Starting phenix.real_space_refine on Sun Sep 29 01:34:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9s_12105/09_2024/7b9s_12105.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9s_12105/09_2024/7b9s_12105.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9s_12105/09_2024/7b9s_12105.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9s_12105/09_2024/7b9s_12105.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9s_12105/09_2024/7b9s_12105.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9s_12105/09_2024/7b9s_12105.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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: 4 Type Number sf(0) Gaussians S 378 5.16 5 C 46572 2.51 5 N 12600 2.21 5 O 12480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 147 residue(s): 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 72030 Number of models: 1 Model: "" Number of chains: 30 Chain: "E" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1305 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 6, 'TRANS': 158} Chain breaks: 3 Chain: "X" Number of atoms: 3469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3469 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 27, 'TRANS': 434} Chain breaks: 1 Chain: "C" Number of atoms: 3107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3107 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 29, 'TRANS': 366} Chain breaks: 1 Chain: "D" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3644 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 455} Chain: "B" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 480 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "H" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1305 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 6, 'TRANS': 158} Chain breaks: 3 Chain: "I" Number of atoms: 3469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3469 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 27, 'TRANS': 434} Chain breaks: 1 Chain: "F" Number of atoms: 3107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3107 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 29, 'TRANS': 366} Chain breaks: 1 Chain: "G" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3644 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 455} Chain: "A" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 480 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "M" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1305 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 6, 'TRANS': 158} Chain breaks: 3 Chain: "N" Number of atoms: 3469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3469 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 27, 'TRANS': 434} Chain breaks: 1 Chain: "K" Number of atoms: 3107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3107 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 29, 'TRANS': 366} Chain breaks: 1 Chain: "L" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3644 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 455} Chain: "J" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 480 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "R" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1305 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 6, 'TRANS': 158} Chain breaks: 3 Chain: "S" Number of atoms: 3469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3469 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 27, 'TRANS': 434} Chain breaks: 1 Chain: "P" Number of atoms: 3107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3107 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 29, 'TRANS': 366} Chain breaks: 1 Chain: "Q" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3644 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 455} Chain: "O" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 480 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "Y" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1305 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 6, 'TRANS': 158} Chain breaks: 3 Chain: "Z" Number of atoms: 3469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3469 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 27, 'TRANS': 434} Chain breaks: 1 Chain: "V" Number of atoms: 3107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3107 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 29, 'TRANS': 366} Chain breaks: 1 Chain: "W" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3644 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 455} Chain: "T" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 480 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "4" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1305 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 6, 'TRANS': 158} Chain breaks: 3 Chain: "5" Number of atoms: 3469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3469 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 27, 'TRANS': 434} Chain breaks: 1 Chain: "2" Number of atoms: 3107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3107 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 29, 'TRANS': 366} Chain breaks: 1 Chain: "3" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3644 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 455} Chain: "1" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 480 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Time building chain proxies: 32.59, per 1000 atoms: 0.45 Number of scatterers: 72030 At special positions: 0 Unit cell: (267.03, 287.67, 125.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 378 16.00 O 12480 8.00 N 12600 7.00 C 46572 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: 13.61 Conformation dependent library (CDL) restraints added in 7.4 seconds 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17460 Finding SS restraints... Secondary structure from input PDB file: 329 helices and 53 sheets defined 59.9% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.92 Creating SS restraints... Processing helix chain 'E' and resid 144 through 151 removed outlier: 4.044A pdb=" N ALA E 147 " --> pdb=" O GLU E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 208 Processing helix chain 'E' and resid 209 through 214 Processing helix chain 'E' and resid 218 through 235 Processing helix chain 'E' and resid 245 through 258 Processing helix chain 'E' and resid 298 through 303 Processing helix chain 'X' and resid 41 through 60 removed outlier: 3.578A pdb=" N MET X 45 " --> pdb=" O PRO X 41 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ASP X 47 " --> pdb=" O SER X 43 " (cutoff:3.500A) Proline residue: X 48 - end of helix Processing helix chain 'X' and resid 117 through 130 Processing helix chain 'X' and resid 134 through 164 removed outlier: 3.678A pdb=" N GLN X 140 " --> pdb=" O VAL X 136 " (cutoff:3.500A) Processing helix chain 'X' and resid 168 through 191 removed outlier: 3.866A pdb=" N PHE X 172 " --> pdb=" O LEU X 168 " (cutoff:3.500A) Processing helix chain 'X' and resid 194 through 196 No H-bonds generated for 'chain 'X' and resid 194 through 196' Processing helix chain 'X' and resid 197 through 218 removed outlier: 4.320A pdb=" N VAL X 209 " --> pdb=" O LEU X 205 " (cutoff:3.500A) Proline residue: X 210 - end of helix removed outlier: 3.520A pdb=" N THR X 218 " --> pdb=" O ALA X 214 " (cutoff:3.500A) Processing helix chain 'X' and resid 224 through 246 removed outlier: 3.859A pdb=" N MET X 243 " --> pdb=" O ALA X 239 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG X 244 " --> pdb=" O MET X 240 " (cutoff:3.500A) Processing helix chain 'X' and resid 249 through 272 removed outlier: 4.082A pdb=" N TYR X 253 " --> pdb=" O ARG X 249 " (cutoff:3.500A) Processing helix chain 'X' and resid 276 through 303 Proline residue: X 296 - end of helix Processing helix chain 'X' and resid 312 through 320 Processing helix chain 'X' and resid 340 through 378 removed outlier: 4.011A pdb=" N SER X 344 " --> pdb=" O GLU X 340 " (cutoff:3.500A) Processing helix chain 'X' and resid 385 through 406 removed outlier: 3.912A pdb=" N LEU X 389 " --> pdb=" O ARG X 385 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU X 390 " --> pdb=" O TRP X 386 " (cutoff:3.500A) Processing helix chain 'X' and resid 408 through 434 removed outlier: 3.734A pdb=" N ILE X 423 " --> pdb=" O ALA X 419 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL X 433 " --> pdb=" O ARG X 429 " (cutoff:3.500A) Processing helix chain 'X' and resid 436 through 460 Proline residue: X 451 - end of helix removed outlier: 4.406A pdb=" N ALA X 458 " --> pdb=" O GLY X 454 " (cutoff:3.500A) Processing helix chain 'X' and resid 461 through 465 Processing helix chain 'X' and resid 467 through 481 Processing helix chain 'X' and resid 484 through 494 Processing helix chain 'C' and resid 36 through 61 removed outlier: 3.861A pdb=" N VAL C 40 " --> pdb=" O PRO C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 72 removed outlier: 3.912A pdb=" N ALA C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 83 removed outlier: 5.085A pdb=" N ALA C 81 " --> pdb=" O ILE C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 90 Processing helix chain 'C' and resid 96 through 133 Processing helix chain 'C' and resid 135 through 142 removed outlier: 3.665A pdb=" N ALA C 140 " --> pdb=" O THR C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 161 removed outlier: 4.385A pdb=" N GLY C 161 " --> pdb=" O ASP C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 203 Processing helix chain 'C' and resid 226 through 245 Processing helix chain 'C' and resid 258 through 270 removed outlier: 3.522A pdb=" N ASP C 263 " --> pdb=" O ASP C 260 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N TRP C 264 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS C 266 " --> pdb=" O ASP C 263 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP C 267 " --> pdb=" O TRP C 264 " (cutoff:3.500A) Proline residue: C 269 - end of helix Processing helix chain 'C' and resid 333 through 338 removed outlier: 4.008A pdb=" N VAL C 337 " --> pdb=" O GLN C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 362 No H-bonds generated for 'chain 'C' and resid 360 through 362' Processing helix chain 'C' and resid 401 through 413 Processing helix chain 'D' and resid 41 through 60 removed outlier: 4.255A pdb=" N ASP D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Proline residue: D 48 - end of helix removed outlier: 4.358A pdb=" N LYS D 51 " --> pdb=" O ASP D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.974A pdb=" N SER D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 164 removed outlier: 3.654A pdb=" N GLN D 140 " --> pdb=" O VAL D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 189 removed outlier: 4.288A pdb=" N PHE D 172 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 219 removed outlier: 4.660A pdb=" N GLY D 200 " --> pdb=" O ASP D 196 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL D 209 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Proline residue: D 210 - end of helix removed outlier: 3.851A pdb=" N ALA D 219 " --> pdb=" O ILE D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 246 removed outlier: 3.849A pdb=" N PHE D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 274 Processing helix chain 'D' and resid 276 through 303 removed outlier: 3.850A pdb=" N HIS D 293 " --> pdb=" O VAL D 289 " (cutoff:3.500A) Proline residue: D 296 - end of helix Processing helix chain 'D' and resid 343 through 345 No H-bonds generated for 'chain 'D' and resid 343 through 345' Processing helix chain 'D' and resid 346 through 374 removed outlier: 4.051A pdb=" N LEU D 350 " --> pdb=" O ARG D 346 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU D 353 " --> pdb=" O LEU D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 403 removed outlier: 3.764A pdb=" N LEU D 389 " --> pdb=" O ARG D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 406 No H-bonds generated for 'chain 'D' and resid 404 through 406' Processing helix chain 'D' and resid 408 through 434 removed outlier: 3.680A pdb=" N ILE D 423 " --> pdb=" O ALA D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 461 Proline residue: D 451 - end of helix Processing helix chain 'D' and resid 467 through 483 removed outlier: 3.761A pdb=" N GLU D 478 " --> pdb=" O VAL D 474 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR D 479 " --> pdb=" O GLU D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 493 Processing helix chain 'D' and resid 494 through 500 Processing helix chain 'B' and resid 19 through 39 Processing helix chain 'B' and resid 47 through 72 removed outlier: 3.712A pdb=" N ARG B 51 " --> pdb=" O GLU B 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 151 removed outlier: 4.044A pdb=" N ALA H 147 " --> pdb=" O GLU H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 208 Processing helix chain 'H' and resid 209 through 214 Processing helix chain 'H' and resid 218 through 235 Processing helix chain 'H' and resid 245 through 258 Processing helix chain 'H' and resid 298 through 303 Processing helix chain 'I' and resid 41 through 60 removed outlier: 3.788A pdb=" N MET I 45 " --> pdb=" O PRO I 41 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ASP I 47 " --> pdb=" O SER I 43 " (cutoff:3.500A) Proline residue: I 48 - end of helix Processing helix chain 'I' and resid 117 through 130 removed outlier: 3.593A pdb=" N LYS I 128 " --> pdb=" O THR I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 164 removed outlier: 3.690A pdb=" N GLN I 140 " --> pdb=" O VAL I 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 191 removed outlier: 3.865A pdb=" N PHE I 172 " --> pdb=" O LEU I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 194 through 196 No H-bonds generated for 'chain 'I' and resid 194 through 196' Processing helix chain 'I' and resid 197 through 218 removed outlier: 4.322A pdb=" N VAL I 209 " --> pdb=" O LEU I 205 " (cutoff:3.500A) Proline residue: I 210 - end of helix removed outlier: 3.523A pdb=" N THR I 218 " --> pdb=" O ALA I 214 " (cutoff:3.500A) Processing helix chain 'I' and resid 224 through 246 removed outlier: 3.855A pdb=" N MET I 243 " --> pdb=" O ALA I 239 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG I 244 " --> pdb=" O MET I 240 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 272 removed outlier: 4.077A pdb=" N TYR I 253 " --> pdb=" O ARG I 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 276 through 303 Proline residue: I 296 - end of helix Processing helix chain 'I' and resid 312 through 320 Processing helix chain 'I' and resid 340 through 378 removed outlier: 3.784A pdb=" N SER I 344 " --> pdb=" O GLU I 340 " (cutoff:3.500A) Processing helix chain 'I' and resid 385 through 406 removed outlier: 3.913A pdb=" N LEU I 389 " --> pdb=" O ARG I 385 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU I 390 " --> pdb=" O TRP I 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 408 through 434 removed outlier: 3.734A pdb=" N ILE I 423 " --> pdb=" O ALA I 419 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL I 433 " --> pdb=" O ARG I 429 " (cutoff:3.500A) Processing helix chain 'I' and resid 436 through 460 Proline residue: I 451 - end of helix removed outlier: 4.410A pdb=" N ALA I 458 " --> pdb=" O GLY I 454 " (cutoff:3.500A) Processing helix chain 'I' and resid 461 through 465 Processing helix chain 'I' and resid 467 through 481 Processing helix chain 'I' and resid 484 through 494 Processing helix chain 'F' and resid 36 through 61 removed outlier: 3.861A pdb=" N VAL F 40 " --> pdb=" O PRO F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 72 removed outlier: 3.913A pdb=" N ALA F 70 " --> pdb=" O LEU F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 83 removed outlier: 5.084A pdb=" N ALA F 81 " --> pdb=" O ILE F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 90 Processing helix chain 'F' and resid 96 through 133 Processing helix chain 'F' and resid 135 through 142 removed outlier: 3.665A pdb=" N ALA F 140 " --> pdb=" O THR F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 161 removed outlier: 4.385A pdb=" N GLY F 161 " --> pdb=" O ASP F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 203 Processing helix chain 'F' and resid 226 through 245 Processing helix chain 'F' and resid 258 through 270 removed outlier: 3.521A pdb=" N ASP F 263 " --> pdb=" O ASP F 260 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TRP F 264 " --> pdb=" O ARG F 261 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS F 266 " --> pdb=" O ASP F 263 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP F 267 " --> pdb=" O TRP F 264 " (cutoff:3.500A) Proline residue: F 269 - end of helix Processing helix chain 'F' and resid 333 through 338 removed outlier: 4.008A pdb=" N VAL F 337 " --> pdb=" O GLN F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 362 No H-bonds generated for 'chain 'F' and resid 360 through 362' Processing helix chain 'F' and resid 401 through 413 Processing helix chain 'G' and resid 41 through 60 removed outlier: 4.259A pdb=" N ASP G 47 " --> pdb=" O SER G 43 " (cutoff:3.500A) Proline residue: G 48 - end of helix removed outlier: 4.357A pdb=" N LYS G 51 " --> pdb=" O ASP G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 127 removed outlier: 3.912A pdb=" N SER G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 164 removed outlier: 3.656A pdb=" N GLN G 140 " --> pdb=" O VAL G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 189 removed outlier: 4.288A pdb=" N PHE G 172 " --> pdb=" O LEU G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 219 removed outlier: 4.662A pdb=" N GLY G 200 " --> pdb=" O ASP G 196 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL G 209 " --> pdb=" O LEU G 205 " (cutoff:3.500A) Proline residue: G 210 - end of helix removed outlier: 3.850A pdb=" N ALA G 219 " --> pdb=" O ILE G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 246 removed outlier: 3.844A pdb=" N PHE G 232 " --> pdb=" O ALA G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 274 Processing helix chain 'G' and resid 276 through 303 removed outlier: 3.911A pdb=" N HIS G 293 " --> pdb=" O VAL G 289 " (cutoff:3.500A) Proline residue: G 296 - end of helix Processing helix chain 'G' and resid 343 through 345 No H-bonds generated for 'chain 'G' and resid 343 through 345' Processing helix chain 'G' and resid 346 through 374 removed outlier: 4.061A pdb=" N LEU G 350 " --> pdb=" O ARG G 346 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU G 353 " --> pdb=" O LEU G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 403 removed outlier: 3.696A pdb=" N LEU G 389 " --> pdb=" O ARG G 385 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 406 No H-bonds generated for 'chain 'G' and resid 404 through 406' Processing helix chain 'G' and resid 408 through 434 removed outlier: 3.679A pdb=" N ILE G 423 " --> pdb=" O ALA G 419 " (cutoff:3.500A) Processing helix chain 'G' and resid 436 through 461 Proline residue: G 451 - end of helix Processing helix chain 'G' and resid 467 through 483 removed outlier: 3.691A pdb=" N GLU G 478 " --> pdb=" O VAL G 474 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR G 479 " --> pdb=" O GLU G 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 484 through 494 Processing helix chain 'G' and resid 494 through 502 Processing helix chain 'A' and resid 19 through 39 Processing helix chain 'A' and resid 47 through 72 removed outlier: 3.712A pdb=" N ARG A 51 " --> pdb=" O GLU A 47 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 151 removed outlier: 4.045A pdb=" N ALA M 147 " --> pdb=" O GLU M 144 " (cutoff:3.500A) Processing helix chain 'M' and resid 205 through 208 Processing helix chain 'M' and resid 209 through 214 Processing helix chain 'M' and resid 218 through 235 Processing helix chain 'M' and resid 245 through 258 Processing helix chain 'M' and resid 298 through 303 Processing helix chain 'N' and resid 41 through 60 removed outlier: 3.684A pdb=" N MET N 45 " --> pdb=" O PRO N 41 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ASP N 47 " --> pdb=" O SER N 43 " (cutoff:3.500A) Proline residue: N 48 - end of helix Processing helix chain 'N' and resid 117 through 130 Processing helix chain 'N' and resid 134 through 164 removed outlier: 3.674A pdb=" N GLN N 140 " --> pdb=" O VAL N 136 " (cutoff:3.500A) Processing helix chain 'N' and resid 168 through 191 removed outlier: 3.861A pdb=" N PHE N 172 " --> pdb=" O LEU N 168 " (cutoff:3.500A) Processing helix chain 'N' and resid 194 through 196 No H-bonds generated for 'chain 'N' and resid 194 through 196' Processing helix chain 'N' and resid 197 through 218 removed outlier: 4.316A pdb=" N VAL N 209 " --> pdb=" O LEU N 205 " (cutoff:3.500A) Proline residue: N 210 - end of helix removed outlier: 3.519A pdb=" N THR N 218 " --> pdb=" O ALA N 214 " (cutoff:3.500A) Processing helix chain 'N' and resid 224 through 246 removed outlier: 3.854A pdb=" N MET N 243 " --> pdb=" O ALA N 239 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG N 244 " --> pdb=" O MET N 240 " (cutoff:3.500A) Processing helix chain 'N' and resid 249 through 272 removed outlier: 4.074A pdb=" N TYR N 253 " --> pdb=" O ARG N 249 " (cutoff:3.500A) Processing