Starting phenix.real_space_refine on Sat Jun 21 04:51:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gaf_29896/06_2025/8gaf_29896.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gaf_29896/06_2025/8gaf_29896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gaf_29896/06_2025/8gaf_29896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gaf_29896/06_2025/8gaf_29896.map" model { file = "/net/cci-nas-00/data/ceres_data/8gaf_29896/06_2025/8gaf_29896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gaf_29896/06_2025/8gaf_29896.cif" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.15, per 1000 atoms: 0.58 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: 6.97 Conformation dependent library (CDL) restraints added in 3.7 seconds 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: 7.83 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: 7.97 Time building geometry restraints manager: 7.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8056 1.34 - 1.45: 3463 1.45 - 1.57: 13360 1.57 - 1.69: 85 1.69 - 1.81: 184 Bond restraints: 25148 Sorted by residual: bond pdb=" CA ASN H 392 " pdb=" CB ASN H 392 " ideal model delta sigma weight residual 1.542 1.530 0.012 8.90e-03 1.26e+04 1.79e+00 bond pdb=" C3' G K 4 " pdb=" O3' G K 4 " ideal model delta sigma weight residual 1.427 1.446 -0.019 1.50e-02 4.44e+03 1.57e+00 bond pdb=" CA GLY N 113 " pdb=" C GLY N 113 " ideal model delta sigma weight residual 1.514 1.531 -0.017 1.41e-02 5.03e+03 1.45e+00 bond pdb=" N ILE M 67 " pdb=" CA ILE M 67 " ideal model delta sigma weight residual 1.459 1.473 -0.014 1.25e-02 6.40e+03 1.23e+00 bond pdb=" N ILE C 247 " pdb=" CA ILE C 247 " ideal model delta sigma weight residual 1.459 1.473 -0.014 1.25e-02 6.40e+03 1.22e+00 ... (remaining 25143 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 33716 1.63 - 3.26: 339 3.26 - 4.89: 42 4.89 - 6.52: 7 6.52 - 8.15: 1 Bond angle restraints: 34105 Sorted by residual: angle pdb=" N VAL N 198 " pdb=" CA VAL N 198 " pdb=" C VAL N 198 " ideal model delta sigma weight residual 113.43 108.53 4.90 1.09e+00 8.42e-01 2.02e+01 angle pdb=" CA ARG B 68 " pdb=" C ARG B 68 " pdb=" N GLU B 69 " ideal model delta sigma weight residual 119.46 116.76 2.70 6.10e-01 2.69e+00 1.96e+01 angle pdb=" C3' G K 4 " pdb=" O3' G K 4 " pdb=" P A K 5 " ideal model delta sigma weight residual 120.20 125.64 -5.44 1.50e+00 4.44e-01 1.31e+01 angle pdb=" C LEU A 235 " pdb=" CA LEU A 235 " pdb=" CB LEU A 235 " ideal model delta sigma weight residual 114.40 110.34 4.06 1.25e+00 6.40e-01 1.05e+01 angle pdb=" C3' A K 9 " pdb=" O3' A K 9 " pdb=" P G K 10 " ideal model delta sigma weight residual 120.20 124.85 -4.65 1.50e+00 4.44e-01 9.63e+00 ... (remaining 34100 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 14539 35.93 - 71.86: 620 71.86 - 107.79: 42 107.79 - 143.72: 2 143.72 - 179.64: 2 Dihedral angle restraints: 15205 sinusoidal: 6691 harmonic: 8514 Sorted by residual: dihedral pdb=" O4' C K 14 " pdb=" C1' C K 14 " pdb=" N1 C K 14 " pdb=" C2 C K 14 " ideal model delta sinusoidal sigma weight residual -128.00 51.64 -179.64 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U K 39 " pdb=" C1' U K 39 " pdb=" N1 U K 39 " pdb=" C2 U K 39 " ideal model delta sinusoidal sigma weight residual -128.00 -34.78 -93.22 1 1.70e+01 3.46e-03 3.51e+01 dihedral pdb=" O4' U K 33 " pdb=" C1' U K 33 " pdb=" N1 U K 33 " pdb=" C2 U K 33 " ideal model delta sinusoidal sigma weight residual -128.00 -42.20 -85.80 1 1.70e+01 3.46e-03 3.08e+01 ... (remaining 15202 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2983 0.041 - 0.083: 525 0.083 - 0.124: 186 0.124 - 0.166: 6 0.166 - 0.207: 1 Chirality restraints: 3701 Sorted by residual: chirality pdb=" C3' G K 4 " pdb=" C4' G K 4 " pdb=" O3' G K 4 " pdb=" C2' G K 4 " both_signs ideal model delta sigma weight residual False -2.74 -2.54 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" P G K 10 " pdb=" OP1 G K 10 " pdb=" OP2 G K 10 " pdb=" O5' G K 10 " both_signs ideal model delta sigma weight residual True 2.41 -2.55 -0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" C3' A K 9 " pdb=" C4' A K 9 " pdb=" O3' A K 9 " pdb=" C2' A K 9 " both_signs ideal model delta sigma weight residual False -2.74 -2.61 -0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 3698 not shown) Planarity restraints: 4355 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU J 59 " -0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO J 60 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO J 60 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO J 60 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 377 " -0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO H 378 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO H 378 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO H 378 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP M 33 " -0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO M 34 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO M 34 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO M 34 " -0.017 5.00e-02 4.00e+02 ... (remaining 4352 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 607 2.69 - 3.24: 22712 3.24 - 3.79: 41141 3.79 - 4.35: 54255 4.35 - 4.90: 87429 Nonbonded interactions: 206144 Sorted by model distance: nonbonded pdb=" O VAL C 125 " pdb=" O2' C K 17 " model vdw 2.133 3.040 nonbonded pdb=" O VAL B 125 " pdb=" O2' G K 11 " model vdw 2.191 3.040 nonbonded pdb=" OD1 ASP A 17 " pdb=" OG1 THR A 172 " model vdw 2.212 3.040 nonbonded pdb=" OG1 THR M 117 " pdb=" OG SER N 75 " model vdw 2.249 3.040 nonbonded pdb=" OD2 ASP D 23 " pdb=" OH TYR I 40 " model vdw 2.251 3.040 ... (remaining 206139 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'B' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'C' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'D' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'E' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'F' and (resid 2 through 74 or resid 94 through 284)) selection = (chain 'M' and (resid 2 through 152 or resid 165 through 284)) } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.950 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 60.050 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5215 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25148 Z= 0.098 Angle : 0.434 8.150 34105 Z= 0.272 Chirality : 0.036 0.207 3701 Planarity : 0.002 0.043 4355 Dihedral : 18.188 179.645 9731 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 2.35 % Allowed : 15.42 % Favored : 82.22 % Rotamer: Outliers : 2.92 % Allowed : 20.27 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.005 0.001 TRP E 203 HIS 0.002 0.000 HIS H 549 PHE 0.011 0.001 PHE D 9 TYR 0.008 0.001 TYR G 9 ARG 0.002 0.000 ARG G 59 Details of bonding type rmsd hydrogen bonds : bond 0.14218 ( 821) hydrogen bonds : angle 5.06101 ( 2352) covalent geometry : bond 0.00162 (25148) covalent geometry : angle 0.43390 (34105) *********************** 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 : 2.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.6790 (mp10) cc_final: 0.6559 (mp10) REVERT: A 139 PRO cc_start: 0.6321 (Cg_exo) cc_final: 0.5965 (Cg_endo) REVERT: A 178 TYR cc_start: 0.5794 (m-80) cc_final: 0.5405 (m-80) REVERT: A 227 TYR cc_start: 0.4952 (m-80) cc_final: 0.4364 (m-80) REVERT: B 209 MET cc_start: 0.5156 (ptt) cc_final: 0.4950 (ptt) REVERT: B 228 VAL cc_start: 0.5579 (t) cc_final: 0.4852 (t) REVERT: C 108 ASP cc_start: 0.7324 (t0) cc_final: 0.6667 (m-30) REVERT: D 141 MET cc_start: 0.4158 (mmm) cc_final: 0.3823 (mpp) REVERT: D 220 GLN cc_start: 0.7342 (tt0) cc_final: 0.7043 (tt0) REVERT: E 52 ASN cc_start: 0.8214 (m-40) cc_final: 0.7766 (m-40) REVERT: E 150 MET cc_start: 0.4544 (mtm) cc_final: 0.3633 (mtm) REVERT: E 183 PHE cc_start: 0.6465 (m-80) cc_final: 0.4854 (m-80) REVERT: E 184 ILE cc_start: 0.7703 (mt) cc_final: 0.7025 (tt) REVERT: E 221 MET cc_start: 0.6261 (mtp) cc_final: 0.5237 (mtt) REVERT: E 222 ASN cc_start: 0.7024 (m-40) cc_final: 0.6632 (m110) REVERT: E 277 LYS cc_start: 0.5641 (mppt) cc_final: 0.5063 (ttmt) REVERT: F 7 TYR cc_start: 0.7983 (m-80) cc_final: 0.7623 (m-80) REVERT: F 16 GLN cc_start: 0.7555 (mm110) cc_final: 0.7298 (mm110) REVERT: F 69 GLU cc_start: 0.5254 (mm-30) cc_final: 0.4707 (mm-30) REVERT: F 129 VAL cc_start: 0.7480 (t) cc_final: 0.7237 (t) REVERT: F 135 ARG cc_start: 0.8980 (ptp-110) cc_final: 0.8278 (mtp180) REVERT: F 227 TYR cc_start: 0.2818 (m-80) cc_final: 0.2196 (m-10) REVERT: F 265 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6474 (mt) REVERT: H 515 LEU cc_start: 0.4500 (OUTLIER) cc_final: 0.4230 (mt) REVERT: H 539 ILE cc_start: 0.6047 (mt) cc_final: 0.5772 (mt) REVERT: I 21 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6485 (mp) REVERT: I 23 LYS cc_start: 0.8071 (tptm) cc_final: 0.7683 (tppp) REVERT: I 25 GLN cc_start: 0.8025 (tm-30) cc_final: 