Starting phenix.real_space_refine on Wed Apr 8 22:25:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nuf_49803/04_2026/9nuf_49803.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nuf_49803/04_2026/9nuf_49803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nuf_49803/04_2026/9nuf_49803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nuf_49803/04_2026/9nuf_49803.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nuf_49803/04_2026/9nuf_49803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nuf_49803/04_2026/9nuf_49803.map" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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 84 5.49 5 S 224 5.16 5 C 28182 2.51 5 N 7686 2.21 5 O 8820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 44996 Number of models: 1 Model: "" Number of chains: 15 Chain: "D" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3094 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 15, 'TRANS': 382} Chain: "E" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3094 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 15, 'TRANS': 382} Chain: "F" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3094 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 15, 'TRANS': 382} Chain: "G" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3094 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 15, 'TRANS': 382} Chain: "H" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3094 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 15, 'TRANS': 382} Chain: "I" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3094 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 15, 'TRANS': 382} Chain: "J" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3094 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 15, 'TRANS': 382} Chain: "K" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3094 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 15, 'TRANS': 382} Chain: "L" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3094 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 15, 'TRANS': 382} Chain: "M" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3094 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 15, 'TRANS': 382} Chain: "N" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3094 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 15, 'TRANS': 382} Chain: "O" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3094 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 15, 'TRANS': 382} Chain: "P" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3094 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 15, 'TRANS': 382} Chain: "Q" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3094 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 15, 'TRANS': 382} Chain: "Z" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1680 Classifications: {'RNA': 84} Modifications used: {'rna2p_pyr': 14, 'rna3p_pyr': 70} Link IDs: {'rna2p': 14, 'rna3p': 69} Time building chain proxies: 10.00, per 1000 atoms: 0.22 Number of scatterers: 44996 At special positions: 0 Unit cell: (133.685, 216.021, 223.104, 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 224 16.00 P 84 15.00 O 8820 8.00 N 7686 7.00 C 28182 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: 3.90 Conformation dependent library (CDL) restraints added in 1.9 seconds 11088 Ramachandran restraints generated. 5544 Oldfield, 0 Emsley, 5544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10388 Finding SS restraints... Secondary structure from input PDB file: 307 helices and 14 sheets defined 69.2% alpha, 3.0% beta 0 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 5.09 Creating SS restraints... Processing helix chain 'D' and resid 3 through 17 Processing helix chain 'D' and resid 25 through 29 removed outlier: 3.565A pdb=" N THR D 28 " --> pdb=" O SER D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 61 removed outlier: 3.662A pdb=" N ARG D 48 " --> pdb=" O SER D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 78 Processing helix chain 'D' and resid 83 through 91 Processing helix chain 'D' and resid 121 through 140 removed outlier: 3.827A pdb=" N MET D 125 " --> pdb=" O ALA D 121 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS D 140 " --> pdb=" O ARG D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 153 removed outlier: 3.596A pdb=" N GLY D 152 " --> pdb=" O SER D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 176 removed outlier: 3.551A pdb=" N ILE D 176 " --> pdb=" O ILE D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 200 removed outlier: 3.653A pdb=" N GLU D 190 " --> pdb=" O ALA D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 208 Processing helix chain 'D' and resid 210 through 224 Processing helix chain 'D' and resid 224 through 240 removed outlier: 4.192A pdb=" N ARG D 228 " --> pdb=" O SER D 224 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS D 240 " --> pdb=" O ILE D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 260 removed outlier: 3.985A pdb=" N TYR D 258 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 275 Processing helix chain 'D' and resid 279 through 286 removed outlier: 5.594A pdb=" N ASN D 285 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLU D 286 " --> pdb=" O ALA D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 305 Processing helix chain 'D' and resid 306 through 311 Proline residue: D 309 - end of helix No H-bonds generated for 'chain 'D' and resid 306 through 311' Processing helix chain 'D' and resid 317 through 321 Processing helix chain 'D' and resid 323 through 326 removed outlier: 3.633A pdb=" N GLY D 326 " --> pdb=" O ALA D 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 323 through 326' Processing helix chain 'D' and resid 327 through 342 removed outlier: 4.472A pdb=" N THR D 340 " --> pdb=" O GLY D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 369 removed outlier: 3.712A pdb=" N HIS D 369 " --> pdb=" O LYS D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 400 Processing helix chain 'E' and resid 4 through 17 Processing helix chain 'E' and resid 25 through 29 removed outlier: 3.587A pdb=" N THR E 28 " --> pdb=" O SER E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 61 removed outlier: 3.732A pdb=" N ARG E 48 " --> pdb=" O SER E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 78 Processing helix chain 'E' and resid 83 through 91 Processing helix chain 'E' and resid 121 through 140 removed outlier: 3.763A pdb=" N MET E 125 " --> pdb=" O ALA E 121 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS E 140 " --> pdb=" O ARG E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 153 removed outlier: 3.656A pdb=" N GLY E 152 " --> pdb=" O SER E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 176 removed outlier: 3.659A pdb=" N ILE E 176 " --> pdb=" O ILE E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 186 through 200 removed outlier: 3.616A pdb=" N GLU E 190 " --> pdb=" O ALA E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 208 removed outlier: 3.647A pdb=" N ALA E 208 " --> pdb=" O PRO E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 224 Processing helix chain 'E' and resid 225 through 240 removed outlier: 3.757A pdb=" N LYS E 240 " --> pdb=" O ILE E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 260 removed outlier: 4.045A pdb=" N TYR E 258 " --> pdb=" O ASP E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 273 Processing helix chain 'E' and resid 279 through 286 removed outlier: 5.778A pdb=" N ASN E 285 " --> pdb=" O LEU E 282 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLU E 286 " --> pdb=" O ALA E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 305 Processing helix chain 'E' and resid 306 through 311 Proline residue: E 309 - end of helix No H-bonds generated for 'chain 'E' and resid 306 through 311' Processing helix chain 'E' and resid 317 through 326 removed outlier: 3.685A pdb=" N ALA E 323 " --> pdb=" O THR E 320 " (cutoff:3.500A) Proline residue: E 324 - end of helix Processing helix chain 'E' and resid 327 through 342 removed outlier: 4.354A pdb=" N THR E 340 " --> pdb=" O GLY E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 369 removed outlier: 3.684A pdb=" N HIS E 369 " --> pdb=" O LYS E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 400 Processing helix chain 'F' and resid 4 through 17 Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.502A pdb=" N THR F 28 " --> pdb=" O SER F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 61 removed outlier: 3.733A pdb=" N ARG F 48 " --> pdb=" O SER F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 78 Processing helix chain 'F' and resid 83 through 91 Processing helix chain 'F' and resid 121 through 140 removed outlier: 3.698A pdb=" N MET F 125 " --> pdb=" O ALA F 121 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS F 140 " --> pdb=" O ARG F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 153 removed outlier: 3.705A pdb=" N GLY F 152 " --> pdb=" O SER F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 176 removed outlier: 3.769A pdb=" N ILE F 176 " --> pdb=" O ILE F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 186 through 200 removed outlier: 3.658A pdb=" N GLU F 190 " --> pdb=" O ALA F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 208 removed outlier: 3.501A pdb=" N PHE F 207 " --> pdb=" O ASN F 204 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA F 208 " --> pdb=" O PRO F 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 204 through 208' Processing helix chain 'F' and resid 210 through 224 Processing helix chain 'F' and resid 224 through 240 removed outlier: 4.101A pdb=" N ARG F 228 " --> pdb=" O SER F 224 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS F 240 " --> pdb=" O ILE F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 260 removed outlier: 4.053A pdb=" N TYR F 258 " --> pdb=" O ASP F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 273 Processing helix chain 'F' and resid 279 through 283 Processing helix chain 'F' and resid 284 through 305 removed outlier: 3.958A pdb=" N GLN F 288 " --> pdb=" O LEU F 284 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER F 289 " --> pdb=" O ASN F 285 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ASP F 290 " --> pdb=" O GLU F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 311 Proline residue: F 309 - end of helix No H-bonds generated for 'chain 'F' and resid 306 through 311' Processing helix chain 'F' and resid 317 through 326 removed outlier: 3.638A pdb=" N ALA F 323 " --> pdb=" O THR F 320 " (cutoff:3.500A) Proline residue: F 324 - end of helix Processing helix chain 'F' and resid 327 through 342 removed outlier: 3.647A pdb=" N TRP F 331 " --> pdb=" O TYR F 327 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THR F 340 " --> pdb=" O GLY F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 356 through 369 removed outlier: 3.867A pdb=" N HIS F 369 " --> pdb=" O LYS F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 400 Processing helix chain 'G' and resid 4 through 17 Processing helix chain 'G' and resid 25 through 29 removed outlier: 3.567A pdb=" N THR G 28 " --> pdb=" O SER G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 61 removed outlier: 3.590A pdb=" N ARG G 48 " --> pdb=" O SER G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 78 Processing helix chain 'G' and resid 83 through 91 Processing helix chain 'G' and resid 121 through 140 removed outlier: 3.914A pdb=" N MET G 125 " --> pdb=" O ALA G 121 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS G 140 " --> pdb=" O ARG G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 153 removed outlier: 3.834A pdb=" N GLY G 152 " --> pdb=" O SER G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 176 removed outlier: 3.808A pdb=" N ILE G 176 " --> pdb=" O ILE G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 186 through 200 removed outlier: 3.574A pdb=" N GLU G 190 " --> pdb=" O ALA G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 208 Processing helix chain 'G' and resid 210 through 224 Processing helix chain 'G' and resid 224 through 240 removed outlier: 4.047A pdb=" N ARG G 228 " --> pdb=" O SER G 224 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS G 240 " --> pdb=" O ILE G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 260 removed outlier: 3.983A pdb=" N TYR G 258 " --> pdb=" O ASP G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 275 Processing helix chain 'G' and resid 279 through 286 removed outlier: 5.714A pdb=" N ASN G 285 " --> pdb=" O LEU G 282 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLU G 286 " --> pdb=" O ALA G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 305 Processing helix chain 'G' and resid 306 through 311 Proline residue: G 309 - end of helix No H-bonds generated for 'chain 'G' and resid 306 through 311' Processing helix chain 'G' and resid 317 through 326 removed outlier: 3.652A pdb=" N ALA G 323 " --> pdb=" O THR G 320 " (cutoff:3.500A) Proline residue: G 324 - end of helix Processing helix chain 'G' and resid 327 through 342 removed outlier: 3.573A pdb=" N TRP G 331 " --> pdb=" O TYR G 327 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR G 340 " --> pdb=" O GLY G 336 " (cutoff:3.500A) Processing helix chain 'G' and resid 356 through 369 removed outlier: 3.513A pdb=" N HIS G 369 " --> pdb=" O LYS G 365 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 400 Processing helix chain 'H' and resid 4 through 17 Processing helix chain 'H' and resid 25 through 29 removed outlier: 3.728A pdb=" N THR H 28 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA H 29 " --> pdb=" O ALA H 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 25 through 29' Processing helix chain 'H' and resid 44 through 61 removed outlier: 3.641A pdb=" N ARG H 48 " --> pdb=" O SER H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 78 Processing helix chain 'H' and resid 83 through 91 Processing helix chain 'H' and resid 121 through 140 removed outlier: 3.812A pdb=" N MET H 125 " --> pdb=" O ALA H 121 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS H 140 " --> pdb=" O ARG H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 153 removed outlier: 3.909A pdb=" N GLY H 152 " --> pdb=" O SER H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 176 removed outlier: 3.914A pdb=" N ILE H 176 " --> pdb=" O ILE H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 179 No H-bonds generated for 'chain 'H' and resid 177 through 179' Processing helix chain 'H' and resid 186 through 200 removed outlier: 3.598A pdb=" N GLU H 190 " --> pdb=" O ALA H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 208 Processing helix chain 'H' and resid 210 through 224 Processing helix chain 'H' and resid 224 through 240 removed outlier: 4.067A pdb=" N ARG H 228 " --> pdb=" O SER H 224 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS H 240 " --> pdb=" O ILE H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 260 removed outlier: 4.019A pdb=" N TYR H 258 " --> pdb=" O ASP H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 264 through 275 Processing helix chain 'H' and resid 279 through 283 Processing helix chain 'H' and resid 284 through 305 removed outlier: 3.911A pdb=" N GLN H 288 " --> pdb=" O LEU H 284 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER H 289 " --> pdb=" O ASN H 285 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ASP H 290 " --> pdb=" O GLU H 286 " (cutoff:3.500A) Processing helix chain 'H' and resid 306 through 311 Proline residue: H 309 - end of helix No H-bonds generated for 'chain 'H' and resid 306 through 311' Processing helix chain 'H' and resid 317 through 326 removed outlier: 3.607A pdb=" N ALA H 323 " --> pdb=" O