helix chain 'N' and resid 276 through 303 Proline residue: N 296 - end of helix Processing helix chain 'N' and resid 312 through 320 Processing helix chain 'N' and resid 340 through 378 removed outlier: 3.941A pdb=" N SER N 344 " --> pdb=" O GLU N 340 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL N 345 " --> pdb=" O GLY N 341 " (cutoff:3.500A) Processing helix chain 'N' and resid 385 through 406 removed outlier: 3.912A pdb=" N LEU N 389 " --> pdb=" O ARG N 385 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU N 390 " --> pdb=" O TRP N 386 " (cutoff:3.500A) Processing helix chain 'N' and resid 408 through 434 removed outlier: 3.737A pdb=" N ILE N 423 " --> pdb=" O ALA N 419 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL N 433 " --> pdb=" O ARG N 429 " (cutoff:3.500A) Processing helix chain 'N' and resid 436 through 460 Proline residue: N 451 - end of helix removed outlier: 4.398A pdb=" N ALA N 458 " --> pdb=" O GLY N 454 " (cutoff:3.500A) Processing helix chain 'N' and resid 461 through 465 Processing helix chain 'N' and resid 467 through 481 Processing helix chain 'N' and resid 484 through 494 Processing helix chain 'K' and resid 36 through 61 removed outlier: 3.861A pdb=" N VAL K 40 " --> pdb=" O PRO K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 72 removed outlier: 3.913A pdb=" N ALA K 70 " --> pdb=" O LEU K 66 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 83 removed outlier: 5.085A pdb=" N ALA K 81 " --> pdb=" O ILE K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 90 Processing helix chain 'K' and resid 96 through 133 Processing helix chain 'K' and resid 135 through 142 removed outlier: 3.664A pdb=" N ALA K 140 " --> pdb=" O THR K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 156 through 161 removed outlier: 4.385A pdb=" N GLY K 161 " --> pdb=" O ASP K 157 " (cutoff:3.500A) Processing helix chain 'K' and resid 189 through 203 Processing helix chain 'K' and resid 226 through 245 Processing helix chain 'K' and resid 258 through 270 removed outlier: 3.520A pdb=" N ASP K 263 " --> pdb=" O ASP K 260 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N TRP K 264 " --> pdb=" O ARG K 261 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS K 266 " --> pdb=" O ASP K 263 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP K 267 " --> pdb=" O TRP K 264 " (cutoff:3.500A) Proline residue: K 269 - end of helix Processing helix chain 'K' and resid 333 through 338 removed outlier: 4.009A pdb=" N VAL K 337 " --> pdb=" O GLN K 333 " (cutoff:3.500A) Processing helix chain 'K' and resid 360 through 362 No H-bonds generated for 'chain 'K' and resid 360 through 362' Processing helix chain 'K' and resid 401 through 413 Processing helix chain 'L' and resid 41 through 60 removed outlier: 4.267A pdb=" N ASP L 47 " --> pdb=" O SER L 43 " (cutoff:3.500A) Proline residue: L 48 - end of helix removed outlier: 4.386A pdb=" N LYS L 51 " --> pdb=" O ASP L 47 " (cutoff:3.500A) Processing helix chain 'L' and resid 119 through 127 removed outlier: 3.904A pdb=" N SER L 127 " --> pdb=" O ALA L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 164 removed outlier: 3.650A pdb=" N GLN L 140 " --> pdb=" O VAL L 136 " (cutoff:3.500A) Processing helix chain 'L' and resid 168 through 189 removed outlier: 4.287A pdb=" N PHE L 172 " --> pdb=" O LEU L 168 " (cutoff:3.500A) Processing helix chain 'L' and resid 196 through 219 removed outlier: 4.660A pdb=" N GLY L 200 " --> pdb=" O ASP L 196 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL L 209 " --> pdb=" O LEU L 205 " (cutoff:3.500A) Proline residue: L 210 - end of helix removed outlier: 3.849A pdb=" N ALA L 219 " --> pdb=" O ILE L 215 " (cutoff:3.500A) Processing helix chain 'L' and resid 228 through 246 removed outlier: 3.845A pdb=" N PHE L 232 " --> pdb=" O ALA L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 249 through 274 Processing helix chain 'L' and resid 276 through 303 removed outlier: 3.848A pdb=" N HIS L 293 " --> pdb=" O VAL L 289 " (cutoff:3.500A) Proline residue: L 296 - end of helix Processing helix chain 'L' and resid 343 through 346 Processing helix chain 'L' and resid 347 through 374 removed outlier: 3.809A pdb=" N GLU L 353 " --> pdb=" O LEU L 349 " (cutoff:3.500A) Processing helix chain 'L' and resid 385 through 403 removed outlier: 3.691A pdb=" N LEU L 389 " --> pdb=" O ARG L 385 " (cutoff:3.500A) Processing helix chain 'L' and resid 404 through 406 No H-bonds generated for 'chain 'L' and resid 404 through 406' Processing helix chain 'L' and resid 408 through 434 removed outlier: 3.642A pdb=" N ILE L 423 " --> pdb=" O ALA L 419 " (cutoff:3.500A) Processing helix chain 'L' and resid 436 through 461 Proline residue: L 451 - end of helix Processing helix chain 'L' and resid 467 through 483 removed outlier: 4.427A pdb=" N GLU L 478 " --> pdb=" O VAL L 474 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR L 479 " --> pdb=" O GLU L 475 " (cutoff:3.500A) Processing helix chain 'L' and resid 484 through 494 Processing helix chain 'L' and resid 494 through 502 Processing helix chain 'J' and resid 19 through 39 Processing helix chain 'J' and resid 47 through 72 removed outlier: 3.711A pdb=" N ARG J 51 " --> pdb=" O GLU J 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 144 through 151 removed outlier: 4.044A pdb=" N ALA R 147 " --> pdb=" O GLU R 144 " (cutoff:3.500A) Processing helix chain 'R' and resid 205 through 208 Processing helix chain 'R' and resid 209 through 214 Processing helix chain 'R' and resid 218 through 235 Processing helix chain 'R' and resid 245 through 258 Processing helix chain 'R' and resid 298 through 303 Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.779A pdb=" N MET S 45 " --> pdb=" O PRO S 41 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASP S 47 " --> pdb=" O SER S 43 " (cutoff:3.500A) Proline residue: S 48 - end of helix Processing helix chain 'S' and resid 117 through 130 Processing helix chain 'S' and resid 134 through 164 removed outlier: 3.677A pdb=" N GLN S 140 " --> pdb=" O VAL S 136 " (cutoff:3.500A) Processing helix chain 'S' and resid 168 through 191 removed outlier: 3.866A pdb=" N PHE S 172 " --> pdb=" O LEU S 168 " (cutoff:3.500A) Processing helix chain 'S' and resid 194 through 196 No H-bonds generated for 'chain 'S' and resid 194 through 196' Processing helix chain 'S' and resid 197 through 218 removed outlier: 4.320A pdb=" N VAL S 209 " --> pdb=" O LEU S 205 " (cutoff:3.500A) Proline residue: S 210 - end of helix removed outlier: 3.520A pdb=" N THR S 218 " --> pdb=" O ALA S 214 " (cutoff:3.500A) Processing helix chain 'S' and resid 224 through 246 removed outlier: 3.858A pdb=" N MET S 243 " --> pdb=" O ALA S 239 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG S 244 " --> pdb=" O MET S 240 " (cutoff:3.500A) Processing helix chain 'S' and resid 249 through 272 removed outlier: 4.080A pdb=" N TYR S 253 " --> pdb=" O ARG S 249 " (cutoff:3.500A) Processing helix chain 'S' and resid 276 through 303 Proline residue: S 296 - end of helix Processing helix chain 'S' and resid 312 through 320 Processing helix chain 'S' and resid 341 through 378 removed outlier: 3.665A pdb=" N VAL S 345 " --> pdb=" O GLY S 341 " (cutoff:3.500A) Processing helix chain 'S' and resid 385 through 406 removed outlier: 3.912A pdb=" N LEU S 389 " --> pdb=" O ARG S 385 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU S 390 " --> pdb=" O TRP S 386 " (cutoff:3.500A) Processing helix chain 'S' and resid 408 through 434 removed outlier: 3.733A pdb=" N ILE S 423 " --> pdb=" O ALA S 419 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL S 433 " --> pdb=" O ARG S 429 " (cutoff:3.500A) Processing helix chain 'S' and resid 436 through 460 Proline residue: S 451 - end of helix removed outlier: 4.405A pdb=" N ALA S 458 " --> pdb=" O GLY S 454 " (cutoff:3.500A) Processing helix chain 'S' and resid 461 through 465 Processing helix chain 'S' and resid 467 through 481 Processing helix chain 'S' and resid 484 through 494 Processing helix chain 'P' and resid 36 through 61 removed outlier: 3.860A pdb=" N VAL P 40 " --> pdb=" O PRO P 36 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 72 removed outlier: 3.913A pdb=" N ALA P 70 " --> pdb=" O LEU P 66 " (cutoff:3.500A) Processing helix chain 'P' and resid 75 through 83 removed outlier: 5.086A pdb=" N ALA P 81 " --> pdb=" O ILE P 77 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 90 Processing helix chain 'P' and resid 96 through 133 Processing helix chain 'P' and resid 135 through 142 removed outlier: 3.664A pdb=" N ALA P 140 " --> pdb=" O THR P 137 " (cutoff:3.500A) Processing helix chain 'P' and resid 156 through 161 removed outlier: 4.385A pdb=" N GLY P 161 " --> pdb=" O ASP P 157 " (cutoff:3.500A) Processing helix chain 'P' and resid 189 through 203 Processing helix chain 'P' and resid 226 through 245 Processing helix chain 'P' and resid 258 through 270 removed outlier: 3.521A pdb=" N ASP P 263 " --> pdb=" O ASP P 260 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TRP P 264 " --> pdb=" O ARG P 261 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS P 266 " --> pdb=" O ASP P 263 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TRP P 267 " --> pdb=" O TRP P 264 " (cutoff:3.500A) Proline residue: P 269 - end of helix Processing helix chain 'P' and resid 333 through 338 removed outlier: 4.008A pdb=" N VAL P 337 " --> pdb=" O GLN P 333 " (cutoff:3.500A) Processing helix chain 'P' and resid 360 through 362 No H-bonds generated for 'chain 'P' and resid 360 through 362' Processing helix chain 'P' and resid 401 through 413 Processing helix chain 'Q' and resid 41 through 60 removed outlier: 4.255A pdb=" N ASP Q 47 " --> pdb=" O SER Q 43 " (cutoff:3.500A) Proline residue: Q 48 - end of helix removed outlier: 4.358A pdb=" N LYS Q 51 " --> pdb=" O ASP Q 47 " (cutoff:3.500A) Processing helix chain 'Q' and resid 119 through 127 removed outlier: 4.053A pdb=" N SER Q 127 " --> pdb=" O ALA Q 123 " (cutoff:3.500A) Processing helix chain 'Q' and resid 134 through 164 removed outlier: 3.654A pdb=" N GLN Q 140 " --> pdb=" O VAL Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 168 through 189 removed outlier: 4.288A pdb=" N PHE Q 172 " --> pdb=" O LEU Q 168 " (cutoff:3.500A) Processing helix chain 'Q' and resid 196 through 219 removed outlier: 4.660A pdb=" N GLY Q 200 " --> pdb=" O ASP Q 196 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL Q 209 " --> pdb=" O LEU Q 205 " (cutoff:3.500A) Proline residue: Q 210 - end of helix removed outlier: 3.851A pdb=" N ALA Q 219 " --> pdb=" O ILE Q 215 " (cutoff:3.500A) Processing helix chain 'Q' and resid 228 through 246 removed outlier: 3.849A pdb=" N PHE Q 232 " --> pdb=" O ALA Q 228 " (cutoff:3.500A) Processing helix chain 'Q' and resid 249 through 274 Processing helix chain 'Q' and resid 276 through 303 removed outlier: 3.853A pdb=" N HIS Q 293 " --> pdb=" O VAL Q 289 " (cutoff:3.500A) Proline residue: Q 296 - end of helix Processing helix chain 'Q' and resid 343 through 345 No H-bonds generated for 'chain 'Q' and resid 343 through 345' Processing helix chain 'Q' and resid 346 through 374 removed outlier: 4.032A pdb=" N LEU Q 350 " --> pdb=" O ARG Q 346 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU Q 353 " --> pdb=" O LEU Q 349 " (cutoff:3.500A) Processing helix chain 'Q' and resid 385 through 403 removed outlier: 3.688A pdb=" N LEU Q 389 " --> pdb=" O ARG Q 385 " (cutoff:3.500A) Processing helix chain 'Q' and resid 408 through 434 removed outlier: 3.677A pdb=" N ILE Q 423 " --> pdb=" O ALA Q 419 " (cutoff:3.500A) Processing helix chain 'Q' and resid 436 through 461 Proline residue: Q 451 - end of helix Processing helix chain 'Q' and resid 467 through 483 removed outlier: 3.728A pdb=" N GLU Q 478 " --> pdb=" O VAL Q 474 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR Q 479 " --> pdb=" O GLU Q 475 " (cutoff:3.500A) Processing helix chain 'Q' and resid 484 through 494 Processing helix chain 'Q' and resid 494 through 501 removed outlier: 3.701A pdb=" N TYR Q 501 " --> pdb=" O GLU Q 497 " (cutoff:3.500A) Processing helix chain 'O' and resid 19 through 39 Processing helix chain 'O' and resid 47 through 72 removed outlier: 3.711A pdb=" N ARG O 51 " --> pdb=" O GLU O 47 " (cutoff:3.500A) Processing helix chain 'Y' and resid 144 through 151 removed outlier: 4.044A pdb=" N ALA Y 147 " --> pdb=" O GLU Y 144 " (cutoff:3.500A) Processing helix chain 'Y' and resid 205 through 208 Processing helix chain 'Y' and resid 209 through 214 Processing helix chain 'Y' and resid 218 through 235 Processing helix chain 'Y' and resid 245 through 258 Processing helix chain 'Y' and resid 298 through 303 Processing helix chain 'Z' and resid 41 through 60 removed outlier: 3.665A pdb=" N MET Z 45 " --> pdb=" O PRO Z 41 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ASP Z 47 " --> pdb=" O SER Z 43 " (cutoff:3.500A) Proline residue: Z 48 - end of helix Processing helix chain 'Z' and resid 117 through 130 removed outlier: 3.695A pdb=" N LYS Z 128 " --> pdb=" O THR Z 124 " (cutoff:3.500A) Processing helix chain 'Z' and resid 134 through 164 removed outlier: 3.684A pdb=" N GLN Z 140 " --> pdb=" O VAL Z 136 " (cutoff:3.500A) Processing helix chain 'Z' and resid 168 through 191 removed outlier: 3.863A pdb=" N PHE Z 172 " --> pdb=" O LEU Z 168 " (cutoff:3.500A) Processing helix chain 'Z' and resid 194 through 196 No H-bonds generated for 'chain 'Z' and resid 194 through 196' Processing helix chain 'Z' and resid 197 through 218 removed outlier: 4.323A pdb=" N VAL Z 209 " --> pdb=" O LEU Z 205 " (cutoff:3.500A) Proline residue: Z 210 - end of helix removed outlier: 3.522A pdb=" N THR Z 218 " --> pdb=" O ALA Z 214 " (cutoff:3.500A) Processing helix chain 'Z' and resid 224 through 246 removed outlier: 3.856A pdb=" N MET Z 243 " --> pdb=" O ALA Z 239 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG Z 244 " --> pdb=" O MET Z 240 " (cutoff:3.500A) Processing helix chain 'Z' and resid 249 through 272 removed outlier: 4.078A pdb=" N TYR Z 253 " --> pdb=" O ARG Z 249 " (cutoff:3.500A) Processing helix chain 'Z' and resid 276 through 303 Proline residue: Z 296 - end of helix Processing helix chain 'Z' and resid 312 through 320 Processing helix chain 'Z' and resid 340 through 378 removed outlier: 3.808A pdb=" N SER Z 344 " --> pdb=" O GLU Z 340 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL Z 345 " --> pdb=" O GLY Z 341 " (cutoff:3.500A) Processing helix chain 'Z' and resid 385 through 406 removed outlier: 3.913A pdb=" N LEU Z 389 " --> pdb=" O ARG Z 385 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU Z 390 " --> pdb=" O TRP Z 386 " (cutoff:3.500A) Processing helix chain 'Z' and resid 408 through 434 removed outlier: 3.734A pdb=" N ILE Z 423 " --> pdb=" O ALA Z 419 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL Z 433 " --> pdb=" O ARG Z 429 " (cutoff:3.500A) Processing helix chain 'Z' and resid 436 through 460 Proline residue: Z 451 - end of helix removed outlier: 4.409A pdb=" N ALA Z 458 " --> pdb=" O GLY Z 454 " (cutoff:3.500A) Processing helix chain 'Z' and resid 461 through 465 Processing helix chain 'Z' and resid 467 through 481 Processing helix chain 'Z' and resid 484 through 494 Processing helix chain 'V' and resid 36 through 61 removed outlier: 3.861A pdb=" N VAL V 40 " --> pdb=" O PRO V 36 " (cutoff:3.500A) Processing helix chain 'V' and resid 62 through 72 removed outlier: 3.912A pdb=" N ALA V 70 " --> pdb=" O LEU V 66 " (cutoff:3.500A) Processing helix chain 'V' and resid 75 through 83 removed outlier: 5.084A pdb=" N ALA V 81 " --> pdb=" O ILE V 77 " (cutoff:3.500A) Processing helix chain 'V' and resid 85 through 90 Processing helix chain 'V' and resid 96 through 133 Processing helix chain 'V' and resid 135 through 142 removed outlier: 3.664A pdb=" N ALA V 140 " --> pdb=" O THR V 137 " (cutoff:3.500A) Processing helix chain 'V' and resid 156 through 161 removed outlier: 4.385A pdb=" N GLY V 161 " --> pdb=" O ASP V 157 " (cutoff:3.500A) Processing helix chain 'V' and resid 189 through 203 Processing helix chain 'V' and resid 226 through 245 Processing helix chain 'V' and resid 258 through 270 removed outlier: 3.522A pdb=" N ASP V 263 " --> pdb=" O ASP V 260 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TRP V 264 " --> pdb=" O ARG V 261 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS V 266 " --> pdb=" O ASP V 263 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP V 267 " --> pdb=" O TRP V 264 " (cutoff:3.500A) Proline residue: V 269 - end of helix Processing helix chain 'V' and resid 333 through 338 removed outlier: 4.008A pdb=" N VAL V 337 " --> pdb=" O GLN V 333 " (cutoff:3.500A) Processing helix chain 'V' and resid 360 through 362 No H-bonds generated for 'chain 'V' and resid 360 through 362' Processing helix chain 'V' and resid 401 through 413 Processing helix chain 'W' and resid 41 through 60 removed outlier: 4.260A pdb=" N ASP W 47 " --> pdb=" O SER W 43 " (cutoff:3.500A) Proline residue: W 48 - end of helix removed outlier: 4.357A pdb=" N LYS W 51 " --> pdb=" O ASP W 47 " (cutoff:3.500A) Processing helix chain 'W' and resid 119 through 127 removed outlier: 4.147A pdb=" N SER W 127 " --> pdb=" O ALA W 123 " (cutoff:3.500A) Processing helix chain 'W' and resid 134 through 164 removed outlier: 3.657A pdb=" N GLN W 140 " --> pdb=" O VAL W 136 " (cutoff:3.500A) Processing helix chain 'W' and resid 168 through 189 removed outlier: 4.286A pdb=" N PHE W 172 " --> pdb=" O LEU W 168 " (cutoff:3.500A) Processing helix chain 'W' and resid 196 through 219 removed outlier: 4.661A pdb=" N GLY W 200 " --> pdb=" O ASP W 196 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL W 209 " --> pdb=" O LEU W 205 " (cutoff:3.500A) Proline residue: W 210 - end of helix removed outlier: 3.851A pdb=" N ALA W 219 " --> pdb=" O ILE W 215 " (cutoff:3.500A) Processing helix chain 'W' and resid 228 through 246 removed outlier: 3.846A pdb=" N PHE W 232 " --> pdb=" O ALA W 228 " (cutoff:3.500A) Processing helix chain 'W' and resid 249 through 274 Processing helix chain 'W' and resid 276 through 303 removed outlier: 3.871A pdb=" N HIS W 293 " --> pdb=" O VAL W 289 " (cutoff:3.500A) Proline residue: W 296 - end of helix Processing helix chain 'W' and resid 343 through 346 Processing helix chain 'W' and resid 347 through 374 removed outlier: 3.769A pdb=" N GLU W 353 " --> pdb=" O LEU W 349 " (cutoff:3.500A) Processing helix chain 'W' and resid 385 through 403 removed outlier: 3.691A pdb=" N LEU W 389 " --> pdb=" O ARG W 385 " (cutoff:3.500A) Processing helix chain 'W' and resid 404 through 406 No H-bonds generated for 'chain 'W' and resid 404 through 406' Processing helix chain 'W' and resid 408 through 434 removed outlier: 3.670A pdb=" N ILE W 423 " --> pdb=" O ALA W 419 " (cutoff:3.500A) Processing helix chain 'W' and resid 436 through 461 Proline residue: W 451 - end of helix Processing helix chain 'W' and resid 467 through 483 removed outlier: 3.950A pdb=" N GLU W 478 " --> pdb=" O VAL W 474 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR W 479 " --> pdb=" O GLU W 475 " (cutoff:3.500A) Processing helix chain 'W' and resid 484 through 494 Processing helix chain 'W' and resid 494 through 502 Processing helix chain 'T' and resid 19 through 39 Processing helix chain 'T' and resid 47 through 72 removed outlier: 3.711A pdb=" N ARG T 51 " --> pdb=" O GLU T 47 " (cutoff:3.500A) Processing helix chain '4' and resid 144 through 151 removed outlier: 4.044A pdb=" N ALA 4 147 " --> pdb=" O GLU 4 144 " (cutoff:3.500A) Processing helix chain '4' and resid 205 through 208 Processing helix chain '4' and resid 209 through 214 Processing helix chain '4' and resid 218 through 235 Processing helix chain '4' and resid 245 through 258 Processing helix chain '4' and resid 298 through 303 Processing helix chain '5' and resid 41 through 60 removed outlier: 3.588A pdb=" N MET 5 45 " --> pdb=" O PRO 5 41 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ASP 5 47 " --> pdb=" O SER 5 43 " (cutoff:3.500A) Proline residue: 5 48 - end of helix Processing helix chain '5' and resid 117 through 130 Processing helix chain '5' and resid 134 through 164 removed outlier: 3.676A pdb=" N GLN 5 140 " --> pdb=" O VAL 5 136 " (cutoff:3.500A) Processing helix chain '5' and resid 168 through 191 removed outlier: 3.861A pdb=" N PHE 5 172 " --> pdb=" O LEU 5 168 " (cutoff:3.500A) Processing helix chain '5' and resid 194 through 196 No H-bonds generated for 'chain '5' and resid 194 through 196' Processing helix chain '5' and resid 197 through 218 removed outlier: 4.316A pdb=" N VAL 5 209 " --> pdb=" O LEU 5 205 " (cutoff:3.500A) Proline residue: 5 210 - end of helix removed outlier: 3.517A pdb=" N THR 5 218 " --> pdb=" O ALA 5 214 " (cutoff:3.500A) Processing helix chain '5' and resid 224 through 246 removed outlier: 3.854A pdb=" N MET 5 243 " --> pdb=" O ALA 5 239 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG 5 244 " --> pdb=" O MET 5 240 " (cutoff:3.500A) Processing helix chain '5' and resid 249 through 272 removed outlier: 4.077A pdb=" N TYR 5 253 " --> pdb=" O ARG 5 249 " (cutoff:3.500A) Processing helix chain '5' and resid 276 through 303 Proline residue: 5 296 - end of helix Processing helix chain '5' and resid 312 through 320 