Starting phenix.real_space_refine on Fri Feb 6 15:52:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iri_60815/02_2026/9iri_60815_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iri_60815/02_2026/9iri_60815.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9iri_60815/02_2026/9iri_60815_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iri_60815/02_2026/9iri_60815_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9iri_60815/02_2026/9iri_60815.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iri_60815/02_2026/9iri_60815.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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 69 5.49 5 S 40 5.16 5 C 16056 2.51 5 N 4540 2.21 5 O 5161 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25866 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2545 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 11, 'TRANS': 316} Chain: "B" Number of atoms: 1444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1444 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 174} Chain: "C" Number of atoms: 2573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2573 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 320} Chain: "D" Number of atoms: 2573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2573 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 320} Chain: "E" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2559 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 318} Chain: "F" Number of atoms: 2573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2573 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 320} Chain: "G" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2566 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 319} Chain: "I" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2559 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 318} Chain: "J" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2536 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 11, 'TRANS': 315} Chain: "K" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2488 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 11, 'TRANS': 308} Chain: "M" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1450 Classifications: {'DNA': 1, 'RNA': 68} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 17, 'rna3p_pur': 19, 'rna3p_pyr': 16} Link IDs: {'rna2p': 31, 'rna3p': 37} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 6.40, per 1000 atoms: 0.25 Number of scatterers: 25866 At special positions: 0 Unit cell: (151.7, 141.86, 156.62, 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 40 16.00 P 69 15.00 O 5161 8.00 N 4540 7.00 C 16056 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: 2.24 Conformation dependent library (CDL) restraints added in 1.2 seconds 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5806 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 53 sheets defined 31.2% alpha, 16.7% beta 4 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 3.16 Creating SS restraints... Processing helix chain 'A' and resid 57 through 62 removed outlier: 3.766A pdb=" N THR A 61 " --> pdb=" O LYS A 57 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER A 62 " --> pdb=" O ASN A 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 57 through 62' Processing helix chain 'A' and resid 63 through 73 removed outlier: 3.532A pdb=" N ASP A 68 " --> pdb=" O PRO A 64 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU A 70 " --> pdb=" O LYS A 66 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS A 73 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 129 removed outlier: 3.759A pdb=" N ASP A 120 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 145 removed outlier: 3.560A pdb=" N GLU A 140 " --> pdb=" O ALA A 136 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN A 141 " --> pdb=" O ARG A 137 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY A 145 " --> pdb=" O ASN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 202 removed outlier: 3.556A pdb=" N LEU A 192 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY A 202 " --> pdb=" O LYS A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.825A pdb=" N ALA A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG A 261 " --> pdb=" O GLY A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 274 removed outlier: 4.081A pdb=" N ALA A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 269 through 274' Processing helix chain 'A' and resid 300 through 304 Processing helix chain 'A' and resid 318 through 329 removed outlier: 3.724A pdb=" N ILE A 323 " --> pdb=" O GLN A 319 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A 324 " --> pdb=" O HIS A 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 35 removed outlier: 4.261A pdb=" N LEU B 20 " --> pdb=" O THR B 16 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU B 24 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL B 31 " --> pdb=" O LYS B 27 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 32 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY B 33 " --> pdb=" O HIS B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 68 removed outlier: 3.528A pdb=" N LEU B 64 " --> pdb=" O THR B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 117 removed outlier: 3.786A pdb=" N LEU B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG B 110 " --> pdb=" O ALA B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 133 removed outlier: 4.014A pdb=" N VAL B 132 " --> pdb=" O PRO B 129 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLU B 133 " --> pdb=" O ASP B 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 129 through 133' Processing helix chain 'C' and resid 57 through 63 removed outlier: 3.996A pdb=" N ASP C 63 " --> pdb=" O ALA C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 72 removed outlier: 3.993A pdb=" N ALA C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU C 70 " --> pdb=" O LYS C 66 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN C 72 " --> pdb=" O ASP C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 129 removed outlier: 4.401A pdb=" N THR C 116 " --> pdb=" O GLN C 112 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN C 129 " --> pdb=" O TYR C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 145 removed outlier: 3.868A pdb=" N ALA C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE C 142 " --> pdb=" O TYR C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 153 removed outlier: 4.629A pdb=" N VAL C 153 " --> pdb=" O TRP C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 201 removed outlier: 3.705A pdb=" N GLN C 194 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ALA C 195 " --> pdb=" O ALA C 191 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY C 199 " --> pdb=" O ALA C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 removed outlier: 3.565A pdb=" N ASN C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 260 Processing helix chain 'C' and resid 269 through 273 removed outlier: 3.871A pdb=" N GLU C 272 " --> pdb=" O ALA C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 309 removed outlier: 3.516A pdb=" N LEU C 303 " --> pdb=" O ASP C 299 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASP C 305 " --> pdb=" O TYR C 301 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ASN C 306 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TRP C 307 " --> pdb=" O LEU C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 329 removed outlier: 3.813A pdb=" N TYR C 321 " --> pdb=" O GLU C 317 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL C 322 " --> pdb=" O GLN C 318 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE C 323 " --> pdb=" O GLN C 319 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA C 324 " --> pdb=" O HIS C 320 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG C 328 " --> pdb=" O ALA C 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 63 removed outlier: 3.573A pdb=" N ASP D 63 " --> pdb=" O ALA D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 73 removed outlier: 3.737A pdb=" N GLU D 70 " --> pdb=" O LYS D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 129 removed outlier: 3.990A pdb=" N ALA D 117 " --> pdb=" O ASP D 113 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 118 " --> pdb=" O TYR D 114 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY D 119 " --> pdb=" O GLN D 115 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE D 121 " --> pdb=" O ALA D 117 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN D 127 " --> pdb=" O THR D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.710A pdb=" N GLY D 145 " --> pdb=" O ASN D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 188 No H-bonds generated for 'chain 'D' and resid 186 through 188' Processing helix chain 'D' and resid 189 through 202 removed outlier: 3.622A pdb=" N GLN D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA D 195 " --> pdb=" O ALA D 191 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU D 197 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY D 202 " --> pdb=" O LYS D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 236 removed outlier: 3.627A pdb=" N ASN D 236 " --> pdb=" O LYS D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 258 removed outlier: 3.515A pdb=" N ILE D 256 " --> pdb=" O HIS D 252 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY D 257 " --> pdb=" O SER D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 274 removed outlier: 4.491A pdb=" N ALA D 273 " --> pdb=" O ALA D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 308 removed outlier: 3.518A pdb=" N LEU D 303 " --> pdb=" O ASP D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 329 removed outlier: 3.523A pdb=" N VAL D 322 " --> pdb=" O GLN D 318 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE D 323 " --> pdb=" O GLN D 319 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA D 324 " --> pdb=" O HIS D 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 63 removed outlier: 3.668A pdb=" N THR E 61 " --> pdb=" O LYS E 57 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASP E 63 " --> pdb=" O ALA E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 73 removed outlier: 3.765A pdb=" N ASP E 68 " --> pdb=" O PRO E 64 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA E 69 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU E 70 " --> pdb=" O LYS E 66 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN E 72 " --> pdb=" O ASP E 68 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS E 73 " --> pdb=" O ALA E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 128 removed outlier: 3.626A pdb=" N GLN E 115 " --> pdb=" O ASP E 111 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP E 120 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR E 123 " --> pdb=" O GLY E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 139 removed outlier: 3.625A pdb=" N ALA E 135 " --> pdb=" O PHE E 131 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG E 137 " --> pdb=" O THR E 133 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA E 139 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 200 removed outlier: 3.537A pdb=" N ALA E 191 " --> pdb=" O GLY E 187 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA E 195 " --> pdb=" O ALA E 191 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE E 196 " --> pdb=" O LEU E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 261 removed outlier: 3.601A pdb=" N ILE E 256 " --> pdb=" O HIS E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 274 removed outlier: 4.098A pdb=" N ALA E 273 " --> pdb=" O ALA E 269 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY E 274 " --> pdb=" O ALA E 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 269 through 274' Processing helix chain 'E' and resid 293 through 297 Processing helix chain 'E' and resid 299 through 309 removed outlier: 4.708A pdb=" N ASP E 305 " --> pdb=" O TYR E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 329 removed outlier: 3.943A pdb=" N VAL E 322 " --> pdb=" O GLN E 318 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE E 323 " --> pdb=" O GLN E 319 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE E 327 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG E 328 " --> pdb=" O ALA E 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 62 Processing helix chain 'F' and resid 63 through 71 removed outlier: 3.530A pdb=" N ASP F 68 " --> pdb=" O PRO F 64 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU F 70 " --> pdb=" O LYS F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 129 removed outlier: 3.697A pdb=" N THR F 116 " --> pdb=" O GLN F 112 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP F 120 " --> pdb=" O THR F 116 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR F 123 " --> pdb=" O GLY F 119 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN F 127 " --> pdb=" O THR F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 145 removed outlier: 3.706A pdb=" N ALA F 136 " --> pdb=" O SER F 132 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG F 137 " --> pdb=" O THR F 133 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN F 141 " --> pdb=" O ARG F 137 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE F 142 " --> pdb=" O TYR F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 177 removed outlier: 3.757A pdb=" N TYR F 177 " --> pdb=" O GLY F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 201 Processing helix chain 'F' and resid 252 