THR H 320 " (cutoff:3.500A) Proline residue: H 324 - end of helix Processing helix chain 'H' and resid 327 through 342 removed outlier: 4.433A pdb=" N THR H 340 " --> pdb=" O GLY H 336 " (cutoff:3.500A) Processing helix chain 'H' and resid 356 through 368 Processing helix chain 'H' and resid 385 through 400 Processing helix chain 'I' and resid 4 through 17 Processing helix chain 'I' and resid 25 through 29 removed outlier: 3.637A pdb=" N THR I 28 " --> pdb=" O SER I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 61 removed outlier: 3.552A pdb=" N ARG I 48 " --> pdb=" O SER I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 78 Processing helix chain 'I' and resid 83 through 91 Processing helix chain 'I' and resid 121 through 140 removed outlier: 3.849A pdb=" N MET I 125 " --> pdb=" O ALA I 121 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS I 140 " --> pdb=" O ARG I 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 148 through 153 removed outlier: 3.869A pdb=" N GLY I 152 " --> pdb=" O SER I 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 176 removed outlier: 3.822A pdb=" N ILE I 176 " --> pdb=" O ILE I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 179 No H-bonds generated for 'chain 'I' and resid 177 through 179' Processing helix chain 'I' and resid 186 through 200 removed outlier: 3.638A pdb=" N GLU I 190 " --> pdb=" O ALA I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 208 removed outlier: 3.505A pdb=" N ALA I 208 " --> pdb=" O PRO I 205 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 224 Processing helix chain 'I' and resid 224 through 240 removed outlier: 4.163A pdb=" N ARG I 228 " --> pdb=" O SER I 224 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS I 240 " --> pdb=" O ILE I 236 " (cutoff:3.500A) Processing helix chain 'I' and resid 246 through 260 removed outlier: 3.912A pdb=" N TYR I 258 " --> pdb=" O ASP I 254 " (cutoff:3.500A) Processing helix chain 'I' and resid 264 through 275 Processing helix chain 'I' and resid 279 through 283 Processing helix chain 'I' and resid 284 through 305 removed outlier: 4.128A pdb=" N GLN I 288 " --> pdb=" O LEU I 284 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N SER I 289 " --> pdb=" O ASN I 285 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ASP I 290 " --> pdb=" O GLU I 286 " (cutoff:3.500A) Processing helix chain 'I' and resid 306 through 311 Proline residue: I 309 - end of helix No H-bonds generated for 'chain 'I' and resid 306 through 311' Processing helix chain 'I' and resid 317 through 322 Processing helix chain 'I' and resid 323 through 326 Processing helix chain 'I' and resid 327 through 342 removed outlier: 4.482A pdb=" N THR I 340 " --> pdb=" O GLY I 336 " (cutoff:3.500A) Processing helix chain 'I' and resid 356 through 368 Processing helix chain 'I' and resid 385 through 400 Processing helix chain 'J' and resid 4 through 17 Processing helix chain 'J' and resid 25 through 29 Processing helix chain 'J' and resid 44 through 61 removed outlier: 3.582A pdb=" N ARG J 48 " --> pdb=" O SER J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 78 Processing helix chain 'J' and resid 83 through 91 Processing helix chain 'J' and resid 121 through 140 removed outlier: 3.809A pdb=" N MET J 125 " --> pdb=" O ALA J 121 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS J 140 " --> pdb=" O ARG J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 153 removed outlier: 3.808A pdb=" N GLY J 152 " --> pdb=" O SER J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 157 through 176 removed outlier: 3.885A pdb=" N ILE J 176 " --> pdb=" O ILE J 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 179 No H-bonds generated for 'chain 'J' and resid 177 through 179' Processing helix chain 'J' and resid 186 through 200 removed outlier: 3.562A pdb=" N GLU J 190 " --> pdb=" O ALA J 186 " (cutoff:3.500A) Processing helix chain 'J' and resid 204 through 208 Processing helix chain 'J' and resid 210 through 224 Processing helix chain 'J' and resid 224 through 240 removed outlier: 4.130A pdb=" N ARG J 228 " --> pdb=" O SER J 224 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS J 240 " --> pdb=" O ILE J 236 " (cutoff:3.500A) Processing helix chain 'J' and resid 246 through 260 removed outlier: 3.945A pdb=" N TYR J 258 " --> pdb=" O ASP J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 264 through 275 Processing helix chain 'J' and resid 279 through 286 removed outlier: 5.731A pdb=" N ASN J 285 " --> pdb=" O LEU J 282 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLU J 286 " --> pdb=" O ALA J 283 " (cutoff:3.500A) Processing helix chain 'J' and resid 287 through 305 removed outlier: 3.538A pdb=" N GLY J 305 " --> pdb=" O TYR J 301 " (cutoff:3.500A) Processing helix chain 'J' and resid 306 through 311 Proline residue: J 309 - end of helix No H-bonds generated for 'chain 'J' and resid 306 through 311' Processing helix chain 'J' and resid 317 through 326 removed outlier: 3.619A pdb=" N ALA J 323 " --> pdb=" O THR J 320 " (cutoff:3.500A) Proline residue: J 324 - end of helix Processing helix chain 'J' and resid 327 through 342 removed outlier: 4.255A pdb=" N THR J 340 " --> pdb=" O GLY J 336 " (cutoff:3.500A) Processing helix chain 'J' and resid 356 through 369 removed outlier: 3.588A pdb=" N HIS J 369 " --> pdb=" O LYS J 365 " (cutoff:3.500A) Processing helix chain 'J' and resid 385 through 400 Processing helix chain 'K' and resid 4 through 17 Processing helix chain 'K' and resid 25 through 29 removed outlier: 3.587A pdb=" N THR K 28 " --> pdb=" O SER K 25 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA K 29 " --> pdb=" O ALA K 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 25 through 29' Processing helix chain 'K' and resid 44 through 61 removed outlier: 3.572A pdb=" N ARG K 48 " --> pdb=" O SER K 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 78 Processing helix chain 'K' and resid 83 through 91 Processing helix chain 'K' and resid 121 through 140 removed outlier: 3.811A pdb=" N MET K 125 " --> pdb=" O ALA K 121 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS K 140 " --> pdb=" O ARG K 136 " (cutoff:3.500A) Processing helix chain 'K' and resid 148 through 153 removed outlier: 3.743A pdb=" N GLY K 152 " --> pdb=" O SER K 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 176 removed outlier: 3.501A pdb=" N LEU K 161 " --> pdb=" O ASP K 157 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE K 176 " --> pdb=" O ILE K 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 179 No H-bonds generated for 'chain 'K' and resid 177 through 179' Processing helix chain 'K' and resid 186 through 200 removed outlier: 3.646A pdb=" N GLU K 190 " --> pdb=" O ALA K 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 204 through 208 Processing helix chain 'K' and resid 210 through 224 Processing helix chain 'K' and resid 224 through 240 removed outlier: 4.145A pdb=" N ARG K 228 " --> pdb=" O SER K 224 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS K 240 " --> pdb=" O ILE K 236 " (cutoff:3.500A) Processing helix chain 'K' and resid 246 through 260 removed outlier: 4.025A pdb=" N TYR K 258 " --> pdb=" O ASP K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 264 through 275 removed outlier: 3.528A pdb=" N LEU K 275 " --> pdb=" O ILE K 271 " (cutoff:3.500A) Processing helix chain 'K' and resid 279 through 286 removed outlier: 5.655A pdb=" N ASN K 285 " --> pdb=" O LEU K 282 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLU K 286 " --> pdb=" O ALA K 283 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 305 Processing helix chain 'K' and resid 306 through 311 Proline residue: K 309 - end of helix No H-bonds generated for 'chain 'K' and resid 306 through 311' Processing helix chain 'K' and resid 316 through 326 removed outlier: 3.561A pdb=" N GLN K 319 " --> pdb=" O GLU K 316 " (cutoff:3.500A) Proline residue: K 324 - end of helix Processing helix chain 'K' and resid 327 through 342 removed outlier: 4.280A pdb=" N THR K 340 " --> pdb=" O GLY K 336 " (cutoff:3.500A) Processing helix chain 'K' and resid 356 through 368 Processing helix chain 'K' and resid 385 through 400 Processing helix chain 'L' and resid 4 through 17 Processing helix chain 'L' and resid 25 through 29 removed outlier: 3.542A pdb=" N THR L 28 " --> pdb=" O SER L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 61 removed outlier: 3.586A pdb=" N ARG L 48 " --> pdb=" O SER L 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 78 Processing helix chain 'L' and resid 83 through 91 Processing helix chain 'L' and resid 121 through 140 removed outlier: 3.816A pdb=" N MET L 125 " --> pdb=" O ALA L 121 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS L 140 " --> pdb=" O ARG L 136 " (cutoff:3.500A) Processing helix chain 'L' and resid 148 through 153 removed outlier: 3.754A pdb=" N GLY L 152 " --> pdb=" O SER L 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 176 removed outlier: 3.888A pdb=" N ILE L 176 " --> pdb=" O ILE L 172 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 200 removed outlier: 3.619A pdb=" N GLU L 190 " --> pdb=" O ALA L 186 " (cutoff:3.500A) Processing helix chain 'L' and resid 204 through 208 removed outlier: 3.503A pdb=" N ALA L 208 " --> pdb=" O PRO L 205 " (cutoff:3.500A) Processing helix chain 'L' and resid 210 through 224 Processing helix chain 'L' and resid 224 through 240 removed outlier: 4.131A pdb=" N ARG L 228 " --> pdb=" O SER L 224 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS L 240 " --> pdb=" O ILE L 236 " (cutoff:3.500A) Processing helix chain 'L' and resid 246 through 260 removed outlier: 3.981A pdb=" N TYR L 258 " --> pdb=" O ASP L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 275 Processing helix chain 'L' and resid 279 through 286 removed outlier: 5.727A pdb=" N ASN L 285 " --> pdb=" O LEU L 282 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLU L 286 " --> pdb=" O ALA L 283 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 305 Processing helix chain 'L' and resid 306 through 311 Proline residue: L 309 - end of helix No H-bonds generated for 'chain 'L' and resid 306 through 311' Processing helix chain 'L' and resid 317 through 326 removed outlier: 3.703A pdb=" N ALA L 323 " --> pdb=" O THR L 320 " (cutoff:3.500A) Proline residue: L 324 - end of helix Processing helix chain 'L' and resid 327 through 342 removed outlier: 4.308A pdb=" N THR L 340 " --> pdb=" O GLY L 336 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 368 Processing helix chain 'L' and resid 385 through 400 Processing helix chain 'M' and resid 4 through 17 Processing helix chain 'M' and resid 25 through 29 removed outlier: 3.571A pdb=" N THR M 28 " --> pdb=" O SER M 25 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA M 29 " --> pdb=" O ALA M 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 25 through 29' Processing helix chain 'M' and resid 44 through 61 removed outlier: 3.717A pdb=" N ARG M 48 " --> pdb=" O SER M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 78 Processing helix chain 'M' and resid 83 through 91 Processing helix chain 'M' and resid 121 through 140 removed outlier: 3.785A pdb=" N MET M 125 " --> pdb=" O ALA M 121 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS M 140 " --> pdb=" O ARG M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 148 through 153 removed outlier: 3.811A pdb=" N GLY M 152 " --> pdb=" O SER M 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 176 removed outlier: 3.904A pdb=" N ILE M 176 " --> pdb=" O ILE M 172 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 179 No H-bonds generated for 'chain 'M' and resid 177 through 179' Processing helix chain 'M' and resid 186 through 200 removed outlier: 3.728A pdb=" N GLU M 190 " --> pdb=" O ALA M 186 " (cutoff:3.500A) Processing helix chain 'M' and resid 204 through 208 removed outlier: 3.515A pdb=" N ALA M 208 " --> pdb=" O PRO M 205 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 224 Processing helix chain 'M' and resid 224 through 240 removed outlier: 4.112A pdb=" N ARG M 228 " --> pdb=" O SER M 224 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS M 240 " --> pdb=" O ILE M 236 " (cutoff:3.500A) Processing helix chain 'M' and resid 246 through 260 removed outlier: 3.967A pdb=" N TYR M 258 " --> pdb=" O ASP M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 275 Processing helix chain 'M' and resid 279 through 283 Processing helix chain 'M' and resid 284 through 305 removed outlier: 3.958A pdb=" N GLN M 288 " --> pdb=" O LEU M 284 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER M 289 " --> pdb=" O ASN M 285 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ASP M 290 " --> pdb=" O GLU M 286 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 311 Proline residue: M 309 - end of helix No H-bonds generated for 'chain 'M' and resid 306 through 311' Processing helix chain 'M' and resid 317 through 326 removed outlier: 3.695A pdb=" N ALA M 323 " --> pdb=" O THR M 320 " (cutoff:3.500A) Proline residue: M 324 - end of helix Processing helix chain 'M' and resid 327 through 342 removed outlier: 4.288A pdb=" N THR M 340 " --> pdb=" O GLY M 336 " (cutoff:3.500A) Processing helix chain 'M' and resid 356 through 370 removed outlier: 3.769A pdb=" N HIS M 369 " --> pdb=" O LYS M 365 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS M 370 " --> pdb=" O SER M 366 " (cutoff:3.500A) Processing helix chain 'M' and resid 385 through 400 Processing helix chain 'N' and resid 4 through 17 removed outlier: 3.612A pdb=" N SER N 13 " --> pdb=" O ALA N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 25 through 29 removed outlier: 3.677A pdb=" N THR N 28 " --> pdb=" O SER N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 61 removed outlier: 3.531A pdb=" N ARG N 48 " --> pdb=" O SER N 44 " (cutoff:3.500A) Processing helix chain 'N' and resid 65 through 78 Processing helix chain 'N' and resid 83 through 91 Processing helix chain 'N' and resid 121 through 140 removed outlier: 3.881A pdb=" N MET N 125 " --> pdb=" O ALA N 121 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS N 140 " --> pdb=" O ARG N 136 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 153 removed outlier: 3.855A pdb=" N GLY N 152 " --> pdb=" O SER N 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 157 through 176 removed outlier: 3.876A pdb=" N ILE N 176 " --> pdb=" O ILE N 172 " (cutoff:3.500A) Processing helix chain 'N' and resid 177 through 179 No H-bonds generated for 'chain 'N' and resid 177 through 179' Processing helix chain 'N' and resid 186 through 200 removed outlier: 3.832A pdb=" N GLU N 190 " --> pdb=" O ALA N 186 " (cutoff:3.500A) Processing helix chain 'N' and resid 204 through 208 removed outlier: 3.533A pdb=" N ALA N 208 " --> pdb=" O PRO N 205 " (cutoff:3.500A) Processing helix chain 'N' and resid 210 through 224 Processing helix chain 'N' and resid 224 through 240 removed outlier: 3.961A pdb=" N ARG N 228 " --> pdb=" O SER N 224 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS N 240 " --> pdb=" O ILE N 236 " (cutoff:3.500A) Processing helix chain 'N' and resid 246 through 260 removed outlier: 3.988A pdb=" N TYR N 258 " --> pdb=" O ASP N 254 " (cutoff:3.500A) Processing helix chain 'N' and resid 264 through 275 Processing helix chain 'N' and resid 279 through 283 Processing helix chain 'N' and resid 284 through 305 removed outlier: 3.910A pdb=" N GLN N 288 " --> pdb=" O LEU N 284 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER N 289 " --> pdb=" O ASN N 285 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASP N 290 " --> pdb=" O GLU N 286 " (cutoff:3.500A) Processing helix chain 'N' and resid 306 through 311 Proline residue: N 309 - end of helix No H-bonds generated for 