Processing helix chain '5' and resid 341 through 378 removed outlier: 3.503A pdb=" N VAL 5 345 " --> pdb=" O GLY 5 341 " (cutoff:3.500A) Processing helix chain '5' and resid 385 through 406 removed outlier: 3.913A pdb=" N LEU 5 389 " --> pdb=" O ARG 5 385 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU 5 390 " --> pdb=" O TRP 5 386 " (cutoff:3.500A) Processing helix chain '5' and resid 408 through 434 removed outlier: 3.738A pdb=" N ILE 5 423 " --> pdb=" O ALA 5 419 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL 5 433 " --> pdb=" O ARG 5 429 " (cutoff:3.500A) Processing helix chain '5' and resid 436 through 460 Proline residue: 5 451 - end of helix removed outlier: 4.401A pdb=" N ALA 5 458 " --> pdb=" O GLY 5 454 " (cutoff:3.500A) Processing helix chain '5' and resid 461 through 465 Processing helix chain '5' and resid 467 through 481 Processing helix chain '5' and resid 484 through 494 Processing helix chain '2' and resid 36 through 61 removed outlier: 3.860A pdb=" N VAL 2 40 " --> pdb=" O PRO 2 36 " (cutoff:3.500A) Processing helix chain '2' and resid 62 through 72 removed outlier: 3.913A pdb=" N ALA 2 70 " --> pdb=" O LEU 2 66 " (cutoff:3.500A) Processing helix chain '2' and resid 75 through 83 removed outlier: 5.085A pdb=" N ALA 2 81 " --> pdb=" O ILE 2 77 " (cutoff:3.500A) Processing helix chain '2' and resid 85 through 90 Processing helix chain '2' and resid 96 through 133 Processing helix chain '2' and resid 135 through 142 removed outlier: 3.664A pdb=" N ALA 2 140 " --> pdb=" O THR 2 137 " (cutoff:3.500A) Processing helix chain '2' and resid 156 through 161 removed outlier: 4.386A pdb=" N GLY 2 161 " --> pdb=" O ASP 2 157 " (cutoff:3.500A) Processing helix chain '2' and resid 189 through 203 Processing helix chain '2' and resid 226 through 245 Processing helix chain '2' and resid 258 through 270 removed outlier: 3.521A pdb=" N ASP 2 263 " --> pdb=" O ASP 2 260 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TRP 2 264 " --> pdb=" O ARG 2 261 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS 2 266 " --> pdb=" O ASP 2 263 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP 2 267 " --> pdb=" O TRP 2 264 " (cutoff:3.500A) Proline residue: 2 269 - end of helix Processing helix chain '2' and resid 333 through 338 removed outlier: 4.008A pdb=" N VAL 2 337 " --> pdb=" O GLN 2 333 " (cutoff:3.500A) Processing helix chain '2' and resid 360 through 362 No H-bonds generated for 'chain '2' and resid 360 through 362' Processing helix chain '2' and resid 401 through 413 Processing helix chain '3' and resid 41 through 60 removed outlier: 3.501A pdb=" N MET 3 45 " --> pdb=" O PRO 3 41 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASP 3 47 " --> pdb=" O SER 3 43 " (cutoff:3.500A) Proline residue: 3 48 - end of helix removed outlier: 4.359A pdb=" N LYS 3 51 " --> pdb=" O ASP 3 47 " (cutoff:3.500A) Processing helix chain '3' and resid 119 through 127 removed outlier: 3.949A pdb=" N SER 3 127 " --> pdb=" O ALA 3 123 " (cutoff:3.500A) Processing helix chain '3' and resid 134 through 164 removed outlier: 3.651A pdb=" N GLN 3 140 " --> pdb=" O VAL 3 136 " (cutoff:3.500A) Processing helix chain '3' and resid 168 through 189 removed outlier: 4.287A pdb=" N PHE 3 172 " --> pdb=" O LEU 3 168 " (cutoff:3.500A) Processing helix chain '3' and resid 196 through 219 removed outlier: 4.660A pdb=" N GLY 3 200 " --> pdb=" O ASP 3 196 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL 3 209 " --> pdb=" O LEU 3 205 " (cutoff:3.500A) Proline residue: 3 210 - end of helix removed outlier: 3.851A pdb=" N ALA 3 219 " --> pdb=" O ILE 3 215 " (cutoff:3.500A) Processing helix chain '3' and resid 228 through 246 removed outlier: 3.844A pdb=" N PHE 3 232 " --> pdb=" O ALA 3 228 " (cutoff:3.500A) Processing helix chain '3' and resid 249 through 274 Processing helix chain '3' and resid 276 through 303 removed outlier: 3.818A pdb=" N HIS 3 293 " --> pdb=" O VAL 3 289 " (cutoff:3.500A) Proline residue: 3 296 - end of helix Processing helix chain '3' and resid 343 through 345 No H-bonds generated for 'chain '3' and resid 343 through 345' Processing helix chain '3' and resid 346 through 374 removed outlier: 4.076A pdb=" N LEU 3 350 " --> pdb=" O ARG 3 346 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU 3 353 " --> pdb=" O LEU 3 349 " (cutoff:3.500A) Processing helix chain '3' and resid 385 through 403 removed outlier: 3.687A pdb=" N LEU 3 389 " --> pdb=" O ARG 3 385 " (cutoff:3.500A) Processing helix chain '3' and resid 404 through 406 No H-bonds generated for 'chain '3' and resid 404 through 406' Processing helix chain '3' and resid 408 through 434 removed outlier: 3.692A pdb=" N ILE 3 423 " --> pdb=" O ALA 3 419 " (cutoff:3.500A) Processing helix chain '3' and resid 436 through 461 Proline residue: 3 451 - end of helix Processing helix chain '3' and resid 467 through 483 removed outlier: 4.139A pdb=" N GLU 3 478 " --> pdb=" O VAL 3 474 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR 3 479 " --> pdb=" O GLU 3 475 " (cutoff:3.500A) Processing helix chain '3' and resid 484 through 494 Processing helix chain '3' and resid 494 through 502 Processing helix chain '1' and resid 19 through 39 Processing helix chain '1' and resid 47 through 72 removed outlier: 3.712A pdb=" N ARG 1 51 " --> pdb=" O GLU 1 47 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 96 through 98 Processing sheet with id=AA2, first strand: chain 'E' and resid 108 through 109 removed outlier: 3.541A pdb=" N ARG E 242 " --> pdb=" O VAL E 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 108 through 109 removed outlier: 4.336A pdb=" N THR E 198 " --> pdb=" O THR E 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'X' and resid 71 through 77 removed outlier: 3.567A pdb=" N LEU X 100 " --> pdb=" O ALA X 24 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 19 through 22 Processing sheet with id=AA6, first strand: chain 'C' and resid 206 through 214 removed outlier: 6.840A pdb=" N TYR C 207 " --> pdb=" O MET C 169 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N MET C 169 " --> pdb=" O TYR C 207 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU C 209 " --> pdb=" O VAL C 167 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL C 167 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS C 211 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N MET C 169 " --> pdb=" O PHE C 394 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N PHE C 394 " --> pdb=" O MET C 169 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N PHE C 393 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N THR C 376 " --> pdb=" O PHE C 393 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL C 373 " --> pdb=" O THR C 368 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LEU C 365 " --> pdb=" O TRP C 220 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER C 222 " --> pdb=" O LEU C 365 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N PHE C 367 " --> pdb=" O SER C 222 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL C 224 " --> pdb=" O PHE C 367 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ASP C 369 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TYR C 221 " --> pdb=" O ASP C 350 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N HIS C 323 " --> pdb=" O THR C 347 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N PHE C 349 " --> pdb=" O HIS C 323 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE C 325 " --> pdb=" O PHE C 349 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N TYR C 287 " --> pdb=" O MET C 252 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL C 254 " --> pdb=" O TYR C 287 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 272 through 277 Processing sheet with id=AA8, first strand: chain 'D' and resid 30 through 37 Processing sheet with id=AA9, first strand: chain 'D' and resid 327 through 328 Processing sheet with id=AB1, first strand: chain 'H' and resid 96 through 98 Processing sheet with id=AB2, first strand: chain 'H' and resid 108 through 109 removed outlier: 3.540A pdb=" N ARG H 242 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 108 through 109 removed outlier: 4.336A pdb=" N THR H 198 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 71 through 77 removed outlier: 8.684A pdb=" N LEU I 100 " --> pdb=" O VAL I 22 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA I 24 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU I 102 " --> pdb=" O ALA I 24 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N MET I 26 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N PHE I 104 " --> pdb=" O MET I 26 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 19 through 22 Processing sheet with id=AB6, first strand: chain 'F' and resid 206 through 214 removed outlier: 6.839A pdb=" N TYR F 207 " --> pdb=" O MET F 169 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N MET F 169 " --> pdb=" O TYR F 207 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU F 209 " --> pdb=" O VAL F 167 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL F 167 " --> pdb=" O LEU F 209 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS F 211 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N MET F 169 " --> pdb=" O PHE F 394 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N PHE F 394 " --> pdb=" O MET F 169 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N PHE F 393 " --> pdb=" O THR F 376 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N THR F 376 " --> pdb=" O PHE F 393 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL F 373 " --> pdb=" O THR F 368 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LEU F 365 " --> pdb=" O TRP F 220 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER F 222 " --> pdb=" O LEU F 365 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N PHE F 367 " --> pdb=" O SER F 222 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL F 224 " --> pdb=" O PHE F 367 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ASP F 369 " --> pdb=" O VAL F 224 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TYR F 221 " --> pdb=" O ASP F 350 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N HIS F 323 " --> pdb=" O THR F 347 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N PHE F 349 " --> pdb=" O HIS F 323 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE F 325 " --> pdb=" O PHE F 349 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N TYR F 287 " --> pdb=" O MET F 252 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL F 254 " --> pdb=" O TYR F 287 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 272 through 277 Processing sheet with id=AB8, first strand: chain 'G' and resid 30 through 37 Processing sheet with id=AB9, first strand: chain 'G' and resid 327 through 328 Processing sheet with id=AC1, first strand: chain 'M' and resid 96 through 98 Processing sheet with id=AC2, first strand: chain 'M' and resid 108 through 109 removed outlier: 3.540A pdb=" N ARG M 242 " --> pdb=" O VAL M 118 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 108 through 109 removed outlier: 4.336A pdb=" N THR M 198 " --> pdb=" O THR M 119 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 30 through 36 removed outlier: 8.645A pdb=" N LEU N 100 " --> pdb=" O VAL N 22 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA N 24 " --> pdb=" O LEU N 100 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N LEU N 102 " --> pdb=" O ALA N 24 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET N 26 " --> pdb=" O LEU N 102 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N PHE N 104 " --> pdb=" O MET N 26 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 19 through 22 Processing sheet with id=AC6, first strand: chain 'K' and resid 206 through 214 removed outlier: 6.839A pdb=" N TYR K 207 " --> pdb=" O MET K 169 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N MET K 169 " --> pdb=" O TYR K 207 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU K 209 " --> pdb=" O VAL K 167 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL K 167 " --> pdb=" O LEU K 209 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS K 211 " --> pdb=" O VAL K 165 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N MET K 169 " --> pdb=" O PHE K 394 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N PHE K 394 " --> pdb=" O MET K 169 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N PHE K 393 " --> pdb=" O THR K 376 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N THR K 376 " --> pdb=" O PHE K 393 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL K 373 " --> pdb=" O THR K 368 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N LEU K 365 " --> pdb=" O TRP K 220 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER K 222 " --> pdb=" O LEU K 365 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N PHE K 367 " --> pdb=" O SER K 222 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL K 224 " --> pdb=" O PHE K 367 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ASP K 369 " --> pdb=" O VAL K 224 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TYR K 221 " --> pdb=" O ASP K 350 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N HIS K 323 " --> pdb=" O THR K 347 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N PHE K 349 " --> pdb=" O HIS K 323 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE K 325 " --> pdb=" O PHE K 349 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N TYR K 287 " --> pdb=" O MET K 252 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL K 254 " --> pdb=" O TYR K 287 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 272 through 277 Processing sheet with id=AC8, first strand: chain 'L' and resid 30 through 37 Processing sheet with id=AC9, first strand: chain 'L' and resid 327 through 328 Processing sheet with id=AD1, first strand: chain 'R' and resid 96 through 98 Processing sheet with id=AD2, first strand: chain 'R' and resid 108 through 109 removed outlier: 3.541A pdb=" N ARG R 242 " --> pdb=" O VAL R 118 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'R' and resid 108 through 109 removed outlier: 4.336A pdb=" N THR R 198 " --> pdb=" O THR R 119 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'S' and resid 71 through 77 removed outlier: 8.612A pdb=" N LEU S 100 " --> pdb=" O VAL S 22 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA S 24 " --> pdb=" O LEU S 100 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N LEU S 102 " --> pdb=" O ALA S 24 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N MET S 26 " --> pdb=" O LEU S 102 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N PHE S 104 " --> pdb=" O MET S 26 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 19 through 22 Processing sheet with id=AD6, first strand: chain 'P' and resid 206 through 214 removed outlier: 6.839A pdb=" N TYR P 207 " --> pdb=" O MET P 169 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N MET P 169 " --> pdb=" O TYR P 207 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU P 209 " --> pdb=" O VAL P 167 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL P 167 " --> pdb=" O LEU P 209 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS P 211 " --> pdb=" O VAL P 165 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N MET P 169 " --> pdb=" O PHE P 394 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N PHE P 394 " --> pdb=" O MET P 169 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N PHE P 393 " --> pdb=" O THR P 376 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N THR P 376 " --> pdb=" O PHE P 393 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL P 373 " --> pdb=" O THR P 368 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LEU P 365 " --> pdb=" O TRP P 220 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER P 222 " --> pdb=" O LEU P 365 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N PHE P 367 " --> pdb=" O SER P 222 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL P 224 " --> pdb=" O PHE P 367 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ASP P 369 " --> pdb=" O VAL P 224 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TYR P 221 " --> pdb=" O ASP P 350 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N HIS P 323 " --> pdb=" O THR P 347 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N PHE P 349 " --> pdb=" O HIS P 323 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE P 325 " --> pdb=" O PHE P 349 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N TYR P 287 " --> pdb=" O MET P 252 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL P 254 " --> pdb=" O TYR P 287 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 272 through 277 Processing sheet with id=AD8, first strand: chain 'Q' and resid 30 through 37 Processing sheet with id=AD9, first strand: chain 'Q' and resid 327 through 328 removed outlier: 3.647A pdb=" N LEU Q 339 " --> pdb=" O THR Q 328 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Y' and resid 96 through 98 Processing sheet with id=AE2, first strand: chain 'Y' and resid 108 through 109 removed outlier: 3.540A pdb=" N ARG Y 242 " --> pdb=" O VAL Y 118 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Y' and resid 108 through 109 removed outlier: 4.336A pdb=" N THR Y 198 " --> pdb=" O THR Y 119 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Z' and resid 71 through 77 removed outlier: 8.746A pdb=" N LEU Z 100 " --> pdb=" O VAL Z 22 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA Z 24 " --> pdb=" O LEU Z 100 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N LEU Z 102 " --> pdb=" O ALA Z 24 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N MET Z 26 " --> pdb=" O LEU Z 102 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N PHE Z 104 " --> pdb=" O MET Z 26 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'V' and resid 19 through 22 Processing sheet with id=AE6, first strand: chain 'V' and resid 206 through 214 removed outlier: 6.839A pdb=" N TYR V 207 " --> pdb=" O MET V 169 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N MET V 169 " --> pdb=" O TYR V 207 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU V 209 " --> pdb=" O VAL V 167 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL V 167 " --> pdb=" O LEU V 209 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS V 211 " --> pdb=" O VAL V 165 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N MET V 169 " --> pdb=" O PHE V 394 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N PHE V 394 " --> pdb=" O MET V 169 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N PHE V 393 " --> pdb=" O THR V 376 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N THR V 376 " --> pdb=" O PHE V 393 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL V 373 " --> pdb=" O THR V 368 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LEU V 365 " --> pdb=" O TRP V 220 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER V 222 " --> pdb=" O LEU V 365 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N PHE V 367 " --> pdb=" O SER V 222 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL V 224 " --> pdb=" O PHE V 367 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ASP V 369 " --> pdb=" O VAL V 224 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TYR V 221 " --> pdb=" O ASP V 350 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N HIS V 323 " --> pdb=" O THR V 347 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N PHE V 349 " --> pdb=" O HIS V 323 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE V 325 " --> pdb=" O PHE V 349 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N TYR V 287 " --> pdb=" O MET V 252 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL V 254 " --> pdb=" O TYR V 287 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'V' and resid 272 through 277 Processing sheet with id=AE8, first strand: chain 'W' and resid 30 through 37 Processing sheet with id=AE9, first strand: chain '4' and resid 96 through 98 Processing sheet with id=AF1, first strand: chain '4' and resid 108 through 109 removed outlier: 3.540A pdb=" N ARG 4 242 " --> pdb=" O VAL 4 118 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain '4' and resid 108 through 109 removed outlier: 4.337A pdb=" N THR 4 198 " --> pdb=" O THR 4 119 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain '5' and resid 71 through 77 removed outlier: 8.654A pdb=" N LEU 5 100 " --> pdb=" O VAL 5 22 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA 5 24 " --> pdb=" O LEU 5 100 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU 5 102 " --> pdb=" O ALA 5 24 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N MET 5 26 " --> pdb=" O LEU 5 102 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N PHE 5 104 " --> pdb=" O MET 5 26 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain '2' and resid 19 through 22 Processing sheet with id=AF5, first strand: chain '2' and resid 206 through 214 removed outlier: 6.840A pdb=" N TYR 2 207 " --> pdb=" O MET 2 169 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N MET 2 169 " --> pdb=" O TYR 2 207 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU 2 209 " --> pdb=" O VAL 2 167 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL 2 167 " --> pdb=" O LEU 2 209 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS 2 211 " --> pdb=" O VAL 2 165 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N MET 2 169 " --> pdb=" O PHE 2 394 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N PHE 2 394 " --> pdb=" O MET 2 169 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N PHE 2 393 " --> pdb=" O THR 2 376 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N THR 2 376 " --> pdb=" O PHE 2 393 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL 2 373 " --> pdb=" O THR 2 368 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LEU 2 365 " --> pdb=" O TRP 2 220 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER 2 222 " --> pdb=" O LEU 2 365 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N PHE 2 367 " --> pdb=" O SER 2 222 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL 2 224 " --> pdb=" O PHE 2 367 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ASP 2 369 " --> pdb=" O VAL 2 224 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TYR 2 221 " --> pdb=" O ASP 2 350 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N HIS 2 323 " --> pdb=" O THR 2 347 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N PHE 2 349 " --> pdb=" O HIS 2 323 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE 2 325 " --> pdb=" O PHE 2 349 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N TYR 2 287 " --> pdb=" O MET 2 252 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL 2 254 " --> pdb=" O TYR 2 287 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain '2' and resid 272 through 277 Processing sheet with id=AF7, first strand: chain '3' and resid 30 through 37 Processing sheet with id=AF8, first strand: chain '3' and resid 327 through 328 4508 hydrogen bonds defined for protein. 