through 261 removed outlier: 3.619A pdb=" N ALA F 259 " --> pdb=" O LYS F 255 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG F 261 " --> pdb=" O GLY F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 274 removed outlier: 3.980A pdb=" N ALA F 273 " --> pdb=" O ALA F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 309 removed outlier: 3.629A pdb=" N TRP F 307 " --> pdb=" O LEU F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 329 removed outlier: 4.205A pdb=" N TYR F 321 " --> pdb=" O GLU F 317 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL F 322 " --> pdb=" O GLN F 318 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU F 326 " --> pdb=" O VAL F 322 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE F 327 " --> pdb=" O ILE F 323 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 62 removed outlier: 3.675A pdb=" N THR G 61 " --> pdb=" O LYS G 57 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER G 62 " --> pdb=" O ASN G 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 57 through 62' Processing helix chain 'G' and resid 63 through 72 removed outlier: 3.666A pdb=" N ALA G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 126 removed outlier: 3.815A pdb=" N GLN G 115 " --> pdb=" O ASP G 111 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA G 117 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP G 120 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 145 removed outlier: 3.736A pdb=" N ASN G 141 " --> pdb=" O ARG G 137 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY G 145 " --> pdb=" O ASN G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 202 removed outlier: 3.726A pdb=" N LEU G 192 " --> pdb=" O ASP G 188 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY G 199 " --> pdb=" O ALA G 195 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA G 201 " --> pdb=" O GLU G 197 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY G 202 " --> pdb=" O LYS G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 261 removed outlier: 3.669A pdb=" N ILE G 256 " --> pdb=" O HIS G 252 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA G 259 " --> pdb=" O LYS G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 299 through 309 removed outlier: 5.073A pdb=" N ASP G 305 " --> pdb=" O TYR G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 317 through 329 removed outlier: 3.996A pdb=" N TYR G 321 " --> pdb=" O GLU G 317 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL G 322 " --> pdb=" O GLN G 318 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG G 328 " --> pdb=" O ALA G 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 62 Processing helix chain 'I' and resid 63 through 69 removed outlier: 3.560A pdb=" N ALA I 69 " --> pdb=" O ALA I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 73 Processing helix chain 'I' and resid 112 through 129 removed outlier: 3.535A pdb=" N GLY I 119 " --> pdb=" O GLN I 115 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP I 120 " --> pdb=" O THR I 116 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE I 122 " --> pdb=" O LEU I 118 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR I 123 " --> pdb=" O GLY I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 145 Processing helix chain 'I' and resid 173 through 177 Processing helix chain 'I' and resid 187 through 200 removed outlier: 3.590A pdb=" N ALA I 191 " --> pdb=" O GLY I 187 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN I 194 " --> pdb=" O ALA I 190 " (cutoff:3.500A) Processing helix chain 'I' and resid 252 through 260 removed outlier: 3.629A pdb=" N ILE I 256 " --> pdb=" O HIS I 252 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY I 257 " --> pdb=" O SER I 253 " (cutoff:3.500A) Processing helix chain 'I' and resid 269 through 274 removed outlier: 4.226A pdb=" N ALA I 273 " --> pdb=" O ALA I 269 " (cutoff:3.500A) Processing helix chain 'I' and resid 293 through 297 Processing helix chain 'I' and resid 299 through 309 Processing helix chain 'I' and resid 318 through 329 removed outlier: 3.827A pdb=" N VAL I 322 " --> pdb=" O GLN I 318 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE I 323 " --> pdb=" O GLN I 319 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE I 327 " --> pdb=" O ILE I 323 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 62 removed outlier: 3.760A pdb=" N SER J 62 " --> pdb=" O ASN J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 71 removed outlier: 3.813A pdb=" N LEU J 67 " --> pdb=" O ASP J 63 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP J 68 " --> pdb=" O PRO J 64 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA J 69 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU J 70 " --> pdb=" O LYS J 66 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE J 71 " --> pdb=" O LEU J 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 63 through 71' Processing helix chain 'J' and resid 111 through 129 removed outlier: 3.665A pdb=" N GLN J 115 " --> pdb=" O ASP J 111 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR J 116 " --> pdb=" O GLN J 112 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP J 120 " --> pdb=" O THR J 116 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR J 123 " --> pdb=" O GLY J 119 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY J 124 " --> pdb=" O ASP J 120 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TYR J 125 " --> pdb=" O ILE J 121 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA J 126 " --> pdb=" O ILE J 122 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN J 127 " --> pdb=" O THR J 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 145 removed outlier: 3.858A pdb=" N ALA J 143 " --> pdb=" O ALA J 139 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY J 145 " --> pdb=" O ASN J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 173 through 177 removed outlier: 3.546A pdb=" N ASP J 176 " --> pdb=" O ASN J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 187 through 200 removed outlier: 4.008A pdb=" N GLN J 194 " --> pdb=" O ALA J 190 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA J 195 " --> pdb=" O ALA J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 231 through 236 removed outlier: 3.785A pdb=" N ARG J 235 " --> pdb=" O ASP J 231 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN J 236 " --> pdb=" O GLU J 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 231 through 236' Processing helix chain 'J' and resid 252 through 261 removed outlier: 3.721A pdb=" N ILE J 256 " --> pdb=" O HIS J 252 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG J 261 " --> pdb=" O GLY J 257 " (cutoff:3.500A) Processing helix chain 'J' and resid 269 through 274 removed outlier: 4.237A pdb=" N ALA J 273 " --> pdb=" O ALA J 269 " (cutoff:3.500A) Processing helix chain 'J' and resid 299 through 307 removed outlier: 3.656A pdb=" N ASP J 305 " --> pdb=" O TYR J 301 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN J 306 " --> pdb=" O THR J 302 " (cutoff:3.500A) Processing helix chain 'J' and resid 315 through 329 removed outlier: 3.657A pdb=" N HIS J 320 " --> pdb=" O PRO J 316 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N TYR J 321 " --> pdb=" O GLU J 317 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL J 322 " --> pdb=" O GLN J 318 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE J 323 " --> pdb=" O GLN J 319 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU J 326 " --> pdb=" O VAL J 322 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 63 removed outlier: 3.969A pdb=" N ASP K 63 " --> pdb=" O ALA K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 69 removed outlier: 3.819A pdb=" N LEU K 67 " --> pdb=" O ASP K 63 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA K 69 " --> pdb=" O ALA K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 129 removed outlier: 3.880A pdb=" N THR K 123 " --> pdb=" O GLY K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 145 removed outlier: 3.539A pdb=" N ALA K 139 " --> pdb=" O ALA K 135 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY K 145 " --> pdb=" O ASN K 141 " (cutoff:3.500A) Processing helix chain 'K' and resid 187 through 202 removed outlier: 4.212A pdb=" N LYS K 198 " --> pdb=" O GLN K 194 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLY K 199 " --> pdb=" O ALA K 195 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ALA K 201 " --> pdb=" O GLU K 197 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY K 202 " --> pdb=" O LYS K 198 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 260 removed outlier: 3.647A pdb=" N ASN K 258 " --> pdb=" O GLN K 254 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU K 260 " --> pdb=" O ILE K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 267 through 271 removed outlier: 4.278A pdb=" N ASP K 271 " --> pdb=" O PRO K 268 " (cutoff:3.500A) Processing helix chain 'K' and resid 299 through 304 Processing helix chain 'K' and resid 304 through 309 removed outlier: 3.605A pdb=" N VAL K 308 " --> pdb=" O LEU K 304 " (cutoff:3.500A) Processing helix chain 'K' and resid 318 through 329 removed outlier: 4.169A pdb=" N VAL K 322 " --> pdb=" O GLN K 318 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE K 323 " --> pdb=" O GLN K 319 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA K 324 " --> pdb=" O HIS K 320 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU K 326 " --> pdb=" O VAL K 322 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG K 328 " --> pdb=" O ALA K 324 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY K 329 " --> pdb=" O THR K 325 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 109 removed outlier: 4.036A pdb=" N VAL A 108 " --> pdb=" O ALA A 15 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE A 16 " --> pdb=" O GLY A 330 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY A 330 " --> pdb=" O PHE A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 22 removed outlier: 3.636A pdb=" N LYS A 92 " --> pdb=" O TYR A 28 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 25 through 30 current: chain 'A' and resid 158 through 164 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 40 removed outlier: 3.636A pdb=" N LYS A 92 " --> pdb=" O TYR A 28 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 44 through 50 Processing sheet with id=AA5, first strand: chain 'A' and resid 283 through 284 removed outlier: 3.565A pdb=" N VAL A 284 " --> pdb=" O LYS A 289 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA7, first strand: chain 'B' and resid 54 through 57 removed outlier: 3.631A pdb=" N TYR B 4 " --> pdb=" O LYS B 86 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS B 86 " --> pdb=" O TYR B 4 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 95 removed outlier: 3.742A pdb=" N LYS B 93 " --> pdb=" O TRP B 183 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 98 through 99 removed outlier: 4.051A pdb=" N ARG B 98 " --> pdb=" O GLU B 157 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 14 through 15 Processing sheet with id=AB2, first strand: chain 'C' and resid 20 through 22 removed outlier: 3.566A pdb=" N ALA C 21 " --> pdb=" O ARG C 98 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE C 208 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR C 163 " --> pdb=" O THR C 209 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 25 through 26 removed outlier: 3.722A pdb=" N ALA C 25 " --> pdb=" O ILE C 251 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 44 through 48 removed outlier: 3.941A pdb=" N LYS C 46 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN C 77 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 283 through 284 removed outlier: 3.650A pdb=" N LYS C 289 " --> pdb=" O VAL C 284 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 20 through 21 removed outlier: 3.566A pdb=" N ALA D 21 " --> pdb=" O ARG D 98 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL D 94 " --> pdb=" O LEU D 26 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU D 26 " --> pdb=" O VAL D 94 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 25 through 30 current: chain 'D' and resid 157 through 164 removed outlier: 4.276A pdb=" N LYS D 164 " --> pdb=" O ARG D 168 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARG D 168 " --> pdb=" O LYS D 164 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 39 through 40 removed outlier: 3.571A pdb=" N THR D 39 " --> pdb=" O ALA D 29 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU D 26 " --> pdb=" O VAL D 94 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL D 94 " --> pdb=" O LEU D 26 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 90 through 99 current: chain 'D' and resid 244 through 245 Processing sheet with id=AB8, first strand: chain 'D' and resid 44 through 50 removed outlier: 3.568A pdb=" N LYS D 46 " --> pdb=" O VAL D 79 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN D 75 " --> pdb=" O GLY D 50 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 226 through 227 removed outlier: 3.996A pdb=" N ILE D 241 " --> pdb=" O GLU D 227 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 262 through 264 Processing sheet with id=AC2, first strand: chain 'E' and resid 108 through 109 removed outlier: 3.624A pdb=" N VAL E 108 " --> pdb=" O ALA E 15 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 20 through 21 Processing sheet with id=AC4, first strand: chain 'E' and resid 39 through 40 removed outlier: 3.755A pdb=" N ALA E 29 " --> pdb=" O THR