0.6989 (tm-30) REVERT: I 122 PHE cc_start: 0.6787 (t80) cc_final: 0.6463 (t80) REVERT: J 123 ASN cc_start: 0.7724 (m-40) cc_final: 0.7339 (m-40) REVERT: M 126 ARG cc_start: 0.5631 (mtm180) cc_final: 0.5046 (mmp80) REVERT: N 43 TRP cc_start: 0.3262 (t60) cc_final: 0.2773 (t60) REVERT: N 50 LYS cc_start: 0.4242 (tptt) cc_final: 0.3749 (tptt) outliers start: 74 outliers final: 11 residues processed: 813 average time/residue: 0.5092 time to fit residues: 611.7882 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 : 3.368 ------------------------------------------------------------------------------- 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 249 optimal weight: 10.0000 chunk 224 optimal weight: 10.0000 chunk 124 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 151 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 232 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 chunk 268 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN A 81 HIS ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 GLN ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN A 208 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 315 GLN H 465 GLN ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 HIS I 76 GLN I 85 HIS ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN J 91 ASN J 94 ASN J 110 GLN M 191 GLN ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 64 ASN N 68 ASN ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 88 GLN N 133 GLN ** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.145705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.129928 restraints weight = 101527.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.132687 restraints weight = 61977.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 72)----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.134388 restraints weight = 41831.560| |-----------------------------------------------------------------------------| r_work (final): 0.4674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6024 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 25148 Z= 0.176 Angle : 0.690 10.482 34105 Z= 0.358 Chirality : 0.045 0.387 3701 Planarity : 0.005 0.107 4355 Dihedral : 13.659 178.205 3939 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.51 % Allowed : 10.64 % Favored : 88.84 % Rotamer: Outliers : 4.46 % Allowed : 24.57 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.14), residues: 2931 helix: -0.26 (0.16), residues: 951 sheet: -1.39 (0.23), residues: 492 loop : -3.33 (0.13), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP H 534 HIS 0.014 0.002 HIS I 92 PHE 0.037 0.002 PHE B 183 TYR 0.021 0.002 TYR H 497 ARG 0.010 0.001 ARG G 263 Details of bonding type rmsd hydrogen bonds : bond 0.03564 ( 821) hydrogen bonds : angle 4.51467 ( 2352) covalent geometry : bond 0.00392 (25148) covalent geometry : angle 0.69003 (34105) *********************** 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 528 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 415 time to evaluate : 3.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 VAL cc_start: 0.6902 (p) cc_final: 0.6682 (p) REVERT: A 171 PHE cc_start: 0.8364 (m-80) cc_final: 0.7437 (m-80) REVERT: A 178 TYR cc_start: 0.6296 (m-80) cc_final: 0.5999 (m-80) REVERT: A 197 ASN cc_start: 0.8176 (p0) cc_final: 0.7958 (m110) REVERT: A 227 TYR cc_start: 0.5627 (m-80) cc_final: 0.4937 (m-80) REVERT: B 3 ILE cc_start: 0.2118 (OUTLIER) cc_final: 0.1533 (mp) REVERT: B 33 ASP cc_start: 0.6211 (OUTLIER) cc_final: 0.6004 (t0) REVERT: C 108 ASP cc_start: 0.7703 (t0) cc_final: 0.6923 (m-30) REVERT: D 132 THR cc_start: 0.6624 (p) cc_final: 0.6176 (p) REVERT: D 141 MET cc_start: 0.4558 (mmm) cc_final: 0.4006 (mpp) REVERT: D 147 ILE cc_start: 0.7384 (pt) cc_final: 0.7173 (pt) REVERT: D 214 HIS cc_start: 0.5988 (m-70) cc_final: 0.5632 (m170) REVERT: D 220 GLN cc_start: 0.7423 (tt0) cc_final: 0.7127 (tt0) REVERT: D 264 TYR cc_start: 0.2633 (OUTLIER) cc_final: 0.1586 (m-10) REVERT: E 52 ASN cc_start: 0.8733 (m-40) cc_final: 0.8263 (m-40) REVERT: E 150 MET cc_start: 0.5410 (mtm) cc_final: 0.4362 (mmp) REVERT: E 188 PHE cc_start: 0.6328 (m-80) cc_final: 0.6023 (m-10) REVERT: E 209 MET cc_start: 0.7418 (tpt) cc_final: 0.7097 (tpt) REVERT: E 220 GLN cc_start: 0.5407 (pp30) cc_final: 0.5060 (tm-30) REVERT: E 221 MET cc_start: 0.5223 (mtp) cc_final: 0.3811 (mtt) REVERT: F 7 TYR cc_start: 0.8155 (m-80) cc_final: 0.7789 (m-80) REVERT: F 41 VAL cc_start: 0.6993 (t) cc_final: 0.6466 (t) REVERT: F 112 PHE cc_start: 0.9153 (m-80) cc_final: 0.8873 (m-80) REVERT: F 135 ARG cc_start: 0.9080 (ptp-110) cc_final: 0.8191 (mtt180) REVERT: F 213 ASP cc_start: 0.2751 (t70) cc_final: 0.1808 (m-30) REVERT: F 227 TYR cc_start: 0.2888 (m-80) cc_final: 0.2254 (m-10) REVERT: F 250 VAL cc_start: 0.4709 (OUTLIER) cc_final: 0.4474 (m) REVERT: G 85 TYR cc_start: 0.5982 (p90) cc_final: 0.5360 (p90) REVERT: H 539 ILE cc_start: 0.6885 (mt) cc_final: 0.6661 (mt) REVERT: H 552 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8005 (pp) REVERT: I 23 LYS cc_start: 0.7932 (tptm) cc_final: 0.7703 (tptt) REVERT: I 25 GLN cc_start: 0.7901 (tm-30) cc_final: 0.6871 (tm-30) REVERT: I 63 LEU cc_start: 0.9071 (mt) cc_final: 0.8813 (pp) REVERT: I 122 PHE cc_start: 0.7264 (t80) cc_final: 0.6677 (t80) REVERT: J 123 ASN cc_start: 0.8029 (m-40) cc_final: 0.7174 (m-40) REVERT: M 12 LEU cc_start: 0.7819 (mm) cc_final: 0.7506 (tp) REVERT: M 120 LYS cc_start: 0.6546 (OUTLIER) cc_final: 0.6332 (ptmt) REVERT: M 237 ASP cc_start: 0.6062 (p0) cc_final: 0.5808 (t70) REVERT: M 244 PHE cc_start: 0.6829 (m-10) cc_final: 0.6587 (m-80) REVERT: N 193 TYR cc_start: 0.5714 (OUTLIER) cc_final: 0.5436 (t80) outliers start: 113 outliers final: 49 residues processed: 503 average time/residue: 0.4815 time to fit residues: 376.7648 Evaluate side-chains 384 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 328 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 207 VAL 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 C residue 15 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 264 TYR Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 231 HIS Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 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 411 LEU Chi-restraints excluded: chain H residue 474 LEU Chi-restraints excluded: chain H residue 489 LEU Chi-restraints excluded: chain H residue 515 LEU Chi-restraints excluded: chain H residue 552 LEU Chi-restraints excluded: chain I residue 4 ASP Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain J residue 85 HIS Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 56 MET Chi-restraints excluded: chain M residue 120 LYS Chi-restraints excluded: chain M residue 153 THR Chi-restraints excluded: chain M residue 180 CYS Chi-restraints excluded: chain M residue 249 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 100 TYR Chi-restraints excluded: chain N residue 193 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 89 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 294 optimal weight: 3.9990 chunk 284 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 159 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 HIS ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 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 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN D 187 HIS D 197 ASN ** 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** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN F 75 ASN ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 ASN F 214 HIS F 234 ASN ** G 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 262 ASN H 486 ASN H 490 ASN H 542 HIS H 567 GLN H 577 ASN I 97 GLN ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 94 ASN M 21 ASN ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 222 ASN ** 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: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.136442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.120492 restraints weight = 101295.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.123124 restraints weight = 60271.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.124887 restraints weight = 40323.677| |-----------------------------------------------------------------------------| r_work (final): 0.4512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 25148 Z= 0.221 Angle : 0.713 10.481 34105 Z= 0.370 Chirality : 0.044 0.236 3701 Planarity : 0.005 0.063 4355 Dihedral : 13.721 177.474 3931 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 24.74 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.32 % Favored : 87.38 % Rotamer: Outliers : 4.81 % Allowed : 25.