'chain 'N' and resid 306 through 311' Processing helix chain 'N' and resid 317 through 326 removed outlier: 3.573A pdb=" N ALA N 323 " --> pdb=" O THR N 320 " (cutoff:3.500A) Proline residue: N 324 - end of helix Processing helix chain 'N' and resid 327 through 342 removed outlier: 4.405A pdb=" N THR N 340 " --> pdb=" O GLY N 336 " (cutoff:3.500A) Processing helix chain 'N' and resid 356 through 369 removed outlier: 3.753A pdb=" N HIS N 369 " --> pdb=" O LYS N 365 " (cutoff:3.500A) Processing helix chain 'N' and resid 385 through 400 Processing helix chain 'O' and resid 4 through 17 Processing helix chain 'O' and resid 25 through 29 removed outlier: 3.631A pdb=" N THR O 28 " --> pdb=" O SER O 25 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA O 29 " --> pdb=" O ALA O 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 25 through 29' Processing helix chain 'O' and resid 44 through 61 removed outlier: 3.675A pdb=" N ARG O 48 " --> pdb=" O SER O 44 " (cutoff:3.500A) Processing helix chain 'O' and resid 65 through 78 Processing helix chain 'O' and resid 83 through 91 Processing helix chain 'O' and resid 121 through 140 removed outlier: 3.826A pdb=" N MET O 125 " --> pdb=" O ALA O 121 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS O 140 " --> pdb=" O ARG O 136 " (cutoff:3.500A) Processing helix chain 'O' and resid 148 through 153 removed outlier: 3.840A pdb=" N GLY O 152 " --> pdb=" O SER O 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 157 through 177 removed outlier: 3.853A pdb=" N ILE O 176 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA O 177 " --> pdb=" O TRP O 173 " (cutoff:3.500A) Processing helix chain 'O' and resid 186 through 200 removed outlier: 3.687A pdb=" N GLU O 190 " --> pdb=" O ALA O 186 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 208 removed outlier: 3.626A pdb=" N ALA O 208 " --> pdb=" O PRO O 205 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 224 Processing helix chain 'O' and resid 224 through 240 removed outlier: 4.103A pdb=" N ARG O 228 " --> pdb=" O SER O 224 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS O 240 " --> pdb=" O ILE O 236 " (cutoff:3.500A) Processing helix chain 'O' and resid 246 through 260 removed outlier: 3.939A pdb=" N TYR O 258 " --> pdb=" O ASP O 254 " (cutoff:3.500A) Processing helix chain 'O' and resid 264 through 273 Processing helix chain 'O' and resid 279 through 286 removed outlier: 5.885A pdb=" N ASN O 285 " --> pdb=" O LEU O 282 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLU O 286 " --> pdb=" O ALA O 283 " (cutoff:3.500A) Processing helix chain 'O' and resid 287 through 305 Processing helix chain 'O' and resid 306 through 311 Proline residue: O 309 - end of helix No H-bonds generated for 'chain 'O' and resid 306 through 311' Processing helix chain 'O' and resid 317 through 326 removed outlier: 3.614A pdb=" N ALA O 323 " --> pdb=" O THR O 320 " (cutoff:3.500A) Proline residue: O 324 - end of helix Processing helix chain 'O' and resid 327 through 342 removed outlier: 4.452A pdb=" N THR O 340 " --> pdb=" O GLY O 336 " (cutoff:3.500A) Processing helix chain 'O' and resid 356 through 369 removed outlier: 3.665A pdb=" N HIS O 369 " --> pdb=" O LYS O 365 " (cutoff:3.500A) Processing helix chain 'O' and resid 385 through 400 Processing helix chain 'P' and resid 4 through 17 Processing helix chain 'P' and resid 25 through 29 Processing helix chain 'P' and resid 44 through 61 removed outlier: 3.568A pdb=" N ARG P 48 " --> pdb=" O SER P 44 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 78 Processing helix chain 'P' and resid 83 through 91 Processing helix chain 'P' and resid 121 through 140 removed outlier: 3.792A pdb=" N MET P 125 " --> pdb=" O ALA P 121 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS P 140 " --> pdb=" O ARG P 136 " (cutoff:3.500A) Processing helix chain 'P' and resid 147 through 153 removed outlier: 4.034A pdb=" N TYR P 151 " --> pdb=" O ASP P 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 157 through 177 removed outlier: 3.549A pdb=" N ILE P 176 " --> pdb=" O ILE P 172 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA P 177 " --> pdb=" O TRP P 173 " (cutoff:3.500A) Processing helix chain 'P' and resid 186 through 200 removed outlier: 3.743A pdb=" N GLU P 190 " --> pdb=" O ALA P 186 " (cutoff:3.500A) Processing helix chain 'P' and resid 204 through 208 removed outlier: 3.531A pdb=" N ALA P 208 " --> pdb=" O PRO P 205 " (cutoff:3.500A) Processing helix chain 'P' and resid 210 through 224 Processing helix chain 'P' and resid 224 through 240 removed outlier: 4.188A pdb=" N ARG P 228 " --> pdb=" O SER P 224 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS P 240 " --> pdb=" O ILE P 236 " (cutoff:3.500A) Processing helix chain 'P' and resid 246 through 260 removed outlier: 3.974A pdb=" N TYR P 258 " --> pdb=" O ASP P 254 " (cutoff:3.500A) Processing helix chain 'P' and resid 264 through 273 Processing helix chain 'P' and resid 279 through 284 Processing helix chain 'P' and resid 287 through 305 Processing helix chain 'P' and resid 306 through 311 Proline residue: P 309 - end of helix No H-bonds generated for 'chain 'P' and resid 306 through 311' Processing helix chain 'P' and resid 317 through 322 removed outlier: 3.832A pdb=" N LYS P 321 " --> pdb=" O SER P 317 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE P 322 " --> pdb=" O ILE P 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 317 through 322' Processing helix chain 'P' and resid 323 through 326 Processing helix chain 'P' and resid 327 through 342 removed outlier: 4.651A pdb=" N THR P 340 " --> pdb=" O GLY P 336 " (cutoff:3.500A) Processing helix chain 'P' and resid 356 through 368 Processing helix chain 'P' and resid 385 through 400 Processing helix chain 'Q' and resid 4 through 17 Processing helix chain 'Q' and resid 25 through 29 removed outlier: 3.504A pdb=" N THR Q 28 " --> pdb=" O SER Q 25 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA Q 29 " --> pdb=" O ALA Q 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 25 through 29' Processing helix chain 'Q' and resid 44 through 61 removed outlier: 3.599A pdb=" N ARG Q 48 " --> pdb=" O SER Q 44 " (cutoff:3.500A) Processing helix chain 'Q' and resid 65 through 78 Processing helix chain 'Q' and resid 83 through 91 Processing helix chain 'Q' and resid 121 through 140 removed outlier: 3.775A pdb=" N MET Q 125 " --> pdb=" O ALA Q 121 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS Q 140 " --> pdb=" O ARG Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 147 through 153 removed outlier: 4.021A pdb=" N TYR Q 151 " --> pdb=" O ASP Q 147 " (cutoff:3.500A) Processing helix chain 'Q' and resid 157 through 176 removed outlier: 3.642A pdb=" N ILE Q 176 " --> pdb=" O ILE Q 172 " (cutoff:3.500A) Processing helix chain 'Q' and resid 177 through 179 No H-bonds generated for 'chain 'Q' and resid 177 through 179' Processing helix chain 'Q' and resid 186 through 200 removed outlier: 3.754A pdb=" N GLU Q 190 " --> pdb=" O ALA Q 186 " (cutoff:3.500A) Processing helix chain 'Q' and resid 204 through 208 Processing helix chain 'Q' and resid 210 through 224 Processing helix chain 'Q' and resid 225 through 240 removed outlier: 3.801A pdb=" N LYS Q 240 " --> pdb=" O ILE Q 236 " (cutoff:3.500A) Processing helix chain 'Q' and resid 246 through 260 removed outlier: 3.995A pdb=" N TYR Q 258 " --> pdb=" O ASP Q 254 " (cutoff:3.500A) Processing helix chain 'Q' and resid 264 through 275 Processing helix chain 'Q' and resid 279 through 286 removed outlier: 5.746A pdb=" N ASN Q 285 " --> pdb=" O LEU Q 282 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLU Q 286 " --> pdb=" O ALA Q 283 " (cutoff:3.500A) Processing helix chain 'Q' and resid 287 through 305 Processing helix chain 'Q' and resid 306 through 311 Proline residue: Q 309 - end of helix No H-bonds generated for 'chain 'Q' and resid 306 through 311' Processing helix chain 'Q' and resid 316 through 326 removed outlier: 3.526A pdb=" N ALA Q 323 " --> pdb=" O THR Q 320 " (cutoff:3.500A) Proline residue: Q 324 - end of helix Processing helix chain 'Q' and resid 327 through 342 removed outlier: 4.552A pdb=" N THR Q 340 " --> pdb=" O GLY Q 336 " (cutoff:3.500A) Processing helix chain 'Q' and resid 356 through 369 removed outlier: 3.694A pdb=" N HIS Q 369 " --> pdb=" O LYS Q 365 " (cutoff:3.500A) Processing helix chain 'Q' and resid 385 through 400 Processing sheet with id=AA1, first strand: chain 'D' and resid 33 through 39 removed outlier: 5.817A pdb=" N THR D 33 " --> pdb=" O GLU D 98 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N VAL D 100 " --> pdb=" O THR D 33 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ILE D 35 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE D 102 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE D 37 " --> pdb=" O ILE D 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'E' and resid 33 through 39 removed outlier: 5.806A pdb=" N THR E 33 " --> pdb=" O GLU E 98 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N VAL E 100 " --> pdb=" O THR E 33 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ILE E 35 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE E 102 " --> pdb=" O ILE E 35 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE E 37 " --> pdb=" O ILE E 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'F' and resid 33 through 39 removed outlier: 5.772A pdb=" N THR F 33 " --> pdb=" O GLU F 98 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N VAL F 100 " --> pdb=" O THR F 33 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ILE F 35 " --> pdb=" O VAL F 100 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ILE F 102 " --> pdb=" O ILE F 35 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE F 37 " --> pdb=" O ILE F 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 33 through 39 removed outlier: 5.795A pdb=" N THR G 33 " --> pdb=" O GLU G 98 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL G 100 " --> pdb=" O THR G 33 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE G 35 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ILE G 102 " --> pdb=" O ILE G 35 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE G 37 " --> pdb=" O ILE G 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'H' and resid 33 through 39 removed outlier: 5.885A pdb=" N THR H 33 " --> pdb=" O GLU H 98 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N VAL H 100 " --> pdb=" O THR H 33 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE H 35 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ILE H 102 " --> pdb=" O ILE H 35 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE H 37 " --> pdb=" O ILE H 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'I' and resid 33 through 39 removed outlier: 5.907A pdb=" N THR I 33 " --> pdb=" O GLU I 98 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N VAL I 100 " --> pdb=" O THR I 33 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE I 35 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE I 102 " --> pdb=" O ILE I 35 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE I 37 " --> pdb=" O ILE I 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'J' and resid 33 through 39 removed outlier: 5.875A pdb=" N THR J 33 " --> pdb=" O GLU J 98 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL J 100 " --> pdb=" O THR J 33 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ILE J 35 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ILE J 102 " --> pdb=" O ILE J 35 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE J 37 " --> pdb=" O ILE J 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'K' and resid 33 through 39 removed outlier: 5.924A pdb=" N THR K 33 " --> pdb=" O GLU K 98 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL K 100 " --> pdb=" O THR K 33 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE K 35 " --> pdb=" O VAL K 100 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ILE K 102 " --> pdb=" O ILE K 35 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE K 37 " --> pdb=" O ILE K 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'L' and resid 33 through 39 removed outlier: 5.937A pdb=" N THR L 33 " --> pdb=" O GLU L 98 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL L 100 " --> pdb=" O THR L 33 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ILE L 35 " --> pdb=" O VAL L 100 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ILE L 102 " --> pdb=" O ILE L 35 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE L 37 " --> pdb=" O ILE L 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'M' and resid 33 through 39 removed outlier: 5.899A pdb=" N THR M 33 " --> pdb=" O GLU M 98 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL M 100 " --> pdb=" O THR M 33 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ILE M 35 " --> pdb=" O VAL M 100 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ILE M 102 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE M 37 " --> pdb=" O ILE M 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'N' and resid 33 through 39 Processing sheet with id=AB3, first strand: chain 'O' and resid 33 through 39 removed outlier: 5.833A pdb=" N THR O 33 " --> pdb=" O GLU O 98 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N VAL O 100 " --> pdb=" O THR O 33 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE O 35 " --> pdb=" O VAL O 100 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE O 102 " --> pdb=" O ILE O 35 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE O 37 " --> pdb=" O ILE O 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'P' and resid 33 through 39 removed outlier: 5.746A pdb=" N THR P 33 " --> pdb=" O GLU P 98 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N VAL P 100 " --> pdb=" O THR P 33 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ILE P 35 " --> pdb=" O VAL P 100 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ILE P 102 " --> pdb=" O ILE P 35 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE P 37 " --> pdb=" O ILE P 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'Q' and resid 33 through 39 removed outlier: 5.714A pdb=" N THR Q 33 " --> pdb=" O GLU Q 98 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL Q 100 " --> pdb=" O THR Q 33 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ILE Q 35 " --> pdb=" O VAL Q 100 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ILE Q 102 " --> pdb=" O ILE Q 35 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE Q 37 " --> pdb=" O ILE Q 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 2414 hydrogen bonds defined for protein. 