E 39 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS E 92 " --> pdb=" O TYR E 28 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 44 through 50 Processing sheet with id=AC6, first strand: chain 'E' and resid 283 through 284 removed outlier: 3.706A pdb=" N VAL E 284 " --> pdb=" O LYS E 289 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS E 289 " --> pdb=" O VAL E 284 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'F' and resid 14 through 15 Processing sheet with id=AC8, first strand: chain 'F' and resid 20 through 22 removed outlier: 3.565A pdb=" N LYS F 92 " --> pdb=" O TYR F 28 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL F 94 " --> pdb=" O LEU F 26 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 25 through 30 current: chain 'F' and resid 157 through 164 Processing sheet with id=AC9, first strand: chain 'F' and resid 39 through 40 removed outlier: 3.523A pdb=" N THR F 39 " --> pdb=" O ALA F 29 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL F 94 " --> pdb=" O LEU F 26 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS F 92 " --> pdb=" O TYR F 28 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 90 through 99 current: chain 'F' and resid 244 through 245 Processing sheet with id=AD1, first strand: chain 'F' and resid 46 through 50 removed outlier: 3.598A pdb=" N LYS F 46 " --> pdb=" O VAL F 79 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 262 through 264 Processing sheet with id=AD3, first strand: chain 'F' and resid 283 through 284 removed outlier: 3.572A pdb=" N VAL F 284 " --> pdb=" O LYS F 289 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 108 through 109 removed outlier: 3.535A pdb=" N VAL G 108 " --> pdb=" O ALA G 15 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE G 16 " --> pdb=" O GLY G 330 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 20 through 22 Processing sheet with id=AD6, first strand: chain 'G' and resid 20 through 22 Processing sheet with id=AD7, first strand: chain 'G' and resid 44 through 50 Processing sheet with id=AD8, first strand: chain 'G' and resid 283 through 284 Processing sheet with id=AD9, first strand: chain 'I' and resid 108 through 109 removed outlier: 3.981A pdb=" N VAL I 108 " --> pdb=" O ALA I 15 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA I 15 " --> pdb=" O VAL I 108 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY I 330 " --> pdb=" O PHE I 16 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 20 through 22 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 25 through 29 current: chain 'I' and resid 158 through 164 Processing sheet with id=AE2, first strand: chain 'I' and resid 39 through 40 removed outlier: 3.501A pdb=" N THR I 39 " --> pdb=" O ALA I 29 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 91 through 99 current: chain 'I' and resid 244 through 245 Processing sheet with id=AE3, first strand: chain 'I' and resid 44 through 50 Processing sheet with id=AE4, first strand: chain 'I' and resid 262 through 264 Processing sheet with id=AE5, first strand: chain 'J' and resid 108 through 109 removed outlier: 3.752A pdb=" N VAL J 108 " --> pdb=" O ALA J 15 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 20 through 22 removed outlier: 3.962A pdb=" N ARG J 98 " --> pdb=" O ALA J 21 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 39 through 40 removed outlier: 3.624A pdb=" N THR J 39 " --> pdb=" O ALA J 29 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE J 93 " --> pdb=" O ALA J 212 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA J 157 " --> pdb=" O GLN J 215 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 43 through 50 removed outlier: 3.550A pdb=" N GLN J 44 " --> pdb=" O VAL J 81 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LYS J 238 " --> pdb=" O LEU J 76 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LYS J 78 " --> pdb=" O LYS J 238 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LYS J 240 " --> pdb=" O LYS J 78 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 161 through 163 removed outlier: 3.638A pdb=" N VAL J 162 " --> pdb=" O TRP J 170 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 244 through 245 removed outlier: 3.791A pdb=" N VAL J 248 " --> pdb=" O VAL J 245 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 262 through 264 Processing sheet with id=AF3, first strand: chain 'K' and resid 14 through 15 removed outlier: 3.753A pdb=" N VAL K 108 " --> pdb=" O ALA K 15 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 20 through 22 removed outlier: 4.455A pdb=" N ALA K 21 " --> pdb=" O ARG K 98 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL K 94 " --> pdb=" O LEU K 26 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU K 26 " --> pdb=" O VAL K 94 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 20 through 22 removed outlier: 4.455A pdb=" N ALA K 21 " --> pdb=" O ARG K 98 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR K 209 " --> pdb=" O THR K 163 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA K 157 " --> pdb=" O GLN K 215 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL K 160 " --> pdb=" O PHE K 172 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE K 172 " --> pdb=" O VAL K 160 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 44 through 50 removed outlier: 3.503A pdb=" N GLN K 77 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASN K 75 " --> pdb=" O GLY K 50 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 244 through 245 Processing sheet with id=AF8, first strand: chain 'K' and resid 283 through 284 685 hydrogen bonds defined for protein. 1839 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 11 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 4.74 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6900 1.33 - 1.45: 5146 1.45 - 1.57: 14237 1.57 - 1.69: 136 1.69 - 1.81: 69 Bond restraints: 26488 Sorted by residual: bond pdb=" C ARG G 292 " pdb=" N GLN G 293 " ideal model delta sigma weight residual 1.330 1.221 0.109 1.47e-02 4.63e+03 5.54e+01 bond pdb=" C ARG I 292 " pdb=" N GLN I 293 " ideal model delta sigma weight residual 1.331 1.210 0.121 2.83e-02 1.25e+03 1.82e+01 bond pdb=" N TRP G 149 " pdb=" CA TRP G 149 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.17e-02 7.31e+03 6.68e+00 bond pdb=" N TRP J 149 " pdb=" CA TRP J 149 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.90e+00 bond pdb=" CB TRP J 149 " pdb=" CG TRP J 149 " ideal model delta sigma weight residual 1.498 1.430 0.068 3.10e-02 1.04e+03 4.86e+00 ... (remaining 26483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.47: 35939 3.47 - 6.95: 277 6.95 - 10.42: 25 10.42 - 13.90: 1 13.90 - 17.37: 1 Bond angle restraints: 36243 Sorted by residual: angle pdb=" N ILE D 263 " pdb=" CA ILE D 263 " pdb=" C ILE D 263 " ideal model delta sigma weight residual 113.71 106.83 6.88 9.50e-01 1.11e+00 5.25e+01 angle pdb=" C LEU E 148 " pdb=" N TRP E 149 " pdb=" CA TRP E 149 " ideal model delta sigma weight residual 121.54 131.51 -9.97 1.91e+00 2.74e-01 2.73e+01 angle pdb=" C LEU G 148 " pdb=" N TRP G 149 " pdb=" CA TRP G 149 " ideal model delta sigma weight residual 121.19 129.16 -7.97 1.59e+00 3.96e-01 2.51e+01 angle pdb=" CA LEU G 228 " pdb=" CB LEU G 228 " pdb=" CG LEU G 228 " ideal model delta sigma weight residual 116.30 133.67 -17.37 3.50e+00 8.16e-02 2.46e+01 angle pdb=" C LEU J 148 " pdb=" N TRP J 149 " pdb=" CA TRP J 149 " ideal model delta sigma weight residual 121.54 130.02 -8.48 1.91e+00 2.74e-01 1.97e+01 ... (remaining 36238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 15597 35.81 - 71.61: 338 71.61 - 107.42: 46 107.42 - 143.22: 1 143.22 - 179.03: 2 Dihedral angle restraints: 15984 sinusoidal: 6931 harmonic: 9053 Sorted by residual: dihedral pdb=" O4' U M 35 " pdb=" C1' U M 35 " pdb=" N1 U M 35 " pdb=" C2 U M 35 " ideal model delta sinusoidal sigma weight residual 232.00 52.97 179.03 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U M 6 " pdb=" C1' U M 6 " pdb=" N1 U M 6 " pdb=" C2 U M 6 " ideal model delta sinusoidal sigma weight residual 232.00 57.86 174.14 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" CA TYR C 267 " pdb=" C TYR C 267 " pdb=" N PRO C 268 " pdb=" CA PRO C 268 " ideal model delta harmonic sigma weight residual -180.00 -142.65 -37.35 0 5.00e+00 4.00e-02 5.58e+01 ... (remaining 15981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3275 0.065 - 0.130: 686 0.130 - 0.196: 94 0.196 - 0.261: 12 0.261 - 0.326: 6 Chirality restraints: 4073 Sorted by residual: chirality pdb=" CB ILE A 93 " pdb=" CA ILE A 93 " pdb=" CG1 ILE A 93 " pdb=" CG2 ILE A 93 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CG LEU I 326 " pdb=" CB LEU I 326 " pdb=" CD1 LEU I 326 " pdb=" CD2 LEU I 326 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CB ILE E 93 " pdb=" CA ILE E 93 " pdb=" CG1 ILE E 93 " pdb=" CG2 ILE E 93 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 4070 not shown) Planarity restraints: 4513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 307 " 0.030 2.00e-02 2.50e+03 2.70e-02 1.82e+01 pdb=" CG TRP G 307 " -0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP G 307 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP G 307 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP G 307 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP G 307 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP G 307 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 307 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 307 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP G 307 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 307 " -0.028 2.00e-02 2.50e+03 2.47e-02 1.52e+01 pdb=" CG TRP E 307 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP E 307 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP E 307 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP E 307 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP E 307 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 307 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 307 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 307 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP E 307 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 307 " -0.027 2.00e-02 2.50e+03 2.07e-02 1.07e+01 pdb=" CG TRP F 307 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP F 307 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP F 307 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 307 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 307 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 307 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 307 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 307 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP F 307 " -0.003 2.00e-02 2.50e+03 ... (remaining 4510 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 350 2.64 - 3.20: 21975 3.20 - 3.77: 38845 3.77 - 4.33: 54120 4.33 - 4.90: 87176 Nonbonded interactions: 202466 Sorted by model distance: nonbonded pdb=" O THR K 96 " pdb=" NH1 ARG K 98 " model vdw 2.070 3.120 nonbonded pdb=" NH1 ARG C 292 " pdb=" O MET C 298 " model vdw 2.071 3.120 nonbonded pdb=" N ARG E 49 " pdb=" OP2 A M 42 " model vdw 2.128 3.120 nonbonded pdb=" O TRP D 149 " pdb=" NH1 ARG D 152 " model vdw 2.133 3.120 nonbonded pdb=" NZ LYS G 92 " pdb=" OE1 GLU G 211 " model vdw 2.143 3.120 ... (remaining 202461 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 13 through 332) selection = (chain 'C' and resid 13 through 332) selection = (chain 'D' and resid 13 through 332) selection = (chain 'E' and resid 13 through 332) selection = (chain 'F' and resid 13 through 332) selection = (chain 'G' and resid 13 through 332) selection = (chain 'I' and resid 13 through 332) selection = (chain 'J' and resid 13 through 332) selection = chain 'K' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 8.