421 3701 Planarity : 0.005 0.060 4355 Dihedral : 13.789 179.944 3927 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 22.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.75 % Favored : 89.05 % Rotamer: Outliers : 3.47 % Allowed : 29.57 % Favored : 66.96 % 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 are not related in a simple way. whole: -2.61 (0.15), residues: 2931 helix: -0.19 (0.17), residues: 953 sheet: -1.28 (0.23), residues: 499 loop : -3.06 (0.14), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 246 TYR 0.035 0.002 TYR I 40 PHE 0.035 0.002 PHE B 66 TRP 0.017 0.002 TRP H 534 HIS 0.010 0.002 HIS I 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (25148) covalent geometry : angle 0.68656 / 0.35 (34105) hydrogen bonds : bond 0.03216 / 2.15 ( 821) hydrogen bonds : angle 5.18429 / 3.69 ( 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 438 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 350 time to evaluate : 0.784 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: A 29 LEU cc_start: 0.8961 (tp) cc_final: 0.8673 (tp) REVERT: A 56 MET cc_start: 0.7590 (ptm) cc_final: 0.7101 (ptm) REVERT: A 102 MET cc_start: 0.7842 (tpp) cc_final: 0.7330 (tpp) REVERT: A 141 MET cc_start: 0.5744 (ptp) cc_final: 0.5433 (ptp) REVERT: A 150 MET cc_start: 0.3221 (ptp) cc_final: 0.2892 (mtt) REVERT: A 178 TYR cc_start: 0.6558 (m-80) cc_final: 0.6223 (m-80) REVERT: A 229 PHE cc_start: 0.6817 (m-80) cc_final: 0.6539 (m-80) REVERT: B 32 ILE cc_start: 0.8734 (tp) cc_final: 0.8498 (tp) REVERT: B 68 ARG cc_start: 0.6025 (OUTLIER) cc_final: 0.5273 (ptp90) REVERT: B 183 PHE cc_start: 0.6726 (m-80) cc_final: 0.6258 (m-80) REVERT: C 108 ASP cc_start: 0.7793 (t0) cc_final: 0.6872 (m-30) REVERT: C 218 ARG cc_start: 0.6030 (OUTLIER) cc_final: 0.4935 (mpp-170) REVERT: D 8 ASP cc_start: 0.5957 (m-30) cc_final: 0.5575 (t0) REVERT: D 116 MET cc_start: 0.5387 (pmm) cc_final: 0.4307 (pmm) REVERT: D 141 MET cc_start: 0.5102 (mmm) cc_final: 0.4499 (mpp) REVERT: D 171 PHE cc_start: 0.7635 (m-80) cc_final: 0.7428 (m-80) REVERT: D 220 GLN cc_start: 0.7579 (tt0) cc_final: 0.6843 (tt0) REVERT: D 239 PRO cc_start: 0.7463 (Cg_exo) cc_final: 0.7248 (Cg_endo) REVERT: D 264 TYR cc_start: 0.2304 (OUTLIER) cc_final: 0.1980 (m-10) REVERT: E 52 ASN cc_start: 0.8966 (m-40) cc_final: 0.8660 (m-40) REVERT: E 90 GLU cc_start: 0.6045 (tt0) cc_final: 0.5426 (tp30) REVERT: E 116 MET cc_start: 0.5885 (pmm) cc_final: 0.5258 (pmm) REVERT: E 132 THR cc_start: 0.6526 (m) cc_final: 0.6244 (m) REVERT: F 4 GLU cc_start: 0.7637 (mp0) cc_final: 0.6834 (tp30) REVERT: F 7 TYR cc_start: 0.8154 (m-80) cc_final: 0.7620 (m-80) REVERT: F 41 VAL cc_start: 0.7257 (t) cc_final: 0.6944 (t) REVERT: F 187 HIS cc_start: 0.7484 (t-170) cc_final: 0.7176 (t-90) REVERT: F 196 GLU cc_start: 0.7631 (mp0) cc_final: 0.7398 (mp0) REVERT: F 221 MET cc_start: 0.4388 (mmm) cc_final: 0.4177 (mmm) REVERT: G 1 MET cc_start: 0.6447 (OUTLIER) cc_final: 0.5824 (ptt) REVERT: G 4 HIS cc_start: 0.5730 (t-90) cc_final: 0.5259 (t-170) REVERT: G 85 TYR cc_start: 0.6554 (p90) cc_final: 0.5966 (p90) REVERT: G 177 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7303 (pm20) REVERT: G 247 MET cc_start: 0.7429 (tmm) cc_final: 0.6977 (tmm) REVERT: H 479 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7889 (tm-30) REVERT: H 497 TYR cc_start: 0.6763 (m-80) cc_final: 0.6422 (m-10) REVERT: H 540 LEU cc_start: 0.6566 (OUTLIER) cc_final: 0.6363 (tt) REVERT: I 21 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8323 (mt) REVERT: I 39 ARG cc_start: 0.7537 (mtm180) cc_final: 0.7135 (mtm180) REVERT: J 3 LEU cc_start: 0.7328 (tp) cc_final: 0.6993 (tt) REVERT: J 77 TRP cc_start: 0.5772 (OUTLIER) cc_final: 0.5131 (t60) REVERT: J 88 ARG cc_start: 0.7391 (tmt170) cc_final: 0.7184 (tpt-90) REVERT: J 123 ASN cc_start: 0.7586 (m-40) cc_final: 0.7109 (m110) REVERT: M 21 ASN cc_start: 0.6541 (t0) cc_final: 0.6269 (t0) REVERT: M 265 LEU cc_start: 0.7235 (mt) cc_final: 0.6903 (mt) REVERT: N 44 LYS cc_start: 0.7152 (mptt) cc_final: 0.6589 (mmtm) REVERT: N 159 LEU cc_start: 0.4506 (OUTLIER) cc_final: 0.4126 (pp) REVERT: N 175 MET cc_start: 0.5911 (OUTLIER) cc_final: 0.5588 (mmt) outliers start: 88 outliers final: 53 residues processed: 408 average time/residue: 0.1701 time to fit residues: 111.5967 Evaluate side-chains 379 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 316 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 A residue 255 VAL Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 203 TRP Chi-restraints excluded: chain B residue 213 ASP 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 25 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 258 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 188 PHE 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 242 SER 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 406 LEU Chi-restraints excluded: chain H residue 411 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 514 ARG Chi-restraints excluded: chain H residue 515 LEU 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 572 LYS Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 77 TRP 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 59 ASN Chi-restraints excluded: chain M residue 64 ASP 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 159 LEU Chi-restraints excluded: chain N residue 175 MET Chi-restraints excluded: chain N residue 193 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 46 optimal weight: 7.9990 chunk 219 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 226 optimal weight: 8.9990 chunk 44 optimal weight: 0.0270 chunk 198 optimal weight: 0.2980 chunk 13 optimal weight: 0.8980 chunk 266 optimal weight: 1.9990 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 HIS A 121 ASN ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 GLN ** 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 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 GLN ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.133669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.117575 restraints weight = 100936.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.120192 restraints weight = 58986.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.121834 restraints weight = 38940.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.123007 restraints weight = 29033.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.123673 restraints weight = 23433.163| |-----------------------------------------------------------------------------| r_work (final): 0.4496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 moved from start: 0.6651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 25148 Z= 0.150 Angle : 0.686 10.227 34105 Z= 0.353 Chirality : 0.044 0.417 3701 Planarity : 0.004 0.058 4355 Dihedral : 13.798 179.760 3926 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 22.33 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.75 % Favored : 89.01 % Rotamer: Outliers : 3.43 % Allowed : 29.77 % Favored : 66.80 % 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 are not related in a simple way. whole: -2.53 (0.15), residues: 2931 helix: -0.11 (0.17), residues: 942 sheet: -1.26 (0.23), residues: 499 loop : -3.00 (0.14), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 57 TYR 0.024 0.002 TYR N 173 PHE 0.031 0.002 PHE N 192 TRP 0.045 0.002 TRP H 534 HIS 0.010 0.002 HIS I 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (25148) covalent geometry : angle 0.68637 / 0.35 (34105) hydrogen bonds : bond 0.03204 / 2.13 ( 821) hydrogen bonds : angle 5.14310 / 3.67 ( 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 418 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 331 time to evaluate : 0.891 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: A 29 LEU cc_start: 0.8848 (tp) cc_final: 0.8613 (tp) REVERT: A 56 MET cc_start: 0.7715 (ptm) cc_final: 0.7167 (ptm) REVERT: A 102 MET cc_start: 0.7866 (tpp) cc_final: 0.7416 (tpp) REVERT: A 141 MET cc_start: 0.5717 (ptp) cc_final: 0.5469 (ptp) REVERT: A 150 MET cc_start: 0.3248 (ptp) cc_final: 0.2923 (mtt) REVERT: A 178 TYR cc_start: 0.6467 (m-80) cc_final: 0.6214 (m-80) REVERT: A 229 PHE cc_start: 0.6739 (m-80) cc_final: 0.6475 (m-80) REVERT: B 32 ILE cc_start: 0.8663 (tp) cc_final: 0.8460 (tp) REVERT: B 68 ARG cc_start: 0.6173 (OUTLIER) cc_final: 0.5470 (ptp90) REVERT: B 183 PHE cc_start: 0.6711 (m-80) cc_final: 0.6293 (m-80) REVERT: C 108 ASP cc_start: 0.7616 (t0) cc_final: 0.6598 (m-30) REVERT: C 218 ARG cc_start: 0.5975 (OUTLIER) cc_final: 0.4800 (mpp-170) REVERT: D 8 ASP cc_start: 0.5814 (m-30) cc_final: 0.5369 (t0) REVERT: D 141 MET cc_start: 0.5197 (mmm) cc_final: 0.4535 (mpp) REVERT: D 171 PHE cc_start: 0.7585 (m-80) cc_final: 0.7330 (m-80) REVERT: D 220 GLN cc_start: 0.7528 (tt0) cc_final: 0.6812 (tt0) REVERT: D 264 TYR cc_start: 0.2258 (OUTLIER) cc_final: 0.1420 (m-10) REVERT: E 52 ASN cc_start: 0.8972 (m-40) cc_final: 0.8467 (m-40) REVERT: E 90 GLU cc_start: 0.6007 (tt0) cc_final: 0.5417 (tp30) REVERT: E 116 MET cc_start: 0.6069 (pmm) cc_final: 0.5430 (pmm) REVERT: F 4 GLU cc_start: 0.7648 (mp0) cc_final: 0.6854 (tp30) REVERT: F 7 TYR cc_start: 0.8204 (m-80) cc_final: 0.7672 (m-80) REVERT: F 41 VAL cc_start: 0.7077 (t) cc_final: 0.6850 (t) REVERT: F 94 LYS cc_start: 0.7250 (OUTLIER) cc_final: 0.6881 (ttmt) REVERT: F 137 ILE cc_start: 0.3785 (OUTLIER) cc_final: 0.3488 (pt) REVERT: F 187 HIS cc_start: 0.7467 (t-170) cc_final: 0.7187 (t-90) REVERT: F 196 GLU cc_start: 0.7612 (mp0) cc_final: 0.7339 (mp0) REVERT: G 1 MET cc_start: 0.6316 (OUTLIER) cc_final: 0.5662 (ptt) REVERT: G 4 HIS cc_start: 0.5747 (t-90) cc_final: 0.5179 (t-170) REVERT: G 85 TYR cc_start: 0.6582 (p90) cc_final: 0.6008 (p90) REVERT: G 177 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7282 (pm20) REVERT: G 247 MET cc_start: 0.7428 (tmm) cc_final: 0.6980 (tmm) REVERT: H 479 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7871 (tm-30) REVERT: I 3 LEU cc_start: 0.7852 (tp) cc_final: 0.7640 (tt) REVERT: I 21 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8375 (mt) REVERT: I 98 GLN cc_start: 0.8293 (tm-30) cc_final: 0.7981 (pp30) REVERT: J 3 LEU cc_start: 0.7252 (tp) cc_final: 0.6867 (tt) REVERT: J 77 TRP cc_start: 0.5807 (OUTLIER) cc_final: 0.5162 (t60) REVERT: J 116 ASP cc_start: 0.6519 (OUTLIER) cc_final: 0.5932 (t0) REVERT: J 123 ASN cc_start: 0.7687 (m-40) cc_final: 0.7126 (m110) REVERT: M 21 ASN cc_start: 0.6447 (t0) cc_final: 0.6194 (t0) REVERT: M 150 MET cc_start: 0.3654 (ptp) cc_final: 0.3404 (ptp) REVERT: M 265 LEU cc_start: 0.7455 (mt) cc_final: 0.7105 (mt) REVERT: N 22 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7341 (mm-30) REVERT: N 44 LYS cc_start: 0.7212 (mptt) cc_final: 0.6662 (mmtm) REVERT: N 74 MET cc_start: 0.4768 (OUTLIER) cc_final: 0.4173 (mmm) REVERT: N 108 MET cc_start: 0.1703 (mmt) cc_final: 0.1437 (mmt) REVERT: N 159 LEU cc_start: 0.4467 (OUTLIER) cc_final: 0.4085 (pp) REVERT: N 175 MET cc_start: 0.6028 (OUTLIER) cc_final: 0.5695 (mmt) outliers start: 87 outliers final: 61 residues processed: 393 average time/residue: 0.1683 time to fit residues: 106.9930 Evaluate side-chains 378 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 304 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 A residue 255 VAL Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 112 PHE Chi-restraints excluded: chain B residue 203 TRP 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 25 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 229 PHE 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 86 VAL Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain F residue 62 HIS Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 94 LYS Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 231 HIS Chi-restraints excluded: chain F residue 242 SER 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 406 LEU 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 474 LEU Chi-restraints excluded: chain H residue 479 GLU Chi-restraints excluded: chain H residue 493 ILE Chi-restraints excluded: chain H residue 514 ARG Chi-restraints excluded: chain H residue 515 LEU