13053 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 31.94 Time building geometry restraints manager: 16.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 23059 1.34 - 1.46: 14162 1.46 - 1.58: 35841 1.58 - 1.70: 0 1.70 - 1.82: 660 Bond restraints: 73722 Sorted by residual: bond pdb=" CB LYS W 472 " pdb=" CG LYS W 472 " ideal model delta sigma weight residual 1.520 1.441 0.079 3.00e-02 1.11e+03 6.86e+00 bond pdb=" C ARG Q 322 " pdb=" N PRO Q 323 " ideal model delta sigma weight residual 1.330 1.360 -0.030 1.19e-02 7.06e+03 6.32e+00 bond pdb=" CB ILE W 499 " pdb=" CG2 ILE W 499 " ideal model delta sigma weight residual 1.521 1.440 0.081 3.30e-02 9.18e+02 6.00e+00 bond pdb=" CB VAL 3 407 " pdb=" CG1 VAL 3 407 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.83e+00 bond pdb=" CG1 ILE L 499 " pdb=" CD1 ILE L 499 " ideal model delta sigma weight residual 1.513 1.432 0.081 3.90e-02 6.57e+02 4.34e+00 ... (remaining 73717 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 97926 2.72 - 5.44: 2496 5.44 - 8.17: 332 8.17 - 10.89: 45 10.89 - 13.61: 13 Bond angle restraints: 100812 Sorted by residual: angle pdb=" CA ARG L 322 " pdb=" CB ARG L 322 " pdb=" CG ARG L 322 " ideal model delta sigma weight residual 114.10 122.46 -8.36 2.00e+00 2.50e-01 1.75e+01 angle pdb=" C ALA 5 28 " pdb=" N ASP 5 29 " pdb=" CA ASP 5 29 " ideal model delta sigma weight residual 121.54 129.26 -7.72 1.91e+00 2.74e-01 1.63e+01 angle pdb=" C ALA S 28 " pdb=" N ASP S 29 " pdb=" CA ASP S 29 " ideal model delta sigma weight residual 121.54 129.20 -7.66 1.91e+00 2.74e-01 1.61e+01 angle pdb=" CA ARG 3 322 " pdb=" CB ARG 3 322 " pdb=" CG ARG 3 322 " ideal model delta sigma weight residual 114.10 122.06 -7.96 2.00e+00 2.50e-01 1.59e+01 angle pdb=" C ALA X 28 " pdb=" N ASP X 29 " pdb=" CA ASP X 29 " ideal model delta sigma weight residual 121.54 129.14 -7.60 1.91e+00 2.74e-01 1.58e+01 ... (remaining 100807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 40620 17.98 - 35.97: 2352 35.97 - 53.95: 433 53.95 - 71.94: 88 71.94 - 89.92: 67 Dihedral angle restraints: 43560 sinusoidal: 16578 harmonic: 26982 Sorted by residual: dihedral pdb=" CA LEU G 325 " pdb=" C LEU G 325 " pdb=" N PRO G 326 " pdb=" CA PRO G 326 " ideal model delta harmonic sigma weight residual 180.00 150.77 29.23 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA PRO N 308 " pdb=" C PRO N 308 " pdb=" N VAL N 309 " pdb=" CA VAL N 309 " ideal model delta harmonic sigma weight residual -180.00 -151.09 -28.91 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA PRO S 308 " pdb=" C PRO S 308 " pdb=" N VAL S 309 " pdb=" CA VAL S 309 " ideal model delta harmonic sigma weight residual -180.00 -151.34 -28.66 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 43557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 9316 0.068 - 0.136: 2308 0.136 - 0.204: 365 0.204 - 0.272: 47 0.272 - 0.340: 12 Chirality restraints: 12048 Sorted by residual: chirality pdb=" CB ILE P 74 " pdb=" CA ILE P 74 " pdb=" CG1 ILE P 74 " pdb=" CG2 ILE P 74 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CB ILE C 74 " pdb=" CA ILE C 74 " pdb=" CG1 ILE C 74 " pdb=" CG2 ILE C 74 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CB ILE K 74 " pdb=" CA ILE K 74 " pdb=" CG1 ILE K 74 " pdb=" CG2 ILE K 74 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.87e+00 ... (remaining 12045 not shown) Planarity restraints: 12642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP I 410 " -0.024 2.00e-02 2.50e+03 4.77e-02 2.27e+01 pdb=" C TRP I 410 " 0.082 2.00e-02 2.50e+03 pdb=" O TRP I 410 " -0.031 2.00e-02 2.50e+03 pdb=" N GLN I 411 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP Z 410 " 0.024 2.00e-02 2.50e+03 4.76e-02 2.26e+01 pdb=" C TRP Z 410 " -0.082 2.00e-02 2.50e+03 pdb=" O TRP Z 410 " 0.031 2.00e-02 2.50e+03 pdb=" N GLN Z 411 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP S 410 " 0.024 2.00e-02 2.50e+03 4.75e-02 2.26e+01 pdb=" C TRP S 410 " -0.082 2.00e-02 2.50e+03 pdb=" O TRP S 410 " 0.031 2.00e-02 2.50e+03 pdb=" N GLN S 411 " 0.028 2.00e-02 2.50e+03 ... (remaining 12639 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 16419 2.80 - 3.32: 73954 3.32 - 3.85: 121622 3.85 - 4.37: 135662 4.37 - 4.90: 231367 Nonbonded interactions: 579024 Sorted by model distance: nonbonded pdb=" O ALA Q 375 " pdb=" NH1 ARG Q 429 " model vdw 2.271 3.120 nonbonded pdb=" NZ LYS P 194 " pdb=" O VAL Q 309 " model vdw 2.272 3.120 nonbonded pdb=" O ALA G 375 " pdb=" NH1 ARG G 429 " model vdw 2.278 3.120 nonbonded pdb=" O ALA 3 375 " pdb=" NH1 ARG 3 429 " model vdw 2.279 3.120 nonbonded pdb=" O ALA D 375 " pdb=" NH1 ARG D 429 " model vdw 2.280 3.120 ... (remaining 579019 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 '1' selection = chain 'A' selection = chain 'B' selection = chain 'J' selection = chain 'O' selection = chain 'T' } ncs_group { reference = chain '2' selection = chain 'C' selection = chain 'F' selection = chain 'K' selection = chain 'P' selection = chain 'V' } ncs_group { reference = (chain '3' and (resid 18 through 323 or resid 339 through 494)) selection = chain '5' selection = (chain 'D' and (resid 18 through 323 or resid 339 through 494)) selection = (chain 'G' and (resid 18 through 323 or resid 339 through 494)) selection = chain 'I' selection = (chain 'L' and (resid 18 through 323 or resid 339 through 494)) selection = chain 'N' selection = (chain 'Q' and (resid 18 through 323 or resid 339 through 494)) selection = chain 'S' selection = (chain 'W' and (resid 18 through 323 or resid 339 through 494)) selection = chain 'X' selection = chain 'Z' } ncs_group { reference = chain '4' selection = chain 'E' selection = chain 'H' selection = chain 'M' selection = chain 'R' selection = chain 'Y' } 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: 7.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 2.030 Check model and map are aligned: 0.420 Set scattering table: 0.490 Process input model: 132.210 Find NCS groups from input model: 2.690 Set up NCS constraints: 0.530 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: 0.020 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 148.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 73722 Z= 0.423 Angle : 1.031 13.610 100812 Z= 0.569 Chirality : 0.061 0.340 12048 Planarity : 0.008 0.092 12642 Dihedral : 12.817 89.919 26100 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.77 % Favored : 96.22 % Rotamer: Outliers : 0.37 % Allowed : 4.27 % Favored : 95.36 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.08), residues: 9306 helix: 0.02 (0.07), residues: 5022 sheet: -0.37 (0.17), residues: 822 loop : -1.22 (0.10), residues: 3462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP 5 317 HIS 0.018 0.002 HIS C 133 PHE 0.034 0.003 PHE Z 396 TYR 0.047 0.005 TYR W 496 ARG 0.072 0.005 ARG 5 84 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 887 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 859 time to evaluate : 6.088 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: E 195 GLU cc_start: 0.7992 (pt0) cc_final: 0.6815 (mp0) REVERT: X 26 MET cc_start: 0.8417 (ptp) cc_final: 0.8206 (ptm) REVERT: C 95 MET cc_start: 0.6450 (ptm) cc_final: 0.6090 (ptp) REVERT: D 299 SER cc_start: 0.9031 (m) cc_final: 0.8577 (p) REVERT: H 195 GLU cc_start: 0.7835 (pt0) cc_final: 0.7018 (mp0) REVERT: I 187 ILE cc_start: 0.9392 (mt) cc_final: 0.9182 (mm) REVERT: I 285 LEU cc_start: 0.9523 (tp) cc_final: 0.9255 (mt) REVERT: I 288 CYS cc_start: 0.9162 (m) cc_final: 0.8735 (m) REVERT: F 17 LYS cc_start: 0.9132 (ptmm) cc_final: 0.8931 (ptmm) REVERT: G 240 MET cc_start: 0.8513 (mtp) cc_final: 0.8287 (mtm) REVERT: G 299 SER cc_start: 0.8969 (m) cc_final: 0.8666 (p) REVERT: G 493 MET cc_start: 0.8307 (mpp) cc_final: 0.8100 (mpp) REVERT: M 107 ILE cc_start: 0.8469 (mm) cc_final: 0.8162 (tp) REVERT: M 195 GLU cc_start: 0.8073 (pt0) cc_final: 0.7428 (pm20) REVERT: N 235 PHE cc_start: 0.8429 (t80) cc_final: 0.8178 (t80) REVERT: N 288 CYS cc_start: 0.9220 (m) cc_final: 0.8858 (m) REVERT: N 299 SER cc_start: 0.9020 (m) cc_final: 0.8775 (p) REVERT: N 373 CYS cc_start: 0.8336 (p) cc_final: 0.7555 (p) REVERT: K 56 MET cc_start: 0.8505 (tpp) cc_final: 0.8281 (ppp) REVERT: L 240 MET cc_start: 0.8507 (mtp) cc_final: 0.8298 (mtp) REVERT: L 299 SER cc_start: 0.8759 (m) cc_final: 0.8352 (p) REVERT: R 195 GLU cc_start: 0.8002 (pt0) cc_final: 0.6709 (mp0) REVERT: S 26 MET cc_start: 0.7976 (ptp) cc_final: 0.7759 (mtp) REVERT: P 95 MET cc_start: 0.6488 (ptm) cc_final: 0.6069 (ptp) REVERT: Q 299 SER cc_start: 0.9002 (m) cc_final: 0.8618 (p) REVERT: Z 45 MET cc_start: 0.8367 (mtm) cc_final: 0.8115 (mtt) REVERT: Z 187 ILE cc_start: 0.9359 (mt) cc_final: 0.9153 (mm) REVERT: Z 285 LEU cc_start: 0.9490 (tp) cc_final: 0.9243 (mt) REVERT: Z 288 CYS cc_start: 0.9136 (m) cc_final: 0.8754 (m) REVERT: Z 292 TYR cc_start: 0.8830 (m-80) cc_final: 0.8473 (m-80) REVERT: V 17 LYS cc_start: 0.9155 (ptmm) cc_final: 0.8938 (ptmm) REVERT: W 240 MET cc_start: 0.8531 (mtp) cc_final: 0.8293 (mtm) REVERT: W 493 MET cc_start: 0.8306 (mpp) cc_final: 0.8011 (mpp) REVERT: 4 195 GLU cc_start: 0.7787 (pt0) cc_final: 0.7087 (mp0) REVERT: 5 26 MET cc_start: 0.8075 (ptp) cc_final: 0.7333 (mtp) REVERT: 5 285 LEU cc_start: 0.9579 (tp) cc_final: 0.9370 (mt) REVERT: 5 288 CYS cc_start: 0.9233 (m) cc_final: 0.8878 (m) REVERT: 5 362 LEU cc_start: 0.9133 (mt) cc_final: 0.8837 (mt) REVERT: 5 373 CYS cc_start: 0.8398 (p) cc_final: 0.7589 (p) REVERT: 3 240 MET cc_start: 0.8497 (mtp) cc_final: 0.8293 (mtp) REVERT: 3 299 SER cc_start: 0.8900 (m) cc_final: 0.8404 (p) REVERT: 1 45 GLU cc_start: 0.7868 (pm20) cc_final: 0.7522 (pm20) outliers start: 28 outliers final: 16 residues processed: 882 average time/residue: 0.6671 time to fit residues: 1013.1374 Evaluate side-chains 573 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 557 time to evaluate : 6.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 96 HIS Chi-restraints excluded: chain X residue 88 SER Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain H residue 96 HIS Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 345 VAL Chi-restraints excluded: chain M residue 96 HIS Chi-restraints excluded: chain R residue 96 HIS Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain Y residue 96 HIS Chi-restraints excluded: chain Z residue 88 SER Chi-restraints excluded: chain Z residue 345 VAL Chi-restraints excluded: chain 4 residue 96 HIS Chi-restraints excluded: chain 5 residue 88 SER Chi-restraints excluded: chain 3 residue 345 VAL Chi-restraints excluded: chain 3 residue 482 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 930 random chunks: chunk 785 optimal weight: 7.9990 chunk 704 optimal weight: 0.9990 chunk 391 optimal weight: 0.9980 chunk 240 optimal weight: 10.0000 chunk 475 optimal weight: 6.9990 chunk 376 optimal weight: 20.0000 chunk 728 optimal weight: 5.9990 chunk 282 optimal weight: 0.9990 chunk 443 optimal weight: 3.9990 chunk 542 optimal weight: 5.9990 chunk 844 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 GLN K 20 ASN ** K 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 22 GLN Z 293 HIS ** V 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 20 ASN ** 2 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 73722 Z= 0.291 Angle : 0.688 13.193 100812 Z= 0.352 Chirality : 0.045 0.304 12048 Planarity : 0.005 0.059 12642 Dihedral : 5.469 55.082 10248 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.55 % Allowed : 8.86 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.09), residues: 9306 helix: 1.46 (0.07), residues: 5154 sheet: -0.01 (0.16), residues: 846 loop : -1.03 (0.11), residues: 3306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 386 HIS 0.006 0.001 HIS K 133 PHE 0.027 0.002 PHE X 396 TYR 0.031 0.002 TYR C 336 ARG 0.005 0.001 ARG L 429 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 647 time to evaluate : 6.180 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: E 195 GLU cc_start: 0.7767 (pt0) cc_final: 0.6374 (mp0) REVERT: X 26 MET cc_start: 0.8101 (ptp) cc_final: 0.7890 (ptm) REVERT: X 288 CYS cc_start: 0.9463 (m) cc_final: 0.8894 (m) REVERT: X 291 MET cc_start: 0.8520 (mmp) cc_final: 0.8274 (mmp) REVERT: X 483 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.7199 (pmm) REVERT: C 53 MET cc_start: 0.8725 (mmt) cc_final: 0.8466 (mmt) REVERT: B 45 GLU cc_start: 0.8333 (pm20) cc_final: 0.7928 (pm20) REVERT: H 195 GLU cc_start: 0.7602 (pt0) cc_final: 0.6529 (mp0) REVERT: I 187 ILE cc_start: 0.9385 (mt) cc_final: 0.9184 (mm) REVERT: I 288 CYS cc_start: 0.9276 (m) cc_final: 0.8774 (m) REVERT: I 291 MET cc_start: 0.8632 (mmp) cc_final: 0.8387 (mmp) REVERT: I 414 THR cc_start: 0.8978 (m) cc_final: 0.8757 (m) REVERT: F 17 LYS cc_start: 0.8957 (ptmm) cc_final: 0.8702 (ptmm) REVERT: F 99 LYS cc_start: 0.8050 (pttp) cc_final: 0.7300 (pptt) REVERT: G 45 MET cc_start: 0.7906 (mmm) cc_final: 0.7611 (mmm) REVERT: G 240 MET cc_start: 0.8489 (mtp) cc_final: 0.8248 (mtm) REVERT: G 299 SER cc_start: 0.9059 (m) cc_final: 0.8667 (p) REVERT: A 44 MET cc_start: 0.8016 (ttt) cc_final: 0.7758 (ttt) REVERT: M 107 ILE cc_start: 0.8387 (mm) cc_final: 0.8115 (tp) REVERT: M 195 GLU cc_start: 0.8016 (pt0) cc_final: 0.6805 (mp0) REVERT: M 252 MET cc_start: 0.6352 (ttp) cc_final: 0.6145 (ttt) REVERT: N 288 CYS cc_start: 0.9253 (m) cc_final: 0.8922 (m) REVERT: N 291 MET cc_start: 0.8373 (mmp) cc_final: 0.8106 (mmp) REVERT: N 299 SER cc_start: 0.9008 (m) cc_final: 0.8788 (p) REVERT: K 53 MET cc_start: 0.8690 (mmt) cc_final: 0.8446 (mmt) REVERT: K 72 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7668 (m-80) REVERT: K 99 LYS cc_start: 0.7894 (pttp) cc_final: 0.7202 (pptt) REVERT: K 194 LYS cc_start: 0.9181 (tptm) cc_final: 0.8977 (tppt) REVERT: K 389 ASP cc_start: 0.8644 (m-30) cc_final: 0.8429 (t70) REVERT: L 240 MET cc_start: 0.8522 (mtp) cc_final: 0.8154 (mtm) REVERT: R 303 TRP cc_start: 0.5572 (m100) cc_final: 0.5037 (t-100) REVERT: S 288 CYS cc_start: 0.9449 (m) cc_final: 0.8884 (m) REVERT: S 483 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.7197 (pmm) REVERT: P 53 MET cc_start: 0.8728 (mmt) cc_final: 0.8489 (mmt) REVERT: P 76 MET cc_start: 0.7431 (pmm) cc_final: 0.7226 (pmm) REVERT: P 95 MET cc_start: 0.6850 (ptm) cc_final: 0.6520 (ptp) REVERT: Q 45 MET cc_start: 0.8046 (mmm) cc_final: 0.7821 (mmm) REVERT: Q 491 TRP cc_start: 0.9291 (OUTLIER) cc_final: 0.7905 (t60) REVERT: Z 45 MET cc_start: 0.8294 (mtm) cc_final: 0.8049 (mtt) REVERT: Z 291 MET cc_start: 0.8589 (mmp) cc_final: 0.8329 (mmp) REVERT: Z 293 HIS cc_start: 0.8764 (OUTLIER) cc_final: 0.8467 (m90) REVERT: V 17 LYS cc_start: 0.8961 (ptmm) cc_final: 0.8712 (ptmm) REVERT: V 95 MET cc_start: 0.6803 (OUTLIER) cc_final: 0.6387 (ptp) REVERT: V 99 LYS cc_start: 0.7909 (pttp) cc_final: 0.7218 (pptt) REVERT: W 45 MET cc_start: 0.7849 (mmm) cc_final: 0.7638 (mmm) REVERT: W 128 LYS cc_start: 0.9377 (ttpp) cc_final: 0.9072 (ptpt) REVERT: W 240 MET cc_start: 0.8466 (mtp) cc_final: 0.8201 (mtm) REVERT: W 485 ILE cc_start: 0.9181 (pt) cc_final: 0.8868 (mt) REVERT: 4 113 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8522 (mm-40) REVERT: 4 195 GLU cc_start: 0.7540 (pt0) cc_final: 0.6681 (mp0) REVERT: 5 26 MET cc_start: 0.7995 (ptp) cc_final: 0.7387 (mtp) REVERT: 5 271 MET cc_start: 0.8449 (tpp) cc_final: 0.8038 (tpp) REVERT: 5 288 CYS cc_start: 0.9283 (m) cc_final: 0.8894 (m) REVERT: 5 291 MET cc_start: 0.8408 (mmp) cc_final: 0.8129 (mmp) REVERT: 2 99 LYS cc_start: 0.7858 (pttp) cc_final: 0.7205 (pptt) REVERT: 2 389 ASP cc_start: 0.8681 (m-30) cc_final: 0.8406 (t70) REVERT: 3 240 MET cc_start: 0.8500 (mtp) cc_final: 0.8151 (mtm) outliers start: 117 outliers final: 50 residues processed: 727 average time/residue: 0.6460 time to fit residues: 829.2580 Evaluate side-chains 602 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 546 time to evaluate : 6.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 96 HIS Chi-restraints excluded: chain X residue 88 SER Chi-restraints excluded: chain X residue 148 VAL Chi-restraints excluded: chain X residue 317 TRP Chi-restraints excluded: chain X residue 483 MET Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain H residue 96 HIS Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 208 LEU Chi-restraints excluded: chain I residue 317 TRP Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain G residue 362 LEU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain M residue 96 HIS Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 126 LEU Chi-restraints excluded: chain N residue 317 TRP Chi-restraints excluded: chain N residue 483 MET Chi-restraints excluded: chain K residue 72 PHE Chi-restraints excluded: chain L residue 208 LEU Chi-restraints excluded: chain L residue 362 LEU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain R residue 96 HIS Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 148 VAL Chi-restraints excluded: chain S residue 317 TRP Chi-restraints excluded: chain S residue 483 MET Chi-restraints excluded: chain Q residue 209 VAL Chi-restraints excluded: chain Q residue 339 LEU Chi-restraints excluded: chain Q residue 491 TRP Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain Y residue 96 HIS Chi-restraints excluded: chain Z residue 26 MET Chi-restraints excluded: chain Z residue 39 HIS Chi-restraints excluded: chain Z residue 126 LEU Chi-restraints excluded: chain Z residue 144 THR Chi-restraints excluded: chain Z residue 208 LEU Chi-restraints excluded: chain Z residue 293 HIS Chi-restraints excluded: chain Z residue 317 TRP Chi-restraints excluded: chain V residue 95 MET Chi-restraints excluded: chain W residue 362 LEU Chi-restraints excluded: chain 4 residue 96 HIS Chi-restraints excluded: chain 5 residue 88 SER Chi-restraints excluded: chain 5 residue 126 LEU Chi-restraints excluded: chain 5 residue 317 TRP Chi-restraints excluded: chain 5 residue 483 MET Chi-restraints excluded: chain 3 residue 309 VAL Chi-restraints excluded: chain 3 residue 362 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 930 random chunks: chunk 469 optimal weight: 3.9990 chunk 262 optimal weight: 8.9990 chunk 702 optimal weight: 0.7980 chunk 575 optimal weight: 8.9990 chunk 232 optimal weight: 0.9980 chunk 846 optimal weight: 5.9990 chunk 913 optimal weight: 1.9990 chunk 753 optimal weight: 0.2980 chunk 839 optimal weight: 1.9990 chunk 288 optimal weight: 2.9990 chunk 678 optimal weight: 9.