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.15), residues: 2931 helix: -0.01 (0.17), residues: 952 sheet: -1.24 (0.24), residues: 490 loop : -3.19 (0.13), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP N 43 HIS 0.031 0.002 HIS E 62 PHE 0.030 0.002 PHE B 183 TYR 0.028 0.002 TYR I 106 ARG 0.012 0.001 ARG M 218 Details of bonding type rmsd hydrogen bonds : bond 0.03564 ( 821) hydrogen bonds : angle 4.88529 ( 2352) covalent geometry : bond 0.00475 (25148) covalent geometry : angle 0.71267 (34105) *********************** 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 505 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 383 time to evaluate : 2.624 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 36 THR cc_start: 0.6824 (OUTLIER) cc_final: 0.6574 (p) REVERT: A 102 MET cc_start: 0.7886 (tpp) cc_final: 0.7470 (tpp) REVERT: A 141 MET cc_start: 0.5448 (ptp) cc_final: 0.4951 (ptp) REVERT: A 178 TYR cc_start: 0.6433 (m-80) cc_final: 0.5993 (m-80) REVERT: A 248 GLN cc_start: 0.6068 (tp40) cc_final: 0.5782 (tp40) REVERT: B 32 ILE cc_start: 0.8523 (tp) cc_final: 0.8311 (tp) REVERT: B 183 PHE cc_start: 0.6250 (m-80) cc_final: 0.5918 (m-10) REVERT: C 56 MET cc_start: 0.4810 (ttp) cc_final: 0.4090 (tpt) REVERT: C 79 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7046 (pp20) REVERT: C 108 ASP cc_start: 0.8106 (t0) cc_final: 0.7444 (m-30) REVERT: D 40 LEU cc_start: 0.8224 (tp) cc_final: 0.7975 (tp) REVERT: D 131 LEU cc_start: 0.7997 (mp) cc_final: 0.7757 (mp) REVERT: D 141 MET cc_start: 0.4707 (mmm) cc_final: 0.4233 (mpp) REVERT: D 147 ILE cc_start: 0.7844 (pt) cc_final: 0.7524 (pt) REVERT: D 171 PHE cc_start: 0.7415 (m-80) cc_final: 0.7204 (m-80) REVERT: D 214 HIS cc_start: 0.6632 (m-70) cc_final: 0.6272 (m170) REVERT: D 220 GLN cc_start: 0.7646 (tt0) cc_final: 0.7260 (tt0) REVERT: D 264 TYR cc_start: 0.3088 (OUTLIER) cc_final: 0.2222 (m-10) REVERT: E 52 ASN cc_start: 0.8887 (m-40) cc_final: 0.8651 (m-40) REVERT: E 134 SER cc_start: 0.7854 (OUTLIER) cc_final: 0.7493 (m) REVERT: E 150 MET cc_start: 0.5235 (mtm) cc_final: 0.3832 (mtm) REVERT: E 209 MET cc_start: 0.6915 (tpt) cc_final: 0.6598 (tpt) REVERT: E 221 MET cc_start: 0.5198 (mtp) cc_final: 0.4990 (mtt) REVERT: F 7 TYR cc_start: 0.8165 (m-80) cc_final: 0.7434 (m-80) REVERT: F 41 VAL cc_start: 0.7298 (t) cc_final: 0.6835 (t) REVERT: F 72 ILE cc_start: 0.7304 (mm) cc_final: 0.7046 (mm) REVERT: F 93 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7610 (tm-30) REVERT: F 112 PHE cc_start: 0.9080 (m-80) cc_final: 0.8676 (m-10) REVERT: F 135 ARG cc_start: 0.9052 (ptp-110) cc_final: 0.8205 (mtt180) REVERT: F 227 TYR cc_start: 0.2842 (m-80) cc_final: 0.2325 (m-10) REVERT: F 250 VAL cc_start: 0.5059 (OUTLIER) cc_final: 0.4825 (m) REVERT: G 4 HIS cc_start: 0.5641 (t-90) cc_final: 0.5400 (t-170) REVERT: G 85 TYR cc_start: 0.6356 (p90) cc_final: 0.5678 (p90) REVERT: G 247 MET cc_start: 0.7186 (tmm) cc_final: 0.6507 (tmm) REVERT: H 463 ASN cc_start: 0.6705 (m-40) cc_final: 0.6480 (m-40) REVERT: I 23 LYS cc_start: 0.8002 (tptm) cc_final: 0.7691 (tttt) REVERT: I 25 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7305 (tm-30) REVERT: I 122 PHE cc_start: 0.7639 (t80) cc_final: 0.7119 (t80) REVERT: J 123 ASN cc_start: 0.7817 (m-40) cc_final: 0.7299 (m-40) REVERT: M 56 MET cc_start: 0.3973 (OUTLIER) cc_final: 0.3363 (mmm) REVERT: M 120 LYS cc_start: 0.6514 (OUTLIER) cc_final: 0.6061 (ptmt) REVERT: M 150 MET cc_start: 0.3043 (ptt) cc_final: 0.2787 (ptp) REVERT: N 70 VAL cc_start: 0.5311 (OUTLIER) cc_final: 0.5040 (p) REVERT: N 159 LEU cc_start: 0.4225 (OUTLIER) cc_final: 0.3798 (pp) outliers start: 122 outliers final: 63 residues processed: 479 average time/residue: 0.4391 time to fit residues: 325.5483 Evaluate side-chains 394 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 322 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 112 PHE Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 230 GLU 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 65 ILE Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 264 TYR Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain F residue 62 HIS Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 203 TRP Chi-restraints excluded: chain F residue 231 HIS Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 15 GLU Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 309 LYS Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 457 THR Chi-restraints excluded: chain H residue 515 LEU Chi-restraints excluded: chain H residue 572 LYS Chi-restraints excluded: chain I residue 4 ASP Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 111 PHE Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 56 MET Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 120 LYS Chi-restraints excluded: chain M residue 153 THR Chi-restraints excluded: chain M residue 180 CYS Chi-restraints excluded: chain M residue 249 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 13 CYS Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 100 TYR 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 166 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 161 optimal weight: 4.9990 chunk 261 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 284 optimal weight: 0.5980 chunk 147 optimal weight: 8.9990 chunk 214 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 115 optimal weight: 0.0070 chunk 104 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.3204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 HIS ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 GLN ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 GLN C 74 ASN C 100 GLN C 212 HIS ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 HIS ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 HIS G 156 ASN H 362 GLN ** H 427 GLN ** 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 62 HIS ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 124 GLN ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.136392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.120419 restraints weight = 102543.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.122893 restraints weight = 60711.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.124665 restraints weight = 40590.697| |-----------------------------------------------------------------------------| r_work (final): 0.4513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6387 moved from start: 0.5705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 25148 Z= 0.150 Angle : 0.641 12.265 34105 Z= 0.327 Chirality : 0.042 0.232 3701 Planarity : 0.004 0.058 4355 Dihedral : 13.761 178.634 3929 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.27 % Favored : 89.49 % Rotamer: Outliers : 4.02 % Allowed : 26.62 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.15), residues: 2931 helix: 0.11 (0.17), residues: 948 sheet: -0.90 (0.25), residues: 455 loop : -3.07 (0.13), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 49 HIS 0.009 0.001 HIS A 62 PHE 0.028 0.002 PHE C 188 TYR 0.021 0.002 TYR C 107 ARG 0.009 0.001 ARG C 68 Details of bonding type rmsd hydrogen bonds : bond 0.03110 ( 821) hydrogen bonds : angle 4.83473 ( 2352) covalent geometry : bond 0.00333 (25148) covalent geometry : angle 0.64117 (34105) *********************** 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 459 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 357 time to evaluate : 3.173 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 102 MET cc_start: 0.8038 (tpp) cc_final: 0.7612 (tpp) REVERT: A 178 TYR cc_start: 0.6316 (m-80) cc_final: 0.6043 (m-80) REVERT: A 248 GLN cc_start: 0.5849 (tp-100) cc_final: 0.5601 (tp40) REVERT: B 183 PHE cc_start: 0.6091 (m-80) cc_final: 0.5721 (m-10) REVERT: B 209 MET cc_start: 0.5537 (ptp) cc_final: 0.5171 (ttp) REVERT: B 210 PHE cc_start: 0.7072 (m-10) cc_final: 0.6611 (m-10) REVERT: C 56 MET cc_start: 0.4914 (OUTLIER) cc_final: 0.4173 (tpt) REVERT: C 108 ASP cc_start: 0.8137 (t0) cc_final: 0.7521 (m-30) REVERT: D 116 MET cc_start: 0.5899 (pmm) cc_final: 0.5078 (pmm) REVERT: D 141 MET cc_start: 0.4781 (mmm) cc_final: 0.4256 (mpp) REVERT: D 214 HIS cc_start: 0.6272 (m-70) cc_final: 0.5945 (m170) REVERT: D 220 GLN cc_start: 0.7337 (tt0) cc_final: 0.6732 (tt0) REVERT: D 227 TYR cc_start: 0.3739 (m-80) cc_final: 0.3521 (m-80) REVERT: D 264 TYR cc_start: 0.2856 (OUTLIER) cc_final: 0.2468 (m-10) REVERT: E 52 ASN cc_start: 0.8816 (m-40) cc_final: 0.8359 (m110) REVERT: E 90 GLU cc_start: 0.6101 (tt0) cc_final: 0.5589 (tp30) REVERT: E 100 GLN cc_start: 0.8357 (mm110) cc_final: 0.8111 (mm110) REVERT: E 132 THR cc_start: 0.6802 (m) cc_final: 0.6457 (m) REVERT: E 134 SER cc_start: 0.7731 (OUTLIER) cc_final: 0.6937 (t) REVERT: E 209 MET cc_start: 0.7144 (tpt) cc_final: 0.6858 (tpt) REVERT: E 221 MET cc_start: 0.5146 (mtp) cc_final: 0.4804 (mtt) REVERT: F 7 TYR cc_start: 0.8179 (m-80) cc_final: 0.7545 (m-80) REVERT: F 93 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7410 (tm-30) REVERT: F 112 PHE cc_start: 0.8990 (m-80) cc_final: 0.8576 (m-10) REVERT: F 135 ARG cc_start: 0.9047 (ptp-110) cc_final: 