Chi-restraints excluded: chain H residue 549 HIS Chi-restraints excluded: chain H residue 550 LEU Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 56 MET Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 77 TRP 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 59 ASN Chi-restraints excluded: chain M residue 64 ASP Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain M residue 211 ASP Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 159 LEU Chi-restraints excluded: chain N residue 175 MET Chi-restraints excluded: chain N residue 193 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 239 optimal weight: 0.8980 chunk 66 optimal weight: 0.4980 chunk 141 optimal weight: 2.9990 chunk 280 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 188 optimal weight: 0.9990 chunk 112 optimal weight: 8.9990 chunk 69 optimal weight: 20.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 HIS ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 HIS ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.133056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.116960 restraints weight = 101452.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.119506 restraints weight = 59180.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.121253 restraints weight = 39434.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.122444 restraints weight = 28962.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.123252 restraints weight = 23094.523| |-----------------------------------------------------------------------------| r_work (final): 0.4486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6452 moved from start: 0.6821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.127 25148 Z= 0.161 Angle : 0.709 12.566 34105 Z= 0.363 Chirality : 0.044 0.413 3701 Planarity : 0.004 0.060 4355 Dihedral : 13.791 178.069 3924 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 22.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.92 % Favored : 88.91 % Rotamer: Outliers : 3.04 % Allowed : 30.60 % Favored : 66.36 % 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 are not related in a simple way. whole: -2.49 (0.15), residues: 2931 helix: -0.12 (0.17), residues: 936 sheet: -1.19 (0.23), residues: 497 loop : -2.94 (0.14), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 57 TYR 0.042 0.002 TYR H 497 PHE 0.035 0.002 PHE B 210 TRP 0.038 0.002 TRP H 534 HIS 0.017 0.002 HIS J 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (25148) covalent geometry : angle 0.70854 / 0.36 (34105) hydrogen bonds : bond 0.03331 / 2.21 ( 821) hydrogen bonds : angle 5.16758 / 3.69 ( 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 399 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 322 time to evaluate : 0.591 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 29 LEU cc_start: 0.8869 (tp) cc_final: 0.8642 (tp) REVERT: A 56 MET cc_start: 0.7675 (ptm) cc_final: 0.7223 (ptm) REVERT: A 102 MET cc_start: 0.7862 (tpp) cc_final: 0.7397 (tpp) REVERT: A 150 MET cc_start: 0.2883 (ptp) cc_final: 0.2557 (mtt) REVERT: A 178 TYR cc_start: 0.6487 (m-80) cc_final: 0.6246 (m-80) REVERT: A 229 PHE cc_start: 0.6914 (m-80) cc_final: 0.6682 (m-80) REVERT: B 4 GLU cc_start: 0.7146 (tm-30) cc_final: 0.6919 (tm-30) REVERT: B 32 ILE cc_start: 0.8689 (tp) cc_final: 0.8475 (tp) REVERT: B 68 ARG cc_start: 0.6226 (OUTLIER) cc_final: 0.5558 (ptp90) REVERT: B 144 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.6145 (mp0) REVERT: B 183 PHE cc_start: 0.6773 (m-80) cc_final: 0.6312 (m-80) REVERT: C 16 GLN cc_start: 0.6979 (OUTLIER) cc_final: 0.6629 (mt0) REVERT: C 141 MET cc_start: 0.5659 (mtm) cc_final: 0.5289 (mtm) REVERT: D 141 MET cc_start: 0.5142 (mmm) cc_final: 0.4416 (mpp) REVERT: D 171 PHE cc_start: 0.7604 (m-80) cc_final: 0.7343 (m-80) REVERT: D 220 GLN cc_start: 0.7650 (tt0) cc_final: 0.6813 (tt0) REVERT: D 264 TYR cc_start: 0.2064 (OUTLIER) cc_final: 0.1522 (m-10) REVERT: E 52 ASN cc_start: 0.9045 (m-40) cc_final: 0.8606 (m-40) REVERT: E 90 GLU cc_start: 0.6058 (tt0) cc_final: 0.5492 (tp30) REVERT: E 116 MET cc_start: 0.6431 (pmm) cc_final: 0.5852 (pmm) REVERT: F 4 GLU cc_start: 0.7601 (mp0) cc_final: 0.6990 (tp30) REVERT: F 7 TYR cc_start: 0.8172 (m-80) cc_final: 0.7640 (m-80) REVERT: F 94 LYS cc_start: 0.7209 (OUTLIER) cc_final: 0.6812 (ttmt) REVERT: F 137 ILE cc_start: 0.3674 (OUTLIER) cc_final: 0.3411 (pt) REVERT: F 196 GLU cc_start: 0.7558 (mp0) cc_final: 0.7355 (mp0) REVERT: G 1 MET cc_start: 0.6348 (OUTLIER) cc_final: 0.5725 (ptt) REVERT: G 4 HIS cc_start: 0.5763 (t-90) cc_final: 0.5156 (t-170) REVERT: G 85 TYR cc_start: 0.6458 (p90) cc_final: 0.5827 (p90) REVERT: G 177 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7294 (pm20) REVERT: G 302 ASP cc_start: 0.5147 (m-30) cc_final: 0.4510 (t70) REVERT: H 358 TYR cc_start: 0.4849 (OUTLIER) cc_final: 0.3008 (m-80) REVERT: H 479 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7868 (tm-30) REVERT: I 21 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8387 (mt) REVERT: J 3 LEU cc_start: 0.7282 (tp) cc_final: 0.6866 (tt) REVERT: J 77 TRP cc_start: 0.5717 (OUTLIER) cc_final: 0.5015 (t60) REVERT: J 116 ASP cc_start: 0.6658 (OUTLIER) cc_final: 0.6379 (t0) REVERT: J 123 ASN cc_start: 0.7668 (m-40) cc_final: 0.7151 (m-40) REVERT: M 21 ASN cc_start: 0.6463 (t0) cc_final: 0.6187 (t0) REVERT: M 150 MET cc_start: 0.3403 (ptp) cc_final: 0.3084 (ptp) REVERT: M 265 LEU cc_start: 0.7537 (mt) cc_final: 0.7021 (mt) REVERT: N 22 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7496 (mm-30) REVERT: N 44 LYS cc_start: 0.7186 (mptt) cc_final: 0.6666 (mmtm) REVERT: N 74 MET cc_start: 0.5290 (mmm) cc_final: 0.4739 (mmm) REVERT: N 108 MET cc_start: 0.1669 (mmt) cc_final: 0.1459 (mmt) REVERT: N 159 LEU cc_start: 0.4237 (OUTLIER) cc_final: 0.3854 (pp) outliers start: 77 outliers final: 53 residues processed: 376 average time/residue: 0.1570 time to fit residues: 94.2773 Evaluate side-chains 373 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 307 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 3 ILE Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 144 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 25 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 258 VAL 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 95 THR Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain F residue 62 HIS Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 94 LYS Chi-restraints excluded: chain F residue 137 ILE 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 338 VAL Chi-restraints excluded: chain H residue 354 ILE Chi-restraints excluded: chain H residue 358 TYR Chi-restraints excluded: chain H residue 406 LEU 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 514 ARG Chi-restraints excluded: chain H residue 515 LEU Chi-restraints excluded: chain H residue 549 HIS Chi-restraints excluded: chain H residue 550 LEU Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain J residue 77 TRP 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 64 ASP Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain M residue 211 ASP 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 159 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 169 optimal weight: 10.0000 chunk 267 optimal weight: 7.9990 chunk 278 optimal weight: 4.9990 chunk 219 optimal weight: 0.8980 chunk 36 optimal weight: 8.9990 chunk 91 optimal weight: 0.5980 chunk 239 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 47 optimal weight: 0.3980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 HIS ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 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** H 538 GLN H 542 HIS ** H 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.133675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.117687 restraints weight = 100674.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.120363 restraints weight = 58378.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.121821 restraints weight = 38305.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.123151 restraints weight = 28872.