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 125 ASN I 293 HIS ** F 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 125 ASN ** V 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 22 GLN ** 2 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 73722 Z= 0.189 Angle : 0.626 13.329 100812 Z= 0.311 Chirality : 0.043 0.252 12048 Planarity : 0.005 0.055 12642 Dihedral : 4.936 51.400 10241 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.12 % Allowed : 10.55 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.09), residues: 9306 helix: 1.88 (0.07), residues: 5124 sheet: -0.21 (0.17), residues: 864 loop : -0.76 (0.11), residues: 3318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP 4 199 HIS 0.022 0.001 HIS Z 293 PHE 0.023 0.001 PHE Z 396 TYR 0.022 0.001 TYR F 336 ARG 0.007 0.000 ARG Z 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 601 time to evaluate : 6.172 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: E 195 GLU cc_start: 0.7903 (pt0) cc_final: 0.6492 (mp0) REVERT: X 26 MET cc_start: 0.7994 (ptp) cc_final: 0.7721 (ptm) REVERT: X 288 CYS cc_start: 0.9447 (m) cc_final: 0.8939 (m) REVERT: X 291 MET cc_start: 0.8515 (mmp) cc_final: 0.8284 (mmp) REVERT: C 95 MET cc_start: 0.6608 (OUTLIER) cc_final: 0.6181 (ptp) REVERT: C 285 MET cc_start: 0.7502 (mmp) cc_final: 0.7148 (mmp) REVERT: H 195 GLU cc_start: 0.7637 (pt0) cc_final: 0.6506 (mp0) REVERT: I 26 MET cc_start: 0.8108 (ptm) cc_final: 0.7250 (mtp) REVERT: I 187 ILE cc_start: 0.9331 (mt) cc_final: 0.9101 (mm) REVERT: I 291 MET cc_start: 0.8582 (mmp) cc_final: 0.8324 (mmp) REVERT: I 464 THR cc_start: 0.4397 (OUTLIER) cc_final: 0.4134 (p) REVERT: F 285 MET cc_start: 0.7373 (mmp) cc_final: 0.6962 (mmm) REVERT: G 45 MET cc_start: 0.8115 (mmm) cc_final: 0.7867 (mmm) REVERT: G 240 MET cc_start: 0.8467 (mtp) cc_final: 0.8204 (mtm) REVERT: G 299 SER cc_start: 0.8959 (m) cc_final: 0.8666 (p) REVERT: N 240 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7853 (mmm) REVERT: N 288 CYS cc_start: 0.9199 (m) cc_final: 0.8958 (p) REVERT: N 291 MET cc_start: 0.8393 (mmp) cc_final: 0.8124 (mmp) REVERT: N 406 TYR cc_start: 0.7664 (m-80) cc_final: 0.7365 (m-10) REVERT: N 464 THR cc_start: 0.4496 (OUTLIER) cc_final: 0.4248 (p) REVERT: N 483 MET cc_start: 0.7479 (OUTLIER) cc_final: 0.7251 (pmm) REVERT: K 148 MET cc_start: 0.7396 (tpt) cc_final: 0.6859 (tpt) REVERT: K 285 MET cc_start: 0.7188 (mmp) cc_final: 0.6790 (mmm) REVERT: L 240 MET cc_start: 0.8486 (mtp) cc_final: 0.8097 (mtm) REVERT: J 52 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8476 (mt0) REVERT: R 303 TRP cc_start: 0.5474 (m100) cc_final: 0.4902 (t-100) REVERT: S 288 CYS cc_start: 0.9431 (m) cc_final: 0.8975 (m) REVERT: P 95 MET cc_start: 0.6674 (ptm) cc_final: 0.6456 (ptp) REVERT: P 148 MET cc_start: 0.7264 (tpt) cc_final: 0.6881 (tpt) REVERT: P 169 MET cc_start: 0.8574 (mpp) cc_final: 0.8336 (mpp) REVERT: P 285 MET cc_start: 0.7452 (mmp) cc_final: 0.7250 (mmm) REVERT: P 400 MET cc_start: 0.8364 (ttp) cc_final: 0.8111 (ttp) REVERT: Q 491 TRP cc_start: 0.9265 (OUTLIER) cc_final: 0.7996 (t60) REVERT: Z 26 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8286 (ptm) REVERT: Z 45 MET cc_start: 0.8394 (mtm) cc_final: 0.8162 (mtt) REVERT: Z 288 CYS cc_start: 0.9240 (m) cc_final: 0.8837 (m) REVERT: Z 291 MET cc_start: 0.8467 (mmp) cc_final: 0.8214 (mmp) REVERT: Z 292 TYR cc_start: 0.9043 (m-80) cc_final: 0.8692 (m-10) REVERT: Z 464 THR cc_start: 0.4332 (OUTLIER) cc_final: 0.4077 (p) REVERT: V 95 MET cc_start: 0.6519 (OUTLIER) cc_final: 0.6201 (ptp) REVERT: V 285 MET cc_start: 0.7440 (mmp) cc_final: 0.7043 (mmm) REVERT: W 45 MET cc_start: 0.8220 (mmm) cc_final: 0.7984 (mmm) REVERT: W 128 LYS cc_start: 0.9368 (ttpp) cc_final: 0.9084 (ptpt) REVERT: W 240 MET cc_start: 0.8475 (mtp) cc_final: 0.8210 (mtm) REVERT: 4 195 GLU cc_start: 0.7671 (pt0) cc_final: 0.6720 (mp0) REVERT: 5 26 MET cc_start: 0.8007 (ptp) cc_final: 0.7250 (mtp) REVERT: 5 240 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7918 (mmm) REVERT: 5 288 CYS cc_start: 0.9210 (m) cc_final: 0.8893 (m) REVERT: 5 291 MET cc_start: 0.8442 (mmp) cc_final: 0.8182 (mmp) REVERT: 5 406 TYR cc_start: 0.7684 (m-80) cc_final: 0.7410 (m-10) REVERT: 5 464 THR cc_start: 0.4489 (OUTLIER) cc_final: 0.4233 (p) REVERT: 5 483 MET cc_start: 0.7418 (OUTLIER) cc_final: 0.7192 (pmm) REVERT: 2 285 MET cc_start: 0.7345 (mmp) cc_final: 0.7048 (mmm) REVERT: 3 240 MET cc_start: 0.8478 (mtp) cc_final: 0.8103 (mtm) outliers start: 160 outliers final: 64 residues processed: 717 average time/residue: 0.6324 time to fit residues: 803.5433 Evaluate side-chains 595 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 518 time to evaluate : 6.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 96 HIS Chi-restraints excluded: chain E residue 199 TRP Chi-restraints excluded: chain X residue 317 TRP Chi-restraints excluded: chain X residue 378 CYS Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain H residue 96 HIS Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 199 TRP Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 208 LEU Chi-restraints excluded: chain I residue 317 TRP Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 464 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 362 LEU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain M residue 96 HIS Chi-restraints excluded: chain M residue 199 TRP Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 240 MET Chi-restraints excluded: chain N residue 317 TRP Chi-restraints excluded: chain N residue 378 CYS Chi-restraints excluded: chain N residue 464 THR Chi-restraints excluded: chain N residue 483 MET Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 362 LEU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 52 GLN Chi-restraints excluded: chain R residue 96 HIS Chi-restraints excluded: chain R residue 199 TRP Chi-restraints excluded: chain S residue 317 TRP Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain P residue 265 VAL Chi-restraints excluded: chain Q residue 148 VAL Chi-restraints excluded: chain Q residue 345 VAL Chi-restraints excluded: chain Q residue 362 LEU Chi-restraints excluded: chain Q residue 401 LEU Chi-restraints excluded: chain Q residue 491 TRP Chi-restraints excluded: chain O residue 35 MET Chi-restraints excluded: chain Y residue 96 HIS Chi-restraints excluded: chain Y residue 199 TRP Chi-restraints excluded: chain Z residue 26 MET Chi-restraints excluded: chain Z residue 39 HIS Chi-restraints excluded: chain Z residue 126 LEU Chi-restraints excluded: chain Z residue 208 LEU Chi-restraints excluded: chain Z residue 317 TRP Chi-restraints excluded: chain Z residue 378 CYS Chi-restraints excluded: chain Z residue 464 THR Chi-restraints excluded: chain V residue 95 MET Chi-restraints excluded: chain V residue 265 VAL Chi-restraints excluded: chain W residue 362 LEU Chi-restraints excluded: chain W residue 474 VAL Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain 4 residue 96 HIS Chi-restraints excluded: chain 4 residue 199 TRP Chi-restraints excluded: chain 5 residue 39 HIS Chi-restraints excluded: chain 5 residue 240 MET Chi-restraints excluded: chain 5 residue 317 TRP Chi-restraints excluded: chain 5 residue 378 CYS Chi-restraints excluded: chain 5 residue 464 THR Chi-restraints excluded: chain 5 residue 483 MET Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 3 residue 148 VAL Chi-restraints excluded: chain 3 residue 208 LEU Chi-restraints excluded: chain 3 residue 309 VAL Chi-restraints excluded: chain 3 residue 362 LEU Chi-restraints excluded: chain 3 residue 482 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 930 random chunks: chunk 835 optimal weight: 7.9990 chunk 636 optimal weight: 6.9990 chunk 439 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 403 optimal weight: 20.0000 chunk 568 optimal weight: 20.0000 chunk 849 optimal weight: 5.9990 chunk 898 optimal weight: 0.5980 chunk 443 optimal weight: 3.9990 chunk 804 optimal weight: 3.9990 chunk 242 optimal weight: 6.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 GLN ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 22 GLN ** P 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 110 HIS ** Z 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 22 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 73722 Z= 0.259 Angle : 0.637 10.741 100812 Z= 0.317 Chirality : 0.044 0.339 12048 Planarity : 0.005 0.054 12642 Dihedral : 4.790 51.370 10239 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.52 % Allowed : 12.49 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.09), residues: 9306 helix: 1.94 (0.07), residues: 5076 sheet: -0.42 (0.16), residues: 984 loop : -0.72 (0.12), residues: 3246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP M 199 HIS 0.006 0.001 HIS C 133 PHE 0.023 0.001 PHE Z 396 TYR 0.022 0.001 TYR K 336 ARG 0.006 0.000 ARG K 291 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 560 time to evaluate : 6.202 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: X 26 MET cc_start: 0.8021 (ptp) cc_final: 0.7685 (ptm) REVERT: X 288 CYS cc_start: 0.9429 (m) cc_final: 0.8972 (m) REVERT: X 291 MET cc_start: 0.8498 (mmp) cc_final: 0.8281 (mmp) REVERT: X 483 MET cc_start: 0.7231 (OUTLIER) cc_final: 0.6966 (pmm) REVERT: C 95 MET cc_start: 0.6563 (OUTLIER) cc_final: 0.6221 (ptp) REVERT: C 110 MET cc_start: 0.8024 (mpp) cc_final: 0.7799 (mpp) REVERT: D 45 MET cc_start: 0.8423 (mmm) cc_final: 0.8186 (mmm) REVERT: H 195 GLU cc_start: 0.7881 (pt0) cc_final: 0.7393 (pm20) REVERT: I 26 MET cc_start: 0.8126 (ptm) cc_final: 0.7250 (mtp) REVERT: I 285 LEU cc_start: 0.9582 (tt) cc_final: 0.9235 (tp) REVERT: I 291 MET cc_start: 0.8638 (mmp) cc_final: 0.8352 (mmp) REVERT: I 293 HIS cc_start: 0.8878 (OUTLIER) cc_final: 0.8160 (m90) REVERT: G 45 MET cc_start: 0.8449 (mmm) cc_final: 0.8126 (mmm) REVERT: G 240 MET cc_start: 0.8448 (mtp) cc_final: 0.8180 (mtm) REVERT: G 299 SER cc_start: 0.9073 (m) cc_final: 0.8709 (p) REVERT: M 195 GLU cc_start: 0.8058 (pt0) cc_final: 0.7229 (pm20) REVERT: N 240 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8004 (mmm) REVERT: N 288 CYS cc_start: 0.9167 (m) cc_final: 0.8959 (p) REVERT: N 291 MET cc_start: 0.8477 (mmp) cc_final: 0.8227 (mmp) REVERT: N 406 TYR cc_start: 0.7797 (m-80) cc_final: 0.7505 (m-10) REVERT: N 464 THR cc_start: 0.3252 (OUTLIER) cc_final: 0.3023 (m) REVERT: L 240 MET cc_start: 0.8514 (mtp) cc_final: 0.8132 (mtm) REVERT: L 290 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.9388 (mm) REVERT: R 303 TRP cc_start: 0.5477 (m100) cc_final: 0.4873 (t-100) REVERT: S 26 MET cc_start: 0.8414 (mtp) cc_final: 0.8196 (mtp) REVERT: S 271 MET cc_start: 0.8238 (tpp) cc_final: 0.7973 (tpp) REVERT: S 288 CYS cc_start: 0.9431 (m) cc_final: 0.8924 (m) REVERT: S 483 MET cc_start: 0.7183 (OUTLIER) cc_final: 0.6922 (pmm) REVERT: P 110 MET cc_start: 0.8034 (mpp) cc_final: 0.7802 (mpp) REVERT: P 148 MET cc_start: 0.7229 (tpt) cc_final: 0.6505 (tpt) REVERT: P 285 MET cc_start: 0.7684 (mmp) cc_final: 0.7478 (mmm) REVERT: P 400 MET cc_start: 0.8318 (ttp) cc_final: 0.8064 (ttp) REVERT: Q 45 MET cc_start: 0.8485 (mmm) cc_final: 0.8211 (mmm) REVERT: Q 491 TRP cc_start: 0.9260 (OUTLIER) cc_final: 0.7999 (t60) REVERT: Z 26 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8192 (ptm) REVERT: Z 45 MET cc_start: 0.8448 (mtm) cc_final: 0.8219 (mtt) REVERT: Z 288 CYS cc_start: 0.9217 (m) cc_final: 0.8781 (m) REVERT: Z 291 MET cc_start: 0.8541 (mmp) cc_final: 0.8290 (mmp) REVERT: Z 292 TYR cc_start: 0.9120 (m-80) cc_final: 0.8768 (m-10) REVERT: W 240 MET cc_start: 0.8460 (mtp) cc_final: 0.8186 (mtm) REVERT: 4 195 GLU cc_start: 0.7769 (pt0) cc_final: 0.6813 (mp0) REVERT: 5 26 MET cc_start: 0.8035 (ptp) cc_final: 0.6990 (mtp) REVERT: 5 240 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8059 (mmm) REVERT: 5 288 CYS cc_start: 0.9169 (m) cc_final: 0.8886 (m) REVERT: 5 291 MET cc_start: 0.8541 (mmp) cc_final: 0.8281 (mmp) REVERT: 5 406 TYR cc_start: 0.7815 (m-80) cc_final: 0.7523 (m-10) REVERT: 5 464 THR cc_start: 0.3160 (OUTLIER) cc_final: 0.2942 (m) REVERT: 2 72 PHE cc_start: 0.7280 (m-80) cc_final: 0.6869 (m-80) REVERT: 2 99 LYS cc_start: 0.7435 (pttp) cc_final: 0.7167 (pptt) REVERT: 2 194 LYS cc_start: 0.9312 (tppt) cc_final: 0.9104 (tppt) REVERT: 3 240 MET cc_start: 0.8497 (mtp) cc_final: 0.8128 (mtm) REVERT: 1 45 GLU cc_start: 0.8021 (pm20) cc_final: 0.7817 (pm20) outliers start: 190 outliers final: 120 residues processed: 699 average time/residue: 0.6120 time to fit residues: 766.4761 Evaluate side-chains 648 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 517 time to evaluate : 6.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 199 TRP Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain X residue 88 SER Chi-restraints excluded: chain X residue 114 VAL Chi-restraints excluded: chain X residue 148 VAL Chi-restraints excluded: chain X residue 179 LEU Chi-restraints excluded: chain X residue 317 TRP Chi-restraints excluded: chain X residue 364 VAL Chi-restraints excluded: chain X residue 373 CYS Chi-restraints excluded: chain X residue 378 CYS Chi-restraints excluded: chain X residue 483 MET Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 336 TYR Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 430 TYR Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain H residue 96 HIS Chi-restraints excluded: chain H residue 199 TRP Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 208 LEU Chi-restraints excluded: chain I residue 252 VAL Chi-restraints excluded: chain I residue 293 HIS Chi-restraints excluded: chain I residue 307 LEU Chi-restraints excluded: chain I residue 317 TRP Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 373 CYS Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 421 LEU Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 362 LEU Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 430 TYR Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain M residue 96 HIS Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 199 TRP Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 88 SER Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain N residue 240 MET Chi-restraints excluded: chain N residue 307 LEU Chi-restraints excluded: chain N residue 317 TRP Chi-restraints excluded: chain N residue 374 LEU Chi-restraints excluded: chain N residue 378 CYS Chi-restraints excluded: chain N residue 464 THR Chi-restraints excluded: chain N residue 483 MET Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 169 MET Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain L residue 229 VAL Chi-restraints excluded: chain L residue 290 LEU Chi-restraints excluded: chain L residue 299 SER Chi-restraints excluded: chain L residue 362 LEU Chi-restraints excluded: chain L residue 369 LEU Chi-restraints excluded: chain L residue 430 TYR Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain S residue 39 HIS Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 148 VAL Chi-restraints excluded: chain S residue 179 LEU Chi-restraints excluded: chain S residue 317 TRP Chi-restraints excluded: chain S residue 364 VAL Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain S residue 483 MET Chi-restraints excluded: chain P residue 169 MET Chi-restraints excluded: chain P residue 265 VAL Chi-restraints excluded: chain P residue 336 TYR Chi-restraints excluded: chain Q residue 229 VAL Chi-restraints excluded: chain Q residue 299 SER Chi-restraints excluded: chain Q residue 345 VAL Chi-restraints excluded: chain Q residue 362 LEU Chi-restraints excluded: chain Q residue 401 LEU Chi-restraints excluded: chain Q residue 430 TYR Chi-restraints excluded: chain Q residue 491 TRP Chi-restraints excluded: chain O residue 35 MET Chi-restraints excluded: chain Y residue 162 ILE Chi-restraints excluded: chain Y residue 199 TRP Chi-restraints excluded: chain Z residue 26 MET Chi-restraints excluded: chain Z residue 39 HIS Chi-restraints excluded: chain Z residue 114 VAL Chi-restraints excluded: chain Z residue 126 LEU Chi-restraints excluded: chain Z residue 144 THR Chi-restraints excluded: chain Z residue 208 LEU Chi-restraints excluded: chain Z residue 252 VAL Chi-restraints excluded: chain Z residue 307 LEU Chi-restraints excluded: chain Z residue 317 TRP Chi-restraints excluded: chain Z residue 364 VAL Chi-restraints excluded: chain Z residue 378 CYS Chi-restraints excluded: chain Z residue 421 LEU Chi-restraints excluded: chain V residue 265 VAL Chi-restraints excluded: chain W residue 229 VAL Chi-restraints excluded: chain W residue 362 LEU Chi-restraints excluded: chain W residue 369 LEU Chi-restraints excluded: chain W residue 430 TYR Chi-restraints excluded: chain W residue 474 VAL Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain T residue 52 GLN Chi-restraints excluded: chain 4 residue 96 HIS Chi-restraints excluded: chain 4 residue 199 TRP Chi-restraints excluded: chain 4 residue 204 MET Chi-restraints excluded: chain 5 residue 39 HIS Chi-restraints excluded: chain 5 residue 240 MET Chi-restraints excluded: chain 5 residue 307 LEU Chi-restraints excluded: chain 5 residue 317 TRP Chi-restraints excluded: chain 5 residue 378 CYS Chi-restraints excluded: chain 5 residue 464 THR Chi-restraints excluded: chain 5 residue 483 MET Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 3 residue 208 LEU Chi-restraints excluded: chain 3 residue 229 VAL Chi-restraints excluded: chain 3 residue 299 SER Chi-restraints excluded: chain 3 residue 309 VAL Chi-restraints excluded: chain 3 residue 362 LEU Chi-restraints excluded: chain 3 residue 369 LEU Chi-restraints excluded: chain 3 residue 430 TYR Chi-restraints excluded: chain 3 residue 482 LEU Chi-restraints excluded: chain 1 residue 52 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 930 random chunks: chunk 748 optimal weight: 0.7980 chunk 510 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 669 optimal weight: 1.9990 chunk 370 optimal weight: 20.0000 chunk 767 optimal weight: 3.9990 chunk 621 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 459 optimal weight: 5.9990 chunk 806 optimal weight: 5.9990 chunk 226 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 399 GLN J 52 GLN ** P 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 399 GLN ** Q 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 125 ASN 2 399 GLN ** 3 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 73722 Z= 0.292 Angle : 0.656 11.237 100812 Z= 0.326 Chirality : 0.044 0.367 12048 Planarity : 0.005 0.053 12642 Dihedral : 4.700 56.747 10233 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.78 % Allowed : 13.11 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.09), residues: 9306 helix: 1.90 (0.07), residues: 5076 sheet: -0.56 (0.15), residues: 984 loop : -0.75 (0.12), residues: 3246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP 4 199 HIS 0.006 0.001 HIS K 133 PHE 0.022 0.001 PHE Z 396 TYR 0.017 0.001 TYR 2 336 ARG 0.006 0.000 ARG S 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 553 time to evaluate : 6.307 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: X 26 MET cc_start: 0.8002 (ptp) cc_final: 0.7563 (ptm) REVERT: X 291 MET cc_start: 0.8449 (mmp) cc_final: 0.8206 (mmp) REVERT: C 95 MET cc_start: 0.6631 (OUTLIER) cc_final: 0.6257 (ptp) REVERT: C 252 MET cc_start: 0.8510 (pmm) cc_final: 0.8135 (pmm) REVERT: D 369 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9255 (mp) REVERT: H 195 GLU cc_start: 0.7794 (pt0) cc_final: 0.7268 (pm20) REVERT: I 26 MET cc_start: 0.8150 (ptm) cc_final: 0.7518 (mtm) REVERT: I 291 MET cc_start: 0.8616 (mmp) cc_final: 0.8346 (mmp) REVERT: I 293 HIS cc_start: 0.8891 (OUTLIER) cc_final: 0.8165 (m90) REVERT: I 320 GLU cc_start: 0.8664 (pp20) cc_final: 0.8409 (pp20) REVERT: F 285 MET cc_start: 0.7440 (mmm) cc_final: 0.6603 (mmm) REVERT: G 240 MET cc_start: 0.8465 (mtp) cc_final: 0.8205 (mtm) REVERT: G 299 SER cc_start: 0.9151 (m) cc_final: 0.8752 (p) REVERT: M 252 MET cc_start: 0.6121 (tpp) cc_final: 0.5318 (ttt) REVERT: N 240 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8060 (mmm) REVERT: N 291 MET cc_start: 0.8576 (mmp) cc_final: 0.8335 (mmp) REVERT: N 406 TYR cc_start: 0.7823 (m-80) cc_final: 0.7526 (m-10) REVERT: K 72 PHE cc_start: 0.7256 (m-80) cc_final: 0.6919 (m-80) REVERT: K 156 LYS cc_start: 0.7403 (mttm) cc_final: 0.7158 (mmmt) REVERT: K 194 LYS cc_start: 0.9297 (tppt) cc_final: 0.8816 (tppt) REVERT: K 285 MET cc_start: 0.7339 (mmm) cc_final: 0.6570 (mmm) REVERT: L 240 MET cc_start: 0.8524 (mtp) cc_final: 0.8158 (mtm) REVERT: L 290 LEU cc_start: 0.9632 (OUTLIER) cc_final: 0.9422 (mm) REVERT: R 303 TRP cc_start: 0.5398 (m100) cc_final: 0.4875 (t-100) REVERT: S 271 MET cc_start: 0.8273 (tpp) cc_final: 0.8021 (tpp) REVERT: S 288 CYS cc_start: 0.9423 (m) cc_final: 0.8945 (m) REVERT: P 148 MET cc_start: 0.6926 (tpt) cc_final: 0.6711 (tpt) REVERT: P 252 MET cc_start: 0.8550 (pmm) cc_final: 0.8098 (pmm) REVERT: P 400 MET cc_start: 0.8330 (ttp) cc_final: 0.8078 (ttp) REVERT: Y 252 MET cc_start: 0.5830 (tpp) cc_final: 0.5258 (ttt) REVERT: Z 291 MET cc_start: 0.8551 (mmp) cc_final: 0.8282 (mmp) REVERT: Z 293 HIS cc_start: 0.8806 (OUTLIER) cc_final: 0.8400 (m-70) REVERT: V 252 MET cc_start: 0.8058 (pmm) cc_final: 0.6908 (pmm) REVERT: V 285 MET cc_start: 0.7449 (mmm) cc_final: 0.6575 (mmm) REVERT: W 45 MET cc_start: 0.8359 (mmm) cc_final: 0.8140 (mmm) REVERT: W 240 MET cc_start: 0.8474 (mtp) cc_final: 0.8201 (mtm) REVERT: 4 195 GLU cc_start: 0.7635 (pt0) cc_final: 0.7110 (pm20) REVERT: 5 240 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8110 (mmm) REVERT: 5 288 CYS cc_start: 0.9200 (m) cc_final: 0.8868 (m) REVERT: 5 406 TYR cc_start: 0.7827 (m-80) cc_final: 0.7542 (m-10) REVERT: 2 72 PHE cc_start: 0.7197 (m-80) cc_final: 0.6799 (m-80) REVERT: 2 194 LYS cc_start: 0.9298 (tppt) cc_final: 0.9075 (tppt) REVERT: 2 285 MET cc_start: 0.7233 (mmm) cc_final: 0.6466 (mmm) REVERT: 2 399 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.6645 (mp10) REVERT: 3 240 MET cc_start: 0.8508 (mtp) cc_final: 0.8140 (mtm) outliers start: 210 outliers final: 152 residues processed: 705 average time/residue: 0.6498 time to fit residues: 819.7808 Evaluate side-chains 672 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 512 time to evaluate : 6.