0.8119 (mtp180) REVERT: F 137 ILE cc_start: 0.3651 (OUTLIER) cc_final: 0.3330 (pt) REVERT: F 187 HIS cc_start: 0.7048 (t-170) cc_final: 0.6797 (t-90) REVERT: F 227 TYR cc_start: 0.2910 (m-80) cc_final: 0.2283 (m-10) REVERT: F 250 VAL cc_start: 0.4904 (OUTLIER) cc_final: 0.4662 (m) REVERT: G 4 HIS cc_start: 0.5669 (t-90) cc_final: 0.5304 (t-170) REVERT: G 85 TYR cc_start: 0.6354 (p90) cc_final: 0.5924 (p90) REVERT: H 358 TYR cc_start: 0.4884 (OUTLIER) cc_final: 0.3979 (m-80) REVERT: H 463 ASN cc_start: 0.6794 (m-40) cc_final: 0.6546 (m-40) REVERT: H 497 TYR cc_start: 0.6507 (m-80) cc_final: 0.6169 (m-10) REVERT: H 552 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8055 (pp) REVERT: I 3 LEU cc_start: 0.7838 (tp) cc_final: 0.7506 (tt) REVERT: I 23 LYS cc_start: 0.7925 (tptm) cc_final: 0.7523 (tttt) REVERT: I 25 GLN cc_start: 0.7962 (tm-30) cc_final: 0.7502 (tp-100) REVERT: I 98 GLN cc_start: 0.8294 (tm-30) cc_final: 0.8017 (tp40) REVERT: I 122 PHE cc_start: 0.7649 (t80) cc_final: 0.7279 (t80) REVERT: J 3 LEU cc_start: 0.7193 (tp) cc_final: 0.6978 (tt) REVERT: J 56 MET cc_start: 0.7500 (mmm) cc_final: 0.7150 (mmm) REVERT: J 88 ARG cc_start: 0.7192 (tmt170) cc_final: 0.6963 (tmt170) REVERT: J 123 ASN cc_start: 0.7598 (m-40) cc_final: 0.7114 (m-40) REVERT: M 244 PHE cc_start: 0.7199 (m-10) cc_final: 0.6710 (m-80) REVERT: N 171 MET cc_start: 0.4665 (mtt) cc_final: 0.4402 (mtt) REVERT: N 192 PHE cc_start: 0.3962 (p90) cc_final: 0.3134 (m-80) REVERT: N 194 GLN cc_start: 0.0888 (OUTLIER) cc_final: 0.0212 (mm110) outliers start: 102 outliers final: 51 residues processed: 436 average time/residue: 0.4133 time to fit residues: 283.7594 Evaluate side-chains 374 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 315 time to evaluate : 2.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 112 PHE Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 213 ASP 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 50 VAL Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 224 ARG Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 264 TYR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain E residue 81 HIS 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 F residue 250 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 358 TYR Chi-restraints excluded: chain H residue 402 THR 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 515 LEU Chi-restraints excluded: chain H residue 549 HIS Chi-restraints excluded: chain H residue 550 LEU Chi-restraints excluded: chain H residue 552 LEU Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 111 PHE Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 153 THR Chi-restraints excluded: chain M residue 249 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 13 CYS Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 194 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 111 optimal weight: 0.0870 chunk 68 optimal weight: 9.9990 chunk 257 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 241 optimal weight: 0.8980 chunk 287 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 171 optimal weight: 3.9990 chunk 201 optimal weight: 0.5980 chunk 20 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 HIS A 121 ASN A 124 GLN ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 HIS ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 GLN C 74 ASN C 220 GLN ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 HIS ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN ** F 83 GLN ** 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 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 124 GLN ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 ASN N 64 ASN ** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.135642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.119805 restraints weight = 101853.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.122325 restraints weight = 59161.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.124131 restraints weight = 38977.707| |-----------------------------------------------------------------------------| r_work (final): 0.4504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 moved from start: 0.6054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 25148 Z= 0.142 Angle : 0.631 10.777 34105 Z= 0.321 Chirality : 0.042 0.245 3701 Planarity : 0.004 0.055 4355 Dihedral : 13.782 179.963 3929 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 20.96 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.19 % Favored : 88.57 % Rotamer: Outliers : 3.63 % Allowed : 27.33 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.15), residues: 2931 helix: 0.19 (0.17), residues: 942 sheet: -1.18 (0.23), residues: 498 loop : -2.94 (0.14), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP J 77 HIS 0.021 0.002 HIS E 81 PHE 0.021 0.002 PHE B 11 TYR 0.033 0.002 TYR I 40 ARG 0.007 0.001 ARG C 224 Details of bonding type rmsd hydrogen bonds : bond 0.03043 ( 821) hydrogen bonds : angle 4.81126 ( 2352) covalent geometry : bond 0.00316 (25148) covalent geometry : angle 0.63125 (34105) *********************** 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 426 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 334 time to evaluate : 2.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.7868 (tpp) cc_final: 0.7500 (tpp) REVERT: A 178 TYR cc_start: 0.6263 (m-80) cc_final: 0.5962 (m-80) REVERT: B 68 ARG cc_start: 0.6168 (OUTLIER) cc_final: 0.5233 (ptp90) REVERT: B 84 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8469 (pm20) REVERT: B 150 MET cc_start: 0.5959 (pmm) cc_final: 0.5672 (pmm) REVERT: B 183 PHE cc_start: 0.6656 (m-80) cc_final: 0.6215 (m-10) REVERT: C 16 GLN cc_start: 0.7065 (OUTLIER) cc_final: 0.6739 (mp10) REVERT: C 56 MET cc_start: 0.4755 (OUTLIER) cc_final: 0.4127 (tpt) REVERT: C 78 ASP cc_start: 0.7001 (m-30) cc_final: 0.6747 (m-30) REVERT: C 79 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7058 (pp20) REVERT: C 108 ASP cc_start: 0.8085 (t0) cc_final: 0.7283 (m-30) REVERT: D 116 MET cc_start: 0.6109 (pmm) cc_final: 0.5561 (pmm) REVERT: D 141 MET cc_start: 0.4682 (mmm) cc_final: 0.4095 (mpp) REVERT: D 214 HIS cc_start: 0.6226 (m-70) cc_final: 0.5956 (m170) REVERT: D 220 GLN cc_start: 0.7454 (tt0) cc_final: 0.7093 (tt0) REVERT: D 227 TYR cc_start: 0.3803 (m-80) cc_final: 0.3562 (m-80) REVERT: D 264 TYR cc_start: 0.3165 (OUTLIER) cc_final: 0.1895 (m-10) REVERT: E 52 ASN cc_start: 0.8833 (m-40) cc_final: 0.8347 (m110) REVERT: E 90 GLU cc_start: 0.6120 (tt0) cc_final: 0.5591 (tp30) REVERT: E 132 THR cc_start: 0.6668 (m) cc_final: 0.6355 (m) REVERT: E 134 SER cc_start: 0.7791 (OUTLIER) cc_final: 0.6882 (t) REVERT: E 221 MET cc_start: 0.5321 (mtp) cc_final: 0.5091 (mmm) REVERT: F 7 TYR cc_start: 0.8131 (m-80) cc_final: 0.7534 (m-80) REVERT: F 93 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7446 (tm-30) REVERT: F 112 PHE cc_start: 0.8997 (m-80) cc_final: 0.8610 (m-10) REVERT: F 135 ARG cc_start: 0.9078 (ptp-110) cc_final: 0.8229 (mtp180) REVERT: F 137 ILE cc_start: 0.3790 (OUTLIER) cc_final: 0.3390 (pt) REVERT: F 227 TYR cc_start: 0.2960 (m-80) cc_final: 0.2369 (m-10) REVERT: F 250 VAL cc_start: 0.4899 (OUTLIER) cc_final: 0.4655 (m) REVERT: G 4 HIS cc_start: 0.5872 (t-90) cc_final: 0.5454 (t-170) REVERT: G 85 TYR cc_start: 0.6384 (p90) cc_final: 0.5833 (p90) REVERT: H 358 TYR cc_start: 0.4738 (OUTLIER) cc_final: 0.3617 (m-80) REVERT: H 463 ASN cc_start: 0.6724 (m-40) cc_final: 0.6516 (m-40) REVERT: H 552 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8208 (pp) REVERT: I 3 LEU cc_start: 0.7837 (tp) cc_final: 0.7573 (tt) REVERT: I 23 LYS cc_start: 0.7934 (tptm) cc_final: 0.7696 (tptt) REVERT: I 122 PHE cc_start: 0.7677 (t80) cc_final: 0.7317 (t80) REVERT: J 3 LEU cc_start: 0.7307 (tp) cc_final: 0.7099 (tt) REVERT: J 56 MET cc_start: 0.7613 (mmm) cc_final: 0.7296 (mmm) REVERT: J 116 ASP cc_start: 0.6567 (OUTLIER) cc_final: 0.6059 (t0) REVERT: J 123 ASN cc_start: 0.7531 (m-40) cc_final: 0.7086 (m-40) REVERT: M 21 ASN cc_start: 0.6433 (t0) cc_final: 0.6145 (t0) REVERT: M 56 MET cc_start: 0.4233 (mmt) cc_final: 0.3965 (mmm) REVERT: M 244 PHE cc_start: 0.7268 (m-10) cc_final: 0.6927 (m-10) REVERT: N 22 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7498 (mm-30) REVERT: N 175 MET cc_start: 0.6277 (mtt) cc_final: 0.5923 (mtt) REVERT: N 192 PHE cc_start: 0.4663 (p90) cc_final: 0.2603 (m-80) REVERT: N 194 GLN cc_start: 0.0339 (OUTLIER) cc_final: -0.0431 (mm110) outliers start: 92 outliers final: 48 residues processed: 400 average time/residue: 0.4174 time to fit residues: 260.8452 Evaluate side-chains 365 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 303 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 112 PHE Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 16 GLN Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 224 ARG Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 264 TYR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain F residue 62 HIS Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 231 HIS Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 250 TYR Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 358 TYR Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 460 LEU Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain H residue 511 THR 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 H residue 552 LEU Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 111 PHE Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 59 ASN Chi-restraints excluded: chain M residue 153 THR Chi-restraints excluded: chain M residue 177 LEU Chi-restraints excluded: chain M residue 265 LEU Chi-restraints excluded: chain N residue 13 CYS Chi-restraints excluded: chain N residue 22 GLU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 194 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 38 optimal weight: 0.6980 chunk 119 optimal weight: 8.9990 chunk 270 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 218 optimal weight: 0.9980 chunk 281 optimal weight: 7.9990 chunk 287 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 267 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 185 optimal weight: 20.