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.123978 restraints weight = 22898.500| |-----------------------------------------------------------------------------| r_work (final): 0.4497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6427 moved from start: 0.6876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.142 25148 Z= 0.151 Angle : 0.712 15.671 34105 Z= 0.363 Chirality : 0.044 0.418 3701 Planarity : 0.004 0.060 4355 Dihedral : 13.808 178.386 3924 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 22.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.58 % Favored : 89.25 % Rotamer: Outliers : 2.96 % Allowed : 30.68 % Favored : 66.36 % 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 are not related in a simple way. whole: -2.45 (0.15), residues: 2931 helix: -0.14 (0.17), residues: 953 sheet: -1.12 (0.23), residues: 492 loop : -2.93 (0.14), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 57 TYR 0.019 0.002 TYR N 173 PHE 0.064 0.002 PHE N 192 TRP 0.037 0.002 TRP H 534 HIS 0.015 0.002 HIS G 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (25148) covalent geometry : angle 0.71225 / 0.36 (34105) hydrogen bonds : bond 0.03333 / 2.18 ( 821) hydrogen bonds : angle 5.12833 / 3.65 ( 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 395 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 320 time to evaluate : 0.705 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 29 LEU cc_start: 0.8988 (tp) cc_final: 0.8735 (tp) REVERT: A 56 MET cc_start: 0.7642 (ptm) cc_final: 0.7210 (ptm) REVERT: A 102 MET cc_start: 0.7704 (tpp) cc_final: 0.7120 (tpp) REVERT: A 141 MET cc_start: 0.5606 (ptp) cc_final: 0.5316 (pmm) REVERT: A 150 MET cc_start: 0.3095 (ptp) cc_final: 0.2762 (mtt) REVERT: A 178 TYR cc_start: 0.6421 (m-80) cc_final: 0.6198 (m-80) REVERT: A 229 PHE cc_start: 0.6836 (m-80) cc_final: 0.6617 (m-80) REVERT: B 32 ILE cc_start: 0.8634 (tp) cc_final: 0.8394 (tp) REVERT: B 68 ARG cc_start: 0.6067 (OUTLIER) cc_final: 0.5364 (ptp90) REVERT: B 141 MET cc_start: 0.4659 (pmm) cc_final: 0.4321 (mmt) REVERT: B 183 PHE cc_start: 0.6694 (m-80) cc_final: 0.6219 (m-80) REVERT: B 221 MET cc_start: 0.6967 (ttt) cc_final: 0.6486 (ttt) REVERT: D 141 MET cc_start: 0.5096 (mmm) cc_final: 0.4361 (mpp) REVERT: D 171 PHE cc_start: 0.7588 (m-80) cc_final: 0.7336 (m-80) REVERT: D 220 GLN cc_start: 0.7552 (tt0) cc_final: 0.6750 (tt0) REVERT: D 264 TYR cc_start: 0.2074 (OUTLIER) cc_final: 0.1497 (m-10) REVERT: E 52 ASN cc_start: 0.9066 (m-40) cc_final: 0.8660 (m-40) REVERT: E 90 GLU cc_start: 0.6089 (tt0) cc_final: 0.5475 (tp30) REVERT: E 116 MET cc_start: 0.6336 (pmm) cc_final: 0.5809 (pmm) REVERT: E 134 SER cc_start: 0.7369 (OUTLIER) cc_final: 0.6438 (t) REVERT: F 4 GLU cc_start: 0.7612 (mp0) cc_final: 0.6998 (tp30) REVERT: F 7 TYR cc_start: 0.8166 (m-80) cc_final: 0.7650 (m-80) REVERT: F 94 LYS cc_start: 0.7199 (OUTLIER) cc_final: 0.6797 (ttmt) REVERT: F 137 ILE cc_start: 0.3788 (OUTLIER) cc_final: 0.3513 (pt) REVERT: G 4 HIS cc_start: 0.5666 (t-90) cc_final: 0.5115 (t-170) REVERT: G 85 TYR cc_start: 0.6457 (p90) cc_final: 0.5838 (p90) REVERT: G 177 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7360 (pm20) REVERT: G 302 ASP cc_start: 0.5215 (m-30) cc_final: 0.4527 (t70) REVERT: H 358 TYR cc_start: 0.4919 (OUTLIER) cc_final: 0.3026 (m-80) REVERT: H 479 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7857 (tm-30) REVERT: I 25 GLN cc_start: 0.7219 (mt0) cc_final: 0.6883 (mm-40) REVERT: J 77 TRP cc_start: 0.5490 (OUTLIER) cc_final: 0.4846 (t60) REVERT: J 123 ASN cc_start: 0.7586 (m-40) cc_final: 0.7089 (m-40) REVERT: M 21 ASN cc_start: 0.6395 (t0) cc_final: 0.6024 (t0) REVERT: M 102 MET cc_start: 0.4680 (pmm) cc_final: 0.4180 (pmm) REVERT: M 150 MET cc_start: 0.3217 (ptp) cc_final: 0.2984 (ptp) REVERT: M 265 LEU cc_start: 0.7491 (mt) cc_final: 0.7070 (mt) REVERT: N 22 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7453 (mm-30) REVERT: N 44 LYS cc_start: 0.7176 (mptt) cc_final: 0.6660 (mmtm) REVERT: N 74 MET cc_start: 0.5235 (OUTLIER) cc_final: 