6915 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 8.43 Time building geometry restraints manager: 5.15 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: 10143 1.33 - 1.45: 9735 1.45 - 1.57: 25412 1.57 - 1.69: 167 1.69 - 1.82: 448 Bond restraints: 45905 Sorted by residual: bond pdb=" C ASP H 375 " pdb=" N GLN H 376 " ideal model delta sigma weight residual 1.331 1.269 0.062 1.42e-02 4.96e+03 1.88e+01 bond pdb=" CA ASN O 109 " pdb=" C ASN O 109 " ideal model delta sigma weight residual 1.530 1.482 0.047 1.10e-02 8.26e+03 1.85e+01 bond pdb=" N ASP L 375 " pdb=" CA ASP L 375 " ideal model delta sigma weight residual 1.456 1.407 0.050 1.16e-02 7.43e+03 1.83e+01 bond pdb=" C PRO O 112 " pdb=" N VAL O 113 " ideal model delta sigma weight residual 1.335 1.295 0.039 1.22e-02 6.72e+03 1.04e+01 bond pdb=" CA ILE J 374 " pdb=" C ILE J 374 " ideal model delta sigma weight residual 1.523 1.482 0.041 1.27e-02 6.20e+03 1.02e+01 ... (remaining 45900 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.42: 61991 4.42 - 8.84: 350 8.84 - 13.26: 31 13.26 - 17.68: 3 17.68 - 22.10: 5 Bond angle restraints: 62380 Sorted by residual: angle pdb=" N ASP H 375 " pdb=" CA ASP H 375 " pdb=" C ASP H 375 " ideal model delta sigma weight residual 109.52 87.42 22.10 1.55e+00 4.16e-01 2.03e+02 angle pdb=" N ASP N 375 " pdb=" CA ASP N 375 " pdb=" C ASP N 375 " ideal model delta sigma weight residual 109.24 87.94 21.30 1.51e+00 4.39e-01 1.99e+02 angle pdb=" N ASP J 375 " pdb=" CA ASP J 375 " pdb=" C ASP J 375 " ideal model delta sigma weight residual 109.14 88.24 20.90 1.49e+00 4.50e-01 1.97e+02 angle pdb=" N ASP L 375 " pdb=" CA ASP L 375 " pdb=" C ASP L 375 " ideal model delta sigma weight residual 108.60 90.75 17.85 1.46e+00 4.69e-01 1.49e+02 angle pdb=" N ASP I 375 " pdb=" CA ASP I 375 " pdb=" C ASP I 375 " ideal model delta sigma weight residual 109.41 91.07 18.34 1.52e+00 4.33e-01 1.46e+02 ... (remaining 62375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.71: 26000 16.71 - 33.42: 1814 33.42 - 50.12: 287 50.12 - 66.83: 126 66.83 - 83.54: 22 Dihedral angle restraints: 28249 sinusoidal: 12149 harmonic: 16100 Sorted by residual: dihedral pdb=" CA ILE E 374 " pdb=" C ILE E 374 " pdb=" N ASP E 375 " pdb=" CA ASP E 375 " ideal model delta harmonic sigma weight residual 180.00 150.05 29.95 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA ILE F 374 " pdb=" C ILE F 374 " pdb=" N ASP F 375 " pdb=" CA ASP F 375 " ideal model delta harmonic sigma weight residual 180.00 150.58 29.42 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA ILE K 374 " pdb=" C ILE K 374 " pdb=" N ASP K 375 " pdb=" CA ASP K 375 " ideal model delta harmonic sigma weight residual 180.00 151.09 28.91 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 28246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 6496 0.082 - 0.164: 657 0.164 - 0.246: 32 0.246 - 0.328: 22 0.328 - 0.410: 3 Chirality restraints: 7210 Sorted by residual: chirality pdb=" CB VAL E 108 " pdb=" CA VAL E 108 " pdb=" CG1 VAL E 108 " pdb=" CG2 VAL E 108 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" CB ILE G 374 " pdb=" CA ILE G 374 " pdb=" CG1 ILE G 374 " pdb=" CG2 ILE G 374 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CA ASP O 375 " pdb=" N ASP O 375 " pdb=" C ASP O 375 " pdb=" CB ASP O 375 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 7207 not shown) Planarity restraints: 7728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN I 285 " 0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" CG ASN I 285 " -0.059 2.00e-02 2.50e+03 pdb=" OD1 ASN I 285 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN I 285 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY O 105 " 0.017 2.00e-02 2.50e+03 3.34e-02 1.12e+01 pdb=" C GLY O 105 " -0.058 2.00e-02 2.50e+03 pdb=" O GLY O 105 " 0.022 2.00e-02 2.50e+03 pdb=" N SER O 106 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY O 373 " -0.014 2.00e-02 2.50e+03 2.92e-02 8.52e+00 pdb=" C GLY O 373 " 0.050 2.00e-02 2.50e+03 pdb=" O GLY O 373 " -0.019 2.00e-02 2.50e+03 pdb=" N ILE O 374 " -0.017 2.00e-02 2.50e+03 ... (remaining 7725 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 318 2.65 - 3.22: 40937 3.22 - 3.78: 70213 3.78 - 4.34: 97884 4.34 - 4.90: 154757 Nonbonded interactions: 364109 Sorted by model distance: nonbonded pdb=" N ASP J 375 " pdb=" O ASP J 375 " model vdw 2.093 2.496 nonbonded pdb=" N ASP H 375 " pdb=" O ASP H 375 " model vdw 2.111 2.496 nonbonded pdb=" N ASP N 375 " pdb=" O ASP N 375 " model vdw 2.140 2.496 nonbonded pdb=" N ASP L 375 " pdb=" O ASP L 375 " model vdw 2.151 2.496 nonbonded pdb=" N ASP I 375 " pdb=" O ASP I 375 " model vdw 2.164 2.496 ... (remaining 364104 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 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 10.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.840 Check model and map are aligned: 0.140 Set scattering table: 0.130 Process input model: 42.970 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 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 : 0.004 0.070 45905 Z= 0.235 Angle : 0.907 22.104 62380 Z= 0.503 Chirality : 0.051 0.410 7210 Planarity : 0.009 0.071 7728 Dihedral : 12.290 83.538 17861 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.10), residues: 5544 helix: -0.52 (0.08), residues: 3164 sheet: 0.43 (0.31), residues: 252 loop : -0.41 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 368 TYR 0.028 0.002 TYR D 327 PHE 0.016 0.002 PHE M 74 TRP 0.016 0.002 TRP H 194 HIS 0.019 0.004 HIS P 369 Details of bonding type rmsd covalent geometry : bond 0.00443 (45905) covalent geometry : angle 0.90652 (62380) hydrogen bonds : bond 0.16150 ( 2414) hydrogen bonds : angle 6.00995 ( 6915) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11088 Ramachandran restraints generated. 5544 Oldfield, 0 Emsley, 5544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11088 Ramachandran restraints generated. 5544 Oldfield, 0 Emsley, 5544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1156 residues out of total 4592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1156 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 264 MET cc_start: 0.5392 (mtp) cc_final: 0.3172 (ttm) REVERT: D 275 LEU cc_start: 0.8528 (mt) cc_final: 0.8132 (tt) REVERT: D 285 ASN cc_start: 0.5627 (m-40) cc_final: 0.5347 (m-40) REVERT: D 287 PHE cc_start: 0.7512 (m-80) cc_final: 0.6718 (m-10) REVERT: D 311 MET cc_start: 0.6400 (ptp) cc_final: 0.5869 (ptp) REVERT: D 391 GLU cc_start: 0.7270 (mm-30) cc_final: 0.7041 (mm-30) REVERT: E 125 MET cc_start: 0.8587 (mtm) cc_final: 0.8214 (mpm) REVERT: E 217 MET cc_start: 0.8405 (tpt) cc_final: 0.8071 (tpt) REVERT: E 354 TYR cc_start: 0.8033 (p90) cc_final: 0.7492 (p90) REVERT: E 377 ASN cc_start: 0.7098 (m110) cc_final: 0.6623 (m-40) REVERT: G 341 ILE cc_start: 0.8085 (mm) cc_final: 0.7751 (mm) REVERT: P 49 TRP cc_start: 0.6905 (t-100) cc_final: 0.6462 (t-100) REVERT: Q 107 MET cc_start: 0.3143 (tmm) cc_final: 0.1694 (ppp) REVERT: Q 197 TYR cc_start: 0.7134 (m-80) cc_final: 0.6862 (m-10) REVERT: Q 213 TRP cc_start: 0.4485 (t60) cc_final: 0.4210 (t60) REVERT: Q 231 MET cc_start: 0.7549 (mmp) cc_final: 0.7119 (tmt) REVERT: Q 327 TYR cc_start: 0.5525 (p90) cc_final: 0.5296 (p90) REVERT: Q 331 TRP cc_start: 0.6790 (t60) cc_final: 0.6543 (t60) outliers start: 0 outliers final: 6 residues processed: 1156 average time/residue: 1.0083 time to fit residues: 1375.5864 Evaluate side-chains 507 residues out of total 4592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 501 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 TYR Chi-restraints excluded: chain D residue 302 ARG Chi-restraints excluded: chain E residue 14 TYR Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain P residue 109 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 394 optimal weight: 1.9990 chunk 430 optimal weight: 1.9990 chunk 41 optimal weight: 20.0000 chunk 265 optimal weight: 0.7980 chunk 523 optimal weight: 20.0000 chunk 497 optimal weight: 2.9990 chunk 414 optimal weight: 1.9990 chunk 310 optimal weight: 0.8980 chunk 488 optimal weight: 8.9990 chunk 366 optimal weight: 3.9990 chunk 223 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 288 GLN D 351 ASN E 15 GLN E 109 ASN E 211 GLN F 285 ASN F 349 ASN ** F 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 257 ASN G 380 ASN G 397 GLN H 15 GLN H 388 GLN ** I 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 377 ASN ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 223 GLN J 285 ASN K 43 ASN M 43 ASN M 397 GLN N 15 GLN N 369 HIS O 369 HIS P 369 HIS ** P 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 257 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.127964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.075788 restraints weight = 103707.000| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.82 r_work: 0.2975 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 45905 Z= 0.166 Angle : 0.659 11.466 62380 Z= 0.346 Chirality : 0.041 0.189 7210 Planarity : 0.005 0.061 7728 Dihedral : 9.868 87.495 7473 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.31 % Allowed : 12.15 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.11), residues: 5544 helix: 0.88 (0.09), residues: 3192 sheet: 0.76 (0.31), residues: 252 loop : 0.12 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 130 TYR 0.024 0.002 TYR D 301 PHE 0.032 0.001 PHE D 360 TRP 0.011 0.001 TRP F 213 HIS 0.007 0.001 HIS M 369 Details of bonding type rmsd covalent geometry : bond 0.00375 (45905) covalent geometry : angle 0.65914 (62380) hydrogen bonds : bond 0.05203 ( 2414) hydrogen bonds : angle 3.85905 ( 6915) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11088 Ramachandran restraints generated. 5544 Oldfield, 0 Emsley, 5544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11088 Ramachandran restraints generated. 5544 Oldfield, 0 Emsley, 5544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 4592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 531 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 122 GLN cc_start: 0.5581 (OUTLIER) cc_final: 0.5209 (mt0) REVERT: D 125 MET cc_start: 0.6333 (pp-130) cc_final: 0.6098 (ppp) REVERT: D 275 LEU cc_start: 0.8355 (mt) cc_final: 0.7822 (tt) REVERT: D 287 PHE cc_start: 0.7583 (m-80) cc_final: 0.7237 (m-10) REVERT: D 322 PHE cc_start: 0.4567 (m-10) cc_final: 0.4301 (m-10) REVERT: D 345 MET cc_start: 0.7278 (mmt) cc_final: 0.7074 (tpp) REVERT: D 399 THR cc_start: 0.4836 (t) cc_final: 0.4372 (m) REVERT: E 14 TYR cc_start: 0.7963 (t80) cc_final: 0.7733 (OUTLIER) REVERT: E 107 MET cc_start: 0.7025 (mmm) cc_final: 0.6824 (mmm) REVERT: E 125 MET cc_start: 0.8835 (mtm) cc_final: 0.8327 (mpm) REVERT: E 217 MET cc_start: 0.8874 (tpt) cc_final: 0.8407 (tpt) REVERT: E 264 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8106 (mpt) REVERT: F 112 PRO cc_start: 0.8246 (Cg_endo) cc_final: 0.7842 (Cg_exo) REVERT: F 125 MET cc_start: 0.8682 (tmm) cc_final: 0.8167 (mpp) REVERT: F 358 MET cc_start: 0.9159 (tmm) cc_final: 0.8884 (tpt) REVERT: G 68 MET cc_start: 0.8968 (mmt) cc_final: 0.8667 (mmp) REVERT: G 107 MET cc_start: 0.7627 (ttt) cc_final: 0.7321 (ttt) REVERT: G 129 MET cc_start: 0.8916 (mpp) cc_final: 0.8454 (mpp) REVERT: G 276 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8269 (mm-30) REVERT: G 358 MET cc_start: 0.8644 (tmm) cc_final: 0.8397 (tmm) REVERT: H 23 ARG cc_start: 0.8857 (mmm-85) cc_final: 0.8589 (mmm-85) REVERT: H 98 GLU cc_start: 0.8811 (pt0) cc_final: 0.8454 (pm20) REVERT: H 109 ASN cc_start: 0.8169 (p0) cc_final: 0.7892 (m110) REVERT: H 250 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8255 (mm-30) REVERT: I 125 MET cc_start: 0.8090 (tmm) cc_final: 0.7793 (tmm) REVERT: I 129 MET cc_start: 0.8973 (mmm) cc_final: 0.8625 (mmm) REVERT: I 187 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7954 (tm-30) REVERT: J 7 GLU cc_start: 0.8231 (tp30) cc_final: 0.7975 (tp30) REVERT: J 125 MET cc_start: 0.8429 (mmt) cc_final: 0.8084 (mmt) REVERT: K 7 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8322 (mp0) REVERT: K 130 ARG cc_start: 0.8901 (ttm110) cc_final: 0.8462 (mtm-85) REVERT: K 131 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8684 (mm) REVERT: K 378 MET cc_start: 0.8938 (mmm) cc_final: 0.8641 (mmm) REVERT: L 6 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8648 (mp0) REVERT: L 114 MET cc_start: 0.8636 (ppp) cc_final: 0.8394 (ppp) REVERT: L 129 MET cc_start: 0.9004 (tpp) cc_final: 0.8603 (tpt) REVERT: M 107 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.7371 (tmt) REVERT: M 264 MET cc_start: 0.9503 (mtm) cc_final: 0.9247 (mtp) REVERT: M 358 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.7907 (tmm) REVERT: M 388 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8307 (pt0) REVERT: N 7 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8496 (mp0) REVERT: O 107 MET cc_start: 0.5084 (tmm) cc_final: 0.4713 (tmt) REVERT: O 197 TYR cc_start: 0.8212 (m-80) cc_final: 0.7778 (m-80) REVERT: O 233 GLU cc_start: 0.9291 (tp30) cc_final: 0.8715 (tp30) REVERT: O 311 MET cc_start: 0.9073 (ptp) cc_final: 0.8830 (ptm) REVERT: O 376 GLN cc_start: 0.7420 (mm-40) cc_final: 0.5956 (mp10) REVERT: P 49 TRP cc_start: 0.6312 (t-100) cc_final: 0.6110 (t-100) REVERT: P 68 MET cc_start: 0.8283 (mtp) cc_final: 0.7673 (ptp) REVERT: P 107 MET cc_start: 0.4498 (ptp) cc_final: 0.4003 (ptp) REVERT: P 114 MET cc_start: 0.6792 (ptt) cc_final: 0.6442 (ptt) REVERT: Q 231 MET cc_start: 0.7593 (mmp) cc_final: 0.7057 (tmt) REVERT: Q 331 TRP cc_start: 0.6716 (t60) cc_final: 0.6496 (t-100) outliers start: 106 outliers final: 22 residues processed: 598 average time/residue: 0.8313 time to fit residues: 599.9228 Evaluate side-chains 457 residues out of total 4592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 428 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 TYR Chi-restraints excluded: chain D residue 79 MET Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 302 ARG Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain G residue 276 GLU Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 131 ILE Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain M residue 358 MET Chi-restraints excluded: chain M residue 388 GLN Chi-restraints excluded: chain M residue 391 GLU Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 7 GLU Chi-restraints excluded: chain N residue 351 ASN Chi-restraints excluded: chain O residue 259 VAL Chi-restraints excluded: chain P residue 236 ILE Chi-restraints excluded: chain Q residue 148 SER Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 238 VAL Chi-restraints excluded: chain Q residue 275 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 525 optimal weight: 0.0170 chunk 483 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 309 optimal weight: 3.9990 chunk 405 optimal weight: 0.9980 chunk 522 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 106 optimal weight: 8.9990 chunk 232 optimal weight: 5.9990 chunk 269 optimal weight: 0.7980 overall best weight: 1.5622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 288 GLN D 351 ASN ** H 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 257 ASN I 285 ASN ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 257 ASN L 257 ASN M 257 ASN ** N 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 376 GLN ** P 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.126128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.073382 restraints weight = 103798.901| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.82 r_work: 0.2924 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 45905 Z= 0.170 Angle : 0.619 11.087 62380 Z= 0.321 Chirality : 0.040 0.170 7210 Planarity : 0.004 0.077 7728 Dihedral : 9.662 86.161 7467 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.40 % Allowed : 13.22 % Favored : 84.39 % 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: 1.31 (0.11), residues: 5544 helix: 1.38 (0.09), residues: 3206 sheet: 1.81 (0.29), residues: 224 loop : 0.10 (0.14), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 23 TYR 0.026 0.002 TYR D 327 PHE 0.018 0.001 PHE O 268 TRP 0.025 0.001 TRP Q 194 HIS 0.011 0.001 HIS N 369 Details of bonding type rmsd covalent geometry : bond 0.00392 (45905) covalent geometry : angle 0.61928 (62380) hydrogen bonds : bond 0.04846 ( 2414) hydrogen bonds : angle 3.62209 ( 6915) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11088 Ramachandran restraints generated. 5544 Oldfield, 0 Emsley, 5544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11088 Ramachandran restraints generated. 