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.890 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 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 : 0.006 0.121 26488 Z= 0.303 Angle : 0.955 17.370 36243 Z= 0.563 Chirality : 0.055 0.326 4073 Planarity : 0.007 0.067 4513 Dihedral : 14.255 179.026 10178 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.16 (0.12), residues: 3126 helix: -4.55 (0.07), residues: 779 sheet: -1.36 (0.22), residues: 537 loop : -2.42 (0.11), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 261 TYR 0.031 0.003 TYR A 138 PHE 0.032 0.003 PHE I 16 TRP 0.072 0.005 TRP G 307 HIS 0.015 0.003 HIS G 320 Details of bonding type rmsd covalent geometry : bond 0.00629 (26488) covalent geometry : angle 0.95533 (36243) hydrogen bonds : bond 0.32906 ( 668) hydrogen bonds : angle 10.92143 ( 1861) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 717 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6971 (m-40) cc_final: 0.6736 (m-40) REVERT: A 215 GLN cc_start: 0.7817 (tt0) cc_final: 0.7198 (tt0) REVERT: A 264 ASP cc_start: 0.7736 (t0) cc_final: 0.7500 (t0) REVERT: A 281 TYR cc_start: 0.7632 (m-10) cc_final: 0.7395 (m-10) REVERT: C 180 ARG cc_start: 0.6473 (mtt180) cc_final: 0.6139 (mtt180) REVERT: C 252 HIS cc_start: 0.7121 (m-70) cc_final: 0.6841 (m-70) REVERT: C 272 GLU cc_start: 0.7055 (pp20) cc_final: 0.6793 (pp20) REVERT: C 278 VAL cc_start: 0.8599 (t) cc_final: 0.8375 (m) REVERT: C 323 ILE cc_start: 0.8025 (tp) cc_final: 0.7799 (tp) REVERT: D 68 ASP cc_start: 0.7450 (m-30) cc_final: 0.7109 (m-30) REVERT: D 77 GLN cc_start: 0.5640 (tp-100) cc_final: 0.5319 (tp-100) REVERT: D 226 GLN cc_start: 0.7149 (mt0) cc_final: 0.6459 (mt0) REVERT: D 271 ASP cc_start: 0.7938 (t0) cc_final: 0.7733 (t0) REVERT: D 334 GLU cc_start: 0.5780 (tm-30) cc_final: 0.5430 (tm-30) REVERT: E 45 GLU cc_start: 0.6268 (tp30) cc_final: 0.5980 (tp30) REVERT: E 47 SER cc_start: 0.8300 (p) cc_final: 0.8034 (p) REVERT: E 78 LYS cc_start: 0.8262 (ttpt) cc_final: 0.7985 (ttpt) REVERT: E 220 GLN cc_start: 0.7917 (mm-40) cc_final: 0.7639 (mm110) REVERT: E 306 ASN cc_start: 0.7561 (m-40) cc_final: 0.7010 (m110) REVERT: E 320 HIS cc_start: 0.7406 (m-70) cc_final: 0.7144 (m90) REVERT: F 66 LYS cc_start: 0.7566 (mttm) cc_final: 0.7227 (mtpp) REVERT: F 79 VAL cc_start: 0.7909 (m) cc_final: 0.7588 (m) REVERT: F 90 THR cc_start: 0.8246 (m) cc_final: 0.7918 (m) REVERT: F 247 ASP cc_start: 0.7728 (m-30) cc_final: 0.7512 (m-30) REVERT: F 283 SER cc_start: 0.7716 (m) cc_final: 0.7387 (t) REVERT: F 293 GLN cc_start: 0.7994 (mm-40) cc_final: 0.7437 (mm110) REVERT: F 331 VAL cc_start: 0.8611 (p) cc_final: 0.8360 (m) REVERT: F 334 GLU cc_start: 0.7498 (tp30) cc_final: 0.7232 (tp30) REVERT: G 66 LYS cc_start: 0.8144 (mtmt) cc_final: 0.7934 (mtmt) REVERT: G 71 ILE cc_start: 0.8520 (mt) cc_final: 0.8309 (mt) REVERT: G 107 SER cc_start: 0.7048 (m) cc_final: 0.6190 (m) REVERT: G 150 ARG cc_start: 0.7765 (ttt-90) cc_final: 0.7529 (ttt-90) REVERT: G 169 SER cc_start: 0.7323 (p) cc_final: 0.7070 (t) REVERT: G 223 PHE cc_start: 0.7795 (m-80) cc_final: 0.7501 (m-80) REVERT: G 267 TYR cc_start: 0.8147 (p90) cc_final: 0.7926 (p90) REVERT: G 302 THR cc_start: 0.7552 (m) cc_final: 0.7006 (m) REVERT: G 306 ASN cc_start: 0.7827 (m-40) cc_final: 0.7429 (m-40) REVERT: I 56 LEU cc_start: 0.8309 (mt) cc_final: 0.7938 (mp) REVERT: I 159 ARG cc_start: 0.7135 (ttt-90) cc_final: 0.6924 (ttt-90) REVERT: I 167 GLU cc_start: 0.7460 (tm-30) cc_final: 0.7243 (tm-30) REVERT: I 172 PHE cc_start: 0.7052 (m-10) cc_final: 0.6615 (m-10) REVERT: I 194 GLN cc_start: 0.7950 (tp40) cc_final: 0.7717 (tp-100) REVERT: I 254 GLN cc_start: 0.8544 (mp10) cc_final: 0.8283 (mp10) REVERT: I 289 LYS cc_start: 0.7552 (ttmm) cc_final: 0.6932 (ttmm) REVERT: I 316 PRO cc_start: 0.8509 (Cg_exo) cc_final: 0.8057 (Cg_endo) REVERT: I 332 PHE cc_start: 0.7747 (m-80) cc_final: 0.7499 (m-80) REVERT: J 14 LEU cc_start: 0.8119 (tp) cc_final: 0.7763 (tm) REVERT: J 109 CYS cc_start: 0.6351 (p) cc_final: 0.5582 (m) REVERT: J 176 ASP cc_start: 0.6768 (t70) cc_final: 0.6563 (t0) REVERT: J 181 GLN cc_start: 0.7156 (tm-30) cc_final: 0.6940 (tm-30) REVERT: J 194 GLN cc_start: 0.7370 (tt0) cc_final: 0.7148 (tt0) REVERT: J 226 GLN cc_start: 0.7597 (mp10) cc_final: 0.7175 (mp10) REVERT: J 243 TYR cc_start: 0.7846 (t80) cc_final: 0.7533 (t80) REVERT: J 253 SER cc_start: 0.8836 (p) cc_final: 0.8525 (m) REVERT: J 315 MET cc_start: 0.7279 (mpp) cc_final: 0.7003 (mpp) REVERT: K 78 LYS cc_start: 0.8225 (ttpt) cc_final: 0.8020 (ttpt) REVERT: K 137 ARG cc_start: 0.7010 (mtt180) cc_final: 0.6718 (ttm170) REVERT: K 151 ASN cc_start: 0.7747 (t0) cc_final: 0.7301 (t0) REVERT: K 171 GLU cc_start: 0.8273 (mp0) cc_final: 0.7956 (mm-30) REVERT: K 298 MET cc_start: 0.6221 (mmt) cc_final: 0.5771 (mmt) outliers start: 0 outliers final: 0 residues processed: 717 average time/residue: 0.6417 time to fit residues: 535.2778 Evaluate side-chains 640 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 640 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 127 GLN A 151 ASN ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 GLN A 306 ASN A 318 GLN B 19 GLN B 150 GLN C 31 ASN C 75 ASN C 141 ASN ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 HIS D 112 GLN ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 GLN E 77 GLN E 102 ASN E 110 ASN F 31 ASN F 102 ASN F 110 ASN F 112 GLN F 115 GLN F 220 GLN F 244 GLN F 258 ASN G 34 GLN G 72 GLN G 105 GLN G 218 ASN ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 GLN I 102 ASN I 218 ASN I 293 GLN J 72 GLN ** J 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 220 GLN J 320 HIS K 35 GLN ** K 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 220 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.186191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.157106 restraints weight = 43816.663| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 3.05 r_work: 0.4016 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 26488 Z= 0.155 Angle : 0.618 9.231 36243 Z= 0.327 Chirality : 0.045 0.192 4073 Planarity : 0.005 0.058 4513 Dihedral : 15.454 171.736 4497 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.35 % Allowed : 12.87 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.13), residues: 3126 helix: -3.09 (0.12), residues: 823 sheet: -0.90 (0.22), residues: 549 loop : -1.86 (0.13), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 152 TYR 0.022 0.002 TYR A 138 PHE 0.017 0.002 PHE E 95 TRP 0.031 0.002 TRP E 307 HIS 0.003 0.001 HIS D 252 Details of bonding type rmsd covalent geometry : bond 0.00334 (26488) covalent geometry : angle 0.61797 (36243) hydrogen bonds : bond 0.04810 ( 668) hydrogen bonds : angle 6.01457 ( 1861) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 673 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.7293 (tp30) cc_final: 0.7016 (tp30) REVERT: A 46 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7794 (ttpp) REVERT: A 127 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7844 (mp10) REVERT: A 156 GLU cc_start: 0.7703 (mp0) cc_final: 0.7181 (mp0) REVERT: A 177 TYR cc_start: 0.8399 (m-10) cc_final: 0.8184 (m-80) REVERT: A 238 LYS cc_start: 0.7549 (mttm) cc_final: 0.7075 (mtpt) REVERT: A 243 TYR cc_start: 0.7822 (t80) cc_final: 0.7447 (t80) REVERT: A 281 TYR cc_start: 0.8135 (m-10) cc_final: 0.7926 (m-10) REVERT: C 35 GLN cc_start: 0.6478 (OUTLIER) cc_final: 0.5128 (mm110) REVERT: C 221 GLU cc_start: 0.8160 (tt0) cc_final: 0.7541 (tp30) REVERT: C 272 GLU cc_start: 0.7542 (pp20) cc_final: 0.7230 (pp20) REVERT: C 291 TYR cc_start: 0.7628 (m-80) cc_final: 0.7261 (m-10) REVERT: C 323 ILE cc_start: 0.8178 (tp) cc_final: 0.7919 (tp) REVERT: D 68 ASP cc_start: 0.7600 (m-30) cc_final: 0.7215 (m-30) REVERT: D 77 GLN cc_start: 0.5759 (tp-100) cc_final: 0.5398 (tm130) REVERT: D 271 ASP cc_start: 0.7897 (t0) cc_final: 0.7674 (t0) REVERT: D 298 MET cc_start: 0.6089 (OUTLIER) cc_final: 0.5813 (tpt) REVERT: D 317 GLU cc_start: 0.7015 (tp30) cc_final: 0.6564 (tp30) REVERT: D 334 GLU cc_start: 0.6245 (tm-30) cc_final: 0.5796 (tm-30) REVERT: E 22 ASN cc_start: 0.7882 (p0) cc_final: 0.7652 (p0) REVERT: E 45 GLU cc_start: 0.6496 (tp30) cc_final: 0.5910 (tp30) REVERT: E 78 LYS cc_start: 0.8488 (ttpt) cc_final: 0.8274 (ttpt) REVERT: E 120 ASP cc_start: 0.7498 (m-30) cc_final: 0.7139 (m-30) REVERT: E 128 GLU cc_start: 0.8018 (tt0) cc_final: 0.7803 (tt0) REVERT: E 323 ILE cc_start: 0.8213 (tt) cc_final: 0.8003 (tt) REVERT: F 79 VAL cc_start: 0.7859 (m) cc_final: 0.7557 (t) REVERT: F 90 THR cc_start: 0.8169 (m) cc_final: 0.7916 (m) REVERT: F 129 GLN cc_start: 0.8541 (mm-40) cc_final: 0.8316 (mm-40) REVERT: F 283 SER cc_start: 0.7910 (m) cc_final: 0.7548 (t) REVERT: F 319 GLN cc_start: 0.8052 (mt0) cc_final: 0.7809 (mt0) REVERT: F 334 GLU cc_start: 0.7736 (tp30) cc_final: 0.7470 (tp30) REVERT: G 66 LYS cc_start: 0.8193 (mtmt) cc_final: 0.7909 (mtmt) REVERT: G 71 ILE cc_start: 0.8676 (mt) cc_final: 0.8446 (mt) REVERT: G 306 ASN cc_start: 0.8068 (m-40) cc_final: 0.7604 (m-40) REVERT: I 55 ARG cc_start: 0.7441 (mtt180) cc_final: 0.7196 (mtt90) REVERT: I 78 LYS cc_start: 0.7982 (ttpp) cc_final: 0.7774 (ttpp) REVERT: I 125 TYR cc_start: 0.7198 (t80) cc_final: 0.6974 (t80) REVERT: I 159 ARG cc_start: 0.7774 (ttt-90) cc_final: 0.7566 (ttt-90) REVERT: I 161 VAL cc_start: 0.8446 (t) cc_final: 0.8245 (t) REVERT: I 167 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7443 (tm-30) REVERT: I 173 ASN cc_start: 0.7550 (t0) cc_final: 0.7277 (t0) REVERT: I 194 GLN cc_start: 0.8284 (tp40) cc_final: 0.8060 (tp40) REVERT: I 279 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7171 (mm-30) REVERT: I 287 ARG cc_start: 0.8112 (mtt90) cc_final: 0.7737 (tpp80) REVERT: I 289 LYS cc_start: 0.7782 (ttmm) cc_final: 0.7292 (ttmm) REVERT: I 310 LYS cc_start: 0.7589 (mppt) cc_final: 0.7178 (mppt) REVERT: I 326 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.6806 (mm) REVERT: I 332 PHE cc_start: 0.7984 (m-80) cc_final: 0.7714 (m-80) REVERT: J 14 LEU cc_start: 0.8253 (tp) cc_final: 0.7855 (tm) REVERT: J 70 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7789 (mp0) REVERT: J 105 GLN cc_start: 0.7629 (pp30) cc_final: 0.7352 (pp30) REVERT: J 109 CYS cc_start: 0.6803 (p) cc_final: 0.5626 (m) REVERT: J 176 ASP cc_start: 0.7292 (t70) cc_final: 0.7041 (t0) REVERT: J 181 GLN cc_start: 0.7457 (tm-30) cc_final: 0.7136 (tm-30) REVERT: J 194 GLN cc_start: 0.7813 (tt0) cc_final: 0.7596 (tt0) REVERT: J 226 GLN cc_start: 0.7889 (mp10) cc_final: 0.7378 (mp10) REVERT: J 243 TYR cc_start: 0.8261 (t80) cc_final: 0.7798 (t80) REVERT: J 244 GLN cc_start: 0.8134 (pp30) cc_final: 0.7876 (pp30) REVERT: K 78 LYS cc_start: 0.8204 (ttpt) cc_final: 0.7894 (ttpt) REVERT: K 137 ARG cc_start: 0.7140 (mtt180) cc_final: 0.6895 (ttm170) REVERT: K 151 ASN cc_start: 0.7755 (t0) cc_final: 0.7302 (t0) REVERT: K 263 ILE cc_start: 0.4118 (mp) cc_final: 0.3891 (mm) outliers start: 59 outliers final: 25 residues processed: 697 average time/residue: 0.6380 time to fit residues: 514.1720 Evaluate side-chains 664 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 635 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 317 GLU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 315 MET Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain I residue 34 GLN Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 326 LEU Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 240 LYS Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain K residue 221 GLU Chi-restraints excluded: chain K residue 251 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 142 optimal weight: 0.0970 chunk 153 optimal weight: 2.9990 chunk 180 optimal weight: 0.7980 chunk 235 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 56 optimal weight: 50.0000 chunk 303 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 224 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 151 ASN ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 GLN C 31 ASN C 252 HIS ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 320 HIS E 110 ASN E 220 GLN E 306 ASN F 77 GLN F 110 ASN F 220 GLN F 244 GLN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 GLN G 102 ASN ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 220 GLN ** G 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN I 129 GLN I 215 GLN I 320 HIS ** J 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.185883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.156795 restraints weight = 44101.882| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 3.07 r_work: 0.4012 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26488 Z= 0.144 Angle : 0.588 9.775 36243 Z= 0.306 Chirality : 0.044 0.226 4073 Planarity : 0.004 0.059 4513 Dihedral : 15.278 172.735 4497 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.19 % Allowed : 16.29 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.14), residues: 3126 helix: -1.90 (0.15), residues: 822 sheet: -0.55 (0.22), residues: 556 loop : -1.62 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 152 TYR 0.034 0.002 TYR C 267 PHE 0.014 0.002 PHE E 95 TRP 0.027 0.002 TRP J 38 HIS 0.003 0.001 HIS J 252 Details of bonding type rmsd covalent geometry : bond 0.00314 (26488) covalent geometry : angle 0.58841 (36243) hydrogen bonds : bond 0.03885 ( 668) hydrogen bonds : angle 5.33063 ( 1861) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 650 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7859 (ttpp) REVERT: A 127 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7793 (mp-120) REVERT: A 243 TYR cc_start: 0.7861 (t80) cc_final: 0.7377 (t80) REVERT: B 19 GLN cc_start: 0.8083 (tp40) cc_final: 0.7491 (tp-100) REVERT: C 35 GLN cc_start: 0.6458 (OUTLIER) cc_final: 0.5834 (pp30) REVERT: C 113 ASP cc_start: 0.6215 (p0) cc_final: 0.5895 (p0) REVERT: C 225 SER cc_start: 0.7482 (p) cc_final: 0.7239 (p) REVERT: C 252 HIS cc_start: 0.7655 (m90) cc_final: 0.7428 (m170) REVERT: C 291 TYR cc_start: 0.7466 (m-80) cc_final: 0.7204 (m-80) REVERT: C 323 ILE cc_start: 0.8197 (tp) cc_final: 0.7903 (tp) REVERT: D 41 ILE cc_start: 0.8535 (mm) cc_final: 0.8249 (pp) REVERT: D 68 ASP cc_start: 0.7587 (m-30) cc_final: 0.7264 (m-30) REVERT: D 208 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.7908 (m-80) REVERT: D 226 GLN cc_start: 0.7567 (mt0) cc_final: 0.6826 (mt0) REVERT: D 298 MET cc_start: 0.6105 (OUTLIER) cc_final: 0.5900 (tpt) REVERT: D 317 GLU cc_start: 0.7049 (tp30) cc_final: 0.6574 (tp30) REVERT: D 334 GLU cc_start: 0.6257 (tm-30) cc_final: 0.5830 (tm-30) REVERT: E 120 ASP cc_start: 0.7544 (m-30) cc_final: 0.7183 (m-30) REVERT: E 128 GLU cc_start: 0.7981 (tt0) cc_final: 0.7769 (tt0) REVERT: E 264 ASP cc_start: 0.8178 (t0) cc_final: 0.7865 (t0) REVERT: E 298 MET cc_start: 0.7138 (OUTLIER) cc_final: 0.6910 (mmm) REVERT: E 317 GLU cc_start: 0.7158 (mm-30) cc_final: 0.6671 (mm-30) REVERT: E 320 HIS cc_start: 0.7608 (m-70) cc_final: 0.7388 (m90) REVERT: E 323 ILE cc_start: 0.8323 (tt) cc_final: 0.8035 (tt) REVERT: F 48 VAL cc_start: 0.8602 (OUTLIER) cc_final: 0.8367 (m) REVERT: F 79 VAL cc_start: 0.7909 (m) cc_final: 0.7584 (t) REVERT: F 90 THR cc_start: 0.8201 (m) cc_final: 0.7941 (m) REVERT: F 240 