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain X residue 88 SER Chi-restraints excluded: chain X residue 114 VAL Chi-restraints excluded: chain X residue 148 VAL Chi-restraints excluded: chain X residue 179 LEU Chi-restraints excluded: chain X residue 191 SER Chi-restraints excluded: chain X residue 317 TRP Chi-restraints excluded: chain X residue 364 VAL Chi-restraints excluded: chain X residue 374 LEU Chi-restraints excluded: chain X residue 378 CYS Chi-restraints excluded: chain X residue 483 MET Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 336 TYR Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 430 TYR Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 199 TRP Chi-restraints excluded: chain H residue 204 MET Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 208 LEU Chi-restraints excluded: chain I residue 252 VAL Chi-restraints excluded: chain I residue 293 HIS Chi-restraints excluded: chain I residue 307 LEU Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 373 CYS Chi-restraints excluded: chain I residue 374 LEU Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 336 TYR Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 362 LEU Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 430 TYR Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain M residue 96 HIS Chi-restraints excluded: chain M residue 199 TRP Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 47 ASP Chi-restraints excluded: chain N residue 88 SER Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain N residue 240 MET Chi-restraints excluded: chain N residue 299 SER Chi-restraints excluded: chain N residue 307 LEU Chi-restraints excluded: chain N residue 317 TRP Chi-restraints excluded: chain N residue 374 LEU Chi-restraints excluded: chain N residue 378 CYS Chi-restraints excluded: chain N residue 483 MET Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 169 MET Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain K residue 336 TYR Chi-restraints excluded: chain L residue 208 LEU Chi-restraints excluded: chain L residue 229 VAL Chi-restraints excluded: chain L residue 290 LEU Chi-restraints excluded: chain L residue 299 SER Chi-restraints excluded: chain L residue 339 LEU Chi-restraints excluded: chain L residue 362 LEU Chi-restraints excluded: chain L residue 430 TYR Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain S residue 39 HIS Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain S residue 148 VAL Chi-restraints excluded: chain S residue 179 LEU Chi-restraints excluded: chain S residue 191 SER Chi-restraints excluded: chain S residue 317 TRP Chi-restraints excluded: chain S residue 364 VAL Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain S residue 483 MET Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 95 MET Chi-restraints excluded: chain P residue 169 MET Chi-restraints excluded: chain P residue 265 VAL Chi-restraints excluded: chain P residue 336 TYR Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain Q residue 229 VAL Chi-restraints excluded: chain Q residue 299 SER Chi-restraints excluded: chain Q residue 345 VAL Chi-restraints excluded: chain Q residue 362 LEU Chi-restraints excluded: chain Q residue 369 LEU Chi-restraints excluded: chain Q residue 401 LEU Chi-restraints excluded: chain Q residue 430 TYR Chi-restraints excluded: chain Q residue 474 VAL Chi-restraints excluded: chain Q residue 491 TRP Chi-restraints excluded: chain O residue 35 MET Chi-restraints excluded: chain O residue 52 GLN Chi-restraints excluded: chain O residue 56 VAL Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain Y residue 162 ILE Chi-restraints excluded: chain Y residue 199 TRP Chi-restraints excluded: chain Y residue 204 MET Chi-restraints excluded: chain Z residue 88 SER Chi-restraints excluded: chain Z residue 114 VAL Chi-restraints excluded: chain Z residue 126 LEU Chi-restraints excluded: chain Z residue 208 LEU Chi-restraints excluded: chain Z residue 252 VAL Chi-restraints excluded: chain Z residue 293 HIS Chi-restraints excluded: chain Z residue 307 LEU Chi-restraints excluded: chain Z residue 317 TRP Chi-restraints excluded: chain Z residue 364 VAL Chi-restraints excluded: chain Z residue 378 CYS Chi-restraints excluded: chain V residue 265 VAL Chi-restraints excluded: chain V residue 336 TYR Chi-restraints excluded: chain W residue 208 LEU Chi-restraints excluded: chain W residue 229 VAL Chi-restraints excluded: chain W residue 345 VAL Chi-restraints excluded: chain W residue 362 LEU Chi-restraints excluded: chain W residue 369 LEU Chi-restraints excluded: chain W residue 400 ILE Chi-restraints excluded: chain W residue 430 TYR Chi-restraints excluded: chain W residue 464 THR Chi-restraints excluded: chain W residue 474 VAL Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain T residue 45 GLU Chi-restraints excluded: chain T residue 52 GLN Chi-restraints excluded: chain 4 residue 199 TRP Chi-restraints excluded: chain 5 residue 39 HIS Chi-restraints excluded: chain 5 residue 240 MET Chi-restraints excluded: chain 5 residue 307 LEU Chi-restraints excluded: chain 5 residue 317 TRP Chi-restraints excluded: chain 5 residue 374 LEU Chi-restraints excluded: chain 5 residue 378 CYS Chi-restraints excluded: chain 5 residue 483 MET Chi-restraints excluded: chain 2 residue 45 LEU Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 336 TYR Chi-restraints excluded: chain 2 residue 399 GLN Chi-restraints excluded: chain 3 residue 78 VAL Chi-restraints excluded: chain 3 residue 208 LEU Chi-restraints excluded: chain 3 residue 229 VAL Chi-restraints excluded: chain 3 residue 299 SER Chi-restraints excluded: chain 3 residue 309 VAL Chi-restraints excluded: chain 3 residue 362 LEU Chi-restraints excluded: chain 3 residue 430 TYR Chi-restraints excluded: chain 3 residue 482 LEU Chi-restraints excluded: chain 1 residue 52 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 930 random chunks: chunk 302 optimal weight: 2.9990 chunk 809 optimal weight: 2.9990 chunk 177 optimal weight: 0.9990 chunk 527 optimal weight: 9.9990 chunk 221 optimal weight: 1.9990 chunk 899 optimal weight: 2.9990 chunk 746 optimal weight: 10.0000 chunk 416 optimal weight: 20.0000 chunk 74 optimal weight: 5.9990 chunk 297 optimal weight: 4.9990 chunk 472 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 333 GLN ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 GLN ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 333 GLN G 125 ASN ** L 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 333 GLN ** Q 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 333 GLN 5 92 GLN ** 2 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 73722 Z= 0.261 Angle : 0.646 11.842 100812 Z= 0.318 Chirality : 0.044 0.307 12048 Planarity : 0.004 0.053 12642 Dihedral : 4.562 59.791 10229 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.80 % Allowed : 13.75 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.09), residues: 9306 helix: 1.91 (0.07), residues: 5076 sheet: -0.64 (0.16), residues: 984 loop : -0.75 (0.12), residues: 3246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP 4 199 HIS 0.006 0.001 HIS I 227 PHE 0.019 0.001 PHE Z 396 TYR 0.014 0.001 TYR P 336 ARG 0.004 0.000 ARG X 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 543 time to evaluate : 6.213 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: E 252 MET cc_start: 0.5767 (ttt) cc_final: 0.5366 (ttt) REVERT: X 26 MET cc_start: 0.8054 (ptp) cc_final: 0.7563 (ptm) REVERT: X 271 MET cc_start: 0.8303 (tpp) cc_final: 0.7971 (tpp) REVERT: X 288 CYS cc_start: 0.9236 (m) cc_final: 0.8909 (p) REVERT: X 291 MET cc_start: 0.8439 (mmp) cc_final: 0.8183 (mmp) REVERT: C 95 MET cc_start: 0.6643 (OUTLIER) cc_final: 0.6241 (ptp) REVERT: D 26 MET cc_start: 0.7158 (mmm) cc_final: 0.6912 (mpp) REVERT: D 45 MET cc_start: 0.8402 (mmm) cc_final: 0.8196 (mmm) REVERT: D 74 MET cc_start: 0.7746 (mpp) cc_final: 0.7149 (mmm) REVERT: H 195 GLU cc_start: 0.7887 (pt0) cc_final: 0.7325 (pm20) REVERT: I 26 MET cc_start: 0.8141 (ptm) cc_final: 0.7484 (mtm) REVERT: I 291 MET cc_start: 0.8578 (mmp) cc_final: 0.8227 (mmp) REVERT: I 293 HIS cc_start: 0.8868 (OUTLIER) cc_final: 0.8177 (m90) REVERT: F 252 MET cc_start: 0.7660 (pmm) cc_final: 0.6753 (pmm) REVERT: F 285 MET cc_start: 0.7497 (mmm) cc_final: 0.6607 (mmm) REVERT: G 130 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.8183 (m-10) REVERT: G 240 MET cc_start: 0.8462 (mtp) cc_final: 0.8190 (mtm) REVERT: G 299 SER cc_start: 0.9135 (m) cc_final: 0.8745 (p) REVERT: M 252 MET cc_start: 0.6134 (tpp) cc_final: 0.5366 (ttt) REVERT: N 240 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.8064 (mmm) REVERT: N 271 MET cc_start: 0.8499 (tpp) cc_final: 0.7992 (tpp) REVERT: N 285 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9260 (mm) REVERT: N 291 MET cc_start: 0.8591 (mmp) cc_final: 0.8371 (mmp) REVERT: N 406 TYR cc_start: 0.7722 (m-80) cc_final: 0.7515 (m-10) REVERT: K 72 PHE cc_start: 0.7305 (m-80) cc_final: 0.6892 (m-80) REVERT: K 156 LYS cc_start: 0.7536 (mttm) cc_final: 0.7315 (mmmt) REVERT: K 194 LYS cc_start: 0.9262 (tppt) cc_final: 0.8769 (tppt) REVERT: K 252 MET cc_start: 0.7706 (pmm) cc_final: 0.7414 (pmm) REVERT: K 285 MET cc_start: 0.7619 (mmm) cc_final: 0.6899 (mmm) REVERT: K 399 GLN cc_start: 0.7157 (OUTLIER) cc_final: 0.6666 (mp10) REVERT: L 240 MET cc_start: 0.8517 (mtp) cc_final: 0.8133 (mtm) REVERT: R 303 TRP cc_start: 0.5463 (m100) cc_final: 0.4906 (t-100) REVERT: S 74 MET cc_start: 0.7818 (tpp) cc_final: 0.7611 (tpp) REVERT: S 288 CYS cc_start: 0.9362 (m) cc_final: 0.8936 (m) REVERT: P 148 MET cc_start: 0.6747 (tpt) cc_final: 0.6352 (tpt) REVERT: P 399 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.6802 (mp10) REVERT: Q 26 MET cc_start: 0.7414 (mmm) cc_final: 0.7162 (mpp) REVERT: Q 74 MET cc_start: 0.7711 (mpp) cc_final: 0.7118 (mmm) REVERT: Y 252 MET cc_start: 0.6111 (tpp) cc_final: 0.5082 (ttt) REVERT: Z 291 MET cc_start: 0.8525 (mmp) cc_final: 0.8275 (mmp) REVERT: V 285 MET cc_start: 0.7426 (mmm) cc_final: 0.6493 (mmm) REVERT: W 45 MET cc_start: 0.8636 (mmm) cc_final: 0.8384 (mmm) REVERT: W 240 MET cc_start: 0.8473 (mtp) cc_final: 0.8195 (mtm) REVERT: 4 195 GLU cc_start: 0.7956 (pt0) cc_final: 0.7235 (pm20) REVERT: 5 240 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8101 (mmm) REVERT: 5 288 CYS cc_start: 0.9201 (m) cc_final: 0.8859 (m) REVERT: 5 406 TYR cc_start: 0.7738 (m-80) cc_final: 0.7537 (m-10) REVERT: 2 72 PHE cc_start: 0.7187 (m-80) cc_final: 0.6814 (m-80) REVERT: 2 194 LYS cc_start: 0.9281 (tppt) cc_final: 0.9067 (tppt) REVERT: 2 285 MET cc_start: 0.7430 (mmm) cc_final: 0.6626 (mmm) REVERT: 3 240 MET cc_start: 0.8496 (mtp) cc_final: 0.8122 (mtm) outliers start: 211 outliers final: 162 residues processed: 702 average time/residue: 0.6217 time to fit residues: 778.7187 Evaluate side-chains 680 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 510 time to evaluate : 6.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 199 TRP Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain X residue 88 SER Chi-restraints excluded: chain X residue 148 VAL Chi-restraints excluded: chain X residue 179 LEU Chi-restraints excluded: chain X residue 191 SER Chi-restraints excluded: chain X residue 307 LEU Chi-restraints excluded: chain X residue 317 TRP Chi-restraints excluded: chain X residue 364 VAL Chi-restraints excluded: chain X residue 373 CYS Chi-restraints excluded: chain X residue 378 CYS Chi-restraints excluded: chain X residue 483 MET Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 336 TYR Chi-restraints excluded: chain C residue 399 GLN Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 430 TYR Chi-restraints excluded: chain D residue 464 THR Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 199 TRP Chi-restraints excluded: chain H residue 204 MET Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 208 LEU Chi-restraints excluded: chain I residue 293 HIS Chi-restraints excluded: chain I residue 307 LEU Chi-restraints excluded: chain I residue 317 TRP Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 374 LEU Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 293 PHE Chi-restraints excluded: chain F residue 336 TYR Chi-restraints excluded: chain G residue 130 PHE Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 345 VAL Chi-restraints excluded: chain G residue 362 LEU Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 430 TYR Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain M residue 96 HIS Chi-restraints excluded: chain M residue 162 ILE Chi-restraints excluded: chain M residue 199 TRP Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 47 ASP Chi-restraints excluded: chain N residue 88 SER Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain N residue 240 MET Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 307 LEU Chi-restraints excluded: chain N residue 317 TRP Chi-restraints excluded: chain N residue 374 LEU Chi-restraints excluded: chain N residue 378 CYS Chi-restraints excluded: chain N residue 483 MET Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 169 MET Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain K residue 336 TYR Chi-restraints excluded: chain K residue 399 GLN Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 208 LEU Chi-restraints excluded: chain L residue 229 VAL Chi-restraints excluded: chain L residue 299 SER Chi-restraints excluded: chain L residue 362 LEU Chi-restraints excluded: chain L residue 430 TYR Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain R residue 199 TRP Chi-restraints excluded: chain S residue 39 HIS Chi-restraints excluded: chain S residue 68 LYS Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 148 VAL Chi-restraints excluded: chain S residue 179 LEU Chi-restraints excluded: chain S residue 191 SER Chi-restraints excluded: chain S residue 317 TRP Chi-restraints excluded: chain S residue 364 VAL Chi-restraints excluded: chain S residue 374 LEU Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain S residue 483 MET Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 169 MET Chi-restraints excluded: chain P residue 265 VAL Chi-restraints excluded: chain P residue 336 TYR Chi-restraints excluded: chain P residue 399 GLN Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain Q residue 229 VAL Chi-restraints excluded: chain Q residue 345 VAL Chi-restraints excluded: chain Q residue 362 LEU Chi-restraints excluded: chain Q residue 369 LEU Chi-restraints excluded: chain Q residue 401 LEU Chi-restraints excluded: chain Q residue 430 TYR Chi-restraints excluded: chain Q residue 474 VAL Chi-restraints excluded: chain Q residue 491 TRP Chi-restraints excluded: chain O residue 35 MET Chi-restraints excluded: chain O residue 52 GLN Chi-restraints excluded: chain O residue 56 VAL Chi-restraints excluded: chain Y residue 162 ILE Chi-restraints excluded: chain Y residue 199 TRP Chi-restraints excluded: chain Y residue 204 MET Chi-restraints excluded: chain Z residue 88 SER Chi-restraints excluded: chain Z residue 114 VAL Chi-restraints excluded: chain Z residue 126 LEU Chi-restraints excluded: chain Z residue 208 LEU Chi-restraints excluded: chain Z residue 307 LEU Chi-restraints excluded: chain Z residue 317 TRP Chi-restraints excluded: chain Z residue 364 VAL Chi-restraints excluded: chain Z residue 374 LEU Chi-restraints excluded: chain Z residue 378 CYS Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 169 MET Chi-restraints excluded: chain V residue 265 VAL Chi-restraints excluded: chain V residue 293 PHE Chi-restraints excluded: chain V residue 336 TYR Chi-restraints excluded: chain W residue 193 THR Chi-restraints excluded: chain W residue 208 LEU Chi-restraints excluded: chain W residue 229 VAL Chi-restraints excluded: chain W residue 345 VAL Chi-restraints excluded: chain W residue 362 LEU Chi-restraints excluded: chain W residue 369 LEU Chi-restraints excluded: chain W residue 400 ILE Chi-restraints excluded: chain W residue 430 TYR Chi-restraints excluded: chain W residue 464 THR Chi-restraints excluded: chain W residue 474 VAL Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain T residue 52 GLN Chi-restraints excluded: chain 4 residue 199 TRP Chi-restraints excluded: chain 5 residue 39 HIS Chi-restraints excluded: chain 5 residue 88 SER Chi-restraints excluded: chain 5 residue 240 MET Chi-restraints excluded: chain 5 residue 307 LEU Chi-restraints excluded: chain 5 residue 317 TRP Chi-restraints excluded: chain 5 residue 378 CYS Chi-restraints excluded: chain 5 residue 483 MET Chi-restraints excluded: chain 2 residue 45 LEU Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 291 ARG Chi-restraints excluded: chain 2 residue 336 TYR Chi-restraints excluded: chain 3 residue 78 VAL Chi-restraints excluded: chain 3 residue 193 THR Chi-restraints excluded: chain 3 residue 208 LEU Chi-restraints excluded: chain 3 residue 229 VAL Chi-restraints excluded: chain 3 residue 299 SER Chi-restraints excluded: chain 3 residue 362 LEU Chi-restraints excluded: chain 3 residue 430 TYR Chi-restraints excluded: chain 3 residue 482 LEU Chi-restraints excluded: chain 1 residue 52 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 930 random chunks: chunk 867 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 512 optimal weight: 6.9990 chunk 657 optimal weight: 9.9990 chunk 509 optimal weight: 3.9990 chunk 757 optimal weight: 9.9990 chunk 502 optimal weight: 9.9990 chunk 896 optimal weight: 20.0000 chunk 560 optimal weight: 6.9990 chunk 546 optimal weight: 6.9990 chunk 413 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN C 410 HIS ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 HIS ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 GLN F 399 GLN F 410 HIS ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 297 GLN K 410 HIS ** L 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 GLN ** P 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 297 GLN P 410 HIS ** Q 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 297 GLN V 399 GLN V 410 HIS ** 2 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 410 HIS ** 3 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.070 73722 Z= 0.603 Angle : 0.877 12.750 100812 Z= 0.440 Chirality : 0.050 0.232 12048 Planarity : 0.006 0.069 12642 Dihedral : 5.292 59.786 10229 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.06 % Allowed : 14.17 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.18 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.09), residues: 9306 helix: 1.01 (0.07), residues: 5166 sheet: -0.87 (0.16), residues: 972 loop : -1.16 (0.11), residues: 3168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 199 HIS 0.009 0.002 HIS W 293 PHE 0.033 0.003 PHE S 396 TYR 0.021 0.002 TYR Q 406 ARG 0.016 0.001 ARG V 97 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 484 time to evaluate : 6.095 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: E 96 HIS cc_start: 0.8180 (OUTLIER) cc_final: 0.7740 (p-80) REVERT: X 26 MET cc_start: 0.8178 (ptp) cc_final: 0.7590 (ptm) REVERT: X 288 CYS cc_start: 0.9329 (m) cc_final: 0.9103 (m) REVERT: X 291 MET cc_start: 0.8625 (mmp) cc_final: 0.8421 (mmp) REVERT: C 252 MET cc_start: 0.8342 (pmm) cc_final: 0.7971 (pmm) REVERT: D 369 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9343 (mp) REVERT: I 26 MET cc_start: 0.8391 (ptm) cc_final: 0.7358 (mtp) REVERT: I 291 MET cc_start: 0.8693 (mmp) cc_final: 0.8366 (mmp) REVERT: I 293 HIS cc_start: 0.8926 (OUTLIER) cc_final: 0.8486 (m90) REVERT: F 252 MET cc_start: 0.8028 (pmm) cc_final: 0.7617 (pmm) REVERT: F 285 MET cc_start: 0.7950 (mmm) cc_final: 0.7307 (mmm) REVERT: F 399 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.6774 (mp10) REVERT: G 130 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.8444 (m-10) REVERT: G 240 MET cc_start: 0.8575 (mtp) cc_final: 0.8164 (mtt) REVERT: G 491 TRP cc_start: 0.9240 (OUTLIER) cc_final: 0.8828 (t60) REVERT: M 252 MET cc_start: 0.6101 (tpp) cc_final: 0.5373 (ttt) REVERT: N 240 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8216 (mmm) REVERT: N 271 MET cc_start: 0.8526 (tpp) cc_final: 0.7921 (tpp) REVERT: N 291 MET cc_start: 0.8616 (mmp) cc_final: 0.8408 (mmp) REVERT: N 406 TYR cc_start: 0.7993 (m-80) cc_final: 0.7674 (m-10) REVERT: K 72 PHE cc_start: 0.7348 (m-80) cc_final: 0.6905 (m-80) REVERT: K 156 LYS cc_start: 0.7480 (mttm) cc_final: 0.7211 (mmmt) REVERT: K 252 MET cc_start: 0.8200 (pmm) cc_final: 0.7987 (pmm) REVERT: K 285 MET cc_start: 0.7848 (mmm) cc_final: 0.7335 (mmm) REVERT: K 389 ASP cc_start: 0.8740 (m-30) cc_final: 0.8475 (t70) REVERT: K 399 GLN cc_start: 0.7398 (OUTLIER) cc_final: 0.6650 (mp10) REVERT: L 240 MET cc_start: 0.8556 (mtp) cc_final: 0.8182 (mtm) REVERT: J 52 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.8918 (pt0) REVERT: R 96 HIS cc_start: 0.7898 (OUTLIER) cc_final: 0.7520 (p-80) REVERT: S 74 MET cc_start: 0.8009 (tpp) cc_final: 0.7768 (tpp) REVERT: S 288 CYS cc_start: 0.9401 (m) cc_final: 0.8962 (m) REVERT: P 148 MET cc_start: 0.6993 (tpt) cc_final: 0.6650 (tpt) REVERT: P 252 MET cc_start: 0.8365 (pmm) cc_final: 0.7971 (pmm) REVERT: Y 252 MET cc_start: 0.5825 (tpp) cc_final: 0.5342 (ttt) REVERT: Z 291 MET cc_start: 0.8653 (mmp) cc_final: 0.8437 (mmp) REVERT: V 252 MET cc_start: 0.7969 (pmm) cc_final: 0.7490 (pmm) REVERT: V 285 MET cc_start: 0.7960 (mmm) cc_final: 0.7316 (mmm) REVERT: V 389 ASP cc_start: 0.9109 (m-30) cc_final: 0.8605 (t70) REVERT: V 399 GLN cc_start: 0.7320 (OUTLIER) cc_final: 0.6627 (mp10) REVERT: W 130 PHE cc_start: 0.8651 (OUTLIER) cc_final: 0.8420 (m-10) REVERT: W 240 MET cc_start: 0.8534 (mtp) cc_final: 0.8103 (mtt) REVERT: W 491 TRP cc_start: 0.9245 (OUTLIER) cc_final: 0.8815 (t60) REVERT: 4 252 MET cc_start: 0.5816 (ttt) cc_final: 0.5427 (ttt) REVERT: 5 74 MET cc_start: 0.8064 (mmm) cc_final: 0.7830 (mmm) REVERT: 5 240 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8271 (mmm) REVERT: 5 271 MET cc_start: 0.8606 (tpp) cc_final: 0.8215 (tpp) REVERT: 5 288 CYS cc_start: 0.9220 (m) cc_final: 0.8886 (m) REVERT: 5 406 TYR cc_start: 0.7984 (m-80) cc_final: 0.7659 (m-10) REVERT: 2 72 PHE cc_start: 0.7156 (m-80) cc_final: 0.6748 (m-80) REVERT: 2 194 LYS cc_start: 0.9402 (tppt) cc_final: 0.8927 (tppt) REVERT: 2 285 MET cc_start: 0.7754 (mmm) cc_final: 0.7235 (mmm) REVERT: 2 389 ASP cc_start: 0.8725 (m-30) cc_final: 0.8412 (t70) REVERT: 3 240 MET cc_start: 0.8539 (mtp) cc_final: 0.8181 (mtm) REVERT: 3 398 PHE cc_start: 0.9550 (OUTLIER) cc_final: 0.9136 (t80) outliers start: 231 outliers final: 173 residues processed: 665 average time/residue: 0.6290 time to fit residues: 745.8901 Evaluate side-chains 655 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 467 time to evaluate : 6.