5544 Oldfield, 0 Emsley, 5544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 4592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 453 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 122 GLN cc_start: 0.5556 (OUTLIER) cc_final: 0.5174 (mt0) REVERT: D 125 MET cc_start: 0.6394 (pp-130) cc_final: 0.6160 (ppp) REVERT: D 213 TRP cc_start: 0.8275 (t60) cc_final: 0.7996 (t60) REVERT: D 257 ASN cc_start: 0.8203 (OUTLIER) cc_final: 0.7703 (m110) REVERT: D 322 PHE cc_start: 0.4554 (m-10) cc_final: 0.4261 (m-80) REVERT: D 330 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7702 (mm) REVERT: D 378 MET cc_start: 0.6732 (ptt) cc_final: 0.6282 (pp-130) REVERT: D 399 THR cc_start: 0.4857 (OUTLIER) cc_final: 0.4378 (m) REVERT: E 107 MET cc_start: 0.7215 (mmm) cc_final: 0.6889 (mmm) REVERT: E 125 MET cc_start: 0.8824 (mtm) cc_final: 0.8195 (mpm) REVERT: E 217 MET cc_start: 0.8863 (tpt) cc_final: 0.8368 (tpt) REVERT: E 264 MET cc_start: 0.8504 (mtp) cc_final: 0.8092 (mpt) REVERT: E 317 SER cc_start: 0.9138 (p) cc_final: 0.8697 (t) REVERT: F 129 MET cc_start: 0.9435 (mtp) cc_final: 0.9230 (mtp) REVERT: F 239 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.7848 (tptp) REVERT: F 264 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8536 (mtm) REVERT: G 68 MET cc_start: 0.8893 (mmt) cc_final: 0.8674 (mmp) REVERT: G 276 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8267 (mm-30) REVERT: G 358 MET cc_start: 0.8612 (tmm) cc_final: 0.8356 (tmm) REVERT: H 23 ARG cc_start: 0.8876 (mmm-85) cc_final: 0.8633 (mmm-85) REVERT: H 98 GLU cc_start: 0.8859 (pt0) cc_final: 0.8453 (pm20) REVERT: H 254 ASP cc_start: 0.9079 (t0) cc_final: 0.8553 (t70) REVERT: H 292 ASN cc_start: 0.8516 (m-40) cc_final: 0.8230 (m110) REVERT: H 303 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8370 (mp0) REVERT: H 365 LYS cc_start: 0.8897 (mtpt) cc_final: 0.8146 (mmtt) REVERT: H 376 GLN cc_start: 0.8417 (mm-40) cc_final: 0.7692 (tm-30) REVERT: I 125 MET cc_start: 0.8084 (tmm) cc_final: 0.7810 (tmm) REVERT: I 187 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7975 (tm-30) REVERT: I 342 ASP cc_start: 0.8786 (t0) cc_final: 0.8467 (t0) REVERT: J 7 GLU cc_start: 0.8415 (tp30) cc_final: 0.8079 (mm-30) REVERT: J 107 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8406 (tpp) REVERT: J 125 MET cc_start: 0.8506 (mmt) cc_final: 0.8194 (mmt) REVERT: J 129 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8990 (mpp) REVERT: J 158 MET cc_start: 0.8134 (mmm) cc_final: 0.7806 (tpt) REVERT: J 342 ASP cc_start: 0.8826 (t70) cc_final: 0.8571 (t0) REVERT: J 351 ASN cc_start: 0.9117 (t0) cc_final: 0.8630 (p0) REVERT: K 36 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8562 (mtm-85) REVERT: K 107 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8560 (ttt) REVERT: K 376 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7846 (tm-30) REVERT: K 378 MET cc_start: 0.8945 (mmm) cc_final: 0.8706 (mmt) REVERT: L 6 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8656 (mp0) REVERT: L 107 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.7552 (tmt) REVERT: L 114 MET cc_start: 0.8539 (ppp) cc_final: 0.8203 (ppp) REVERT: L 129 MET cc_start: 0.8978 (tpp) cc_final: 0.8557 (tpt) REVERT: L 216 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8639 (mp0) REVERT: L 378 MET cc_start: 0.9106 (mmm) cc_final: 0.8850 (mmm) REVERT: M 358 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.7997 (tmm) REVERT: N 114 MET cc_start: 0.8461 (pp-130) cc_final: 0.8236 (ppp) REVERT: N 129 MET cc_start: 0.9549 (mpp) cc_final: 0.9242 (mpp) REVERT: N 190 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8371 (mt-10) REVERT: N 378 MET cc_start: 0.8317 (tpt) cc_final: 0.7763 (mpm) REVERT: O 80 TYR cc_start: 0.8454 (p90) cc_final: 0.8210 (p90) REVERT: O 82 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8064 (mp0) REVERT: O 114 MET cc_start: 0.8094 (ppp) cc_final: 0.6833 (ppp) REVERT: O 197 TYR cc_start: 0.8328 (m-80) cc_final: 0.7963 (m-80) REVERT: O 233 GLU cc_start: 0.9301 (tp30) cc_final: 0.8791 (tp30) REVERT: P 49 TRP cc_start: 0.6397 (t-100) cc_final: 0.6098 (t-100) REVERT: P 68 MET cc_start: 0.8278 (mtp) cc_final: 0.7852 (ptt) REVERT: P 107 MET cc_start: 0.4480 (ptp) cc_final: 0.4059 (ptp) REVERT: P 114 MET cc_start: 0.7002 (ptt) cc_final: 0.6636 (ptt) REVERT: P 272 ARG cc_start: 0.8441 (tpp80) cc_final: 0.8061 (tpp-160) REVERT: P 356 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8680 (tm-30) REVERT: Q 107 MET cc_start: 0.4941 (tmt) cc_final: 0.4562 (tmt) REVERT: Q 231 MET cc_start: 0.7669 (mmp) cc_final: 0.7121 (tmt) REVERT: Q 298 MET cc_start: 0.9115 (ttp) cc_final: 0.8525 (tmm) REVERT: Q 331 TRP cc_start: 0.6827 (t60) cc_final: 0.6500 (t-100) outliers start: 110 outliers final: 31 residues processed: 525 average time/residue: 0.7245 time to fit residues: 460.0943 Evaluate side-chains 449 residues out of total 4592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 399 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 TYR Chi-restraints excluded: chain D residue 79 MET Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 302 ARG Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain E residue 14 TYR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain F residue 239 LYS Chi-restraints excluded: chain F residue 264 MET Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain G residue 276 GLU Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain H residue 36 ARG Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 303 GLU Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 107 MET Chi-restraints excluded: chain J residue 129 MET Chi-restraints excluded: chain K residue 36 ARG Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 107 MET Chi-restraints excluded: chain K residue 376 GLN Chi-restraints excluded: chain L residue 107 MET Chi-restraints excluded: chain L residue 216 GLU Chi-restraints excluded: chain L residue 303 GLU Chi-restraints excluded: chain M residue 21 ASP Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 358 MET Chi-restraints excluded: chain M residue 391 GLU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 190 GLU Chi-restraints excluded: chain N residue 271 ILE Chi-restraints excluded: chain O residue 82 GLU Chi-restraints excluded: chain O residue 259 VAL Chi-restraints excluded: chain P residue 356 GLU Chi-restraints excluded: chain Q residue 106 SER Chi-restraints excluded: chain Q residue 148 SER Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 238 VAL Chi-restraints excluded: chain Q residue 275 LEU Chi-restraints excluded: chain Q residue 389 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 477 optimal weight: 0.0270 chunk 245 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 552 optimal weight: 6.9990 chunk 187 optimal weight: 1.9990 chunk 209 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 419 optimal weight: 1.9990 chunk 251 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 369 optimal weight: 0.9990 overall best weight: 1.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 288 GLN D 397 GLN E 15 GLN E 285 ASN ** H 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 257 ASN ** I 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 122 GLN K 285 ASN ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 122 GLN ** N 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 223 GLN ** P 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.125904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.073631 restraints weight = 103514.514| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.79 r_work: 0.2922 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 45905 Z= 0.156 Angle : 0.605 12.414 62380 Z= 0.310 Chirality : 0.040 0.176 7210 Planarity : 0.004 0.076 7728 Dihedral : 9.538 60.853 7465 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.87 % Allowed : 14.13 % Favored : 83.99 % 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: 1.59 (0.11), residues: 5544 helix: 1.64 (0.09), residues: 3164 sheet: 0.95 (0.30), residues: 252 loop : 0.29 (0.14), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 130 TYR 0.015 0.001 TYR O 258 PHE 0.026 0.001 PHE D 333 TRP 0.034 0.001 TRP Q 194 HIS 0.007 0.001 HIS N 369 Details of bonding type rmsd covalent geometry : bond 0.00359 (45905) covalent geometry : angle 0.60530 (62380) hydrogen bonds : bond 0.04515 ( 2414) hydrogen bonds : angle 3.51898 ( 6915) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11088 Ramachandran restraints generated. 5544 Oldfield, 0 Emsley, 5544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11088 Ramachandran restraints generated. 5544 Oldfield, 0 Emsley, 5544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 4592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 445 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 122 GLN cc_start: 0.5569 (OUTLIER) cc_final: 0.5179 (mt0) REVERT: D 125 MET cc_start: 0.6328 (pp-130) cc_final: 0.6085 (ppp) REVERT: D 213 TRP cc_start: 0.8272 (t60) cc_final: 0.8032 (t60) REVERT: D 257 ASN cc_start: 0.8170 (OUTLIER) cc_final: 0.7652 (m110) REVERT: D 275 LEU cc_start: 0.8202 (mp) cc_final: 0.7901 (pp) REVERT: D 322 PHE cc_start: 0.4621 (m-10) cc_final: 0.4375 (m-80) REVERT: D 327 TYR cc_start: 0.7627 (p90) cc_final: 0.7408 (p90) REVERT: D 378 MET cc_start: 0.6706 (ptt) cc_final: 0.6276 (pp-130) REVERT: D 399 THR cc_start: 0.4610 (OUTLIER) cc_final: 0.4156 (m) REVERT: E 107 MET cc_start: 0.7010 (mmm) cc_final: 0.6640 (mmm) REVERT: E 125 MET cc_start: 0.8796 (mtm) cc_final: 0.8148 (mpm) REVERT: E 217 MET cc_start: 0.8872 (tpt) cc_final: 0.8407 (tpt) REVERT: E 264 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8093 (mpt) REVERT: E 311 MET cc_start: 0.7938 (mmm) cc_final: 0.7621 (mpt) REVERT: E 317 SER cc_start: 0.9124 (p) cc_final: 0.8637 (t) REVERT: F 112 PRO cc_start: 0.8163 (Cg_endo) cc_final: 0.7726 (Cg_exo) REVERT: F 129 MET cc_start: 0.9447 (mtp) cc_final: 0.9226 (mtp) REVERT: F 331 TRP cc_start: 0.8298 (t60) cc_final: 0.7941 (t60) REVERT: F 342 ASP cc_start: 0.8269 (m-30) cc_final: 0.8055 (m-30) REVERT: F 358 MET cc_start: 0.9246 (tmm) cc_final: 0.8952 (tpt) REVERT: F 368 ARG cc_start: 0.7312 (mtt180) cc_final: 0.7109 (ttm110) REVERT: G 20 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7853 (mmt-90) REVERT: G 21 ASP cc_start: 0.9020 (m-30) cc_final: 0.8395 (m-30) REVERT: G 78 SER cc_start: 0.9376 (OUTLIER) cc_final: 0.9171 (p) REVERT: G 129 MET cc_start: 0.8983 (mpp) cc_final: 0.8757 (mpp) REVERT: G 276 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8121 (mm-30) REVERT: G 358 MET cc_start: 0.8646 (tmm) cc_final: 0.8344 (tmm) REVERT: G 361 ARG cc_start: 0.8541 (mtm110) cc_final: 0.8336 (mtm110) REVERT: H 23 ARG cc_start: 0.8875 (mmm-85) cc_final: 0.8644 (mmm-85) REVERT: H 254 ASP cc_start: 0.9077 (t0) cc_final: 0.8558 (t70) REVERT: H 292 ASN cc_start: 0.8540 (m-40) cc_final: 0.8246 (m110) REVERT: H 303 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8374 (mp0) REVERT: H 365 LYS cc_start: 0.8895 (mtpt) cc_final: 0.8149 (mmtt) REVERT: H 376 GLN cc_start: 0.8424 (mm-40) cc_final: 0.7722 (tm-30) REVERT: I 125 MET cc_start: 0.8127 (tmm) cc_final: 0.7826 (tmt) REVERT: I 187 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8048 (tm-30) REVERT: J 7 GLU cc_start: 0.8464 (tp30) cc_final: 0.7639 (tp30) REVERT: J 114 MET cc_start: 0.7713 (ppp) cc_final: 0.7425 (ppp) REVERT: J 125 MET cc_start: 0.8517 (mmt) cc_final: 0.8239 (mmt) REVERT: J 158 MET cc_start: 0.8124 (mmm) cc_final: 0.7798 (tpt) REVERT: K 36 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8530 (mtm-85) REVERT: K 376 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7981 (tm-30) REVERT: K 378 MET cc_start: 0.8942 (mmm) cc_final: 0.8740 (mmt) REVERT: L 6 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8720 (mp0) REVERT: L 114 MET cc_start: 0.8641 (ppp) cc_final: 0.8364 (pp-130) REVERT: L 129 MET cc_start: 0.8994 (tpp) cc_final: 0.8570 (tpt) REVERT: M 104 VAL cc_start: 0.7956 (OUTLIER) cc_final: 0.7668 (p) REVERT: M 107 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.7272 (tmt) REVERT: M 114 MET cc_start: 0.9097 (tmm) cc_final: 0.8143 (ppp) REVERT: M 358 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8053 (tmm) REVERT: N 7 GLU cc_start: 0.8930 (mp0) cc_final: 0.8464 (mp0) REVERT: N 125 MET cc_start: 0.9068 (mmt) cc_final: 0.8767 (mmm) REVERT: N 129 MET cc_start: 0.9564 (mpp) cc_final: 0.9228 (mpp) REVERT: N 378 MET cc_start: 0.8261 (tpt) cc_final: 0.7731 (mpm) REVERT: O 82 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8128 (mp0) REVERT: O 122 GLN cc_start: 0.8674 (mp10) cc_final: 0.8459 (pm20) REVERT: O 197 TYR cc_start: 0.8316 (m-80) cc_final: 0.7953 (m-80) REVERT: O 233 GLU cc_start: 0.9302 (tp30) cc_final: 0.8817 (tp30) REVERT: O 376 GLN cc_start: 0.6819 (mm110) cc_final: 0.5771 (mp10) REVERT: O 378 MET cc_start: 0.7623 (tmm) cc_final: 0.7291 (pmm) REVERT: P 49 TRP cc_start: 0.6382 (t-100) cc_final: 0.6116 (t-100) REVERT: P 68 MET cc_start: 0.8273 (mtp) cc_final: 0.7913 (ptp) REVERT: P 107 MET cc_start: 0.4553 (ptp) cc_final: 0.4216 (ptp) REVERT: P 114 MET cc_start: 0.7102 (ptt) cc_final: 0.6757 (ptt) REVERT: P 272 ARG cc_start: 0.8500 (tpp80) cc_final: 0.8117 (tpp-160) REVERT: Q 107 MET cc_start: 0.4709 (tmt) cc_final: 0.4409 (tmt) REVERT: Q 231 MET cc_start: 0.7516 (mmp) cc_final: 0.7050 (tmt) REVERT: Q 298 MET cc_start: 0.9105 (ttp) cc_final: 0.8452 (tmm) REVERT: Q 311 MET cc_start: 0.8111 (mmp) cc_final: 0.7627 (mmm) outliers start: 86 outliers final: 31 residues processed: 505 average time/residue: 0.7207 time to fit residues: 441.2685 Evaluate side-chains 441 residues out of total 4592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 396 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 TYR Chi-restraints excluded: chain D residue 79 MET Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 302 ARG Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 276 GLU Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 342 ASP Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 36 ARG Chi-restraints excluded: chain H residue 303 GLU Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain I residue 341 ILE Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain K residue 36 ARG Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 376 GLN Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 303 GLU Chi-restraints excluded: chain M residue 21 ASP Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain M residue 358 MET Chi-restraints excluded: chain M residue 391 GLU Chi-restraints excluded: chain O residue 82 GLU Chi-restraints excluded: chain Q residue 148 SER Chi-restraints excluded: chain Q residue 238 VAL Chi-restraints excluded: chain Q residue 262 THR Chi-restraints excluded: chain Q residue 389 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 375 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 331 optimal weight: 0.7980 chunk 209 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 409 optimal weight: 0.7980 chunk 107 optimal weight: 8.9990 chunk 524 optimal weight: 4.9990 chunk 363 optimal weight: 1.9990 chunk 417 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 288 GLN D 376 GLN ** F 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 GLN ** H 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 109 ASN K 122 GLN ** N 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.126156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.073859 restraints weight = 103738.293| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.81 r_work: 0.2931 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 45905 Z= 0.137 Angle : 0.592 12.030 62380 Z= 0.302 Chirality : 0.039 0.203 7210 Planarity : 0.004 0.051 7728 Dihedral : 9.492 60.734 7465 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.18 % Allowed : 15.07 % Favored : 82.75 % 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 (0.11), residues: 5544 helix: 1.75 (0.09), residues: 3164 sheet: 2.02 (0.28), residues: 224 loop : 0.22 (0.14), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J 23 TYR 0.023 0.001 TYR D 80 PHE 0.019 0.001 PHE E 333 TRP 0.026 0.001 TRP D 173 HIS 0.005 0.001 HIS N 369 Details of bonding type rmsd covalent geometry : bond 0.00310 (45905) covalent geometry : angle 0.59203 (62380) hydrogen bonds : bond 0.04199 ( 2414) hydrogen bonds : angle 3.43556 ( 6915) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11088 Ramachandran restraints generated. 