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.7906 (ttpp) REVERT: F 283 SER cc_start: 0.7955 (m) cc_final: 0.7589 (t) REVERT: F 293 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8230 (mm-40) REVERT: F 334 GLU cc_start: 0.7658 (tp30) cc_final: 0.7398 (tp30) REVERT: G 55 ARG cc_start: 0.8463 (tpp80) cc_final: 0.8203 (ttt90) REVERT: G 66 LYS cc_start: 0.8151 (mtmt) cc_final: 0.7804 (mtmt) REVERT: G 71 ILE cc_start: 0.8629 (mt) cc_final: 0.8396 (mt) REVERT: G 261 ARG cc_start: 0.8232 (ptt-90) cc_final: 0.7986 (ptt-90) REVERT: G 281 TYR cc_start: 0.8578 (m-80) cc_final: 0.8364 (m-80) REVERT: G 298 MET cc_start: 0.7713 (mmm) cc_final: 0.7365 (mmm) REVERT: G 306 ASN cc_start: 0.8081 (m-40) cc_final: 0.7658 (m-40) REVERT: I 49 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.6123 (ptp90) REVERT: I 125 TYR cc_start: 0.7102 (t80) cc_final: 0.6858 (t80) REVERT: I 129 GLN cc_start: 0.7836 (mt0) cc_final: 0.7632 (mt0) REVERT: I 167 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7381 (tm-30) REVERT: I 173 ASN cc_start: 0.7500 (t0) cc_final: 0.7275 (t0) REVERT: I 194 GLN cc_start: 0.8245 (tp40) cc_final: 0.8032 (tp40) REVERT: I 287 ARG cc_start: 0.8202 (mtt90) cc_final: 0.7999 (mtt180) REVERT: I 289 LYS cc_start: 0.7876 (ttmm) cc_final: 0.7365 (ttmm) REVERT: I 323 ILE cc_start: 0.7007 (OUTLIER) cc_final: 0.6777 (mp) REVERT: I 332 PHE cc_start: 0.7950 (m-80) cc_final: 0.7628 (m-80) REVERT: J 14 LEU cc_start: 0.8207 (tp) cc_final: 0.7813 (tm) REVERT: J 19 LYS cc_start: 0.8671 (mmtt) cc_final: 0.8418 (mmtt) REVERT: J 109 CYS cc_start: 0.6786 (p) cc_final: 0.5567 (m) REVERT: J 175 GLU cc_start: 0.6541 (pm20) cc_final: 0.6242 (pm20) REVERT: J 176 ASP cc_start: 0.7238 (t70) cc_final: 0.6997 (t0) REVERT: J 181 GLN cc_start: 0.7457 (tm-30) cc_final: 0.7135 (tm-30) REVERT: J 189 LEU cc_start: 0.6826 (tp) cc_final: 0.6561 (tp) REVERT: J 226 GLN cc_start: 0.7966 (mp10) cc_final: 0.7531 (mp10) REVERT: J 243 TYR cc_start: 0.8194 (t80) cc_final: 0.7854 (t80) REVERT: J 244 GLN cc_start: 0.8121 (pp30) cc_final: 0.7864 (pp30) REVERT: J 254 GLN cc_start: 0.8290 (pm20) cc_final: 0.8029 (pm20) REVERT: J 298 MET cc_start: 0.7102 (ttm) cc_final: 0.6869 (tpp) REVERT: K 19 LYS cc_start: 0.7035 (mmmm) cc_final: 0.6471 (mmmm) REVERT: K 78 LYS cc_start: 0.8197 (ttpt) cc_final: 0.7879 (ttpt) REVERT: K 137 ARG cc_start: 0.7161 (mtt180) cc_final: 0.6930 (ttm170) REVERT: K 151 ASN cc_start: 0.7760 (t0) cc_final: 0.7333 (t0) REVERT: K 315 MET cc_start: 0.4703 (tpp) cc_final: 0.4497 (tpp) outliers start: 80 outliers final: 38 residues processed: 672 average time/residue: 0.6438 time to fit residues: 499.8839 Evaluate side-chains 656 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 608 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 211 GLU Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 240 LYS Chi-restraints excluded: chain F residue 293 GLN Chi-restraints excluded: chain F residue 315 MET Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain I residue 49 ARG Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 323 ILE Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 253 SER Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 326 LEU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 196 ILE Chi-restraints excluded: chain K residue 221 GLU Chi-restraints excluded: chain K residue 251 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 168 optimal weight: 0.8980 chunk 167 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 chunk 225 optimal weight: 1.9990 chunk 196 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 chunk 166 optimal weight: 0.7980 chunk 248 optimal weight: 9.9990 chunk 203 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 151 ASN A 244 GLN B 142 GLN C 31 ASN C 252 HIS ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 ASN E 220 GLN F 77 GLN F 110 ASN F 115 GLN F 220 GLN F 244 GLN F 258 ASN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 ASN G 220 GLN ** G 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN I 102 ASN I 215 GLN I 218 ASN ** J 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 194 GLN ** J 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 GLN ** K 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.184666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.155597 restraints weight = 43545.604| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 3.05 r_work: 0.3989 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 26488 Z= 0.193 Angle : 0.614 13.317 36243 Z= 0.319 Chirality : 0.046 0.262 4073 Planarity : 0.004 0.054 4513 Dihedral : 15.192 175.297 4497 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.86 % Allowed : 17.77 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.14), residues: 3126 helix: -1.40 (0.17), residues: 816 sheet: -0.43 (0.23), residues: 548 loop : -1.54 (0.14), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 328 TYR 0.025 0.002 TYR G 243 PHE 0.017 0.002 PHE J 172 TRP 0.027 0.002 TRP I 307 HIS 0.005 0.001 HIS G 320 Details of bonding type rmsd covalent geometry : bond 0.00420 (26488) covalent geometry : angle 0.61374 (36243) hydrogen bonds : bond 0.03823 ( 668) hydrogen bonds : angle 5.27325 ( 1861) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 629 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7982 (ttpp) REVERT: A 156 GLU cc_start: 0.7833 (mp0) cc_final: 0.7514 (mp0) REVERT: A 216 LEU cc_start: 0.8572 (mt) cc_final: 0.8295 (mp) REVERT: A 239 SER cc_start: 0.8440 (m) cc_final: 0.8005 (t) REVERT: A 243 TYR cc_start: 0.7939 (t80) cc_final: 0.7378 (t80) REVERT: B 19 GLN cc_start: 0.8086 (tp40) cc_final: 0.7497 (tp-100) REVERT: C 35 GLN cc_start: 0.6660 (OUTLIER) cc_final: 0.6001 (pp30) REVERT: C 125 TYR cc_start: 0.6273 (t80) cc_final: 0.5805 (t80) REVERT: C 251 ILE cc_start: 0.8001 (mt) cc_final: 0.7683 (mm) REVERT: C 323 ILE cc_start: 0.8371 (tp) cc_final: 0.8096 (tp) REVERT: D 68 ASP cc_start: 0.7564 (m-30) cc_final: 0.7245 (m-30) REVERT: D 208 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.7931 (m-80) REVERT: D 226 GLN cc_start: 0.7578 (mt0) cc_final: 0.6899 (mt0) REVERT: D 317 GLU cc_start: 0.7087 (tp30) cc_final: 0.6603 (tp30) REVERT: D 334 GLU cc_start: 0.6231 (tm-30) cc_final: 0.5763 (tm-30) REVERT: E 120 ASP cc_start: 0.7582 (m-30) cc_final: 0.7243 (m-30) REVERT: E 264 ASP cc_start: 0.8171 (t0) cc_final: 0.7909 (t0) REVERT: E 265 ASP cc_start: 0.7564 (p0) cc_final: 0.7331 (p0) REVERT: F 48 VAL cc_start: 0.8603 (OUTLIER) cc_final: 0.8392 (m) REVERT: F 49 ARG cc_start: 0.7903 (ttm-80) cc_final: 0.7598 (ptm160) REVERT: F 90 THR cc_start: 0.8239 (m) cc_final: 0.7985 (m) REVERT: F 240 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.7963 (ttpp) REVERT: F 283 SER cc_start: 0.7981 (m) cc_final: 0.7665 (t) REVERT: F 293 GLN cc_start: 0.8697 (mm110) cc_final: 0.8375 (mm-40) REVERT: F 334 GLU cc_start: 0.7701 (tp30) cc_final: 0.7391 (tp30) REVERT: G 55 ARG cc_start: 0.8518 (tpp80) cc_final: 0.8223 (ttt90) REVERT: G 66 LYS cc_start: 0.8169 (mtmt) cc_final: 0.7813 (mtmt) REVERT: G 71 ILE cc_start: 0.8629 (mt) cc_final: 0.8385 (mt) REVERT: G 281 TYR cc_start: 0.8609 (m-80) cc_final: 0.8299 (m-80) REVERT: G 298 MET cc_start: 0.7689 (mmm) cc_final: 0.7345 (mmm) REVERT: G 306 ASN cc_start: 0.8093 (m-40) cc_final: 0.7669 (m-40) REVERT: I 49 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.6074 (ptp90) REVERT: I 167 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7406 (tm-30) REVERT: I 173 ASN cc_start: 0.7525 (t0) cc_final: 0.7283 (t0) REVERT: I 194 GLN cc_start: 0.8295 (tp40) cc_final: 0.8076 (tp40) REVERT: I 289 LYS cc_start: 0.7967 (ttmm) cc_final: 0.7525 (ttmm) REVERT: I 310 LYS cc_start: 0.7592 (mppt) cc_final: 0.7282 (mppt) REVERT: I 323 ILE cc_start: 0.6953 (OUTLIER) cc_final: 0.6734 (mp) REVERT: I 326 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6820 (mm) REVERT: I 332 PHE cc_start: 0.7949 (m-80) cc_final: 0.7616 (m-80) REVERT: J 14 LEU cc_start: 0.8218 (tp) cc_final: 0.7883 (tm) REVERT: J 19 LYS cc_start: 0.8639 (mmtt) cc_final: 0.8438 (mmtt) REVERT: J 105 GLN cc_start: 0.7727 (pp30) cc_final: 0.7422 (pp30) REVERT: J 109 CYS cc_start: 0.6822 (p) cc_final: 0.5616 (m) REVERT: J 115 GLN cc_start: 0.7024 (tm-30) cc_final: 0.6718 (tm-30) REVERT: J 175 GLU cc_start: 0.6702 (pm20) cc_final: 0.6273 (pm20) REVERT: J 176 ASP cc_start: 0.7185 (t70) cc_final: 0.6935 (t0) REVERT: J 181 GLN cc_start: 0.7440 (tm-30) cc_final: 0.7158 (tm-30) REVERT: J 189 LEU cc_start: 0.6838 (tp) cc_final: 0.6608 (tp) REVERT: J 208 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7269 (m-80) REVERT: J 226 GLN cc_start: 0.8004 (mp10) cc_final: 0.7501 (mp10) REVERT: J 243 TYR cc_start: 0.8180 (t80) cc_final: 0.7868 (t80) REVERT: J 279 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7369 (pt0) REVERT: K 19 LYS cc_start: 0.6937 (mmmm) cc_final: 0.6328 (mmmm) REVERT: K 78 LYS cc_start: 0.8304 (ttpt) cc_final: 0.7956 (ttpt) REVERT: K 103 LEU cc_start: 0.7333 (mm) cc_final: 0.7126 (mm) REVERT: K 151 ASN cc_start: 0.7810 (t0) cc_final: 0.7474 (t0) REVERT: K 165 LYS cc_start: 0.7311 (mppt) cc_final: 0.7031 (mmtm) outliers start: 97 outliers final: 43 residues processed: 677 average time/residue: 0.6345 time to fit residues: 496.8279 Evaluate side-chains 658 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 606 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 164 LYS Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 240 LYS Chi-restraints excluded: chain F residue 315 MET Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain I residue 49 ARG Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 309 ILE Chi-restraints excluded: chain I residue 323 ILE Chi-restraints excluded: chain I residue 326 LEU Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 208 PHE Chi-restraints excluded: chain J residue 253 SER Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 326 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 84 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 165 optimal weight: 1.9990 chunk 208 optimal weight: 0.8980 chunk 254 optimal weight: 3.9990 chunk 247 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 89 optimal weight: 0.0570 chunk 105 optimal weight: 6.9990 chunk 314 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 167 optimal weight: 0.0060 chunk 34 optimal weight: 7.9990 overall best weight: 0.9918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 151 ASN ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN C 129 GLN ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 GLN ** E 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 GLN F 110 ASN F 115 GLN F 194 GLN F 220 GLN F 244 GLN F 258 ASN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 319 GLN ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 ASN G 220 GLN ** G 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN I 102 ASN I 110 ASN I 129 GLN I 215 GLN ** I 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 318 GLN ** J 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 151 ASN K 35 GLN K 141 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.184211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.155156 restraints weight = 43465.956| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 3.06 r_work: 0.3983 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 26488 Z= 0.199 Angle : 0.620 10.548 36243 Z= 0.323 Chirality : 0.046 0.242 4073 Planarity : 0.005 0.099 4513 Dihedral : 15.149 175.570 4497 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.22 % Allowed : 18.76 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.14), residues: 3126 helix: -1.06 (0.17), residues: 810 sheet: -0.45 (0.22), residues: 561 loop : -1.40 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 328 TYR 0.032 0.002 TYR G 125 PHE 0.030 0.002 PHE C 95 TRP 0.032 0.002 TRP I 38 HIS 0.005 0.001 HIS G 320 Details of bonding type rmsd covalent geometry : bond 0.00438 (26488) covalent geometry : angle 0.62013 (36243) hydrogen bonds : bond 0.03809 ( 668) hydrogen bonds : angle 5.20832 ( 1861) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 649 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7924 (ttpp) REVERT: A 156 GLU cc_start: 0.7816 (mp0) cc_final: 0.7513 (mp0) REVERT: A 239 SER cc_start: 0.8416 (m) cc_final: 0.7960 (t) REVERT: A 243 TYR cc_start: 0.7932 (t80) cc_final: 0.7372 (t80) REVERT: B 19 GLN cc_start: 0.8110 (tp40) cc_final: 0.7533 (tp-100) REVERT: C 35 GLN cc_start: 0.6812 (OUTLIER) cc_final: 0.6124 (pp30) REVERT: C 251 ILE cc_start: 0.8002 (mt) cc_final: 0.7655 (mm) REVERT: C 287 ARG cc_start: 0.7497 (mmt180) cc_final: 0.7008 (mmt180) REVERT: C 323 ILE cc_start: 0.8336 (tp) cc_final: 0.8084 (tp) REVERT: D 77 GLN cc_start: 0.5987 (tp-100) cc_final: 0.5520 (tm130) REVERT: D 90 THR cc_start: 0.7248 (m) cc_final: 0.7019 (m) REVERT: D 208 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.7871 (m-80) REVERT: D 226 GLN cc_start: 0.7555 (mt0) cc_final: 0.6865 (mt0) REVERT: D 301 TYR cc_start: 0.6851 (m-80) cc_final: 0.6567 (m-80) REVERT: D 317 GLU cc_start: 0.7215 (tp30) cc_final: 0.6687 (tp30) REVERT: D 334 GLU cc_start: 0.6235 (tm-30) cc_final: 0.5786 (tm-30) REVERT: E 120 ASP cc_start: 0.7619 (m-30) cc_final: 0.7308 (m-30) REVERT: E 264 ASP cc_start: 0.8209 (t0) cc_final: 0.7975 (t0) REVERT: E 265 ASP cc_start: 0.7641 (p0) cc_final: 0.7431 (p0) REVERT: E 301 TYR cc_start: 0.7816 (m-10) cc_final: 0.7499 (m-10) REVERT: F 48 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8366 (m) REVERT: F 49 ARG cc_start: 0.7902 (ttm-80) cc_final: 0.7560 (ptm160) REVERT: F 90 THR cc_start: 0.8188 (m) cc_final: 0.7932 (m) REVERT: F 196 ILE cc_start: 0.8112 (mm) cc_final: 0.7877 (mp) REVERT: F 240 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.7927 (ttpp) REVERT: F 283 SER cc_start: 0.7975 (m) cc_final: 0.7676 (t) REVERT: F 293 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8215 (mt0) REVERT: F 296 GLU cc_start: 0.7750 (mp0) cc_final: 0.7498 (mp0) REVERT: F 319 GLN cc_start: 0.8063 (mt0) cc_final: 0.7841 (mt0) REVERT: F 334 GLU cc_start: 0.7670 (tp30) cc_final: 0.7343 (tp30) REVERT: G 66 LYS cc_start: 0.8163 (mtmt) cc_final: 0.7801 (mtmt) REVERT: G 71 ILE cc_start: 0.8614 (mt) cc_final: 0.8369 (mt) REVERT: G 281 TYR cc_start: 0.8577 (m-80) cc_final: 0.8321 (m-80) REVERT: G 298 MET cc_start: 0.7683 (mmm) cc_final: 0.7411 (mmm) REVERT: G 306 ASN cc_start: 0.8157 (m-40) cc_final: 0.7755 (m-40) REVERT: I 49 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.6111 (ptp90) REVERT: I 167 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7465 (tm-30) REVERT: I 173 ASN cc_start: 0.7557 (t0) cc_final: 0.7356 (t0) REVERT: I 194 GLN cc_start: 0.8266 (tp40) cc_final: 0.7991 (tp40) REVERT: I 241 ILE cc_start: 0.8307 (mt) cc_final: 0.7987 (tt) REVERT: I 289 LYS cc_start: 0.7980 (ttmm) cc_final: 0.7558 (ttmm) REVERT: I 310 LYS cc_start: 0.7654 (mppt) cc_final: 0.7403 (mppt) REVERT: I 318 GLN cc_start: 0.8390 (mt0) cc_final: 0.8120 (mt0) REVERT: I 323 ILE cc_start: 0.6858 (OUTLIER) cc_final: 0.6619 (mp) REVERT: I 332 PHE cc_start: 0.7958 (m-80) cc_final: 0.7630 (m-80) REVERT: J 14 LEU cc_start: 0.8260 (tp) cc_final: 0.7896 (tm) REVERT: J 19 LYS cc_start: 0.8611 (mmtt) cc_final: 0.8353 (mmtt) REVERT: J 105 GLN cc_start: 0.7731 (pp30) cc_final: 0.7447 (pp30) REVERT: J 109 CYS cc_start: 0.6846 (p) cc_final: 0.5629 (m) REVERT: J 175 GLU cc_start: 0.6641 (pm20) cc_final: 0.6219 (pm20) REVERT: J 176 ASP cc_start: 0.7162 (t70) cc_final: 0.6915 (t0) REVERT: J 181 GLN cc_start: 0.7469 (tm-30) cc_final: 0.7226 (tm-30) REVERT: J 189 LEU cc_start: 0.6820 (tp) cc_final: 0.6605 (tp) REVERT: J 208 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.7507 (m-80) REVERT: J 226 GLN cc_start: 0.8023 (mp10) cc_final: 0.7630 (mp10) REVERT: J 243 TYR cc_start: 0.8154 (t80) cc_final: 0.7908 (t80) REVERT: J 244 GLN cc_start: 0.8034 (pp30) cc_final: 0.7812 (pp30) REVERT: J 254 GLN cc_start: 0.8330 (pm20) cc_final: 0.8108 (pm20) REVERT: J 279 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7437 (pt0) REVERT: K 19 LYS cc_start: 0.6838 (mmmm) cc_final: 0.6240 (mmmm) REVERT: K 49 ARG cc_start: 0.7438 (ptm160) cc_final: 0.7234 (ptp-170) REVERT: K 78 LYS cc_start: 0.8306 (ttpt) cc_final: 0.7968 (ttpt) REVERT: K 137 ARG cc_start: 0.6966 (mtm180) cc_final: 0.6482 (ttm170) REVERT: K 150 ARG cc_start: 0.7056 (ttt180) cc_final: 0.6841 (ttt-90) REVERT: K 152 ARG cc_start: 0.7947 (ttt180) cc_final: 0.7324 (mmm-85) REVERT: K 165 LYS cc_start: 0.7305 (mppt) cc_final: 0.6976 (mmtm) REVERT: K 251 ILE cc_start: 0.7429 (OUTLIER) cc_final: 0.6893 (mp) REVERT: K 297 LYS cc_start: 0.7080 (OUTLIER) cc_final: 0.6864 (ptpp) outliers start: 106 outliers final: 58 residues processed: 691 average time/residue: 0.6570 time to fit residues: 525.1693 Evaluate side-chains 693 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 624 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 165 LYS Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 240 LYS Chi-restraints excluded: chain F residue 254 GLN Chi-restraints excluded: chain F residue 293 GLN Chi-restraints excluded: chain F residue 315 MET Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 253 SER Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 49 ARG Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 286 SER Chi-restraints excluded: chain I residue 309 ILE Chi-restraints excluded: chain I residue 323 ILE Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 27 MET Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 208 PHE Chi-restraints excluded: chain J residue 253 SER Chi-restraints excluded: chain J residue 308 VAL Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 326 LEU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 196 ILE Chi-restraints excluded: chain K residue 251 ILE Chi-restraints excluded: chain K residue 297 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 55 optimal weight: 20.0000 chunk 165 optimal weight: 0.7980 chunk 87 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 179 optimal weight: 0.0000 chunk 33 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 chunk 224 optimal weight: 0.6980 chunk 168 optimal weight: 1.9990 chunk 232 optimal weight: 0.4980 chunk 289 optimal weight: 9.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 151 ASN ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN E 220 GLN E 318 GLN F 77 GLN F 110 ASN F 115 GLN F 220 GLN F 244 GLN F 258 ASN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 220 GLN ** G 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 GLN I 110 ASN I 215 GLN I 320 HIS ** J 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.185879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.156737 restraints weight = 43785.776| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 3.07 r_work: 0.4009 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26488 Z= 0.137 Angle : 0.587 10.306 36243 Z= 0.305 Chirality : 0.044 0.246 4073 Planarity : 0.004 0.097 4513 Dihedral : 15.035 175.538 4497 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.94 % Allowed : 19.84 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.14), residues: 3126 helix: -0.67 (0.18), residues: 812 sheet: -0.35 (0.22), residues: 557 loop : -1.29 (0.14), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 18 TYR 0.027 0.002 TYR G 243 PHE 0.030 0.001 PHE C 95 TRP 0.034 0.001 TRP I 38 HIS 0.003 0.001 HIS G 320 Details of bonding type rmsd covalent geometry : bond 0.00306 (26488) covalent geometry : angle 0.58723 (36243) hydrogen bonds : bond 0.03326 ( 668) hydrogen bonds : angle 4.90992 ( 1861) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 624 time to evaluate : 0.993 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: A 46 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7902 (ttpp) REVERT: A 197 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6916 (tt0) REVERT: A 216 LEU cc_start: 0.8568 (mt) cc_final: 0.8303 (mp) REVERT: A 239 SER cc_start: 0.8394 (m) cc_final: 0.7935 (t) REVERT: A 243 TYR cc_start: 0.7861 (t80) cc_final: 0.7369 (t80) REVERT: A 318 GLN cc_start: 0.8132 (mp10) cc_final: 0.7762 (mm-40) REVERT: B 1 MET cc_start: 0.4250 (mmp) cc_final: 0.3721 (mmp) REVERT: B 19 GLN cc_start: 0.8128 (tp40) cc_final: 0.7555 (tp-100) REVERT: B 86 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7690 (mppt) REVERT: C 31 ASN cc_start: 0.5508 (t0) cc_final: 0.4896 (t0) REVERT: C 35 GLN cc_start: 0.6573 (OUTLIER) cc_final: 0.5951 (pp30) REVERT: C 251 ILE cc_start: 0.7961 (mt) cc_final: 0.7633 (mm) REVERT: C 272 GLU cc_start: 0.7704 (pp20) cc_final: 0.7465 (pp20) REVERT: C 323 ILE cc_start: 0.8380 (tp) cc_final: 0.8164 (tp) REVERT: C 326 LEU cc_start: 0.8570 (mt) cc_final: 0.8347 (mt) REVERT: D 73 LYS cc_start: 0.8274 (mttt) cc_final: 0.7919 (mttt) REVERT: D 90 THR cc_start: 0.7063 (m) cc_final: 0.6851 (m) REVERT: D 208 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.7849 (m-80) REVERT: D 226 GLN cc_start: 0.7524 (mt0) cc_final: 0.6859 (mt0) REVERT: D 301 TYR cc_start: 0.6861 (m-80) cc_final: 0.6642 (m-80) REVERT: D 317 GLU cc_start: 0.7129 (tp30) cc_final: 0.6662 (tp30) REVERT: D 334 GLU cc_start: 0.6258 (tm-30) cc_final: 0.5786 (tm-30) REVERT: E 120 ASP cc_start: 0.7598 (m-30) cc_final: 0.7279 (m-30) REVERT: E 264 ASP cc_start: 0.8208 (t0) cc_final: 0.7947 (t0) REVERT: E 301 TYR cc_start: 0.7804 (m-10) cc_final: 0.7438 (m-10) REVERT: F 48 VAL cc_start: 0.8522 (OUTLIER) cc_final: 0.8273 (m) REVERT: F 49 ARG cc_start: 0.7870 (ttm-80) cc_final: 0.7529 (ptm160) REVERT: F 90 THR cc_start: 0.8117 (m) cc_final: 0.7867 (m) REVERT: F 283 SER cc_start: 0.7908 (m) cc_final: 0.7603 (t) REVERT: F 293 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8346 (mm-40) REVERT: F 334 GLU cc_start: 0.7716 (tp30) cc_final: 0.7443 (mm-30) REVERT: G 66 LYS cc_start: 0.8102 (mtmt) cc_final: 0.7808 (mtmt) REVERT: G 71 ILE cc_start: 0.8589 (mt) cc_final: 0.8341 (mt) REVERT: G 281 TYR cc_start: 0.8559 (m-80) cc_final: 0.8255 (m-80) REVERT: G 298 MET cc_start: 0.7703 (mmm) cc_final: 0.7437 (mmm) REVERT: G 306 ASN cc_start: 0.8123 (m-40) cc_final: 0.7725 (m-40) REVERT: I 49 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.6030 (ptp90) REVERT: I 167 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7401 (tm-30) REVERT: I 173 ASN cc_start: 0.7491 (t0) cc_final: 0.7270 (t0) REVERT: I 194 GLN cc_start: 0.8203 (tp40) cc_final: 0.7953 (tp40) REVERT: I 287 ARG cc_start: 0.8113 (mtt180) cc_final: 0.7768 (tpp80) REVERT: I 289 LYS cc_start: 0.7977 (ttmm) cc_final: 0.7557 (ttmm) REVERT: I 292 ARG cc_start: 0.8276 (mtt-85) cc_final: 0.7834 (ttm170) REVERT: I 298 MET cc_start: 0.5171 (mtm) cc_final: 0.4857 (mtm) REVERT: I 323 ILE cc_start: 0.6707 (OUTLIER) cc_final: 0.6484 (mp) REVERT: I 332 PHE cc_start: 0.7938 (m-80) cc_final: 0.7596 (m-80) REVERT: J 14 LEU cc_start: 0.8209 (tp) cc_final: 0.7838 (tm) REVERT: J 19 LYS cc_start: 0.8620 (mmtt) cc_final: 0.8398 (mmtt) REVERT: J 105 GLN cc_start: 0.7747 (pp30) cc_final: 0.7440 (pp30) REVERT: J 109 CYS cc_start: 0.6879 (p) cc_final: 0.5581 (m) REVERT: J 175 GLU cc_start: 0.6612 (pm20) cc_final: 0.6287 (pm20) REVERT: J 176 ASP cc_start: 0.7208 (t70) cc_final: 0.6969 (t0) REVERT: J 181 GLN cc_start: 0.7477 (tm-30) cc_final: 0.7257 (tm-30) REVERT: J 189 LEU cc_start: 0.6795 (tp) cc_final: 0.6574 (tp) REVERT: J 220 GLN cc_start: 0.7720 (tp-100) cc_final: 0.7489 (tp-100) REVERT: J 226 GLN cc_start: 0.8017 (mp10) cc_final: 0.7597 (mp10) REVERT: J 243 TYR cc_start: 0.8152 (t80) cc_final: 0.7898 (t80) REVERT: J 244 GLN cc_start: 0.8048 (pp30) cc_final: 0.7813 (pp30) REVERT: J 254 GLN cc_start: 0.8300 (pm20) cc_final: 0.8083 (pm20) REVERT: J 279 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7402 (pt0) REVERT: K 19 LYS cc_start: 0.6766 (mmmm) cc_final: 0.6205 (mmmm) REVERT: K 49 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.7061 (ptp-170) REVERT: K 78 LYS cc_start: 0.8298 (ttpt) cc_final: 0.7918 (ttpt) REVERT: K 150 ARG cc_start: 0.7081 (ttt180) cc_final: 0.6872 (ttt-90) REVERT: K 152 ARG cc_start: 0.7876 (ttt180) cc_final: 0.7252 (mmm-85) REVERT: K 251 ILE cc_start: 0.7557 (OUTLIER) cc_final: 0.6908 (mp) REVERT: K 297 LYS cc_start: 0.7026 (OUTLIER) cc_final: 0.6819 (ptpp) outliers start: 99 outliers final: 56 residues processed: 667 average time/residue: 0.6700 time to fit residues: 516.3978 Evaluate side-chains 681 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 613 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 267 TYR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 110 ASN Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 165 LYS Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 211 GLU Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 254 GLN Chi-restraints excluded: chain F residue 293 GLN Chi-restraints excluded: chain F residue 315 MET Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 197 GLU Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain I residue 34 GLN Chi-restraints excluded: chain I residue 49 ARG Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 286 SER Chi-restraints excluded: chain I residue 323 ILE Chi-restraints excluded: chain J residue 27 MET Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 240 LYS Chi-restraints excluded: chain J residue 253 SER Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 326 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 49 ARG Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 196 ILE Chi-restraints excluded: chain K residue 221 GLU Chi-restraints excluded: chain K residue 251 ILE Chi-restraints excluded: chain K residue 297 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 31 optimal weight: 1.9990 chunk 267 optimal weight: 9.9990 chunk 250 optimal weight: 3.9990 chunk 252 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 283 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 316 optimal weight: 3.9990 chunk 198 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 151 ASN ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 318 GLN F 77 GLN ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 GLN F 220 GLN F 244 GLN F 258 ASN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 220 GLN ** G 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN ** I 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 215 GLN I 218 ASN I 258 ASN I 320 HIS ** J 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.182948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.153611 restraints weight = 43662.109| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 3.07 r_work: 0.3966 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 26488 Z= 0.252 Angle : 0.672 12.046 36243 Z= 0.351 Chirality : 0.047 0.264 4073 Planarity : 0.005 0.066 4513 Dihedral : 15.209 175.498 4497 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 4.18 % Allowed : 20.64 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.14), residues: 3126 helix: -0.83 (0.18), residues: 814 sheet: -0.45 (0.22), residues: 564 loop : -1.42 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 18 TYR 0.034 0.002 TYR G 243 PHE 0.038 0.002 PHE C 95 TRP 