0.4602 (mmm) REVERT: N 159 LEU cc_start: 0.4765 (OUTLIER) cc_final: 0.4433 (pp) REVERT: N 175 MET cc_start: 0.6062 (OUTLIER) cc_final: 0.5632 (mmt) outliers start: 75 outliers final: 55 residues processed: 372 average time/residue: 0.1593 time to fit residues: 94.6072 Evaluate side-chains 367 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 301 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 A residue 255 VAL Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 12 LEU 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 144 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 25 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 243 LEU 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 250 VAL Chi-restraints excluded: chain D residue 264 TYR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain F residue 62 HIS Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 94 LYS Chi-restraints excluded: chain F residue 137 ILE 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 338 VAL Chi-restraints excluded: chain H residue 354 ILE Chi-restraints excluded: chain H residue 358 TYR Chi-restraints excluded: chain H residue 406 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 514 ARG Chi-restraints excluded: chain H residue 515 LEU Chi-restraints excluded: chain H residue 549 HIS Chi-restraints excluded: chain H residue 550 LEU Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain J residue 38 ASP Chi-restraints excluded: chain J residue 77 TRP Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 111 PHE Chi-restraints excluded: chain M residue 64 ASP Chi-restraints excluded: chain M residue 211 ASP Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 159 LEU 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: 2.9990 chunk 286 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 85 optimal weight: 0.7980 chunk 127 optimal weight: 9.9990 chunk 230 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 75 optimal weight: 0.0050 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 HIS ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 HIS ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 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** ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 ASN ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.132005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.116019 restraints weight = 101388.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.118759 restraints weight = 58776.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.120514 restraints weight = 38358.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.121586 restraints weight = 27736.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.122255 restraints weight = 22111.226| |-----------------------------------------------------------------------------| r_work (final): 0.4469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 moved from start: 0.7103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.124 25148 Z= 0.168 Angle : 0.714 15.243 34105 Z= 0.364 Chirality : 0.044 0.412 3701 Planarity : 0.004 0.060 4355 Dihedral : 13.779 178.535 3924 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 23.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.19 % Favored : 88.64 % Rotamer: Outliers : 2.84 % Allowed : 30.99 % Favored : 66.17 % 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 are not related in a simple way. whole: -2.40 (0.15), residues: 2931 helix: -0.11 (0.17), residues: 952 sheet: -1.14 (0.23), residues: 502 loop : -2.86 (0.14), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 51 TYR 0.022 0.002 TYR I 40 PHE 0.054 0.002 PHE N 192 TRP 0.035 0.002 TRP H 534 HIS 0.011 0.002 HIS G 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (25148) covalent geometry : angle 0.71442 / 0.36 (34105) hydrogen bonds : bond 0.03353 / 2.20 ( 821) hydrogen bonds : angle 5.13350 / 3.65 ( 2352) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4950.92 seconds wall clock time: 86 minutes 23.35 seconds (5183.35 seconds total)