5544 Oldfield, 0 Emsley, 5544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11088 Ramachandran restraints generated. 5544 Oldfield, 0 Emsley, 5544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 4592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 430 time to evaluate : 1.035 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: D 122 GLN cc_start: 0.5627 (OUTLIER) cc_final: 0.5246 (mt0) REVERT: D 125 MET cc_start: 0.6325 (pp-130) cc_final: 0.6079 (ppp) REVERT: D 213 TRP cc_start: 0.8319 (t60) cc_final: 0.8108 (t60) REVERT: D 257 ASN cc_start: 0.8025 (OUTLIER) cc_final: 0.7250 (m110) REVERT: D 264 MET cc_start: 0.1809 (mtm) cc_final: 0.1285 (mtm) REVERT: D 322 PHE cc_start: 0.4568 (m-10) cc_final: 0.4102 (m-80) REVERT: D 327 TYR cc_start: 0.7709 (p90) cc_final: 0.7488 (p90) REVERT: D 345 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.7124 (tpp) REVERT: D 378 MET cc_start: 0.6756 (ptt) cc_final: 0.6393 (pp-130) REVERT: D 399 THR cc_start: 0.4440 (OUTLIER) cc_final: 0.3922 (m) REVERT: E 107 MET cc_start: 0.6955 (mmm) cc_final: 0.6579 (mmm) REVERT: E 125 MET cc_start: 0.8792 (mtm) cc_final: 0.8167 (mpm) REVERT: E 217 MET cc_start: 0.8872 (tpt) cc_final: 0.8408 (tpt) REVERT: E 264 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8095 (mpt) REVERT: E 317 SER cc_start: 0.9079 (p) cc_final: 0.8545 (t) REVERT: F 107 MET cc_start: 0.7786 (tmm) cc_final: 0.7460 (tmm) REVERT: F 112 PRO cc_start: 0.8183 (Cg_endo) cc_final: 0.7512 (Cg_exo) REVERT: F 129 MET cc_start: 0.9484 (mtp) cc_final: 0.9161 (mmm) REVERT: F 331 TRP cc_start: 0.8322 (t60) cc_final: 0.7988 (t60) REVERT: F 342 ASP cc_start: 0.8290 (m-30) cc_final: 0.8044 (m-30) REVERT: F 358 MET cc_start: 0.9250 (tmm) cc_final: 0.8976 (tpt) REVERT: G 20 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7807 (mmt-90) REVERT: G 129 MET cc_start: 0.8986 (mpp) cc_final: 0.8761 (mpp) REVERT: G 276 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8084 (mm-30) REVERT: G 341 ILE cc_start: 0.7839 (mm) cc_final: 0.7465 (mt) REVERT: G 358 MET cc_start: 0.8685 (tmm) cc_final: 0.8393 (tmm) REVERT: G 376 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8085 (tm-30) REVERT: H 23 ARG cc_start: 0.8858 (mmm-85) cc_final: 0.8637 (mmm-85) REVERT: H 250 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8361 (mm-30) REVERT: H 254 ASP cc_start: 0.9077 (t0) cc_final: 0.8562 (t70) REVERT: H 292 ASN cc_start: 0.8560 (m-40) cc_final: 0.8269 (m110) REVERT: H 303 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8334 (mp0) REVERT: H 365 LYS cc_start: 0.8869 (mtpt) cc_final: 0.8111 (mmtt) REVERT: H 376 GLN cc_start: 0.8403 (mm-40) cc_final: 0.7639 (tm-30) REVERT: I 17 LYS cc_start: 0.8542 (tppp) cc_final: 0.8278 (mmtt) REVERT: I 125 MET cc_start: 0.8205 (tmm) cc_final: 0.7727 (tmm) REVERT: I 129 MET cc_start: 0.9148 (mmm) cc_final: 0.8693 (mmm) REVERT: I 187 GLU cc_start: 0.8387 (tm-30) cc_final: 0.8033 (tm-30) REVERT: I 303 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8248 (tm-30) REVERT: J 7 GLU cc_start: 0.8445 (tp30) cc_final: 0.8085 (tp30) REVERT: J 114 MET cc_start: 0.7716 (ppp) cc_final: 0.7499 (ppp) REVERT: J 125 MET cc_start: 0.8443 (mmt) cc_final: 0.8227 (mmt) REVERT: J 158 MET cc_start: 0.8110 (mmm) cc_final: 0.7784 (tpt) REVERT: J 342 ASP cc_start: 0.8736 (t0) cc_final: 0.8506 (t0) REVERT: K 376 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7982 (tm-30) REVERT: K 378 MET cc_start: 0.8906 (mmm) cc_final: 0.8672 (mmt) REVERT: L 6 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8713 (mp0) REVERT: L 107 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.7723 (tmt) REVERT: L 114 MET cc_start: 0.8711 (ppp) cc_final: 0.8400 (pp-130) REVERT: L 129 MET cc_start: 0.8981 (tpp) cc_final: 0.8530 (tpt) REVERT: M 107 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.7218 (tmt) REVERT: N 7 GLU cc_start: 0.8938 (mp0) cc_final: 0.8430 (mp0) REVERT: N 125 MET cc_start: 0.9094 (mmt) cc_final: 0.8781 (mmm) REVERT: N 129 MET cc_start: 0.9563 (mpp) cc_final: 0.9191 (mpp) REVERT: N 378 MET cc_start: 0.8200 (tpt) cc_final: 0.7731 (mpm) REVERT: O 82 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8216 (mp0) REVERT: O 197 TYR cc_start: 0.8309 (m-80) cc_final: 0.7969 (m-80) REVERT: O 233 GLU cc_start: 0.9293 (tp30) cc_final: 0.8848 (tp30) REVERT: O 299 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.8729 (mm) REVERT: O 376 GLN cc_start: 0.6929 (mm110) cc_final: 0.6192 (mp10) REVERT: O 378 MET cc_start: 0.7650 (tmm) cc_final: 0.7357 (pmm) REVERT: P 49 TRP cc_start: 0.6346 (t-100) cc_final: 0.6112 (t-100) REVERT: P 68 MET cc_start: 0.8273 (mtp) cc_final: 0.7927 (ptp) REVERT: P 107 MET cc_start: 0.4534 (ptp) cc_final: 0.3826 (ppp) REVERT: P 114 MET cc_start: 0.7207 (ptt) cc_final: 0.6843 (ptt) REVERT: P 272 ARG cc_start: 0.8515 (tpp80) cc_final: 0.8174 (tpp80) REVERT: Q 21 ASP cc_start: 0.8643 (t70) cc_final: 0.8314 (t70) REVERT: Q 107 MET cc_start: 0.4883 (OUTLIER) cc_final: 0.4439 (tmt) REVERT: Q 231 MET cc_start: 0.7528 (mmp) cc_final: 0.7067 (tmt) REVERT: Q 298 MET cc_start: 0.9123 (ttp) cc_final: 0.8507 (tmm) REVERT: Q 311 MET cc_start: 0.8058 (mmp) cc_final: 0.7612 (mmm) outliers start: 100 outliers final: 35 residues processed: 490 average time/residue: 0.6144 time to fit residues: 365.5825 Evaluate side-chains 449 residues out of total 4592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 400 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 TYR Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 302 ARG Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 276 GLU Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 377 ASN Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 36 ARG Chi-restraints excluded: chain H residue 303 GLU Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain I residue 341 ILE Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain J residue 375 ASP Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 376 GLN Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 107 MET Chi-restraints excluded: chain L residue 223 GLN Chi-restraints excluded: chain L residue 303 GLU Chi-restraints excluded: chain L residue 342 ASP Chi-restraints excluded: chain M residue 21 ASP Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain O residue 82 GLU Chi-restraints excluded: chain O residue 176 ILE Chi-restraints excluded: chain O residue 299 LEU Chi-restraints excluded: chain Q residue 106 SER Chi-restraints excluded: chain Q residue 107 MET Chi-restraints excluded: chain Q residue 148 SER Chi-restraints excluded: chain Q residue 238 VAL Chi-restraints excluded: chain Q residue 296 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 336 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 470 optimal weight: 6.9990 chunk 467 optimal weight: 9.9990 chunk 398 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 chunk 334 optimal weight: 0.4980 chunk 243 optimal weight: 0.2980 chunk 240 optimal weight: 4.9990 chunk 532 optimal weight: 8.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.126615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.074492 restraints weight = 103818.590| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.80 r_work: 0.2944 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 45905 Z= 0.124 Angle : 0.590 12.174 62380 Z= 0.299 Chirality : 0.039 0.252 7210 Planarity : 0.004 0.059 7728 Dihedral : 9.454 60.606 7465 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.83 % Allowed : 16.07 % Favored : 82.10 % 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: 1.81 (0.11), residues: 5544 helix: 1.82 (0.09), residues: 3164 sheet: 2.15 (0.28), residues: 224 loop : 0.25 (0.14), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG J 23 TYR 0.018 0.001 TYR E 14 PHE 0.028 0.001 PHE D 333 TRP 0.035 0.001 TRP D 173 HIS 0.004 0.001 HIS N 369 Details of bonding type rmsd covalent geometry : bond 0.00278 (45905) covalent geometry : angle 0.59047 (62380) hydrogen bonds : bond 0.03967 ( 2414) hydrogen bonds : angle 3.37754 ( 6915) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11088 Ramachandran restraints generated. 5544 Oldfield, 0 Emsley, 5544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11088 Ramachandran restraints generated. 5544 Oldfield, 0 Emsley, 5544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 4592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 437 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 122 GLN cc_start: 0.5668 (OUTLIER) cc_final: 0.5327 (mt0) REVERT: D 125 MET cc_start: 0.6333 (pp-130) cc_final: 0.6037 (ppp) REVERT: D 166 ILE cc_start: 0.7872 (mt) cc_final: 0.7517 (pp) REVERT: D 322 PHE cc_start: 0.4489 (m-10) cc_final: 0.4227 (m-80) REVERT: D 378 MET cc_start: 0.6699 (ptt) cc_final: 0.6334 (pp-130) REVERT: D 399 THR cc_start: 0.4331 (OUTLIER) cc_final: 0.3845 (m) REVERT: E 107 MET cc_start: 0.6776 (mmm) cc_final: 0.6505 (mmm) REVERT: E 125 MET cc_start: 0.8800 (mtm) cc_final: 0.8203 (mpm) REVERT: E 217 MET cc_start: 0.8874 (tpt) cc_final: 0.8357 (tpt) REVERT: E 264 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.8151 (mpt) REVERT: E 317 SER cc_start: 0.9069 (p) cc_final: 0.8630 (t) REVERT: F 107 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7466 (tmm) REVERT: F 112 PRO cc_start: 0.8180 (Cg_endo) cc_final: 0.7673 (Cg_exo) REVERT: F 125 MET cc_start: 0.8594 (tmm) cc_final: 0.8078 (mpp) REVERT: F 331 TRP cc_start: 0.8314 (t60) cc_final: 0.8000 (t60) REVERT: F 342 ASP cc_start: 0.8309 (m-30) cc_final: 0.8023 (m-30) REVERT: F 358 MET cc_start: 0.9220 (tmm) cc_final: 0.8942 (tpt) REVERT: G 68 MET cc_start: 0.8946 (mmp) cc_final: 0.8690 (mmp) REVERT: G 129 MET cc_start: 0.8990 (mpp) cc_final: 0.8756 (mpp) REVERT: G 341 ILE cc_start: 0.7948 (mm) cc_final: 0.7499 (mt) REVERT: G 358 MET cc_start: 0.8685 (tmm) cc_final: 0.8326 (tmm) REVERT: G 376 GLN cc_start: 0.8530 (mm-40) cc_final: 0.8129 (tm-30) REVERT: H 23 ARG cc_start: 0.8875 (mmm-85) cc_final: 0.8668 (mmm-85) REVERT: H 114 MET cc_start: 0.7839 (ppp) cc_final: 0.7566 (ppp) REVERT: H 250 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8357 (mm-30) REVERT: H 254 ASP cc_start: 0.9073 (t0) cc_final: 0.8561 (t70) REVERT: H 303 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8321 (mp0) REVERT: H 365 LYS cc_start: 0.8867 (mtpt) cc_final: 0.8092 (mmtt) REVERT: H 376 GLN cc_start: 0.8405 (mm-40) cc_final: 0.7697 (tm-30) REVERT: I 7 GLU cc_start: 0.8248 (tp30) cc_final: 0.7548 (tm-30) REVERT: I 17 LYS cc_start: 0.8499 (tppp) cc_final: 0.8239 (mmtt) REVERT: I 125 MET cc_start: 0.8216 (tmm) cc_final: 0.7810 (tmm) REVERT: I 129 MET cc_start: 0.9207 (mmm) cc_final: 0.8967 (mmm) REVERT: I 187 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8029 (tm-30) REVERT: I 303 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8226 (tm-30) REVERT: J 7 GLU cc_start: 0.8459 (tp30) cc_final: 0.7647 (tp30) REVERT: J 158 MET cc_start: 0.8075 (mmm) cc_final: 0.7749 (tpt) REVERT: J 342 ASP cc_start: 0.8732 (t0) cc_final: 0.8500 (t0) REVERT: J 378 MET cc_start: 0.9273 (mmm) cc_final: 0.9017 (tpp) REVERT: K 376 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.8005 (tm-30) REVERT: K 378 MET cc_start: 0.8881 (mmm) cc_final: 0.8677 (mmt) REVERT: L 6 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8711 (mp0) REVERT: L 107 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.7683 (tmt) REVERT: L 114 MET cc_start: 0.8760 (ppp) cc_final: 0.8437 (pp-130) REVERT: L 129 MET cc_start: 0.8974 (tpp) cc_final: 0.8537 (tpt) REVERT: M 107 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.7140 (tmt) REVERT: N 7 GLU cc_start: 0.8939 (mp0) cc_final: 0.8050 (mp0) REVERT: N 107 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8144 (tmt) REVERT: N 125 MET cc_start: 0.9070 (mmt) cc_final: 0.8818 (mmm) REVERT: N 378 MET cc_start: 0.8107 (tpt) cc_final: 0.7741 (mpm) REVERT: O 197 TYR cc_start: 0.8317 (m-80) cc_final: 0.7983 (m-80) REVERT: O 233 GLU cc_start: 0.9293 (tp30) cc_final: 0.8860 (tp30) REVERT: O 376 GLN cc_start: 0.6701 (mm110) cc_final: 0.6019 (mp10) REVERT: O 378 MET cc_start: 0.7648 (tmm) cc_final: 0.7344 (pmm) REVERT: P 68 MET cc_start: 0.8280 (mtp) cc_final: 0.7780 (ptm) REVERT: P 107 MET cc_start: 0.4573 (ptp) cc_final: 0.3760 (ppp) REVERT: P 114 MET cc_start: 0.7276 (ptt) cc_final: 0.6937 (ptt) REVERT: P 272 ARG cc_start: 0.8547 (tpp80) cc_final: 0.8289 (tpp80) REVERT: Q 107 MET cc_start: 0.4836 (OUTLIER) cc_final: 0.4577 (tmt) REVERT: Q 231 MET cc_start: 0.7497 (mmp) cc_final: 0.7079 (tmt) REVERT: Q 298 MET cc_start: 0.9120 (ttp) cc_final: 0.8504 (tmm) REVERT: Q 311 MET cc_start: 0.8045 (mmp) cc_final: 0.7569 (mmm) outliers start: 84 outliers final: 36 residues processed: 488 average time/residue: 0.5456 time to fit residues: 326.6657 Evaluate side-chains 443 residues out of total 4592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 397 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 TYR Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 302 ARG Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 342 ASP Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 36 ARG Chi-restraints excluded: chain H residue 303 GLU Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain I residue 341 ILE Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 376 GLN Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 107 MET Chi-restraints excluded: chain L residue 159 SER Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain M residue 216 GLU Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain M residue 388 GLN Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain O residue 176 ILE Chi-restraints excluded: chain O residue 384 LEU Chi-restraints excluded: chain Q residue 106 SER Chi-restraints excluded: chain Q residue 107 MET Chi-restraints excluded: chain Q residue 148 SER Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 238 VAL Chi-restraints excluded: chain Q residue 296 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 180 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 333 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 202 optimal weight: 2.9990 chunk 477 optimal weight: 9.9990 chunk 292 optimal weight: 0.2980 chunk 79 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 363 optimal weight: 1.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 292 ASN ** I 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 397 GLN ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 199 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.125058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.072291 restraints weight = 103235.615| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.81 r_work: 0.2894 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 45905 Z= 0.186 Angle : 0.638 14.966 62380 Z= 0.322 Chirality : 0.041 0.273 7210 Planarity : 0.004 0.057 7728 Dihedral : 9.423 60.810 7465 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.94 % Allowed : 16.57 % Favored : 81.49 % 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: 1.55 (0.11), residues: 5544 helix: 1.70 (0.09), residues: 3248 sheet: 1.19 (0.30), residues: 252 loop : 0.00 (0.14), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG J 23 TYR 0.023 0.002 TYR E 14 PHE 0.021 0.001 PHE D 333 TRP 0.039 0.001 TRP Q 194 HIS 0.006 0.001 HIS L 370 Details of bonding type rmsd covalent geometry : bond 0.00435 (45905) covalent geometry : angle 0.63824 (62380) hydrogen bonds : bond 0.04626 ( 2414) hydrogen bonds : angle 3.52473 ( 6915) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11088 Ramachandran restraints generated. 