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 GLN F 81 HIS ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 HIS ** H 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 538 GLN H 542 HIS ** I 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 94 ASN M 208 ASN ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.133830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.117551 restraints weight = 100160.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.119982 restraints weight = 58397.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.121733 restraints weight = 38767.583| |-----------------------------------------------------------------------------| r_work (final): 0.4468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.6542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 25148 Z= 0.149 Angle : 0.649 11.173 34105 Z= 0.330 Chirality : 0.042 0.236 3701 Planarity : 0.004 0.052 4355 Dihedral : 13.807 179.229 3927 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 21.69 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.85 % Favored : 88.95 % Rotamer: Outliers : 3.67 % Allowed : 27.37 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.15), residues: 2931 helix: 0.13 (0.17), residues: 959 sheet: -1.11 (0.24), residues: 469 loop : -2.94 (0.14), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP J 77 HIS 0.014 0.001 HIS A 145 PHE 0.027 0.002 PHE D 261 TYR 0.027 0.002 TYR I 40 ARG 0.010 0.001 ARG E 135 Details of bonding type rmsd hydrogen bonds : bond 0.03087 ( 821) hydrogen bonds : angle 4.92304 ( 2352) covalent geometry : bond 0.00336 (25148) covalent geometry : angle 0.64873 (34105) *********************** 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 428 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 335 time to evaluate : 3.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.8022 (tpp) cc_final: 0.7650 (tpp) REVERT: A 116 MET cc_start: 0.5896 (OUTLIER) cc_final: 0.5560 (tmm) REVERT: A 178 TYR cc_start: 0.6291 (m-80) cc_final: 0.5910 (m-80) REVERT: A 220 GLN cc_start: 0.7409 (OUTLIER) cc_final: 0.6632 (tp-100) REVERT: B 68 ARG cc_start: 0.6189 (OUTLIER) cc_final: 0.5582 (ptp90) REVERT: B 84 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8495 (pm20) REVERT: B 150 MET cc_start: 0.6207 (pmm) cc_final: 0.5578 (pmm) REVERT: B 183 PHE cc_start: 0.6667 (m-80) cc_final: 0.6286 (m-80) REVERT: B 218 ARG cc_start: 0.5969 (OUTLIER) cc_final: 0.4825 (mtm180) REVERT: C 16 GLN cc_start: 0.7043 (OUTLIER) cc_final: 0.6669 (mp10) REVERT: C 78 ASP cc_start: 0.6989 (m-30) cc_final: 0.6706 (m-30) REVERT: C 93 GLU cc_start: 0.7618 (tp30) cc_final: 0.7350 (tm-30) REVERT: C 209 MET cc_start: 0.6677 (tpp) cc_final: 0.6391 (tpp) REVERT: D 141 MET cc_start: 0.4797 (mmm) cc_final: 0.4162 (mpp) REVERT: D 214 HIS cc_start: 0.6295 (m-70) cc_final: 0.6066 (m170) REVERT: D 227 TYR cc_start: 0.3671 (m-80) cc_final: 0.3419 (m-80) REVERT: D 264 TYR cc_start: 0.2777 (OUTLIER) cc_final: 0.1895 (m-10) REVERT: E 52 ASN cc_start: 0.8886 (m-40) cc_final: 0.8389 (m110) REVERT: E 90 GLU cc_start: 0.6112 (tt0) cc_final: 0.5570 (tp30) REVERT: E 134 SER cc_start: 0.7650 (OUTLIER) cc_final: 0.6838 (t) REVERT: E 199 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7998 (tp) REVERT: F 7 TYR cc_start: 0.8268 (m-80) cc_final: 0.7716 (m-80) REVERT: F 93 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7355 (tm-30) REVERT: F 112 PHE cc_start: 0.8765 (m-80) cc_final: 0.8453 (m-10) REVERT: F 137 ILE cc_start: 0.3972 (OUTLIER) cc_final: 0.3543 (pt) REVERT: F 227 TYR cc_start: 0.2614 (m-80) cc_final: 0.2127 (m-10) REVERT: F 250 VAL cc_start: 0.4358 (OUTLIER) cc_final: 0.4114 (m) REVERT: G 4 HIS cc_start: 0.5996 (t-90) cc_final: 0.5497 (t-170) REVERT: G 25 PHE cc_start: 0.5275 (m-80) cc_final: 0.5049 (m-80) REVERT: G 85 TYR cc_start: 0.6506 (p90) cc_final: 0.5915 (p90) REVERT: H 358 TYR cc_start: 0.4723 (OUTLIER) cc_final: 0.3227 (m-80) REVERT: H 463 ASN cc_start: 0.6772 (m-40) cc_final: 0.6571 (m-40) REVERT: H 479 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7833 (tm-30) REVERT: I 3 LEU cc_start: 0.7945 (tp) cc_final: 0.7682 (tt) REVERT: I 23 LYS cc_start: 0.8004 (tptm) cc_final: 0.7683 (tptt) REVERT: I 98 GLN cc_start: 0.8302 (tm-30) cc_final: 0.8046 (pp30) REVERT: J 3 LEU cc_start: 0.7458 (tp) cc_final: 0.7213 (tt) REVERT: J 116 ASP cc_start: 0.6732 (m-30) cc_final: 0.6098 (t0) REVERT: J 123 ASN cc_start: 0.7495 (m-40) cc_final: 0.7058 (m110) REVERT: M 21 ASN cc_start: 0.6318 (t0) cc_final: 0.6032 (t0) REVERT: N 175 MET cc_start: 0.6344 (mtt) cc_final: 0.6103 (mtt) outliers start: 93 outliers final: 57 residues processed: 404 average time/residue: 0.4589 time to fit residues: 296.1835 Evaluate side-chains 367 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 297 time to evaluate : 4.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 155 GLU 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 16 GLN Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 224 ARG 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 264 TYR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 199 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 F residue 250 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 250 TYR Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 358 TYR Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 460 LEU Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain H residue 479 GLU Chi-restraints excluded: chain H residue 493 ILE Chi-restraints excluded: chain H residue 511 THR Chi-restraints excluded: chain H residue 515 LEU Chi-restraints excluded: chain H residue 530 VAL 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 119 LYS Chi-restraints excluded: chain J residue 38 ASP Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain J residue 111 PHE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 59 ASN Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 153 THR Chi-restraints excluded: chain M residue 177 LEU Chi-restraints excluded: chain N residue 13 CYS Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 140 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 256 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 258 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 250 optimal weight: 10.0000 chunk 249 optimal weight: 10.0000 chunk 230 optimal weight: 0.7980 chunk 75 optimal weight: 0.0970 chunk 246 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 overall best weight: 3.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 28 ASN ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 GLN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 GLN ** D 220 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 191 GLN ** 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 145 HIS ** F 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 ASN H 427 GLN ** H 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 577 ASN ** I 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 121 ASN ** M 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 ASN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.122936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.105981 restraints weight = 99063.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.108533 restraints weight = 58803.