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 96 HIS Chi-restraints excluded: chain E residue 199 TRP Chi-restraints excluded: chain E residue 204 MET Chi-restraints excluded: chain X residue 88 SER Chi-restraints excluded: chain X residue 148 VAL Chi-restraints excluded: chain X residue 179 LEU Chi-restraints excluded: chain X residue 191 SER Chi-restraints excluded: chain X residue 307 LEU Chi-restraints excluded: chain X residue 317 TRP Chi-restraints excluded: chain X residue 364 VAL Chi-restraints excluded: chain X residue 374 LEU Chi-restraints excluded: chain X residue 378 CYS Chi-restraints excluded: chain X residue 421 LEU Chi-restraints excluded: chain X residue 483 MET Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 336 TYR Chi-restraints excluded: chain C residue 399 GLN Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 430 TYR Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain H residue 96 HIS Chi-restraints excluded: chain H residue 199 TRP Chi-restraints excluded: chain H residue 204 MET Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 208 LEU Chi-restraints excluded: chain I residue 293 HIS Chi-restraints excluded: chain I residue 307 LEU Chi-restraints excluded: chain I residue 317 TRP Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 374 LEU Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 336 TYR Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain G residue 130 PHE Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 345 VAL Chi-restraints excluded: chain G residue 362 LEU Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 400 ILE Chi-restraints excluded: chain G residue 430 TYR Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain G residue 491 TRP Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain M residue 96 HIS Chi-restraints excluded: chain M residue 162 ILE Chi-restraints excluded: chain N residue 47 ASP Chi-restraints excluded: chain N residue 88 SER Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain N residue 240 MET Chi-restraints excluded: chain N residue 299 SER Chi-restraints excluded: chain N residue 374 LEU Chi-restraints excluded: chain N residue 378 CYS Chi-restraints excluded: chain N residue 483 MET Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 169 MET Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain K residue 336 TYR Chi-restraints excluded: chain K residue 399 GLN Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 208 LEU Chi-restraints excluded: chain L residue 229 VAL Chi-restraints excluded: chain L residue 299 SER Chi-restraints excluded: chain L residue 339 LEU Chi-restraints excluded: chain L residue 362 LEU Chi-restraints excluded: chain L residue 492 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 52 GLN Chi-restraints excluded: chain R residue 96 HIS Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain S residue 39 HIS Chi-restraints excluded: chain S residue 68 LYS Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 148 VAL Chi-restraints excluded: chain S residue 179 LEU Chi-restraints excluded: chain S residue 191 SER Chi-restraints excluded: chain S residue 307 LEU Chi-restraints excluded: chain S residue 317 TRP Chi-restraints excluded: chain S residue 364 VAL Chi-restraints excluded: chain S residue 374 LEU Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain S residue 421 LEU Chi-restraints excluded: chain S residue 483 MET Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 169 MET Chi-restraints excluded: chain P residue 265 VAL Chi-restraints excluded: chain P residue 336 TYR Chi-restraints excluded: chain P residue 399 GLN Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain Q residue 229 VAL Chi-restraints excluded: chain Q residue 299 SER Chi-restraints excluded: chain Q residue 345 VAL Chi-restraints excluded: chain Q residue 362 LEU Chi-restraints excluded: chain Q residue 401 LEU Chi-restraints excluded: chain Q residue 430 TYR Chi-restraints excluded: chain Q residue 464 THR Chi-restraints excluded: chain Q residue 474 VAL Chi-restraints excluded: chain Q residue 491 TRP Chi-restraints excluded: chain O residue 35 MET Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 52 GLN Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain Y residue 162 ILE Chi-restraints excluded: chain Y residue 204 MET Chi-restraints excluded: chain Z residue 88 SER Chi-restraints excluded: chain Z residue 114 VAL Chi-restraints excluded: chain Z residue 126 LEU Chi-restraints excluded: chain Z residue 144 THR Chi-restraints excluded: chain Z residue 208 LEU Chi-restraints excluded: chain Z residue 252 VAL Chi-restraints excluded: chain Z residue 307 LEU Chi-restraints excluded: chain Z residue 317 TRP Chi-restraints excluded: chain Z residue 364 VAL Chi-restraints excluded: chain Z residue 374 LEU Chi-restraints excluded: chain Z residue 378 CYS Chi-restraints excluded: chain V residue 169 MET Chi-restraints excluded: chain V residue 265 VAL Chi-restraints excluded: chain V residue 336 TYR Chi-restraints excluded: chain V residue 399 GLN Chi-restraints excluded: chain W residue 130 PHE Chi-restraints excluded: chain W residue 193 THR Chi-restraints excluded: chain W residue 208 LEU Chi-restraints excluded: chain W residue 229 VAL Chi-restraints excluded: chain W residue 345 VAL Chi-restraints excluded: chain W residue 362 LEU Chi-restraints excluded: chain W residue 369 LEU Chi-restraints excluded: chain W residue 400 ILE Chi-restraints excluded: chain W residue 430 TYR Chi-restraints excluded: chain W residue 464 THR Chi-restraints excluded: chain W residue 491 TRP Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain T residue 45 GLU Chi-restraints excluded: chain T residue 52 GLN Chi-restraints excluded: chain 4 residue 199 TRP Chi-restraints excluded: chain 4 residue 204 MET Chi-restraints excluded: chain 5 residue 39 HIS Chi-restraints excluded: chain 5 residue 88 SER Chi-restraints excluded: chain 5 residue 114 VAL Chi-restraints excluded: chain 5 residue 240 MET Chi-restraints excluded: chain 5 residue 374 LEU Chi-restraints excluded: chain 5 residue 378 CYS Chi-restraints excluded: chain 5 residue 483 MET Chi-restraints excluded: chain 2 residue 45 LEU Chi-restraints excluded: chain 2 residue 169 MET Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 291 ARG Chi-restraints excluded: chain 2 residue 336 TYR Chi-restraints excluded: chain 3 residue 47 ASP Chi-restraints excluded: chain 3 residue 78 VAL Chi-restraints excluded: chain 3 residue 193 THR Chi-restraints excluded: chain 3 residue 208 LEU Chi-restraints excluded: chain 3 residue 229 VAL Chi-restraints excluded: chain 3 residue 299 SER Chi-restraints excluded: chain 3 residue 362 LEU Chi-restraints excluded: chain 3 residue 398 PHE Chi-restraints excluded: chain 3 residue 464 THR Chi-restraints excluded: chain 3 residue 491 TRP Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 52 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 930 random chunks: chunk 554 optimal weight: 0.5980 chunk 357 optimal weight: 9.9990 chunk 535 optimal weight: 0.0040 chunk 270 optimal weight: 8.9990 chunk 176 optimal weight: 5.9990 chunk 173 optimal weight: 30.0000 chunk 569 optimal weight: 0.9980 chunk 610 optimal weight: 1.9990 chunk 443 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 704 optimal weight: 3.9990 overall best weight: 1.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 HIS ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 240 GLN ** F 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 31 GLN ** Z 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 240 GLN ** V 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 73722 Z= 0.208 Angle : 0.654 14.453 100812 Z= 0.320 Chirality : 0.043 0.363 12048 Planarity : 0.004 0.054 12642 Dihedral : 4.674 59.528 10229 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.24 % Allowed : 15.39 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.09), residues: 9306 helix: 1.69 (0.07), residues: 5142 sheet: -0.88 (0.16), residues: 972 loop : -0.93 (0.12), residues: 3192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 199 HIS 0.006 0.001 HIS S 117 PHE 0.016 0.001 PHE I 396 TYR 0.011 0.001 TYR P 336 ARG 0.009 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 534 time to evaluate : 6.356 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: X 26 MET cc_start: 0.8047 (ptp) cc_final: 0.7521 (ptm) REVERT: X 288 CYS cc_start: 0.9223 (m) cc_final: 0.8968 (m) REVERT: X 291 MET cc_start: 0.8474 (mmp) cc_final: 0.8192 (mmp) REVERT: C 252 MET cc_start: 0.8171 (pmm) cc_final: 0.7737 (pmm) REVERT: D 26 MET cc_start: 0.7138 (mmm) cc_final: 0.6812 (mpp) REVERT: D 74 MET cc_start: 0.7792 (mpp) cc_final: 0.7554 (mpp) REVERT: H 96 HIS cc_start: 0.8338 (OUTLIER) cc_final: 0.7835 (p90) REVERT: I 26 MET cc_start: 0.8168 (ptm) cc_final: 0.7513 (mtp) REVERT: I 291 MET cc_start: 0.8589 (mmp) cc_final: 0.8261 (mmp) REVERT: I 293 HIS cc_start: 0.8871 (OUTLIER) cc_final: 0.8216 (m90) REVERT: F 252 MET cc_start: 0.7628 (pmm) cc_final: 0.6673 (pmm) REVERT: F 285 MET cc_start: 0.7676 (mmm) cc_final: 0.6995 (mmm) REVERT: G 50 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8179 (tp) REVERT: G 130 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.8413 (m-10) REVERT: G 240 MET cc_start: 0.8447 (mtp) cc_final: 0.8183 (mtm) REVERT: G 299 SER cc_start: 0.9099 (m) cc_final: 0.8715 (p) REVERT: G 491 TRP cc_start: 0.9108 (OUTLIER) cc_final: 0.8845 (t60) REVERT: M 252 MET cc_start: 0.6112 (tpp) cc_final: 0.5425 (ttt) REVERT: N 240 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.8114 (mmm) REVERT: N 271 MET cc_start: 0.8566 (tpp) cc_final: 0.8209 (tpp) REVERT: N 291 MET cc_start: 0.8564 (mmp) cc_final: 0.8343 (mmp) REVERT: N 406 TYR cc_start: 0.7762 (m-80) cc_final: 0.7473 (m-10) REVERT: K 72 PHE cc_start: 0.7251 (m-80) cc_final: 0.6876 (m-80) REVERT: K 194 LYS cc_start: 0.9243 (tppt) cc_final: 0.8823 (tppt) REVERT: K 285 MET cc_start: 0.7665 (mmm) cc_final: 0.7188 (mmm) REVERT: L 26 MET cc_start: 0.7444 (mmm) cc_final: 0.7112 (mpp) REVERT: L 130 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.7997 (m-10) REVERT: L 240 MET cc_start: 0.8480 (mtp) cc_final: 0.8082 (mtm) REVERT: S 74 MET cc_start: 0.8012 (tpp) cc_final: 0.7758 (tpp) REVERT: S 288 CYS cc_start: 0.9333 (m) cc_final: 0.8960 (m) REVERT: P 148 MET cc_start: 0.6887 (tpt) cc_final: 0.6434 (tpt) REVERT: P 252 MET cc_start: 0.8213 (pmm) cc_final: 0.7749 (pmm) REVERT: P 399 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7238 (mp10) REVERT: Q 74 MET cc_start: 0.7843 (mpp) cc_final: 0.7575 (mpp) REVERT: Y 252 MET cc_start: 0.5797 (tpp) cc_final: 0.5344 (ttt) REVERT: Z 243 MET cc_start: 0.8961 (mmm) cc_final: 0.8658 (tpp) REVERT: Z 291 MET cc_start: 0.8503 (mmp) cc_final: 0.8259 (mmp) REVERT: V 252 MET cc_start: 0.7804 (pmm) cc_final: 0.6719 (pmm) REVERT: V 285 MET cc_start: 0.7685 (mmm) cc_final: 0.7015 (mmm) REVERT: W 50 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8214 (tp) REVERT: W 240 MET cc_start: 0.8462 (mtp) cc_final: 0.8189 (mtm) REVERT: W 491 TRP cc_start: 0.9106 (OUTLIER) cc_final: 0.8807 (t60) REVERT: 5 240 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8209 (mmm) REVERT: 5 271 MET cc_start: 0.8469 (tpp) cc_final: 0.8016 (tpp) REVERT: 5 288 CYS cc_start: 0.9179 (m) cc_final: 0.8827 (m) REVERT: 5 406 TYR cc_start: 0.7787 (m-80) cc_final: 0.7511 (m-10) REVERT: 2 72 PHE cc_start: 0.7125 (m-80) cc_final: 0.6779 (m-80) REVERT: 2 285 MET cc_start: 0.7670 (mmm) cc_final: 0.7153 (mmm) REVERT: 3 240 MET cc_start: 0.8462 (mtp) cc_final: 0.8082 (mtm) REVERT: 1 61 SER cc_start: 0.9368 (m) cc_final: 0.8959 (t) outliers start: 169 outliers final: 133 residues processed: 655 average time/residue: 0.6258 time to fit residues: 727.6057 Evaluate side-chains 654 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 510 time to evaluate : 6.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 199 TRP Chi-restraints excluded: chain X residue 88 SER Chi-restraints excluded: chain X residue 179 LEU Chi-restraints excluded: chain X residue 307 LEU Chi-restraints excluded: chain X residue 317 TRP Chi-restraints excluded: chain X residue 364 VAL Chi-restraints excluded: chain X residue 378 CYS Chi-restraints excluded: chain X residue 421 LEU Chi-restraints excluded: chain X residue 483 MET Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 336 TYR Chi-restraints excluded: chain C residue 399 GLN Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 430 TYR Chi-restraints excluded: chain D residue 464 THR Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain H residue 96 HIS Chi-restraints excluded: chain H residue 199 TRP Chi-restraints excluded: chain H residue 204 MET Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 208 LEU Chi-restraints excluded: chain I residue 293 HIS Chi-restraints excluded: chain I residue 307 LEU Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 336 TYR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 130 PHE Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 362 LEU Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 430 TYR Chi-restraints excluded: chain G residue 491 TRP Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain M residue 96 HIS Chi-restraints excluded: chain M residue 162 ILE Chi-restraints excluded: chain M residue 199 TRP Chi-restraints excluded: chain N residue 47 ASP Chi-restraints excluded: chain N residue 88 SER Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain N residue 208 LEU Chi-restraints excluded: chain N residue 240 MET Chi-restraints excluded: chain N residue 374 LEU Chi-restraints excluded: chain N residue 378 CYS Chi-restraints excluded: chain N residue 483 MET Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 169 MET Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 130 PHE Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 208 LEU Chi-restraints excluded: chain L residue 299 SER Chi-restraints excluded: chain L residue 362 LEU Chi-restraints excluded: chain L residue 430 TYR Chi-restraints excluded: chain R residue 199 TRP Chi-restraints excluded: chain S residue 39 HIS Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 307 LEU Chi-restraints excluded: chain S residue 317 TRP Chi-restraints excluded: chain S residue 364 VAL Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain S residue 421 LEU Chi-restraints excluded: chain S residue 483 MET Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 169 MET Chi-restraints excluded: chain P residue 265 VAL Chi-restraints excluded: chain P residue 336 TYR Chi-restraints excluded: chain P residue 399 GLN Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain Q residue 229 VAL Chi-restraints excluded: chain Q residue 362 LEU Chi-restraints excluded: chain Q residue 401 LEU Chi-restraints excluded: chain Q residue 430 TYR Chi-restraints excluded: chain Q residue 474 VAL Chi-restraints excluded: chain Q residue 491 TRP Chi-restraints excluded: chain O residue 52 GLN Chi-restraints excluded: chain Y residue 107 ILE Chi-restraints excluded: chain Y residue 162 ILE Chi-restraints excluded: chain Y residue 199 TRP Chi-restraints excluded: chain Y residue 204 MET Chi-restraints excluded: chain Z residue 88 SER Chi-restraints excluded: chain Z residue 114 VAL Chi-restraints excluded: chain Z residue 126 LEU Chi-restraints excluded: chain Z residue 208 LEU Chi-restraints excluded: chain Z residue 252 VAL Chi-restraints excluded: chain Z residue 307 LEU Chi-restraints excluded: chain Z residue 317 TRP Chi-restraints excluded: chain Z residue 378 CYS Chi-restraints excluded: chain V residue 169 MET Chi-restraints excluded: chain V residue 265 VAL Chi-restraints excluded: chain V residue 336 TYR Chi-restraints excluded: chain W residue 50 LEU Chi-restraints excluded: chain W residue 193 THR Chi-restraints excluded: chain W residue 208 LEU Chi-restraints excluded: chain W residue 229 VAL Chi-restraints excluded: chain W residue 362 LEU Chi-restraints excluded: chain W residue 369 LEU Chi-restraints excluded: chain W residue 430 TYR Chi-restraints excluded: chain W residue 491 TRP Chi-restraints excluded: chain T residue 45 GLU Chi-restraints excluded: chain T residue 52 GLN Chi-restraints excluded: chain 4 residue 199 TRP Chi-restraints excluded: chain 5 residue 26 MET Chi-restraints excluded: chain 5 residue 39 HIS Chi-restraints excluded: chain 5 residue 88 SER Chi-restraints excluded: chain 5 residue 114 VAL Chi-restraints excluded: chain 5 residue 240 MET Chi-restraints excluded: chain 5 residue 257 VAL Chi-restraints excluded: chain 5 residue 374 LEU Chi-restraints excluded: chain 5 residue 378 CYS Chi-restraints excluded: chain 5 residue 483 MET Chi-restraints excluded: chain 2 residue 45 LEU Chi-restraints excluded: chain 2 residue 169 MET Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 336 TYR Chi-restraints excluded: chain 3 residue 78 VAL Chi-restraints excluded: chain 3 residue 193 THR Chi-restraints excluded: chain 3 residue 208 LEU Chi-restraints excluded: chain 3 residue 299 SER Chi-restraints excluded: chain 3 residue 362 LEU Chi-restraints excluded: chain 3 residue 430 TYR Chi-restraints excluded: chain 1 residue 52 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 930 random chunks: chunk 815 optimal weight: 4.9990 chunk 858 optimal weight: 1.9990 chunk 783 optimal weight: 10.0000 chunk 835 optimal weight: 10.0000 chunk 502 optimal weight: 5.9990 chunk 363 optimal weight: 3.9990 chunk 655 optimal weight: 0.6980 chunk 256 optimal weight: 0.0470 chunk 754 optimal weight: 2.9990 chunk 790 optimal weight: 20.0000 chunk 832 optimal weight: 9.9990 overall best weight: 1.