0.046 0.002 TRP I 38 HIS 0.006 0.001 HIS G 320 Details of bonding type rmsd covalent geometry : bond 0.00553 (26488) covalent geometry : angle 0.67250 (36243) hydrogen bonds : bond 0.04128 ( 668) hydrogen bonds : angle 5.26165 ( 1861) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 643 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7851 (ttpp) REVERT: A 216 LEU cc_start: 0.8523 (mt) cc_final: 0.8291 (mp) REVERT: A 239 SER cc_start: 0.8442 (m) cc_final: 0.7955 (t) REVERT: A 243 TYR cc_start: 0.7958 (t80) cc_final: 0.7354 (t80) REVERT: A 318 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7605 (mp10) REVERT: B 1 MET cc_start: 0.4546 (mmp) cc_final: 0.4222 (mmt) REVERT: B 19 GLN cc_start: 0.8108 (tp40) cc_final: 0.7548 (tp-100) REVERT: C 35 GLN cc_start: 0.6774 (OUTLIER) cc_final: 0.5756 (pp30) REVERT: C 251 ILE cc_start: 0.8012 (mt) cc_final: 0.7678 (mm) REVERT: C 272 GLU cc_start: 0.7704 (pp20) cc_final: 0.7458 (pp20) REVERT: C 317 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7953 (mp0) REVERT: D 77 GLN cc_start: 0.6018 (tp-100) cc_final: 0.5595 (tm-30) REVERT: D 90 THR cc_start: 0.7350 (m) cc_final: 0.7141 (m) REVERT: D 208 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.7865 (m-80) REVERT: D 226 GLN cc_start: 0.7554 (mt0) cc_final: 0.6835 (mt0) REVERT: D 317 GLU cc_start: 0.7241 (tp30) cc_final: 0.6810 (tp30) REVERT: D 334 GLU cc_start: 0.6282 (tm-30) cc_final: 0.5796 (tm-30) REVERT: E 120 ASP cc_start: 0.7727 (m-30) cc_final: 0.7427 (m-30) REVERT: E 197 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6866 (tp30) REVERT: E 264 ASP cc_start: 0.8238 (t0) cc_final: 0.8002 (t0) REVERT: E 301 TYR cc_start: 0.7854 (m-10) cc_final: 0.7623 (m-10) REVERT: F 48 VAL cc_start: 0.8582 (OUTLIER) cc_final: 0.8350 (m) REVERT: F 49 ARG cc_start: 0.7904 (ttm-80) cc_final: 0.7595 (ptm160) REVERT: F 90 THR cc_start: 0.8272 (m) cc_final: 0.8014 (m) REVERT: F 283 SER cc_start: 0.7939 (m) cc_final: 0.7654 (t) REVERT: F 293 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8410 (mt0) REVERT: F 334 GLU cc_start: 0.7748 (tp30) cc_final: 0.7393 (tp30) REVERT: G 66 LYS cc_start: 0.8199 (mtmt) cc_final: 0.7921 (mtmt) REVERT: G 71 ILE cc_start: 0.8613 (mt) cc_final: 0.8405 (mt) REVERT: G 89 ASP cc_start: 0.6793 (p0) cc_final: 0.6557 (p0) REVERT: G 281 TYR cc_start: 0.8652 (m-80) cc_final: 0.8343 (m-80) REVERT: G 298 MET cc_start: 0.7739 (mmm) cc_final: 0.7539 (mmm) REVERT: G 306 ASN cc_start: 0.8178 (m-40) cc_final: 0.7831 (m-40) REVERT: I 49 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.6163 (ptp90) REVERT: I 167 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7465 (tm-30) REVERT: I 173 ASN cc_start: 0.7560 (t0) cc_final: 0.7348 (t0) REVERT: I 194 GLN cc_start: 0.8354 (tp40) cc_final: 0.8090 (tp40) REVERT: I 289 LYS cc_start: 0.7990 (ttmm) cc_final: 0.7601 (ttmm) REVERT: I 332 PHE cc_start: 0.7939 (m-80) cc_final: 0.7629 (m-80) REVERT: J 14 LEU cc_start: 0.8269 (tp) cc_final: 0.7898 (tm) REVERT: J 19 LYS cc_start: 0.8625 (mmtt) cc_final: 0.8347 (mmtt) REVERT: J 105 GLN cc_start: 0.7836 (pp30) cc_final: 0.7542 (pp30) REVERT: J 109 CYS cc_start: 0.6866 (p) cc_final: 0.5621 (m) REVERT: J 176 ASP cc_start: 0.7188 (t70) cc_final: 0.6911 (t0) REVERT: J 181 GLN cc_start: 0.7427 (tm-30) cc_final: 0.7157 (tm-30) REVERT: J 189 LEU cc_start: 0.6796 (tp) cc_final: 0.6588 (tp) REVERT: J 208 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7756 (m-80) REVERT: J 226 GLN cc_start: 0.7957 (mp10) cc_final: 0.7566 (mp10) REVERT: J 243 TYR cc_start: 0.8174 (t80) cc_final: 0.7969 (t80) REVERT: K 19 LYS cc_start: 0.6808 (mmmm) cc_final: 0.6254 (mmmm) REVERT: K 49 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7211 (ptp-170) REVERT: K 78 LYS cc_start: 0.8374 (ttpt) cc_final: 0.8038 (ttpt) REVERT: K 152 ARG cc_start: 0.8006 (ttt180) cc_final: 0.7386 (mmm-85) REVERT: K 251 ILE cc_start: 0.7472 (OUTLIER) cc_final: 0.6808 (mp) REVERT: K 263 ILE cc_start: 0.4419 (mm) cc_final: 0.3899 (mp) REVERT: K 297 LYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6942 (ptpp) REVERT: K 315 MET cc_start: 0.4654 (tpp) cc_final: 0.4404 (tpp) outliers start: 105 outliers final: 67 residues processed: 690 average time/residue: 0.6628 time to fit residues: 528.9803 Evaluate side-chains 708 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 628 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 317 GLU Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 165 LYS Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 211 GLU Chi-restraints excluded: chain F residue 293 GLN Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 197 GLU Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 239 SER Chi-restraints excluded: chain G residue 253 SER Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 49 ARG Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 286 SER Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 27 MET Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 208 PHE Chi-restraints excluded: chain J residue 240 LYS Chi-restraints excluded: chain J residue 253 SER Chi-restraints excluded: chain J residue 308 VAL Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 326 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 49 ARG Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 196 ILE Chi-restraints excluded: chain K residue 221 GLU Chi-restraints excluded: chain K residue 251 ILE Chi-restraints excluded: chain K residue 297 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 317 optimal weight: 10.0000 chunk 258 optimal weight: 0.8980 chunk 146 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 232 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 205 optimal weight: 1.9990 chunk 14 optimal weight: 0.1980 chunk 47 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 GLN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN I 34 GLN I 215 GLN I 318 GLN ** J 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 220 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 = 0.4425 r_free = 0.4425 target = 0.184038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.154769 restraints weight = 43996.516| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 3.08 r_work: 0.3984 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 26488 Z= 0.194 Angle : 0.653 10.211 36243 Z= 0.337 Chirality : 0.046 0.263 4073 Planarity : 0.004 0.062 4513 Dihedral : 15.172 174.952 4497 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.02 % Allowed : 21.51 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.14), residues: 3126 helix: -0.75 (0.18), residues: 810 sheet: -0.34 (0.22), residues: 554 loop : -1.34 (0.14), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 152 TYR 0.035 0.002 TYR G 243 PHE 0.039 0.002 PHE C 95 TRP 0.043 0.002 TRP I 38 HIS 0.005 0.001 HIS G 320 Details of bonding type rmsd covalent geometry : bond 0.00431 (26488) covalent geometry : angle 0.65313 (36243) hydrogen bonds : bond 0.03683 ( 668) hydrogen bonds : angle 5.11352 ( 1861) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 637 time to evaluate : 0.934 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 46 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7831 (ttpp) REVERT: A 127 GLN cc_start: 0.8091 (mm-40) cc_final: 0.7881 (mp-120) REVERT: A 216 LEU cc_start: 0.8509 (mt) cc_final: 0.8252 (mp) REVERT: A 239 SER cc_start: 0.8426 (m) cc_final: 0.7937 (t) REVERT: A 243 TYR cc_start: 0.7913 (t80) cc_final: 0.7324 (t80) REVERT: A 318 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7866 (mm-40) REVERT: B 1 MET cc_start: 0.4318 (mmp) cc_final: 0.4011 (mmt) REVERT: B 19 GLN cc_start: 0.8112 (tp40) cc_final: 0.7551 (tp-100) REVERT: C 35 GLN cc_start: 0.6715 (OUTLIER) cc_final: 0.5775 (pp30) REVERT: C 251 ILE cc_start: 0.7983 (mt) cc_final: 0.7662 (mm) REVERT: C 272 GLU cc_start: 0.7675 (pp20) cc_final: 0.7428 (pp20) REVERT: D 90 THR cc_start: 0.7296 (m) cc_final: 0.7072 (m) REVERT: D 208 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.7814 (m-80) REVERT: D 226 GLN cc_start: 0.7530 (mt0) cc_final: 0.6779 (mt0) REVERT: D 301 TYR cc_start: 0.6826 (m-80) cc_final: 0.5924 (t80) REVERT: D 317 GLU cc_start: 0.7216 (tp30) cc_final: 0.6787 (tp30) REVERT: D 334 GLU cc_start: 0.6247 (tm-30) cc_final: 0.5763 (tm-30) REVERT: E 197 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6863 (tp30) REVERT: E 264 ASP cc_start: 0.8240 (t0) cc_final: 0.8013 (t0) REVERT: E 301 TYR cc_start: 0.7824 (m-10) cc_final: 0.7524 (m-10) REVERT: F 48 VAL cc_start: 0.8575 (OUTLIER) cc_final: 0.8326 (m) REVERT: F 49 ARG cc_start: 0.7873 (ttm-80) cc_final: 0.7577 (ptm160) REVERT: F 57 LYS cc_start: 0.5808 (tmtm) cc_final: 0.5524 (tmtm) REVERT: F 90 THR cc_start: 0.8213 (m) cc_final: 0.7962 (m) REVERT: F 283 SER cc_start: 0.7937 (m) cc_final: 0.7642 (t) REVERT: F 293 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8217 (mt0) REVERT: F 296 GLU cc_start: 0.7672 (mp0) cc_final: 0.7468 (mp0) REVERT: F 334 GLU cc_start: 0.7739 (tp30) cc_final: 0.7391 (tp30) REVERT: G 66 LYS cc_start: 0.8143 (mtmt) cc_final: 0.7735 (mtmt) REVERT: G 71 ILE cc_start: 0.8605 (mt) cc_final: 0.8354 (mt) REVERT: G 78 LYS cc_start: 0.8543 (mtpp) cc_final: 0.8329 (ttmm) REVERT: G 89 ASP cc_start: 0.6793 (p0) cc_final: 0.6556 (p0) REVERT: G 128 GLU cc_start: 0.8281 (tt0) cc_final: 0.8068 (tm-30) REVERT: G 281 TYR cc_start: 0.8608 (m-80) cc_final: 0.8306 (m-80) REVERT: G 306 ASN cc_start: 0.8154 (m-40) cc_final: 0.7766 (m-40) REVERT: I 49 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.6135 (ptp90) REVERT: I 167 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7386 (tm-30) REVERT: I 173 ASN cc_start: 0.7516 (t0) cc_final: 0.7301 (t0) REVERT: I 279 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7151 (mm-30) REVERT: I 289 LYS cc_start: 0.7962 (ttmm) cc_final: 0.7583 (ttmm) REVERT: I 328 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.4674 (tmt90) REVERT: I 332 PHE cc_start: 0.7910 (m-80) cc_final: 0.7631 (m-80) REVERT: J 14 LEU cc_start: 0.8237 (tp) cc_final: 0.7867 (tm) REVERT: J 19 LYS cc_start: 0.8609 (mmtt) cc_final: 0.8305 (mmtt) REVERT: J 105 GLN cc_start: 0.7861 (pp30) cc_final: 0.7546 (pp30) REVERT: J 109 CYS cc_start: 0.6875 (p) cc_final: 0.5634 (m) REVERT: J 176 ASP cc_start: 0.7181 (t70) cc_final: 0.6973 (t0) REVERT: J 181 GLN cc_start: 0.7409 (tm-30) cc_final: 0.7152 (tm-30) REVERT: J 189 LEU cc_start: 0.6825 (tp) cc_final: 0.6618 (tp) REVERT: J 226 GLN cc_start: 0.7999 (mp10) cc_final: 0.7580 (mp10) REVERT: J 243 TYR cc_start: 0.8146 (t80) cc_final: 0.7900 (t80) REVERT: J 254 GLN cc_start: 0.8329 (pm20) cc_final: 0.8115 (pm20) REVERT: J 279 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7575 (pt0) REVERT: J 292 ARG cc_start: 0.7952 (mtt90) cc_final: 0.7685 (mtt90) REVERT: K 19 LYS cc_start: 0.6827 (mmmm) cc_final: 0.6293 (mmmm) REVERT: K 78 LYS cc_start: 0.8348 (ttpt) cc_final: 0.7995 (ttpt) REVERT: K 152 ARG cc_start: 0.7963 (ttt180) cc_final: 0.7343 (mmm-85) REVERT: K 315 MET cc_start: 0.4680 (tpp) cc_final: 0.4422 (tpp) outliers start: 101 outliers final: 62 residues processed: 683 average time/residue: 0.6740 time to fit residues: 531.7649 Evaluate side-chains 694 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 623 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 267 TYR Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 165 LYS Chi-restraints excluded: chain F residue 173 ASN Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 211 GLU Chi-restraints excluded: chain F residue 293 GLN Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 197 GLU Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 239 SER Chi-restraints excluded: chain G residue 253 SER Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain I residue 34 GLN Chi-restraints excluded: chain I residue 49 ARG Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 286 SER Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 328 ARG Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 27 MET Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 240 LYS Chi-restraints excluded: chain J residue 253 SER Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 196 ILE Chi-restraints excluded: chain K residue 221 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 32 optimal weight: 3.9990 chunk 304 optimal weight: 0.1980 chunk 149 optimal weight: 0.8980 chunk 258 optimal weight: 2.9990 chunk 195 optimal weight: 0.5980 chunk 127 optimal weight: 0.8980 chunk 270 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 211 optimal weight: 0.9990 chunk 267 optimal weight: 6.9990 chunk 168 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 GLN F 220 GLN F 258 ASN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 319 GLN ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 220 GLN ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN I 215 GLN ** J 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.185103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.155999 restraints weight = 43800.152| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 3.08 r_work: 0.3997 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26488 Z= 0.161 Angle : 0.651 10.922 36243 Z= 0.333 Chirality : 0.045 0.268 4073 Planarity : 0.005 0.101 4513 Dihedral : 15.087 175.391 4497 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.31 % Allowed : 22.87 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.15), residues: 3126 helix: -0.59 (0.18), residues: 807 sheet: -0.25 (0.22), residues: 554 loop : -1.29 (0.14), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 