5544 Oldfield, 0 Emsley, 5544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11088 Ramachandran restraints generated. 5544 Oldfield, 0 Emsley, 5544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 4592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 402 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 122 GLN cc_start: 0.5641 (OUTLIER) cc_final: 0.5277 (mt0) REVERT: D 125 MET cc_start: 0.6238 (pp-130) cc_final: 0.5979 (ppp) REVERT: D 166 ILE cc_start: 0.7806 (mt) cc_final: 0.7447 (pp) REVERT: D 257 ASN cc_start: 0.7867 (OUTLIER) cc_final: 0.7303 (m110) REVERT: D 378 MET cc_start: 0.6657 (ptt) cc_final: 0.6318 (pp-130) REVERT: D 399 THR cc_start: 0.4132 (OUTLIER) cc_final: 0.3690 (m) REVERT: E 68 MET cc_start: 0.7511 (pmm) cc_final: 0.6903 (ptt) REVERT: E 107 MET cc_start: 0.6731 (OUTLIER) cc_final: 0.6410 (mmm) REVERT: E 217 MET cc_start: 0.8866 (tpt) cc_final: 0.8346 (tpt) REVERT: E 264 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.8147 (mpt) REVERT: E 317 SER cc_start: 0.9083 (p) cc_final: 0.8556 (t) REVERT: F 112 PRO cc_start: 0.8192 (Cg_endo) cc_final: 0.7362 (Cg_exo) REVERT: F 129 MET cc_start: 0.9522 (mtp) cc_final: 0.9260 (mmm) REVERT: F 331 TRP cc_start: 0.8305 (t60) cc_final: 0.7990 (t60) REVERT: F 342 ASP cc_start: 0.8270 (m-30) cc_final: 0.7967 (m-30) REVERT: G 20 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7868 (mmt-90) REVERT: G 68 MET cc_start: 0.8983 (mmp) cc_final: 0.8757 (mmp) REVERT: G 129 MET cc_start: 0.8977 (mpp) cc_final: 0.8756 (mpp) REVERT: G 341 ILE cc_start: 0.8028 (mm) cc_final: 0.7621 (mt) REVERT: G 358 MET cc_start: 0.8670 (tmm) cc_final: 0.8248 (tmm) REVERT: G 361 ARG cc_start: 0.8547 (mtm110) cc_final: 0.8220 (mtm110) REVERT: G 376 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8143 (tm-30) REVERT: H 23 ARG cc_start: 0.8890 (mmm-85) cc_final: 0.8664 (mmm-85) REVERT: H 250 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8413 (mm-30) REVERT: H 254 ASP cc_start: 0.9076 (t0) cc_final: 0.8606 (t70) REVERT: H 376 GLN cc_start: 0.8564 (mm-40) cc_final: 0.7700 (tm-30) REVERT: I 7 GLU cc_start: 0.8379 (tp30) cc_final: 0.7748 (tm-30) REVERT: I 17 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8342 (mmtm) REVERT: I 125 MET cc_start: 0.8222 (tmm) cc_final: 0.7815 (tmm) REVERT: I 129 MET cc_start: 0.9203 (mmm) cc_final: 0.8978 (mmm) REVERT: I 187 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8128 (tm-30) REVERT: J 6 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8463 (pt0) REVERT: J 158 MET cc_start: 0.8226 (mmm) cc_final: 0.7901 (tpt) REVERT: J 272 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8783 (ttt180) REVERT: J 342 ASP cc_start: 0.8814 (t0) cc_final: 0.8566 (t0) REVERT: J 378 MET cc_start: 0.9306 (mmm) cc_final: 0.9066 (tpp) REVERT: K 36 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8580 (mtm-85) REVERT: K 376 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8110 (tm-30) REVERT: K 378 MET cc_start: 0.8915 (mmm) cc_final: 0.8694 (mmt) REVERT: L 6 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8665 (mp0) REVERT: L 114 MET cc_start: 0.8869 (ppp) cc_final: 0.8463 (pp-130) REVERT: L 129 MET cc_start: 0.9001 (tpp) cc_final: 0.8563 (tpt) REVERT: M 107 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.7351 (tmt) REVERT: M 114 MET cc_start: 0.8888 (ttp) cc_final: 0.8383 (ptp) REVERT: M 358 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8082 (tmm) REVERT: N 7 GLU cc_start: 0.8951 (mp0) cc_final: 0.8450 (mp0) REVERT: N 114 MET cc_start: 0.8602 (pp-130) cc_final: 0.8304 (pp-130) REVERT: N 125 MET cc_start: 0.9055 (mmt) cc_final: 0.8827 (mmm) REVERT: N 129 MET cc_start: 0.9545 (mpp) cc_final: 0.9306 (mpp) REVERT: N 378 MET cc_start: 0.8226 (tpt) cc_final: 0.7850 (mpm) REVERT: O 114 MET cc_start: 0.8051 (pmt) cc_final: 0.7094 (pp-130) REVERT: O 197 TYR cc_start: 0.8359 (m-80) cc_final: 0.8063 (m-80) REVERT: O 233 GLU cc_start: 0.9310 (tp30) cc_final: 0.8434 (tp30) REVERT: O 398 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7799 (pp20) REVERT: P 68 MET cc_start: 0.8274 (mtp) cc_final: 0.7738 (ptm) REVERT: P 107 MET cc_start: 0.4704 (ptp) cc_final: 0.4199 (ptp) REVERT: P 114 MET cc_start: 0.7234 (ptt) cc_final: 0.6988 (ptt) REVERT: P 125 MET cc_start: 0.7078 (mpt) cc_final: 0.6860 (mmm) REVERT: P 299 LEU cc_start: 0.9290 (mm) cc_final: 0.8855 (tp) REVERT: Q 83 ARG cc_start: 0.5056 (mtm-85) cc_final: 0.4797 (pmt170) REVERT: Q 107 MET cc_start: 0.4693 (OUTLIER) cc_final: 0.4422 (tmt) REVERT: Q 231 MET cc_start: 0.7503 (mmp) cc_final: 0.7047 (tmt) REVERT: Q 298 MET cc_start: 0.9139 (ttp) cc_final: 0.8568 (tmm) REVERT: Q 311 MET cc_start: 0.8067 (mmp) cc_final: 0.7590 (mmm) outliers start: 89 outliers final: 38 residues processed: 456 average time/residue: 0.5612 time to fit residues: 309.6137 Evaluate side-chains 440 residues out of total 4592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 388 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 79 MET Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 302 ARG Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 377 ASN Chi-restraints excluded: chain H residue 36 ARG Chi-restraints excluded: chain I residue 17 LYS Chi-restraints excluded: chain I residue 341 ILE Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 272 ARG Chi-restraints excluded: chain K residue 36 ARG Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 376 GLN Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 159 SER Chi-restraints excluded: chain L residue 303 GLU Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain M residue 311 MET Chi-restraints excluded: chain M residue 358 MET Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain O residue 259 VAL Chi-restraints excluded: chain O residue 384 LEU Chi-restraints excluded: chain O residue 398 GLU Chi-restraints excluded: chain Q residue 106 SER Chi-restraints excluded: chain Q residue 107 MET Chi-restraints excluded: chain Q residue 148 SER Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 238 VAL Chi-restraints excluded: chain Q residue 259 VAL Chi-restraints excluded: chain Q residue 262 THR Chi-restraints excluded: chain Q residue 296 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 451 optimal weight: 0.6980 chunk 434 optimal weight: 6.9990 chunk 220 optimal weight: 0.9990 chunk 264 optimal weight: 0.0370 chunk 88 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 11 optimal weight: 0.0470 chunk 459 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 chunk 286 optimal weight: 0.9980 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 199 GLN E 200 GLN ** F 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 GLN H 292 ASN ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 199 GLN ** N 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 200 GLN P 200 GLN Q 212 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.127340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.075382 restraints weight = 103500.297| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.83 r_work: 0.2963 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 45905 Z= 0.114 Angle : 0.617 14.084 62380 Z= 0.307 Chirality : 0.039 0.260 7210 Planarity : 0.004 0.067 7728 Dihedral : 9.406 60.493 7463 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.50 % Allowed : 17.60 % Favored : 80.90 % 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: 1.81 (0.12), residues: 5544 helix: 1.84 (0.09), residues: 3192 sheet: 1.30 (0.30), residues: 252 loop : 0.30 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG J 23 TYR 0.022 0.001 TYR E 14 PHE 0.019 0.001 PHE G 11 TRP 0.029 0.001 TRP Q 194 HIS 0.004 0.001 HIS N 369 Details of bonding type rmsd covalent geometry : bond 0.00250 (45905) covalent geometry : angle 0.61654 (62380) hydrogen bonds : bond 0.03638 ( 2414) hydrogen bonds : angle 3.34100 ( 6915) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11088 Ramachandran restraints generated. 5544 Oldfield, 0 Emsley, 5544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11088 Ramachandran restraints generated. 5544 Oldfield, 0 Emsley, 5544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 4592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 429 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 122 GLN cc_start: 0.5715 (OUTLIER) cc_final: 0.5440 (mt0) REVERT: D 125 MET cc_start: 0.6127 (pp-130) cc_final: 0.5915 (ppp) REVERT: D 166 ILE cc_start: 0.7673 (mt) cc_final: 0.7293 (pp) REVERT: D 257 ASN cc_start: 0.7821 (OUTLIER) cc_final: 0.7221 (m110) REVERT: D 378 MET cc_start: 0.6648 (ptt) cc_final: 0.6307 (pp-130) REVERT: D 399 THR cc_start: 0.3983 (OUTLIER) cc_final: 0.3547 (m) REVERT: E 68 MET cc_start: 0.7554 (pmm) cc_final: 0.6941 (ptt) REVERT: E 217 MET cc_start: 0.8868 (tpt) cc_final: 0.8349 (tpt) REVERT: E 264 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8105 (mpt) REVERT: E 317 SER cc_start: 0.9044 (p) cc_final: 0.8455 (t) REVERT: F 112 PRO cc_start: 0.8157 (Cg_endo) cc_final: 0.7707 (Cg_exo) REVERT: F 114 MET cc_start: 0.7334 (ppp) cc_final: 0.7119 (ppp) REVERT: F 125 MET cc_start: 0.8634 (tmm) cc_final: 0.8117 (mpp) REVERT: F 342 ASP cc_start: 0.8331 (m-30) cc_final: 0.8015 (m-30) REVERT: G 20 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7758 (mmt-90) REVERT: G 21 ASP cc_start: 0.8995 (m-30) cc_final: 0.8411 (m-30) REVERT: G 68 MET cc_start: 0.8936 (mmp) cc_final: 0.8724 (mmp) REVERT: G 129 MET cc_start: 0.8983 (mpp) cc_final: 0.8758 (mpp) REVERT: G 341 ILE cc_start: 0.8055 (mm) cc_final: 0.7688 (mt) REVERT: G 358 MET cc_start: 0.8726 (tmm) cc_final: 0.8271 (tmm) REVERT: G 361 ARG cc_start: 0.8541 (mtm110) cc_final: 0.8212 (mtm110) REVERT: G 376 GLN cc_start: 0.8486 (mm-40) cc_final: 0.8227 (tm-30) REVERT: H 107 MET cc_start: 0.8620 (ttt) cc_final: 0.8273 (tmt) REVERT: H 250 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8339 (mm-30) REVERT: H 254 ASP cc_start: 0.9069 (t0) cc_final: 0.8561 (t70) REVERT: H 365 LYS cc_start: 0.8904 (mtpt) cc_final: 0.8104 (mmtt) REVERT: H 376 GLN cc_start: 0.8513 (mm-40) cc_final: 0.7666 (tm-30) REVERT: I 17 LYS cc_start: 0.8429 (tppp) cc_final: 0.8144 (mmtm) REVERT: I 125 MET cc_start: 0.8232 (tmm) cc_final: 0.7809 (tmm) REVERT: I 129 MET cc_start: 0.9225 (mmm) cc_final: 0.9003 (mmm) REVERT: I 187 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8001 (tm-30) REVERT: J 7 GLU cc_start: 0.8540 (tp30) cc_final: 0.7652 (tp30) REVERT: J 158 MET cc_start: 0.7983 (mmm) cc_final: 0.7683 (tpt) REVERT: J 272 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8738 (ttt180) REVERT: J 342 ASP cc_start: 0.8747 (t0) cc_final: 0.8508 (t0) REVERT: J 378 MET cc_start: 0.9283 (mmm) cc_final: 0.9061 (tpp) REVERT: K 376 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.8039 (tm-30) REVERT: K 378 MET cc_start: 0.8893 (mmm) cc_final: 0.8670 (mmt) REVERT: L 6 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8713 (mp0) REVERT: L 107 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.7973 (tmt) REVERT: L 114 MET cc_start: 0.8861 (ppp) cc_final: 0.8455 (pp-130) REVERT: L 129 MET cc_start: 0.8961 (tpp) cc_final: 0.8502 (tpt) REVERT: M 107 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.6979 (tmt) REVERT: M 114 MET cc_start: 0.8749 (ttp) cc_final: 0.8453 (ptm) REVERT: N 7 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8474 (mp0) REVERT: N 107 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8247 (tmt) REVERT: N 114 MET cc_start: 0.8663 (pp-130) cc_final: 0.8389 (pp-130) REVERT: N 129 MET cc_start: 0.9533 (mpp) cc_final: 0.9281 (mpp) REVERT: N 378 MET cc_start: 0.8156 (tpt) cc_final: 0.7901 (mpm) REVERT: O 12 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8189 (mpt-90) REVERT: O 114 MET cc_start: 0.8019 (pmt) cc_final: 0.7086 (pp-130) REVERT: O 197 TYR cc_start: 0.8334 (m-80) cc_final: 0.8016 (m-80) REVERT: O 233 GLU cc_start: 0.9280 (tp30) cc_final: 0.8435 (tp30) REVERT: O 378 MET cc_start: 0.7585 (tmm) cc_final: 0.6474 (mmt) REVERT: O 384 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.6926 (mt) REVERT: O 398 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7944 (pp20) REVERT: P 68 MET cc_start: 0.8226 (mtp) cc_final: 0.7686 (ptm) REVERT: P 107 MET cc_start: 0.4406 (ptp) cc_final: 0.3590 (ppp) REVERT: P 114 MET cc_start: 0.7233 (ptt) cc_final: 0.6891 (ptt) REVERT: Q 17 LYS cc_start: 0.9294 (mmmm) cc_final: 0.8627 (tppt) REVERT: Q 83 ARG cc_start: 0.5115 (mtm-85) cc_final: 0.4862 (pmt170) REVERT: Q 107 MET cc_start: 0.4500 (OUTLIER) cc_final: 0.4146 (tmt) REVERT: Q 231 MET cc_start: 0.7504 (mmp) cc_final: 0.7078 (tmt) REVERT: Q 264 MET cc_start: 0.7533 (mpp) cc_final: 0.7128 (pmm) REVERT: Q 311 MET cc_start: 0.8073 (mmp) cc_final: 0.7665 (mmm) outliers start: 69 outliers final: 28 residues processed: 470 average time/residue: 0.5416 time to fit residues: 308.9650 Evaluate side-chains 436 residues out of total 4592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 393 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 TYR Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 302 ARG Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain F residue 345 MET Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 342 ASP Chi-restraints excluded: chain H residue 36 ARG Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 272 ARG Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 376 GLN Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 107 MET Chi-restraints excluded: chain L residue 303 GLU Chi-restraints excluded: chain M residue 21 ASP Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain M residue 158 MET Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain N residue 7 GLU Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain O residue 12 ARG Chi-restraints excluded: chain O residue 176 ILE Chi-restraints excluded: chain O residue 384 LEU Chi-restraints excluded: chain O residue 398 GLU Chi-restraints excluded: chain Q residue 107 MET Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 238 VAL Chi-restraints excluded: chain Q residue 259 VAL Chi-restraints excluded: chain Q residue 296 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 550 optimal weight: 3.9990 chunk 505 optimal weight: 0.9980 chunk 376 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 494 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 232 optimal weight: 2.9990 chunk 405 optimal weight: 0.9990 chunk 409 optimal weight: 3.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 292 ASN ** I 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.125939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.073501 restraints weight = 103187.056| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.81 r_work: 0.2928 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 45905 Z= 0.156 Angle : 0.645 14.296 62380 Z= 0.321 Chirality : 0.040 0.300 7210 Planarity : 0.004 0.067 7728 Dihedral : 9.376 60.613 7463 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.37 % Allowed : 18.31 % Favored : 80.31 % 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: 1.80 (0.12), residues: 5544 helix: 1.85 (0.09), residues: 3192 sheet: 1.32 (0.30), residues: 252 loop : 0.26 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG J 23 TYR 0.022 0.001 TYR F 310 PHE 0.035 0.001 PHE D 333 TRP 0.026 0.001 TRP Q 194 HIS 0.004 0.001 HIS L 370 Details of bonding type rmsd covalent geometry : bond 0.00362 (45905) covalent geometry : angle 0.64451 (62380) hydrogen bonds : bond 0.04151 ( 2414) hydrogen bonds : angle 3.43768 ( 6915) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11088 Ramachandran restraints generated. 