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 HIS ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 92 GLN ** Z 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 333 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 73722 Z= 0.235 Angle : 0.661 16.441 100812 Z= 0.323 Chirality : 0.043 0.419 12048 Planarity : 0.004 0.056 12642 Dihedral : 4.534 57.540 10229 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.33 % Allowed : 15.51 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.09), residues: 9306 helix: 1.77 (0.07), residues: 5136 sheet: -0.95 (0.16), residues: 924 loop : -0.92 (0.11), residues: 3246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP 4 199 HIS 0.009 0.001 HIS H 96 PHE 0.019 0.001 PHE I 396 TYR 0.009 0.001 TYR Z 292 ARG 0.007 0.000 ARG S 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 530 time to evaluate : 6.195 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: X 26 MET cc_start: 0.8073 (ptp) cc_final: 0.7521 (ptm) REVERT: X 288 CYS cc_start: 0.9251 (m) cc_final: 0.8923 (p) REVERT: X 291 MET cc_start: 0.8460 (mmp) cc_final: 0.8257 (mmp) REVERT: C 156 LYS cc_start: 0.7494 (mttm) cc_final: 0.7233 (mmmt) REVERT: C 252 MET cc_start: 0.8232 (pmm) cc_final: 0.7829 (pmm) REVERT: D 26 MET cc_start: 0.7132 (mmm) cc_final: 0.6798 (mpp) REVERT: D 74 MET cc_start: 0.7877 (mpp) cc_final: 0.7654 (mpp) REVERT: H 252 MET cc_start: 0.6003 (tpp) cc_final: 0.5163 (ttt) REVERT: I 26 MET cc_start: 0.8231 (ptm) cc_final: 0.7567 (mtp) REVERT: I 291 MET cc_start: 0.8589 (mmp) cc_final: 0.8262 (mmp) REVERT: I 293 HIS cc_start: 0.8868 (OUTLIER) cc_final: 0.8105 (m90) REVERT: F 252 MET cc_start: 0.7780 (pmm) cc_final: 0.6782 (pmm) REVERT: F 285 MET cc_start: 0.7620 (mmm) cc_final: 0.6949 (mmm) REVERT: G 130 PHE cc_start: 0.8586 (OUTLIER) cc_final: 0.8331 (m-10) REVERT: G 240 MET cc_start: 0.8505 (mtp) cc_final: 0.8242 (mtm) REVERT: G 299 SER cc_start: 0.9109 (m) cc_final: 0.8721 (p) REVERT: G 491 TRP cc_start: 0.9107 (OUTLIER) cc_final: 0.8798 (t60) REVERT: M 107 ILE cc_start: 0.8398 (mt) cc_final: 0.8090 (tp) REVERT: M 252 MET cc_start: 0.6113 (OUTLIER) cc_final: 0.5411 (ttt) REVERT: N 240 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8091 (mmm) REVERT: N 271 MET cc_start: 0.8536 (tpp) cc_final: 0.8177 (tpp) REVERT: N 291 MET cc_start: 0.8520 (mmp) cc_final: 0.8287 (mmp) REVERT: N 406 TYR cc_start: 0.7608 (m-80) cc_final: 0.7394 (m-10) REVERT: K 72 PHE cc_start: 0.7229 (m-80) cc_final: 0.6881 (m-80) REVERT: K 156 LYS cc_start: 0.7594 (mttm) cc_final: 0.7278 (mmmt) REVERT: K 194 LYS cc_start: 0.9254 (tppt) cc_final: 0.8772 (tppt) REVERT: K 285 MET cc_start: 0.7674 (mmm) cc_final: 0.7232 (mmm) REVERT: K 399 GLN cc_start: 0.7294 (OUTLIER) cc_final: 0.6635 (mp10) REVERT: L 26 MET cc_start: 0.7449 (mmm) cc_final: 0.7110 (mpp) REVERT: L 240 MET cc_start: 0.8480 (mtp) cc_final: 0.8101 (mtm) REVERT: R 303 TRP cc_start: 0.5188 (m100) cc_final: 0.4648 (t-100) REVERT: S 74 MET cc_start: 0.8027 (tpp) cc_final: 0.7776 (tpp) REVERT: S 288 CYS cc_start: 0.9391 (m) cc_final: 0.8885 (m) REVERT: P 148 MET cc_start: 0.6957 (tpt) cc_final: 0.6485 (tpt) REVERT: P 252 MET cc_start: 0.8275 (pmm) cc_final: 0.7839 (pmm) REVERT: P 399 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.7369 (mp10) REVERT: Q 74 MET cc_start: 0.7884 (mpp) cc_final: 0.7662 (mpp) REVERT: Y 252 MET cc_start: 0.5793 (OUTLIER) cc_final: 0.5335 (ttt) REVERT: Z 26 MET cc_start: 0.8385 (ptm) cc_final: 0.7136 (mtp) REVERT: Z 243 MET cc_start: 0.9046 (mmm) cc_final: 0.8810 (tpp) REVERT: Z 291 MET cc_start: 0.8500 (mmp) cc_final: 0.8262 (mmp) REVERT: V 252 MET cc_start: 0.7872 (pmm) cc_final: 0.6823 (pmm) REVERT: V 285 MET cc_start: 0.7631 (mmm) cc_final: 0.6981 (mmm) REVERT: W 240 MET cc_start: 0.8514 (mtp) cc_final: 0.8246 (mtm) REVERT: W 491 TRP cc_start: 0.9092 (OUTLIER) cc_final: 0.8771 (t60) REVERT: 5 88 SER cc_start: 0.8981 (OUTLIER) cc_final: 0.8721 (t) REVERT: 5 240 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.8130 (mmm) REVERT: 5 271 MET cc_start: 0.8547 (tpp) cc_final: 0.8098 (tpp) REVERT: 5 288 CYS cc_start: 0.9203 (m) cc_final: 0.8842 (m) REVERT: 5 406 TYR cc_start: 0.7751 (m-80) cc_final: 0.7503 (m-10) REVERT: 2 72 PHE cc_start: 0.6938 (m-80) cc_final: 0.6595 (m-80) REVERT: 2 285 MET cc_start: 0.7598 (mmm) cc_final: 0.7077 (mmm) REVERT: 3 130 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.8101 (m-80) REVERT: 3 240 MET cc_start: 0.8460 (mtp) cc_final: 0.8092 (mtm) REVERT: 3 491 TRP cc_start: 0.9211 (OUTLIER) cc_final: 0.8148 (t60) REVERT: 3 493 MET cc_start: 0.8715 (mmm) cc_final: 0.8299 (mmm) outliers start: 176 outliers final: 145 residues processed: 662 average time/residue: 0.6231 time to fit residues: 734.5918 Evaluate side-chains 676 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 518 time to evaluate : 6.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 199 TRP Chi-restraints excluded: chain X residue 88 SER Chi-restraints excluded: chain X residue 179 LEU Chi-restraints excluded: chain X residue 307 LEU Chi-restraints excluded: chain X residue 364 VAL Chi-restraints excluded: chain X residue 374 LEU Chi-restraints excluded: chain X residue 378 CYS Chi-restraints excluded: chain X residue 421 LEU Chi-restraints excluded: chain X residue 483 MET Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 336 TYR Chi-restraints excluded: chain C residue 399 GLN Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 430 TYR Chi-restraints excluded: chain D residue 464 THR Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain H residue 199 TRP Chi-restraints excluded: chain H residue 204 MET Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 208 LEU Chi-restraints excluded: chain I residue 293 HIS Chi-restraints excluded: chain I residue 307 LEU Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 130 PHE Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 362 LEU Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 430 TYR Chi-restraints excluded: chain G residue 491 TRP Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain M residue 162 ILE Chi-restraints excluded: chain M residue 199 TRP Chi-restraints excluded: chain M residue 252 MET Chi-restraints excluded: chain N residue 47 ASP Chi-restraints excluded: chain N residue 88 SER Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain N residue 208 LEU Chi-restraints excluded: chain N residue 240 MET Chi-restraints excluded: chain N residue 307 LEU Chi-restraints excluded: chain N residue 374 LEU Chi-restraints excluded: chain N residue 378 CYS Chi-restraints excluded: chain N residue 483 MET Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 152 GLN Chi-restraints excluded: chain K residue 169 MET Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain K residue 399 GLN Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 133 ILE Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 208 LEU Chi-restraints excluded: chain L residue 229 VAL Chi-restraints excluded: chain L residue 299 SER Chi-restraints excluded: chain L residue 362 LEU Chi-restraints excluded: chain L residue 430 TYR Chi-restraints excluded: chain L residue 491 TRP Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain R residue 199 TRP Chi-restraints excluded: chain S residue 39 HIS Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 179 LEU Chi-restraints excluded: chain S residue 307 LEU Chi-restraints excluded: chain S residue 317 TRP Chi-restraints excluded: chain S residue 364 VAL Chi-restraints excluded: chain S residue 374 LEU Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain S residue 421 LEU Chi-restraints excluded: chain S residue 483 MET Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 169 MET Chi-restraints excluded: chain P residue 265 VAL Chi-restraints excluded: chain P residue 336 TYR Chi-restraints excluded: chain P residue 399 GLN Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain Q residue 229 VAL Chi-restraints excluded: chain Q residue 362 LEU Chi-restraints excluded: chain Q residue 401 LEU Chi-restraints excluded: chain Q residue 430 TYR Chi-restraints excluded: chain Q residue 464 THR Chi-restraints excluded: chain Q residue 474 VAL Chi-restraints excluded: chain Q residue 491 TRP Chi-restraints excluded: chain O residue 52 GLN Chi-restraints excluded: chain O residue 56 VAL Chi-restraints excluded: chain Y residue 107 ILE Chi-restraints excluded: chain Y residue 162 ILE Chi-restraints excluded: chain Y residue 199 TRP Chi-restraints excluded: chain Y residue 204 MET Chi-restraints excluded: chain Y residue 252 MET Chi-restraints excluded: chain Z residue 88 SER Chi-restraints excluded: chain Z residue 114 VAL Chi-restraints excluded: chain Z residue 126 LEU Chi-restraints excluded: chain Z residue 208 LEU Chi-restraints excluded: chain Z residue 252 VAL Chi-restraints excluded: chain Z residue 307 LEU Chi-restraints excluded: chain Z residue 317 TRP Chi-restraints excluded: chain Z residue 364 VAL Chi-restraints excluded: chain Z residue 378 CYS Chi-restraints excluded: chain V residue 169 MET Chi-restraints excluded: chain V residue 265 VAL Chi-restraints excluded: chain W residue 193 THR Chi-restraints excluded: chain W residue 208 LEU Chi-restraints excluded: chain W residue 229 VAL Chi-restraints excluded: chain W residue 362 LEU Chi-restraints excluded: chain W residue 369 LEU Chi-restraints excluded: chain W residue 430 TYR Chi-restraints excluded: chain W residue 491 TRP Chi-restraints excluded: chain T residue 45 GLU Chi-restraints excluded: chain T residue 52 GLN Chi-restraints excluded: chain 4 residue 199 TRP Chi-restraints excluded: chain 5 residue 26 MET Chi-restraints excluded: chain 5 residue 39 HIS Chi-restraints excluded: chain 5 residue 88 SER Chi-restraints excluded: chain 5 residue 114 VAL Chi-restraints excluded: chain 5 residue 240 MET Chi-restraints excluded: chain 5 residue 257 VAL Chi-restraints excluded: chain 5 residue 374 LEU Chi-restraints excluded: chain 5 residue 378 CYS Chi-restraints excluded: chain 5 residue 483 MET Chi-restraints excluded: chain 2 residue 45 LEU Chi-restraints excluded: chain 2 residue 169 MET Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 3 residue 78 VAL Chi-restraints excluded: chain 3 residue 130 PHE Chi-restraints excluded: chain 3 residue 133 ILE Chi-restraints excluded: chain 3 residue 193 THR Chi-restraints excluded: chain 3 residue 208 LEU Chi-restraints excluded: chain 3 residue 229 VAL Chi-restraints excluded: chain 3 residue 299 SER Chi-restraints excluded: chain 3 residue 362 LEU Chi-restraints excluded: chain 3 residue 430 TYR Chi-restraints excluded: chain 3 residue 482 LEU Chi-restraints excluded: chain 3 residue 491 TRP Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 52 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 930 random chunks: chunk 548 optimal weight: 8.9990 chunk 883 optimal weight: 20.0000 chunk 539 optimal weight: 0.9980 chunk 419 optimal weight: 10.0000 chunk 614 optimal weight: 3.9990 chunk 926 optimal weight: 2.9990 chunk 852 optimal weight: 9.9990 chunk 737 optimal weight: 2.9990 chunk 76 optimal weight: 0.0870 chunk 569 optimal weight: 10.0000 chunk 452 optimal weight: 2.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 HIS ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 399 GLN ** N 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 240 GLN ** 2 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 73722 Z= 0.240 Angle : 0.672 16.120 100812 Z= 0.327 Chirality : 0.044 0.426 12048 Planarity : 0.004 0.055 12642 Dihedral : 4.441 52.005 10227 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.19 % Allowed : 15.91 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.09), residues: 9306 helix: 1.81 (0.07), residues: 5136 sheet: -0.72 (0.17), residues: 864 loop : -0.88 (0.11), residues: 3306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP W 491 HIS 0.006 0.001 HIS S 227 PHE 0.018 0.001 PHE I 396 TYR 0.010 0.001 TYR Z 292 ARG 0.007 0.000 ARG X 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 522 time to evaluate : 6.200 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: X 26 MET cc_start: 0.8061 (ptp) cc_final: 0.7509 (ptm) REVERT: X 271 MET cc_start: 0.8475 (tpp) cc_final: 0.8263 (tpp) REVERT: X 288 CYS cc_start: 0.9248 (m) cc_final: 0.8933 (p) REVERT: X 291 MET cc_start: 0.8462 (mmp) cc_final: 0.8191 (mmp) REVERT: C 156 LYS cc_start: 0.7583 (mttm) cc_final: 0.7297 (mmmt) REVERT: C 252 MET cc_start: 0.8263 (pmm) cc_final: 0.7855 (pmm) REVERT: C 399 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.6960 (mp10) REVERT: D 26 MET cc_start: 0.7128 (mmm) cc_final: 0.6798 (mpp) REVERT: D 74 MET cc_start: 0.7964 (mpp) cc_final: 0.7761 (mpp) REVERT: I 26 MET cc_start: 0.8227 (ptm) cc_final: 0.7549 (mtp) REVERT: I 291 MET cc_start: 0.8575 (mmp) cc_final: 0.8266 (mmp) REVERT: I 293 HIS cc_start: 0.8859 (OUTLIER) cc_final: 0.8090 (m90) REVERT: F 252 MET cc_start: 0.7804 (pmm) cc_final: 0.6800 (pmm) REVERT: F 285 MET cc_start: 0.7613 (mmm) cc_final: 0.6945 (mmm) REVERT: F 399 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.6704 (mp10) REVERT: G 50 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8174 (tp) REVERT: G 240 MET cc_start: 0.8502 (mtp) cc_final: 0.8240 (mtm) REVERT: G 299 SER cc_start: 0.9101 (m) cc_final: 0.8722 (p) REVERT: G 491 TRP cc_start: 0.9100 (OUTLIER) cc_final: 0.8785 (t60) REVERT: M 107 ILE cc_start: 0.8408 (mt) cc_final: 0.8098 (tp) REVERT: M 252 MET cc_start: 0.6114 (OUTLIER) cc_final: 0.5414 (ttt) REVERT: N 240 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8119 (mmm) REVERT: N 271 MET cc_start: 0.8534 (tpp) cc_final: 0.8192 (tpp) REVERT: N 291 MET cc_start: 0.8504 (mmp) cc_final: 0.8276 (mmp) REVERT: N 406 TYR cc_start: 0.7589 (m-80) cc_final: 0.7367 (m-10) REVERT: K 56 MET cc_start: 0.9147 (ppp) cc_final: 0.8479 (mmt) REVERT: K 72 PHE cc_start: 0.7248 (m-80) cc_final: 0.6918 (m-80) REVERT: K 156 LYS cc_start: 0.7591 (mttm) cc_final: 0.7271 (mmmt) REVERT: K 194 LYS cc_start: 0.9241 (tppt) cc_final: 0.8778 (tppt) REVERT: K 285 MET cc_start: 0.7676 (mmm) cc_final: 0.7237 (mmm) REVERT: K 399 GLN cc_start: 0.7166 (OUTLIER) cc_final: 0.6541 (mp10) REVERT: L 26 MET cc_start: 0.7442 (mmm) cc_final: 0.7105 (mpp) REVERT: L 130 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7972 (m-10) REVERT: L 240 MET cc_start: 0.8489 (mtp) cc_final: 0.8113 (mtm) REVERT: R 303 TRP cc_start: 0.5144 (m100) cc_final: 0.4621 (t-100) REVERT: S 74 MET cc_start: 0.8016 (tpp) cc_final: 0.7776 (tpp) REVERT: S 288 CYS cc_start: 0.9394 (m) cc_final: 0.8877 (m) REVERT: P 148 MET cc_start: 0.6939 (tpt) cc_final: 0.6469 (tpt) REVERT: P 252 MET cc_start: 0.8303 (pmm) cc_final: 0.7824 (pmm) REVERT: P 399 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7421 (mp10) REVERT: Q 74 MET cc_start: 0.7945 (mpp) cc_final: 0.7744 (mpp) REVERT: Q 128 LYS cc_start: 0.9465 (ttpp) cc_final: 0.9199 (pptt) REVERT: Y 252 MET cc_start: 0.5791 (OUTLIER) cc_final: 0.5331 (ttt) REVERT: Z 26 MET cc_start: 0.8378 (ptm) cc_final: 0.7202 (mtp) REVERT: Z 291 MET cc_start: 0.8498 (mmp) cc_final: 0.8271 (mmp) REVERT: V 252 MET cc_start: 0.7907 (pmm) cc_final: 0.6867 (pmm) REVERT: V 285 MET cc_start: 0.7615 (mmm) cc_final: 0.6946 (mmm) REVERT: W 50 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8298 (tp) REVERT: W 240 MET cc_start: 0.8509 (mtp) cc_final: 0.8245 (mtm) REVERT: W 491 TRP cc_start: 0.9103 (OUTLIER) cc_final: 0.8778 (t60) REVERT: 4 252 MET cc_start: 0.5914 (tpp) cc_final: 0.5074 (ttt) REVERT: 5 88 SER cc_start: 0.9037 (OUTLIER) cc_final: 0.8827 (t) REVERT: 5 240 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8127 (mmm) REVERT: 5 271 MET cc_start: 0.8542 (tpp) cc_final: 0.8128 (tpp) REVERT: 5 288 CYS cc_start: 0.9210 (m) cc_final: 0.8799 (m) REVERT: 5 406 TYR cc_start: 0.7690 (m-80) cc_final: 0.7440 (m-10) REVERT: 2 72 PHE cc_start: 0.6862 (m-80) cc_final: 0.6617 (m-80) REVERT: 2 285 MET cc_start: 0.7595 (mmm) cc_final: 0.7093 (mmm) REVERT: 3 240 MET cc_start: 0.8468 (mtp) cc_final: 0.8100 (mtm) REVERT: 3 491 TRP cc_start: 0.9212 (OUTLIER) cc_final: 0.8151 (t60) outliers start: 165 outliers final: 141 residues processed: 647 average time/residue: 0.6205 time to fit residues: 715.2179 Evaluate side-chains 672 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 515 time to evaluate : 6.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 199 TRP Chi-restraints excluded: chain X residue 88 SER Chi-restraints excluded: chain X residue 179 LEU Chi-restraints excluded: chain X residue 307 LEU Chi-restraints excluded: chain X residue 317 TRP Chi-restraints excluded: chain X residue 364 VAL Chi-restraints excluded: chain X residue 374 LEU Chi-restraints excluded: chain X residue 378 CYS Chi-restraints excluded: chain X residue 421 LEU Chi-restraints excluded: chain X residue 483 MET Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 399 GLN Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 430 TYR Chi-restraints excluded: chain D residue 464 THR Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain H residue 199 TRP Chi-restraints excluded: chain H residue 204 MET Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 208 LEU Chi-restraints excluded: chain I residue 293 HIS Chi-restraints excluded: chain I residue 307 LEU Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 345 VAL Chi-restraints excluded: chain G residue 362 LEU Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 430 TYR Chi-restraints excluded: chain G residue 491 TRP Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain M residue 162 ILE Chi-restraints excluded: chain M residue 252 MET Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 88 SER Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain N residue 208 LEU Chi-restraints excluded: chain N residue 240 MET Chi-restraints excluded: chain N residue 307 LEU Chi-restraints excluded: chain N residue 374 LEU Chi-restraints excluded: chain N residue 378 CYS Chi-restraints excluded: chain N residue 483 MET Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 152 GLN Chi-restraints excluded: chain K residue 169 MET Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain K residue 399 GLN Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 130 PHE Chi-restraints excluded: chain L residue 133 ILE Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 208 LEU Chi-restraints excluded: chain L residue 229 VAL Chi-restraints excluded: chain L residue 299 SER Chi-restraints excluded: chain L residue 362 LEU Chi-restraints excluded: chain L residue 430 TYR Chi-restraints excluded: chain L residue 491 TRP Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain R residue 199 TRP Chi-restraints excluded: chain S residue 39 HIS Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 148 VAL Chi-restraints excluded: chain S residue 179 LEU Chi-restraints excluded: chain S residue 307 LEU Chi-restraints excluded: chain S residue 364 VAL Chi-restraints excluded: chain S residue 374 LEU Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain S residue 421 LEU Chi-restraints excluded: chain S residue 483 MET Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 169 MET Chi-restraints excluded: chain P residue 265 VAL Chi-restraints excluded: chain P residue 399 GLN Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain Q residue 229 VAL Chi-restraints excluded: chain Q residue 362 LEU Chi-restraints excluded: chain Q residue 401 LEU Chi-restraints excluded: chain Q residue 430 TYR Chi-restraints excluded: chain Q residue 474 VAL Chi-restraints excluded: chain Q residue 491 TRP Chi-restraints excluded: chain O residue 52 GLN Chi-restraints excluded: chain O residue 56 VAL Chi-restraints excluded: chain Y residue 107 ILE Chi-restraints excluded: chain Y residue 162 ILE Chi-restraints excluded: chain Y residue 199 TRP Chi-restraints excluded: chain Y residue 204 MET Chi-restraints excluded: chain Y residue 252 MET Chi-restraints excluded: chain Z residue 88 SER Chi-restraints excluded: chain Z residue 114 VAL Chi-restraints excluded: chain Z residue 126 LEU Chi-restraints excluded: chain Z residue 208 LEU Chi-restraints excluded: chain Z residue 252 VAL Chi-restraints excluded: chain Z residue 307 LEU Chi-restraints excluded: chain Z residue 364 VAL Chi-restraints excluded: chain Z residue 378 CYS Chi-restraints excluded: chain V residue 169 MET Chi-restraints excluded: chain V residue 265 VAL Chi-restraints excluded: chain W residue 50 LEU Chi-restraints excluded: chain W residue 193 THR Chi-restraints excluded: chain W residue 208 LEU Chi-restraints excluded: chain W residue 229 VAL Chi-restraints excluded: chain W residue 362 LEU Chi-restraints excluded: chain W residue 369 LEU Chi-restraints excluded: chain W residue 430 TYR Chi-restraints excluded: chain W residue 491 TRP Chi-restraints excluded: chain T residue 45 GLU Chi-restraints excluded: chain T residue 52 GLN Chi-restraints excluded: chain 4 residue 199 TRP Chi-restraints excluded: chain 5 residue 26 MET Chi-restraints excluded: chain 5 residue 88 SER Chi-restraints excluded: chain 5 residue 114 VAL Chi-restraints excluded: chain 5 residue 240 MET Chi-restraints excluded: chain 5 residue 257 VAL Chi-restraints excluded: chain 5 residue 374 LEU Chi-restraints excluded: chain 5 residue 378 CYS Chi-restraints excluded: chain 5 residue 483 MET Chi-restraints excluded: chain 2 residue 45 LEU Chi-restraints excluded: chain 2 residue 169 MET Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 3 residue 133 ILE Chi-restraints excluded: chain 3 residue 193 THR Chi-restraints excluded: chain 3 residue 208 LEU Chi-restraints excluded: chain 3 residue 229 VAL Chi-restraints excluded: chain 3 residue 299 SER Chi-restraints excluded: chain 3 residue 362 LEU Chi-restraints excluded: chain 3 residue 430 TYR Chi-restraints excluded: chain 3 residue 482 LEU Chi-restraints excluded: chain 3 residue 491 TRP Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 52 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 930 random chunks: chunk 586 optimal weight: 0.4980 chunk 785 optimal weight: 8.9990 chunk 226 optimal weight: 3.9990 chunk 680 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 205 optimal weight: 0.2980 chunk 738 optimal weight: 5.9990 chunk 309 optimal weight: 8.9990 chunk 758 optimal weight: 0.8980 chunk 93 optimal weight: 0.1980 chunk 136 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 GLN ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 140 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.087134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.064358 restraints weight = 354145.804| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 4.16 r_work: 0.3210 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 73722 Z= 0.168 Angle : 0.650 16.236 100812 Z= 0.313 Chirality : 0.043 0.430 12048 Planarity : 0.004 0.056 12642 Dihedral : 4.265 50.214 10227 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.84 % Allowed : 16.34 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.09), residues: 9306 helix: 1.93 (0.07), residues: 5148 sheet: -0.66 (0.17), residues: 858 loop : -0.87 (0.11), residues: 3300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 199 HIS 0.005 0.001 HIS X 117 PHE 0.015 0.001 PHE I 396 TYR 0.010 0.001 TYR Z 292 ARG 0.007 0.000 ARG S 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15769.23 seconds wall clock time: 272 minutes 55.93 seconds (16375.93 seconds total)