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.110156 restraints weight = 38401.448| |-----------------------------------------------------------------------------| r_work (final): 0.4280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.8289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 25148 Z= 0.283 Angle : 0.844 11.305 34105 Z= 0.435 Chirality : 0.049 0.294 3701 Planarity : 0.006 0.117 4355 Dihedral : 14.215 178.076 3926 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 34.23 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.69 % Favored : 87.10 % Rotamer: Outliers : 4.69 % Allowed : 28.08 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.14), residues: 2931 helix: -0.31 (0.16), residues: 948 sheet: -1.40 (0.25), residues: 411 loop : -2.84 (0.14), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP J 77 HIS 0.016 0.003 HIS B 231 PHE 0.034 0.003 PHE C 188 TYR 0.033 0.003 TYR H 497 ARG 0.011 0.001 ARG C 126 Details of bonding type rmsd hydrogen bonds : bond 0.04388 ( 821) hydrogen bonds : angle 5.66876 ( 2352) covalent geometry : bond 0.00612 (25148) covalent geometry : angle 0.84439 (34105) *********************** 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 474 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 355 time to evaluate : 3.523 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: A 36 THR cc_start: 0.7826 (OUTLIER) cc_final: 0.7540 (p) REVERT: A 93 GLU cc_start: 0.7520 (tp30) cc_final: 0.7070 (tp30) REVERT: A 102 MET cc_start: 0.7736 (tpp) cc_final: 0.7277 (tpp) REVERT: A 124 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.8049 (mm-40) REVERT: A 178 TYR cc_start: 0.6461 (m-80) cc_final: 0.5927 (m-80) REVERT: B 68 ARG cc_start: 0.6536 (OUTLIER) cc_final: 0.5845 (ptp90) REVERT: B 150 MET cc_start: 0.6616 (pmm) cc_final: 0.5676 (pmm) REVERT: B 183 PHE cc_start: 0.6579 (m-80) cc_final: 0.6151 (m-80) REVERT: C 141 MET cc_start: 0.5029 (mtm) cc_final: 0.4591 (mtm) REVERT: D 141 MET cc_start: 0.5591 (mmm) cc_final: 0.5146 (mpp) REVERT: D 167 MET cc_start: 0.5683 (mmm) cc_final: 0.5342 (mmm) REVERT: D 169 ARG cc_start: 0.7967 (ptp90) cc_final: 0.7720 (ptp90) REVERT: D 227 TYR cc_start: 0.4735 (m-80) cc_final: 0.4452 (m-80) REVERT: D 264 TYR cc_start: 0.2736 (OUTLIER) cc_final: 0.2481 (m-10) REVERT: E 52 ASN cc_start: 0.8877 (m-40) cc_final: 0.8373 (m-40) REVERT: E 90 GLU cc_start: 0.6478 (tt0) cc_final: 0.6127 (tp30) REVERT: E 100 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8142 (mm110) REVERT: E 134 SER cc_start: 0.8635 (OUTLIER) cc_final: 0.7746 (t) REVERT: F 7 TYR cc_start: 0.8256 (m-80) cc_final: 0.7659 (m-80) REVERT: F 93 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7374 (tm-30) REVERT: F 112 PHE cc_start: 0.8683 (m-80) cc_final: 0.8431 (m-10) REVERT: F 169 ARG cc_start: 0.7082 (mmt-90) cc_final: 0.6457 (mmp80) REVERT: F 170 LYS cc_start: 0.4996 (mmtt) cc_final: 0.4673 (mptt) REVERT: F 227 TYR cc_start: 0.3077 (m-80) cc_final: 0.2704 (m-10) REVERT: F 250 VAL cc_start: 0.4587 (OUTLIER) cc_final: 0.4353 (m) REVERT: G 4 HIS cc_start: 0.6858 (t-90) cc_final: 0.6437 (t-170) REVERT: G 85 TYR cc_start: 0.6481 (p90) cc_final: 0.5899 (p90) REVERT: G 160 ARG cc_start: 0.5501 (mtt180) cc_final: 0.5291 (mmt90) REVERT: G 177 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7379 (pm20) REVERT: G 278 ARG cc_start: 0.6338 (ptt180) cc_final: 0.5909 (ptt180) REVERT: G 307 LEU cc_start: 0.3220 (OUTLIER) cc_final: 0.2871 (tp) REVERT: H 358 TYR cc_start: 0.6339 (OUTLIER) cc_final: 0.4787 (m-80) REVERT: H 463 ASN cc_start: 0.7411 (m-40) cc_final: 0.7035 (m-40) REVERT: H 479 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7976 (tm-30) REVERT: I 13 VAL cc_start: 0.8246 (p) cc_final: 0.7841 (m) REVERT: I 23 LYS cc_start: 0.8104 (tptm) cc_final: 0.7720 (tptt) REVERT: I 25 GLN cc_start: 0.7949 (tm-30) cc_final: 0.7472 (tp-100) REVERT: I 40 TYR cc_start: 0.7493 (m-80) cc_final: 0.7140 (m-80) REVERT: I 116 ASP cc_start: 0.7932 (t0) cc_final: 0.7552 (t0) REVERT: J 3 LEU cc_start: 0.7888 (tp) cc_final: 0.7608 (tt) REVERT: J 123 ASN cc_start: 0.7580 (m-40) cc_final: 0.7235 (m110) REVERT: N 137 GLN cc_start: 0.4711 (tt0) cc_final: 0.4444 (mp10) REVERT: N 175 MET cc_start: 0.6422 (mtt) cc_final: 0.6094 (mtt) outliers start: 119 outliers final: 71 residues processed: 446 average time/residue: 0.5532 time to fit residues: 387.0777 Evaluate side-chains 393 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 313 time to evaluate : 4.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 PHE Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 112 PHE Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 170 LYS 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 50 VAL Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 243 LEU 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 D residue 281 LYS Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 86 VAL 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 188 PHE Chi-restraints excluded: chain F residue 45 CYS Chi-restraints excluded: chain F residue 62 HIS Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 203 TRP Chi-restraints excluded: chain F residue 231 HIS Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 307 LEU Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 358 TYR Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 479 GLU Chi-restraints excluded: chain H residue 493 ILE Chi-restraints excluded: chain H residue 511 THR Chi-restraints excluded: chain H residue 530 VAL Chi-restraints excluded: chain H residue 539 ILE 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 29 ASN Chi-restraints excluded: chain I residue 56 MET Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 38 ASP Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain J residue 111 PHE Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 59 ASN Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 152 VAL Chi-restraints excluded: chain M residue 177 LEU Chi-restraints excluded: chain M residue 249 VAL Chi-restraints excluded: chain M residue 265 LEU 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 98 VAL Chi-restraints excluded: chain N residue 140 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 159 optimal weight: 6.9990 chunk 237 optimal weight: 5.9990 chunk 292 optimal weight: 6.9990 chunk 240 optimal weight: 6.9990 chunk 162 optimal weight: 8.9990 chunk 127 optimal weight: 8.9990 chunk 269 optimal weight: 0.9990 chunk 221 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 28 ASN A 62 HIS ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 HIS ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN D 83 GLN ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 HIS ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 HIS F 208 ASN F 212 HIS G 104 HIS H 577 ASN I 6 ASN ** I 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN J 81 GLN ** J 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 199 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.122930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.106360 restraints weight = 98272.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.108626 restraints weight = 56542.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.110216 restraints weight = 37319.585| |-----------------------------------------------------------------------------| r_work (final): 0.4292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.8644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 25148 Z= 0.231 Angle : 0.771 13.015 34105 Z= 0.396 Chirality : 0.046 0.270 3701 Planarity : 0.005 0.055 4355 Dihedral : 14.212 176.035 3924 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 30.69 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.57 % Favored : 88.23 % Rotamer: Outliers : 3.47 % Allowed : 30.99 % Favored : 65.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.14), residues: 2931 helix: -0.47 (0.16), residues: 963 sheet: -1.52 (0.24), residues: 434 loop : -2.92 (0.14), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP H 534 HIS 0.010 0.002 HIS B 231 PHE 0.028 0.003 PHE A 171 TYR 0.035 0.002 TYR H 497 ARG 0.009 0.001 ARG C 169 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 821) hydrogen bonds : angle 5.65855 ( 2352) covalent geometry : bond 0.00504 (25148) covalent geometry : angle 0.77143 (34105) *********************** 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 415 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 327 time to evaluate : 2.652 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: A 93 GLU cc_start: 0.7536 (tp30) cc_final: 0.7110 (tp30) REVERT: A 102 MET cc_start: 0.7762 (tpp) cc_final: 0.7160 (tpp) REVERT: A 116 MET cc_start: 0.6783 (ptm) cc_final: 0.5946 (tmm) REVERT: A 178 TYR cc_start: 0.6589 (m-80) cc_final: 0.5773 (m-80) REVERT: B 68 ARG cc_start: 0.6456 (OUTLIER) cc_final: 0.5748 (ptp90) REVERT: B 183 PHE cc_start: 0.6692 (m-80) cc_final: 0.6278 (m-80) REVERT: D 116 MET cc_start: 0.5757 (pmm) cc_final: 0.5417 (pmm) REVERT: D 141 MET cc_start: 0.5460 (mmm) cc_final: 0.5030 (mpp) REVERT: D 167 MET cc_start: 0.5813 (mmm) cc_final: 0.5323 (mmm) REVERT: D 227 TYR cc_start: 0.4618 (m-80) cc_final: 0.4400 (m-80) REVERT: E 52 ASN cc_start: 0.8995 (m-40) cc_final: 0.8578 (m-40) REVERT: E 90 GLU cc_start: 0.6339 (tt0) cc_final: 0.5921 (tp30) REVERT: F 7 TYR cc_start: 0.8230 (m-80) cc_final: 0.7854 (m-80) REVERT: F 169 ARG cc_start: 0.6879 (mmt-90) cc_final: 0.6294 (mmp80) REVERT: F 170 LYS cc_start: 0.4907 (mmtt) cc_final: 0.4636 (mptt) REVERT: F 229 PHE cc_start: 0.4802 (OUTLIER) cc_final: 0.4539 (m-80) REVERT: G 4 HIS cc_start: 0.6811 (t-90) cc_final: 0.6239 (t-170) REVERT: G 85 TYR cc_start: 0.6767 (p90) cc_final: 0.6190 (p90) REVERT: G 177 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7386 (pm20) REVERT: G 278 ARG cc_start: 0.6269 (ptt180) cc_final: 0.5770 (ptt180) REVERT: H 358 TYR cc_start: 0.6454 (OUTLIER) cc_final: 0.4641 (m-80) REVERT: H 463 ASN cc_start: 0.7351 (m-40) cc_final: 0.7035 (m-40) REVERT: H 479 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7999 (tm-30) REVERT: I 13 VAL cc_start: 0.8323 (p) cc_final: 0.7938 (m) REVERT: I 21 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8175 (mt) REVERT: I 40 TYR cc_start: 0.7553 (m-80) cc_final: 0.7073 (m-80) REVERT: J 18 PHE cc_start: 0.7174 (t80) cc_final: 0.6826 (t80) REVERT: J 56 MET cc_start: 0.8227 (mmm) cc_final: 0.7985 (mmm) REVERT: J 81 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.7275 (mt0) REVERT: J 123 ASN cc_start: 0.7766 (m-40) cc_final: 0.7330 (m110) REVERT: M 29 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8959 (pp) outliers start: 88 outliers final: 60 residues processed: 399 average time/residue: 0.3697 time to fit residues: 232.4287 Evaluate side-chains 361 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 294 time to evaluate : 2.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 179 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 250 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 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 203 TRP Chi-restraints excluded: chain F residue 229 PHE Chi-restraints excluded: chain F residue 231 HIS Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 358 TYR Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 470 VAL Chi-restraints excluded: chain H residue 479 GLU Chi-restraints excluded: chain H residue 493 ILE Chi-restraints excluded: chain H residue 530 VAL 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 29 ASN Chi-restraints excluded: chain J residue 38 ASP Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain J residue 111 PHE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 59 ASN Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 152 VAL Chi-restraints excluded: chain M residue 177 LEU Chi-restraints excluded: chain M residue 249 VAL Chi-restraints excluded: chain M residue 255 VAL Chi-restraints excluded: chain M residue 265 LEU 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 98 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 265 optimal weight: 0.6980 chunk 207 optimal weight: 5.9990 chunk 232 optimal weight: 0.7980 chunk 292 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 230 optimal weight: 2.9990 chunk 175 optimal weight: 20.0000 chunk 0 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 HIS ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 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 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 HIS ** 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 104 HIS ** I 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 GLN ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN ** J 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 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 = 0.4515 r_free = 0.4515 target = 0.123698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.107016 restraints weight = 99884.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.109215 restraints weight = 56443.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.110932 restraints weight = 37541.152| |-----------------------------------------------------------------------------| r_work (final): 0.4303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.8811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 25148 Z= 0.198 Angle : 0.755 10.200 34105 Z= 0.385 Chirality : 0.046 0.242 3701 Planarity : 0.005 0.056 4355 Dihedral : 14.234 176.472 3924 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 29.67 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.60 % Favored : 88.20 % Rotamer: Outliers : 3.35 % Allowed : 31.31 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.14), residues: 2931 helix: -0.42 (0.16), residues: 951 sheet: -1.63 (0.23), residues: 463 loop : -2.90 (0.14), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP H 534 HIS 0.008 0.002 HIS A 145 PHE 0.050 0.003 PHE C 112 TYR 0.028 0.002 TYR H 497 ARG 0.007 0.001 ARG J 39 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 821) hydrogen bonds : angle 5.58512 ( 2352) covalent geometry : bond 0.00445 (25148) covalent geometry : angle 0.75502 (34105) *********************** 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 391 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 306 time to evaluate : 3.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.7566 (tp30) cc_final: 0.7132 (tp30) REVERT: A 102 MET cc_start: 0.7756 (tpp) cc_final: 0.7102 (tpp) REVERT: A 116 MET cc_start: 0.6864 (ptm) cc_final: 0.6301 (tmm) REVERT: A 178 TYR cc_start: 0.6504 (m-80) cc_final: 0.5779 (m-80) REVERT: B 68 ARG cc_start: 0.6264 (OUTLIER) cc_final: 0.5649 (ptp90) REVERT: B 183 PHE cc_start: 0.6749 (m-80) cc_final: 0.6387 (m-80) REVERT: C 141 MET cc_start: 0.5899 (mtm) cc_final: 0.5344 (mtm) REVERT: D 116 MET cc_start: 0.6115 (pmm) cc_final: 0.5607 (pmm) REVERT: D 141 MET cc_start: 0.5397 (mmm) cc_final: 0.4977 (mpp) REVERT: D 167 MET cc_start: 0.5564 (mmm) cc_final: 0.5166 (mmm) REVERT: D 169 ARG cc_start: 0.8061 (ptp-170) cc_final: 0.7783 (ptp-170) REVERT: D 227 TYR cc_start: 0.4560 (m-80) cc_final: 0.4349 (m-80) REVERT: E 52 ASN cc_start: 0.8909 (m-40) cc_final: 0.8469 (m-40) REVERT: E 90 GLU cc_start: 0.6432 (tt0) cc_final: 0.5974 (tp30) REVERT: E 150 MET cc_start: 0.3248 (mmp) cc_final: 0.2927 (mtt) REVERT: E 220 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.6569 (tm-30) REVERT: F 7 TYR cc_start: 0.8209 (m-80) cc_final: 0.7781 (m-80) REVERT: F 169 ARG cc_start: 0.7013 (mmt-90) cc_final: 0.6486 (mmp80) REVERT: F 170 LYS cc_start: 0.4858 (mmtt) cc_final: 0.4556 (mptt) REVERT: F 178 TYR cc_start: 0.6908 (OUTLIER) cc_final: 0.6593 (t80) REVERT: F 229 PHE cc_start: 0.4875 (OUTLIER) cc_final: 0.4631 (m-80) REVERT: G 1 MET cc_start: 0.6634 (ptt) cc_final: 0.6423 (ptt) REVERT: G 4 HIS cc_start: 0.6428 (t-90) cc_final: 0.5802 (t-170) REVERT: G 85 TYR cc_start: 0.6691 (p90) cc_final: 0.6163 (p90) REVERT: G 177 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7436 (pt0) REVERT: G 278 ARG cc_start: 0.6265 (ptt180) cc_final: 0.5795 (ptt180) REVERT: G 307 LEU cc_start: 0.3683 (OUTLIER) cc_final: 0.3292 (tp) REVERT: H 358 TYR cc_start: 0.6664 (OUTLIER) cc_final: 0.4837 (m-80) REVERT: H 463 ASN cc_start: 0.7379 (m-40) cc_final: 0.7167 (m-40) REVERT: H 479 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7934 (tm-30) REVERT: H 513 MET cc_start: 0.5859 (mmp) cc_final: 0.5370 (mmp) REVERT: I 13 VAL cc_start: 0.8245 (p) cc_final: 0.7845 (m) REVERT: I 21 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8168 (mt) REVERT: I 40 TYR cc_start: 0.7384 (m-80) cc_final: 0.6997 (m-80) REVERT: J 18 PHE cc_start: 0.7129 (t80) cc_final: 0.6812 (t80) REVERT: J 123 ASN cc_start: 0.7748 (m-40) cc_final: 0.7327 (m110) REVERT: N 51 VAL cc_start: 0.5456 (OUTLIER) cc_final: 0.5155 (t) outliers start: 85 outliers final: 59 residues processed: 372 average time/residue: 0.3769 time to fit residues: 220.5829 Evaluate side-chains 364 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 296 time to evaluate : 2.