152 TYR 0.034 0.002 TYR G 243 PHE 0.041 0.002 PHE C 95 TRP 0.044 0.002 TRP I 38 HIS 0.004 0.001 HIS G 320 Details of bonding type rmsd covalent geometry : bond 0.00359 (26488) covalent geometry : angle 0.65063 (36243) hydrogen bonds : bond 0.03463 ( 668) hydrogen bonds : angle 4.96836 ( 1861) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 630 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7834 (ttpp) REVERT: A 216 LEU cc_start: 0.8499 (mt) cc_final: 0.8224 (mp) REVERT: A 239 SER cc_start: 0.8406 (m) cc_final: 0.7894 (t) REVERT: A 243 TYR cc_start: 0.7876 (t80) cc_final: 0.7354 (t80) REVERT: A 298 MET cc_start: 0.8347 (mmt) cc_final: 0.8103 (tpt) REVERT: A 318 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7735 (mm-40) REVERT: B 19 GLN cc_start: 0.8174 (tp40) cc_final: 0.7590 (tp-100) REVERT: C 35 GLN cc_start: 0.6702 (OUTLIER) cc_final: 0.5889 (pp30) REVERT: C 251 ILE cc_start: 0.7939 (mt) cc_final: 0.7621 (mm) REVERT: C 272 GLU cc_start: 0.7686 (pp20) cc_final: 0.7439 (pp20) REVERT: D 77 GLN cc_start: 0.6044 (tp-100) cc_final: 0.5700 (tm-30) REVERT: D 208 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.7820 (m-80) REVERT: D 226 GLN cc_start: 0.7591 (mt0) cc_final: 0.6834 (mt0) REVERT: D 317 GLU cc_start: 0.7190 (tp30) cc_final: 0.6753 (tp30) REVERT: D 334 GLU cc_start: 0.6243 (tm-30) cc_final: 0.5767 (tm-30) REVERT: E 120 ASP cc_start: 0.7649 (m-30) cc_final: 0.7341 (m-30) REVERT: E 197 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6840 (tp30) REVERT: E 301 TYR cc_start: 0.7785 (m-10) cc_final: 0.7426 (m-10) REVERT: F 48 VAL cc_start: 0.8565 (OUTLIER) cc_final: 0.8307 (m) REVERT: F 90 THR cc_start: 0.8193 (m) cc_final: 0.7935 (m) REVERT: F 283 SER cc_start: 0.7882 (m) cc_final: 0.7583 (t) REVERT: F 293 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8153 (mt0) REVERT: F 296 GLU cc_start: 0.7626 (mp0) cc_final: 0.7399 (mp0) REVERT: F 334 GLU cc_start: 0.7734 (tp30) cc_final: 0.7379 (tp30) REVERT: G 66 LYS cc_start: 0.8130 (mtmt) cc_final: 0.7692 (mtmt) REVERT: G 71 ILE cc_start: 0.8589 (mt) cc_final: 0.8345 (mt) REVERT: G 73 LYS cc_start: 0.8412 (mmmm) cc_final: 0.8201 (mmmm) REVERT: G 78 LYS cc_start: 0.8547 (mtpp) cc_final: 0.8239 (ttmm) REVERT: G 89 ASP cc_start: 0.6780 (p0) cc_final: 0.6548 (p0) REVERT: G 128 GLU cc_start: 0.8298 (tt0) cc_final: 0.8070 (tm-30) REVERT: G 281 TYR cc_start: 0.8573 (m-80) cc_final: 0.8275 (m-80) REVERT: G 306 ASN cc_start: 0.8121 (m-40) cc_final: 0.7726 (m-40) REVERT: I 49 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.6081 (ptp90) REVERT: I 115 GLN cc_start: 0.8005 (mp10) cc_final: 0.7788 (pm20) REVERT: I 167 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7436 (tm-30) REVERT: I 173 ASN cc_start: 0.7505 (t0) cc_final: 0.7288 (t0) REVERT: I 279 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7069 (mm-30) REVERT: I 289 LYS cc_start: 0.7982 (ttmm) cc_final: 0.7603 (ttmm) REVERT: I 328 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.4684 (tmt90) REVERT: I 332 PHE cc_start: 0.7903 (m-80) cc_final: 0.7618 (m-80) REVERT: J 14 LEU cc_start: 0.8214 (tp) cc_final: 0.7832 (tm) REVERT: J 19 LYS cc_start: 0.8610 (mmtt) cc_final: 0.8278 (mmtt) REVERT: J 105 GLN cc_start: 0.7853 (pp30) cc_final: 0.7533 (pp30) REVERT: J 109 CYS cc_start: 0.6876 (p) cc_final: 0.5564 (m) REVERT: J 176 ASP cc_start: 0.7147 (t70) cc_final: 0.6931 (t0) REVERT: J 181 GLN cc_start: 0.7440 (tm-30) cc_final: 0.7181 (tm-30) REVERT: J 189 LEU cc_start: 0.6812 (tp) cc_final: 0.6599 (tp) REVERT: J 226 GLN cc_start: 0.7986 (mp10) cc_final: 0.7557 (mp10) REVERT: J 243 TYR cc_start: 0.8096 (t80) cc_final: 0.7853 (t80) REVERT: J 254 GLN cc_start: 0.8328 (pm20) cc_final: 0.8125 (pm20) REVERT: J 279 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7526 (pt0) REVERT: K 19 LYS cc_start: 0.6836 (mmmm) cc_final: 0.6327 (mmmm) REVERT: K 78 LYS cc_start: 0.8342 (ttpt) cc_final: 0.7961 (ttpt) REVERT: K 152 ARG cc_start: 0.7952 (ttt180) cc_final: 0.7327 (mmm-85) REVERT: K 315 MET cc_start: 0.4679 (tpp) cc_final: 0.4408 (tpp) outliers start: 83 outliers final: 64 residues processed: 663 average time/residue: 0.6813 time to fit residues: 521.8017 Evaluate side-chains 689 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 616 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 267 TYR Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 165 LYS Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 211 GLU Chi-restraints excluded: chain F residue 293 GLN Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 125 TYR Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 197 GLU Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 239 SER Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain I residue 44 GLN Chi-restraints excluded: chain I residue 49 ARG Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 328 ARG Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 27 MET Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 240 LYS Chi-restraints excluded: chain J residue 253 SER Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 326 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 196 ILE Chi-restraints excluded: chain K residue 221 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 180 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 229 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 chunk 315 optimal weight: 2.9990 chunk 276 optimal weight: 0.7980 chunk 291 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 224 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 GLN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN I 34 GLN I 215 GLN ** J 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.184760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.155990 restraints weight = 43779.116| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 3.06 r_work: 0.3996 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 26488 Z= 0.173 Angle : 0.668 10.414 36243 Z= 0.342 Chirality : 0.046 0.269 4073 Planarity : 0.005 0.117 4513 Dihedral : 15.082 177.100 4497 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.15 % Allowed : 23.55 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.15), residues: 3126 helix: -0.54 (0.18), residues: 802 sheet: -0.21 (0.22), residues: 554 loop : -1.31 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 292 TYR 0.035 0.002 TYR G 243 PHE 0.047 0.002 PHE E 300 TRP 0.049 0.002 TRP I 38 HIS 0.005 0.001 HIS G 320 Details of bonding type rmsd covalent geometry : bond 0.00386 (26488) covalent geometry : angle 0.66757 (36243) hydrogen bonds : bond 0.03561 ( 668) hydrogen bonds : angle 4.97723 ( 1861) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 622 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7863 (ttpp) REVERT: A 127 GLN cc_start: 0.8116 (mm-40) cc_final: 0.7903 (mp-120) REVERT: A 216 LEU cc_start: 0.8519 (mt) cc_final: 0.8272 (mp) REVERT: A 239 SER cc_start: 0.8399 (m) cc_final: 0.7890 (t) REVERT: A 243 TYR cc_start: 0.7877 (t80) cc_final: 0.7343 (t80) REVERT: A 298 MET cc_start: 0.8334 (mmt) cc_final: 0.8098 (tpt) REVERT: A 318 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7759 (mm-40) REVERT: B 19 GLN cc_start: 0.8162 (tp40) cc_final: 0.7575 (tp-100) REVERT: C 35 GLN cc_start: 0.6521 (OUTLIER) cc_final: 0.5798 (pp30) REVERT: C 251 ILE cc_start: 0.7939 (mt) cc_final: 0.7625 (mm) REVERT: C 272 GLU cc_start: 0.7661 (pp20) cc_final: 0.7413 (pp20) REVERT: D 77 GLN cc_start: 0.6071 (tp-100) cc_final: 0.5839 (tm-30) REVERT: D 208 PHE cc_start: 0.8468 (OUTLIER) cc_final: 0.7812 (m-80) REVERT: D 226 GLN cc_start: 0.7598 (mt0) cc_final: 0.6850 (mt0) REVERT: D 317 GLU cc_start: 0.7201 (tp30) cc_final: 0.6744 (tp30) REVERT: E 120 ASP cc_start: 0.7643 (m-30) cc_final: 0.7339 (m-30) REVERT: E 197 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6856 (tp30) REVERT: E 301 TYR cc_start: 0.7752 (m-10) cc_final: 0.7479 (m-10) REVERT: F 48 VAL cc_start: 0.8548 (OUTLIER) cc_final: 0.8293 (m) REVERT: F 90 THR cc_start: 0.8215 (m) cc_final: 0.7959 (m) REVERT: F 228 LEU cc_start: 0.8124 (tp) cc_final: 0.7704 (tt) REVERT: F 283 SER cc_start: 0.7885 (m) cc_final: 0.7583 (t) REVERT: F 293 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8144 (mt0) REVERT: F 296 GLU cc_start: 0.7607 (mp0) cc_final: 0.7374 (mp0) REVERT: F 334 GLU cc_start: 0.7759 (tp30) cc_final: 0.7395 (tp30) REVERT: G 66 LYS cc_start: 0.8130 (mtmt) cc_final: 0.7707 (mtmt) REVERT: G 71 ILE cc_start: 0.8592 (mt) cc_final: 0.8344 (mt) REVERT: G 78 LYS cc_start: 0.8501 (mtpp) cc_final: 0.8205 (ttmm) REVERT: G 89 ASP cc_start: 0.6751 (p0) cc_final: 0.6517 (p0) REVERT: G 128 GLU cc_start: 0.8294 (tt0) cc_final: 0.8088 (tm-30) REVERT: G 281 TYR cc_start: 0.8555 (m-80) cc_final: 0.8246 (m-80) REVERT: G 298 MET cc_start: 0.7774 (mmm) cc_final: 0.7292 (tmm) REVERT: G 306 ASN cc_start: 0.8138 (m-40) cc_final: 0.7738 (m-40) REVERT: I 49 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.6098 (ptp90) REVERT: I 167 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7375 (tm-30) REVERT: I 173 ASN cc_start: 0.7506 (t0) cc_final: 0.7283 (t0) REVERT: I 198 LYS cc_start: 0.7965 (tptm) cc_final: 0.7716 (mptm) REVERT: I 279 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7098 (mm-30) REVERT: I 289 LYS cc_start: 0.7971 (ttmm) cc_final: 0.7587 (ttmm) REVERT: I 310 LYS cc_start: 0.7551 (mppt) cc_final: 0.7349 (mppt) REVERT: I 320 HIS cc_start: 0.7719 (m170) cc_final: 0.7445 (m170) REVERT: I 328 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.4725 (tmt90) REVERT: I 332 PHE cc_start: 0.7906 (m-80) cc_final: 0.7617 (m-80) REVERT: J 14 LEU cc_start: 0.8195 (tp) cc_final: 0.7801 (tm) REVERT: J 19 LYS cc_start: 0.8612 (mmtt) cc_final: 0.8285 (mmtt) REVERT: J 105 GLN cc_start: 0.7886 (pp30) cc_final: 0.7565 (pp30) REVERT: J 109 CYS cc_start: 0.6907 (p) cc_final: 0.5540 (m) REVERT: J 176 ASP cc_start: 0.7125 (t70) cc_final: 0.6922 (t0) REVERT: J 181 GLN cc_start: 0.7427 (tm-30) cc_final: 0.7168 (tm-30) REVERT: J 189 LEU cc_start: 0.6830 (tp) cc_final: 0.6609 (tp) REVERT: J 226 GLN cc_start: 0.7954 (mp10) cc_final: 0.7641 (mp10) REVERT: J 243 TYR cc_start: 0.8083 (t80) cc_final: 0.7819 (t80) REVERT: J 254 GLN cc_start: 0.8324 (pm20) cc_final: 0.8121 (pm20) REVERT: J 279 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7517 (pt0) REVERT: J 292 ARG cc_start: 0.7957 (mtt90) cc_final: 0.7669 (mtt90) REVERT: K 19 LYS cc_start: 0.6919 (mmmm) cc_final: 0.6417 (mmmm) REVERT: K 78 LYS cc_start: 0.8360 (ttpt) cc_final: 0.7976 (ttpt) REVERT: K 152 ARG cc_start: 0.7947 (ttt180) cc_final: 0.7329 (mmm-85) REVERT: K 315 MET cc_start: 0.4703 (tpp) cc_final: 0.4444 (tpp) outliers start: 79 outliers final: 63 residues processed: 655 average time/residue: 0.6750 time to fit residues: 512.9444 Evaluate side-chains 695 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 623 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 267 TYR Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 165 LYS Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 211 GLU Chi-restraints excluded: chain F residue 293 GLN Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 197 GLU Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 239 SER Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain I residue 34 GLN Chi-restraints excluded: chain I residue 44 GLN Chi-restraints excluded: chain I residue 49 ARG Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 328 ARG Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 27 MET Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 240 LYS Chi-restraints excluded: chain J residue 253 SER Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 326 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 196 ILE Chi-restraints excluded: chain K residue 221 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 274 optimal weight: 0.0070 chunk 160 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 310 optimal weight: 6.9990 chunk 197 optimal weight: 0.9980 chunk 269 optimal weight: 1.9990 chunk 292 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 203 optimal weight: 0.0770 chunk 50 optimal weight: 0.0770 overall best weight: 0.4114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 GLN F 115 GLN F 129 GLN ** F 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 293 GLN I 22 ASN I 34 GLN I 110 ASN I 215 GLN I 258 ASN I 318 GLN ** J 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 306 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.187073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.158163 restraints weight = 44012.278| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 3.09 r_work: 0.4026 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26488 Z= 0.125 Angle : 0.643 10.142 36243 Z= 0.328 Chirality : 0.044 0.265 4073 Planarity : 0.004 0.072 4513 Dihedral : 14.961 175.845 4497 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.03 % Allowed : 23.67 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.15), residues: 3126 helix: -0.25 (0.19), residues: 808 sheet: -0.28 (0.22), residues: 584 loop : -1.19 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 95 TYR 0.033 0.002 TYR G 243 PHE 0.042 0.001 PHE C 95 TRP 0.043 0.002 TRP J 307 HIS 0.004 0.001 HIS I 320 Details of bonding type rmsd covalent geometry : bond 0.00283 (26488) covalent geometry : angle 0.64285 (36243) hydrogen bonds : bond 0.03144 ( 668) hydrogen bonds : angle 4.75069 ( 1861) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11487.16 seconds wall clock time: 195 minutes 51.83 seconds (11751.83 seconds total)