5544 Oldfield, 0 Emsley, 5544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11088 Ramachandran restraints generated. 5544 Oldfield, 0 Emsley, 5544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 4592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 402 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 122 GLN cc_start: 0.5722 (OUTLIER) cc_final: 0.5415 (mt0) REVERT: D 125 MET cc_start: 0.6013 (pp-130) cc_final: 0.5745 (ppp) REVERT: D 166 ILE cc_start: 0.7703 (mt) cc_final: 0.7314 (pp) REVERT: D 257 ASN cc_start: 0.7912 (OUTLIER) cc_final: 0.7638 (m110) REVERT: D 378 MET cc_start: 0.6661 (ptt) cc_final: 0.6318 (pp-130) REVERT: D 399 THR cc_start: 0.3626 (OUTLIER) cc_final: 0.3271 (m) REVERT: E 68 MET cc_start: 0.7557 (pmm) cc_final: 0.6959 (ptt) REVERT: E 107 MET cc_start: 0.6643 (mmm) cc_final: 0.5631 (mmm) REVERT: E 217 MET cc_start: 0.8854 (tpt) cc_final: 0.8336 (tpt) REVERT: E 264 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8069 (mpt) REVERT: E 317 SER cc_start: 0.9055 (p) cc_final: 0.8840 (p) REVERT: F 112 PRO cc_start: 0.8127 (Cg_endo) cc_final: 0.7680 (Cg_exo) REVERT: F 125 MET cc_start: 0.8622 (tmm) cc_final: 0.8083 (mpp) REVERT: F 342 ASP cc_start: 0.8307 (m-30) cc_final: 0.7981 (m-30) REVERT: G 68 MET cc_start: 0.8953 (mmp) cc_final: 0.8745 (mmp) REVERT: G 129 MET cc_start: 0.8990 (mpp) cc_final: 0.8763 (mpp) REVERT: G 341 ILE cc_start: 0.8148 (mm) cc_final: 0.7804 (mt) REVERT: G 358 MET cc_start: 0.8736 (tmm) cc_final: 0.8366 (tmm) REVERT: G 361 ARG cc_start: 0.8555 (mtm110) cc_final: 0.8338 (mtm110) REVERT: G 376 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8210 (tm-30) REVERT: H 107 MET cc_start: 0.8485 (ttt) cc_final: 0.8141 (tmt) REVERT: H 250 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8392 (mm-30) REVERT: H 254 ASP cc_start: 0.9068 (t0) cc_final: 0.8584 (t70) REVERT: H 303 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8211 (mp0) REVERT: H 365 LYS cc_start: 0.8936 (mtpt) cc_final: 0.8134 (mmtt) REVERT: H 376 GLN cc_start: 0.8481 (mm-40) cc_final: 0.7726 (tm-30) REVERT: I 7 GLU cc_start: 0.8321 (tp30) cc_final: 0.7729 (tm-30) REVERT: I 17 LYS cc_start: 0.8591 (tppp) cc_final: 0.8301 (mmtm) REVERT: I 125 MET cc_start: 0.8230 (tmm) cc_final: 0.7808 (tmm) REVERT: I 129 MET cc_start: 0.9207 (mmm) cc_final: 0.8974 (mmm) REVERT: I 187 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8069 (tm-30) REVERT: J 6 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8490 (pt0) REVERT: J 7 GLU cc_start: 0.8545 (tp30) cc_final: 0.7731 (tp30) REVERT: J 158 MET cc_start: 0.8130 (mmm) cc_final: 0.7816 (tpt) REVERT: J 272 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8766 (ttt180) REVERT: J 342 ASP cc_start: 0.8791 (t0) cc_final: 0.8544 (t0) REVERT: J 378 MET cc_start: 0.9316 (mmm) cc_final: 0.9076 (tpp) REVERT: K 376 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8122 (tm-30) REVERT: K 378 MET cc_start: 0.8938 (mmm) cc_final: 0.8702 (mmt) REVERT: L 6 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8707 (mp0) REVERT: L 107 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.7893 (tmt) REVERT: L 114 MET cc_start: 0.8884 (ppp) cc_final: 0.8481 (pp-130) REVERT: L 129 MET cc_start: 0.8970 (tpp) cc_final: 0.8513 (tpt) REVERT: M 107 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.7100 (tmt) REVERT: M 114 MET cc_start: 0.8949 (ttp) cc_final: 0.8715 (ptp) REVERT: N 7 GLU cc_start: 0.8989 (mp0) cc_final: 0.8494 (mp0) REVERT: N 107 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8154 (tmt) REVERT: N 114 MET cc_start: 0.8602 (pp-130) cc_final: 0.8360 (ppp) REVERT: N 129 MET cc_start: 0.9519 (mpp) cc_final: 0.9251 (mpp) REVERT: N 378 MET cc_start: 0.8135 (tpt) cc_final: 0.7891 (mpm) REVERT: O 12 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8184 (mpt-90) REVERT: O 114 MET cc_start: 0.8126 (pmt) cc_final: 0.7157 (pp-130) REVERT: O 197 TYR cc_start: 0.8398 (m-80) cc_final: 0.8120 (m-80) REVERT: O 233 GLU cc_start: 0.9285 (tp30) cc_final: 0.8434 (tp30) REVERT: O 378 MET cc_start: 0.7474 (tmm) cc_final: 0.6379 (mmt) REVERT: O 384 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.6950 (mt) REVERT: O 398 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7911 (pp20) REVERT: P 68 MET cc_start: 0.8172 (mtp) cc_final: 0.7623 (ptm) REVERT: P 107 MET cc_start: 0.4396 (ptp) cc_final: 0.3913 (ptp) REVERT: P 114 MET cc_start: 0.7278 (ptt) cc_final: 0.7007 (ptt) REVERT: P 299 LEU cc_start: 0.9267 (mm) cc_final: 0.8856 (tp) REVERT: Q 17 LYS cc_start: 0.9301 (mmmm) cc_final: 0.8588 (tppt) REVERT: Q 83 ARG cc_start: 0.5055 (mtm-85) cc_final: 0.4793 (pmt170) REVERT: Q 107 MET cc_start: 0.4467 (OUTLIER) cc_final: 0.4142 (tmt) REVERT: Q 231 MET cc_start: 0.7523 (mmp) cc_final: 0.7061 (tmt) REVERT: Q 264 MET cc_start: 0.7588 (mpp) cc_final: 0.7142 (pmm) REVERT: Q 311 MET cc_start: 0.8055 (mmp) cc_final: 0.7650 (mmm) outliers start: 63 outliers final: 33 residues processed: 444 average time/residue: 0.5468 time to fit residues: 294.4418 Evaluate side-chains 439 residues out of total 4592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 392 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 TYR Chi-restraints excluded: chain D residue 79 MET Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 342 ASP Chi-restraints excluded: chain H residue 36 ARG Chi-restraints excluded: chain H residue 303 GLU Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 272 ARG Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 376 GLN Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 107 MET Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 303 GLU Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain M residue 158 MET Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain O residue 12 ARG Chi-restraints excluded: chain O residue 176 ILE Chi-restraints excluded: chain O residue 384 LEU Chi-restraints excluded: chain O residue 398 GLU Chi-restraints excluded: chain P residue 282 LEU Chi-restraints excluded: chain Q residue 107 MET Chi-restraints excluded: chain Q residue 148 SER Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 238 VAL Chi-restraints excluded: chain Q residue 259 VAL Chi-restraints excluded: chain Q residue 262 THR Chi-restraints excluded: chain Q residue 296 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 23 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 chunk 423 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 187 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 321 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 292 ASN ** I 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 257 ASN ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.126209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.073483 restraints weight = 104402.862| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.84 r_work: 0.2935 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 45905 Z= 0.141 Angle : 0.653 13.724 62380 Z= 0.323 Chirality : 0.040 0.292 7210 Planarity : 0.004 0.070 7728 Dihedral : 9.342 60.546 7459 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.28 % Allowed : 18.49 % Favored : 80.23 % 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: 1.80 (0.12), residues: 5544 helix: 1.85 (0.09), residues: 3192 sheet: 1.31 (0.30), residues: 252 loop : 0.26 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG J 23 TYR 0.020 0.001 TYR E 14 PHE 0.035 0.001 PHE D 333 TRP 0.025 0.001 TRP D 173 HIS 0.003 0.001 HIS N 369 Details of bonding type rmsd covalent geometry : bond 0.00327 (45905) covalent geometry : angle 0.65265 (62380) hydrogen bonds : bond 0.03997 ( 2414) hydrogen bonds : angle 3.43213 ( 6915) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11088 Ramachandran restraints generated. 5544 Oldfield, 0 Emsley, 5544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11088 Ramachandran restraints generated. 5544 Oldfield, 0 Emsley, 5544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 4592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 400 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 122 GLN cc_start: 0.5703 (OUTLIER) cc_final: 0.5410 (mt0) REVERT: D 125 MET cc_start: 0.6015 (pp-130) cc_final: 0.5794 (ppp) REVERT: D 166 ILE cc_start: 0.7616 (mt) cc_final: 0.7228 (pp) REVERT: D 257 ASN cc_start: 0.7886 (OUTLIER) cc_final: 0.7607 (m110) REVERT: D 378 MET cc_start: 0.6628 (ptt) cc_final: 0.6279 (pp-130) REVERT: D 399 THR cc_start: 0.3638 (OUTLIER) cc_final: 0.3186 (m) REVERT: E 68 MET cc_start: 0.7596 (pmm) cc_final: 0.7011 (ptt) REVERT: E 107 MET cc_start: 0.6591 (mmm) cc_final: 0.5684 (mmm) REVERT: E 109 ASN cc_start: 0.7152 (OUTLIER) cc_final: 0.6862 (p0) REVERT: E 217 MET cc_start: 0.8860 (tpt) cc_final: 0.8337 (tpt) REVERT: E 264 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8092 (mpt) REVERT: E 317 SER cc_start: 0.8969 (p) cc_final: 0.8710 (p) REVERT: F 112 PRO cc_start: 0.8013 (Cg_endo) cc_final: 0.7557 (Cg_exo) REVERT: F 114 MET cc_start: 0.7432 (ppp) cc_final: 0.7207 (ppp) REVERT: F 125 MET cc_start: 0.8635 (tmm) cc_final: 0.8112 (mpp) REVERT: F 342 ASP cc_start: 0.8335 (m-30) cc_final: 0.8005 (m-30) REVERT: G 129 MET cc_start: 0.8989 (mpp) cc_final: 0.8758 (mpp) REVERT: G 341 ILE cc_start: 0.8200 (mm) cc_final: 0.7875 (mt) REVERT: G 358 MET cc_start: 0.8744 (tmm) cc_final: 0.8364 (tmm) REVERT: G 361 ARG cc_start: 0.8560 (mtm110) cc_final: 0.8339 (mtm110) REVERT: G 376 GLN cc_start: 0.8507 (mm-40) cc_final: 0.8183 (tm-30) REVERT: H 107 MET cc_start: 0.8564 (ttt) cc_final: 0.8175 (tmt) REVERT: H 250 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8392 (mm-30) REVERT: H 254 ASP cc_start: 0.9069 (t0) cc_final: 0.8580 (t70) REVERT: H 303 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8186 (mp0) REVERT: H 342 ASP cc_start: 0.8805 (t0) cc_final: 0.8552 (t0) REVERT: H 365 LYS cc_start: 0.8915 (mtpt) cc_final: 0.8111 (mmtt) REVERT: H 376 GLN cc_start: 0.8449 (mm-40) cc_final: 0.7738 (tm-30) REVERT: I 7 GLU cc_start: 0.8299 (tp30) cc_final: 0.7735 (tm-30) REVERT: I 17 LYS cc_start: 0.8600 (tppp) cc_final: 0.8298 (mmtm) REVERT: I 125 MET cc_start: 0.8242 (tmm) cc_final: 0.7822 (tmm) REVERT: I 129 MET cc_start: 0.9218 (mmm) cc_final: 0.8984 (mmm) REVERT: I 187 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8081 (tm-30) REVERT: J 7 GLU cc_start: 0.8579 (tp30) cc_final: 0.7754 (tp30) REVERT: J 158 MET cc_start: 0.8113 (mmm) cc_final: 0.7810 (tpt) REVERT: J 272 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8762 (ttt180) REVERT: J 342 ASP cc_start: 0.8796 (t0) cc_final: 0.8546 (t0) REVERT: J 378 MET cc_start: 0.9340 (mmm) cc_final: 0.9100 (tpp) REVERT: K 376 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.8088 (tm-30) REVERT: K 378 MET cc_start: 0.8919 (mmm) cc_final: 0.8686 (mmt) REVERT: L 6 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8740 (mp0) REVERT: L 107 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.7893 (tmt) REVERT: L 114 MET cc_start: 0.8911 (ppp) cc_final: 0.8530 (pp-130) REVERT: L 129 MET cc_start: 0.8966 (tpp) cc_final: 0.8504 (tpt) REVERT: M 107 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7024 (tmt) REVERT: M 114 MET cc_start: 0.8928 (ttp) cc_final: 0.8590 (ptm) REVERT: N 7 GLU cc_start: 0.8991 (mp0) cc_final: 0.8504 (mp0) REVERT: N 107 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8276 (tmt) REVERT: N 114 MET cc_start: 0.8623 (pp-130) cc_final: 0.8401 (ppp) REVERT: N 129 MET cc_start: 0.9513 (mpp) cc_final: 0.9225 (mpp) REVERT: N 378 MET cc_start: 0.8183 (tpt) cc_final: 0.7915 (mpm) REVERT: O 12 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.8230 (mpt-90) REVERT: O 14 TYR cc_start: 0.9422 (t80) cc_final: 0.9149 (t80) REVERT: O 114 MET cc_start: 0.8184 (pmt) cc_final: 0.7233 (pp-130) REVERT: O 197 TYR cc_start: 0.8405 (m-80) cc_final: 0.8139 (m-80) REVERT: O 233 GLU cc_start: 0.9274 (tp30) cc_final: 0.8413 (tp30) REVERT: O 303 GLU cc_start: 0.8696 (mp0) cc_final: 0.8472 (mp0) REVERT: O 378 MET cc_start: 0.7435 (tmm) cc_final: 0.6346 (mmt) REVERT: O 384 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.6978 (mt) REVERT: O 398 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7951 (pp20) REVERT: P 68 MET cc_start: 0.8161 (mtp) cc_final: 0.7624 (ptm) REVERT: P 107 MET cc_start: 0.4521 (ptp) cc_final: 0.3993 (ptp) REVERT: P 114 MET cc_start: 0.7303 (ptt) cc_final: 0.6960 (ptt) REVERT: P 231 MET cc_start: 0.7893 (ptm) cc_final: 0.7467 (ppp) REVERT: P 299 LEU cc_start: 0.9251 (mm) cc_final: 0.8800 (tp) REVERT: Q 17 LYS cc_start: 0.9313 (mmmm) cc_final: 0.8596 (tppt) REVERT: Q 83 ARG cc_start: 0.5048 (mtm-85) cc_final: 0.4784 (pmt170) REVERT: Q 107 MET cc_start: 0.4369 (OUTLIER) cc_final: 0.4041 (tmt) REVERT: Q 129 MET cc_start: 0.9089 (ppp) cc_final: 0.8864 (mpp) REVERT: Q 231 MET cc_start: 0.7493 (mmp) cc_final: 0.7049 (tmt) REVERT: Q 264 MET cc_start: 0.7593 (mpp) cc_final: 0.7174 (pmm) REVERT: Q 311 MET cc_start: 0.8079 (mmp) cc_final: 0.7710 (mmm) outliers start: 59 outliers final: 34 residues processed: 439 average time/residue: 0.4954 time to fit residues: 264.0499 Evaluate side-chains 439 residues out of total 4592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 390 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 TYR Chi-restraints excluded: chain D residue 79 MET Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 342 ASP Chi-restraints excluded: chain H residue 36 ARG Chi-restraints excluded: chain H residue 303 GLU Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 272 ARG Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 376 GLN Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 107 MET Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 303 GLU Chi-restraints excluded: chain M residue 21 ASP Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain M residue 158 MET Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain O residue 12 ARG Chi-restraints excluded: chain O residue 384 LEU Chi-restraints excluded: chain O residue 398 GLU Chi-restraints excluded: chain Q residue 107 MET Chi-restraints excluded: chain Q residue 148 SER Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 238 VAL Chi-restraints excluded: chain Q residue 259 VAL Chi-restraints excluded: chain Q residue 262 THR Chi-restraints excluded: chain Q residue 296 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 300 optimal weight: 0.7980 chunk 414 optimal weight: 6.9990 chunk 215 optimal weight: 0.6980 chunk 42 optimal weight: 10.0000 chunk 268 optimal weight: 3.9990 chunk 241 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 286 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 366 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 292 ASN ** I 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.126682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.074209 restraints weight = 104130.076| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.84 r_work: 0.2950 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 45905 Z= 0.127 Angle : 0.651 14.754 62380 Z= 0.321 Chirality : 0.039 0.301 7210 Planarity : 0.004 0.079 7728 Dihedral : 9.341 60.388 7459 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.28 % Allowed : 18.45 % Favored : 80.27 % 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: 1.82 (0.12), residues: 5544 helix: 1.86 (0.09), residues: 3192 sheet: 1.32 (0.30), residues: 252 loop : 0.28 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG K 130 TYR 0.020 0.001 TYR F 310 PHE 0.034 0.001 PHE D 333 TRP 0.045 0.001 TRP E 331 HIS 0.003 0.001 HIS J 370 Details of bonding type rmsd covalent geometry : bond 0.00289 (45905) covalent geometry : angle 0.65104 (62380) hydrogen bonds : bond 0.03840 ( 2414) hydrogen bonds : angle 3.40836 ( 6915) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15023.18 seconds wall clock time: 255 minutes 12.42 seconds (15312.42 seconds total)