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 220 GLN Chi-restraints excluded: chain F residue 62 HIS Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 178 TYR Chi-restraints excluded: chain F residue 203 TRP Chi-restraints excluded: chain F residue 229 PHE Chi-restraints excluded: chain F residue 231 HIS Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 307 LEU Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 358 TYR Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 479 GLU Chi-restraints excluded: chain H residue 493 ILE Chi-restraints excluded: chain H residue 530 VAL 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 29 ASN Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain J residue 38 ASP Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain J residue 111 PHE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 59 ASN Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 152 VAL Chi-restraints excluded: chain M residue 177 LEU Chi-restraints excluded: chain M residue 249 VAL Chi-restraints excluded: chain M residue 255 VAL Chi-restraints excluded: chain M residue 265 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 6 GLU 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 193 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 15 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 75 optimal weight: 0.0470 chunk 282 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 chunk 146 optimal weight: 0.1980 chunk 157 optimal weight: 5.9990 chunk 164 optimal weight: 8.9990 chunk 237 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 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 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN D 83 GLN ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 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 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 GLN F 83 GLN F 181 HIS G 4 HIS I 29 ASN ** I 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 130 GLN ** 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 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN ** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.127499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.111106 restraints weight = 98541.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.113608 restraints weight = 56021.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.115343 restraints weight = 36762.485| |-----------------------------------------------------------------------------| r_work (final): 0.4376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.8640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 25148 Z= 0.149 Angle : 0.740 18.763 34105 Z= 0.371 Chirality : 0.045 0.223 3701 Planarity : 0.005 0.058 4355 Dihedral : 14.202 174.934 3923 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 24.76 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.06 % Favored : 89.73 % Rotamer: Outliers : 2.13 % Allowed : 32.89 % Favored : 64.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.14), residues: 2931 helix: -0.35 (0.16), residues: 961 sheet: -1.46 (0.23), residues: 475 loop : -2.88 (0.14), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP H 534 HIS 0.007 0.001 HIS N 136 PHE 0.038 0.003 PHE C 210 TYR 0.025 0.002 TYR I 40 ARG 0.008 0.001 ARG J 39 Details of bonding type rmsd hydrogen bonds : bond 0.03448 ( 821) hydrogen bonds : angle 5.47276 ( 2352) covalent geometry : bond 0.00343 (25148) covalent geometry : angle 0.73954 (34105) ********************** 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 375 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 321 time to evaluate : 5.311 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: A 93 GLU cc_start: 0.7453 (tp30) cc_final: 0.7043 (tp30) REVERT: A 102 MET cc_start: 0.7771 (tpp) cc_final: 0.7128 (tpp) REVERT: A 116 MET cc_start: 0.6312 (ptm) cc_final: 0.5986 (ppp) REVERT: A 171 PHE cc_start: 0.8459 (m-80) cc_final: 0.8222 (m-80) REVERT: A 178 TYR cc_start: 0.6377 (m-80) cc_final: 0.5659 (m-80) REVERT: A 209 MET cc_start: 0.5033 (tpp) cc_final: 0.4361 (tpp) REVERT: A 221 MET cc_start: 0.5578 (mmm) cc_final: 0.5281 (mtp) REVERT: B 68 ARG cc_start: 0.6263 (OUTLIER) cc_final: 0.6050 (ptp90) REVERT: B 179 ARG cc_start: 0.7374 (ttt180) cc_final: 0.6803 (ttt180) REVERT: B 183 PHE cc_start: 0.6699 (m-80) cc_final: 0.6235 (m-10) REVERT: C 141 MET cc_start: 0.5844 (mtm) cc_final: 0.5452 (mtm) REVERT: C 221 MET cc_start: 0.7302 (ttm) cc_final: 0.7031 (ttm) REVERT: D 116 MET cc_start: 0.6063 (pmm) cc_final: 0.5227 (pmm) REVERT: D 141 MET cc_start: 0.4938 (mmm) cc_final: 0.4476 (mpp) REVERT: D 150 MET cc_start: 0.4614 (ptp) cc_final: 0.4229 (ptp) REVERT: D 167 MET cc_start: 0.5647 (mmm) cc_final: 0.5196 (mmm) REVERT: D 227 TYR cc_start: 0.4360 (m-80) cc_final: 0.4145 (m-80) REVERT: E 52 ASN cc_start: 0.9010 (m-40) cc_final: 0.8550 (m-40) REVERT: E 90 GLU cc_start: 0.6303 (tt0) cc_final: 0.5902 (tp30) REVERT: E 100 GLN cc_start: 0.8662 (mm-40) cc_final: 0.8257 (mm110) REVERT: E 102 MET cc_start: 0.7597 (mmt) cc_final: 0.7276 (mmt) REVERT: E 135 ARG cc_start: 0.7908 (mtt-85) cc_final: 0.7549 (mmt180) REVERT: F 7 TYR cc_start: 0.8259 (m-80) cc_final: 0.7871 (m-80) REVERT: F 140 ILE cc_start: 0.4135 (pt) cc_final: 0.3717 (tp) REVERT: F 169 ARG cc_start: 0.6886 (mmt-90) cc_final: 0.6458 (mmp80) REVERT: F 170 LYS cc_start: 0.4935 (mmtt) cc_final: 0.4610 (mptt) REVERT: F 178 TYR cc_start: 0.6802 (OUTLIER) cc_final: 0.6182 (t80) REVERT: F 229 PHE cc_start: 0.4838 (OUTLIER) cc_final: 0.4623 (m-80) REVERT: G 4 HIS cc_start: 0.6011 (t70) cc_final: 0.5637 (t-170) REVERT: G 85 TYR cc_start: 0.6688 (p90) cc_final: 0.6149 (p90) REVERT: G 89 LEU cc_start: 0.4592 (mt) cc_final: 0.4204 (mt) REVERT: G 177 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7382 (pm20) REVERT: G 307 LEU cc_start: 0.3686 (OUTLIER) cc_final: 0.3294 (tp) REVERT: H 358 TYR cc_start: 0.6529 (OUTLIER) cc_final: 0.4876 (m-80) REVERT: H 463 ASN cc_start: 0.7028 (m-40) cc_final: 0.6785 (m-40) REVERT: H 479 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7892 (tm-30) REVERT: I 13 VAL cc_start: 0.8151 (p) cc_final: 0.7772 (m) REVERT: I 21 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8097 (mt) REVERT: I 40 TYR cc_start: 0.7560 (m-80) cc_final: 0.7091 (m-80) REVERT: J 3 LEU cc_start: 0.7541 (tp) cc_final: 0.7235 (tt) REVERT: J 77 TRP cc_start: 0.4137 (OUTLIER) cc_final: 0.3505 (t60) REVERT: J 123 ASN cc_start: 0.7841 (m-40) cc_final: 0.7451 (m110) REVERT: N 51 VAL cc_start: 0.5510 (OUTLIER) cc_final: 0.5233 (t) outliers start: 54 outliers final: 33 residues processed: 361 average time/residue: 0.4786 time to fit residues: 278.9104 Evaluate side-chains 336 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 294 time to evaluate : 5.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 68 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 179 ARG Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain F residue 62 HIS Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 178 TYR Chi-restraints excluded: chain F residue 203 TRP Chi-restraints excluded: chain F residue 229 PHE Chi-restraints excluded: chain F residue 231 HIS Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 307 LEU Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 358 TYR Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 479 GLU Chi-restraints excluded: chain H residue 493 ILE Chi-restraints excluded: chain H residue 530 VAL 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 51 VAL Chi-restraints excluded: chain J residue 77 TRP Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 152 VAL 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 175 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 235 optimal weight: 5.9990 chunk 187 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 295 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 226 optimal weight: 10.0000 chunk 31 optimal weight: 0.0010 chunk 20 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 40 optimal weight: 0.6980 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 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 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 HIS ** I 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 GLN ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 130 GLN ** 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 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 103 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.125858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.109442 restraints weight = 99431.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.112145 restraints weight = 57543.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.113786 restraints weight = 36892.619| |-----------------------------------------------------------------------------| r_work (final): 0.4345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.8799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 25148 Z= 0.168 Angle : 0.743 18.017 34105 Z= 0.374 Chirality : 0.045 0.334 3701 Planarity : 0.005 0.056 4355 Dihedral : 14.121 176.249 3922 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 26.87 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.58 % Favored : 89.22 % Rotamer: Outliers : 2.01 % Allowed : 33.16 % Favored : 64.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.15), residues: 2931 helix: -0.33 (0.16), residues: 969 sheet: -1.45 (0.23), residues: 471 loop : -2.82 (0.14), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP H 357 HIS 0.007 0.001 HIS A 145 PHE 0.040 0.003 PHE C 112 TYR 0.057 0.002 TYR I 106 ARG 0.007 0.001 ARG J 39 Details of bonding type rmsd hydrogen bonds : bond 0.03499 ( 821) hydrogen bonds : angle 5.49690 ( 2352) covalent geometry : bond 0.00387 (25148) covalent geometry : angle 0.74307 (34105) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10952.80 seconds wall clock time: 200 minutes 5.61 seconds (12005.61 seconds total)