Starting phenix.real_space_refine on Wed Aug 27 02:15:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c5x_45234/08_2025/9c5x_45234.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c5x_45234/08_2025/9c5x_45234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c5x_45234/08_2025/9c5x_45234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c5x_45234/08_2025/9c5x_45234.map" model { file = "/net/cci-nas-00/data/ceres_data/9c5x_45234/08_2025/9c5x_45234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c5x_45234/08_2025/9c5x_45234.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.068 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 132 5.16 5 C 29460 2.51 5 N 7644 2.21 5 O 8754 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 45990 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1423 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 165} Chain: "B" Number of atoms: 1423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1423 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 165} Chain: "C" Number of atoms: 1423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1423 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 165} Chain: "D" Number of atoms: 1423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1423 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 165} Chain: "E" Number of atoms: 1423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1423 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 165} Chain: "F" Number of atoms: 1423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1423 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 165} Chain: "G" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1506 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain: "H" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1506 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain: "I" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1506 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain: "J" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1506 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain: "K" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1506 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain: "L" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1506 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain: "M" Number of atoms: 4736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4736 Classifications: {'peptide': 585} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 561} Chain: "N" Number of atoms: 4736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4736 Classifications: {'peptide': 585} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 561} Chain: "O" Number of atoms: 4736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4736 Classifications: {'peptide': 585} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 561} Chain: "P" Number of atoms: 4736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4736 Classifications: {'peptide': 585} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 561} Chain: "Q" Number of atoms: 4736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4736 Classifications: {'peptide': 585} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 561} Chain: "R" Number of atoms: 4736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4736 Classifications: {'peptide': 585} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 561} Time building chain proxies: 11.46, per 1000 atoms: 0.25 Number of scatterers: 45990 At special positions: 0 Unit cell: (143.88, 143.88, 208.19, 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 132 16.00 O 8754 8.00 N 7644 7.00 C 29460 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: 4.55 Conformation dependent library (CDL) restraints added in 2.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10812 Finding SS restraints... Secondary structure from input PDB file: 228 helices and 47 sheets defined 38.3% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 267 through 272 Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 327 through 341 removed outlier: 3.712A pdb=" N LEU A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER A 332 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU A 333 " --> pdb=" O ASN A 329 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A 337 " --> pdb=" O GLU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 422 through 430 removed outlier: 3.641A pdb=" N LEU A 426 " --> pdb=" O ASN A 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 307 removed outlier: 5.358A pdb=" N ILE B 299 " --> pdb=" O ASP B 295 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LEU B 300 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 341 removed outlier: 3.754A pdb=" N TYR B 334 " --> pdb=" O ASN B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 360 Processing helix chain 'B' and resid 382 through 392 Processing helix chain 'B' and resid 422 through 430 Processing helix chain 'C' and resid 297 through 310 removed outlier: 4.468A pdb=" N LYS C 308 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 340 removed outlier: 3.706A pdb=" N TYR C 334 " --> pdb=" O ASN C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 360 Processing helix chain 'C' and resid 382 through 392 Processing helix chain 'C' and resid 422 through 430 removed outlier: 3.591A pdb=" N LEU C 426 " --> pdb=" O ASN C 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 272 Processing helix chain 'D' and resid 273 through 277 removed outlier: 3.682A pdb=" N ASN D 276 " --> pdb=" O PRO D 273 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE D 277 " --> pdb=" O SER D 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 273 through 277' Processing helix chain 'D' and resid 293 through 310 removed outlier: 6.014A pdb=" N ILE D 299 " --> pdb=" O ASP D 295 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LEU D 300 " --> pdb=" O ASP D 296 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LYS D 308 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 329 No H-bonds generated for 'chain 'D' and resid 327 through 329' Processing helix chain 'D' and resid 330 through 341 removed outlier: 3.605A pdb=" N TYR D 334 " --> pdb=" O ASN D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 361 Processing helix chain 'D' and resid 382 through 392 Processing helix chain 'D' and resid 422 through 430 Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 288 through 291 removed outlier: 4.031A pdb=" N ILE E 291 " --> pdb=" O PRO E 288 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 288 through 291' Processing helix chain 'E' and resid 297 through 306 Processing helix chain 'E' and resid 328 through 341 removed outlier: 4.143A pdb=" N SER E 332 " --> pdb=" O VAL E 328 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU E 333 " --> pdb=" O ASN E 329 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG E 341 " --> pdb=" O ARG E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'E' and resid 367 through 370 Processing helix chain 'E' and resid 382 through 392 Processing helix chain 'E' and resid 422 through 430 removed outlier: 3.589A pdb=" N LEU E 426 " --> pdb=" O ASN E 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 272 Processing helix chain 'F' and resid 288 through 291 removed outlier: 3.579A pdb=" N ILE F 291 " --> pdb=" O PRO F 288 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 288 through 291' Processing helix chain 'F' and resid 297 through 310 removed outlier: 4.084A pdb=" N LYS F 308 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 330 Processing helix chain 'F' and resid 331 through 341 Processing helix chain 'F' and resid 382 through 392 removed outlier: 3.736A pdb=" N TYR F 391 " --> pdb=" O LYS F 387 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS F 392 " --> pdb=" O CYS F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 430 Processing helix chain 'G' and resid 258 through 276 Proline residue: G 273 - end of helix removed outlier: 3.522A pdb=" N ASN G 276 " --> pdb=" O VAL G 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 310 Processing helix chain 'G' and resid 328 through 340 removed outlier: 4.040A pdb=" N GLU G 333 " --> pdb=" O ASN G 329 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR G 334 " --> pdb=" O ASN G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 355 through 360 Processing helix chain 'G' and resid 386 through 392 removed outlier: 3.596A pdb=" N ASN G 390 " --> pdb=" O ILE G 386 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS G 392 " --> pdb=" O CYS G 388 " (cutoff:3.500A) Processing helix chain 'G' and resid 422 through 430 Processing helix chain 'H' and resid 259 through 276 removed outlier: 3.856A pdb=" N VAL H 266 " --> pdb=" O GLN H 262 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG H 267 " --> pdb=" O LEU H 263 " (cutoff:3.500A) Proline residue: H 273 - end of helix removed outlier: 3.614A pdb=" N ASN H 276 " --> pdb=" O VAL H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 287 through 291 removed outlier: 3.695A pdb=" N ILE H 291 " --> pdb=" O PRO H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 310 removed outlier: 6.356A pdb=" N ILE H 299 " --> pdb=" O ASP H 295 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LEU H 300 " --> pdb=" O ASP H 296 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS H 308 " --> pdb=" O ASP H 304 " (cutoff:3.500A) Processing helix chain 'H' and resid 327 through 340 removed outlier: 3.537A pdb=" N SER H 332 " --> pdb=" O VAL H 328 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU H 333 " --> pdb=" O ASN H 329 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR H 334 " --> pdb=" O ASN H 330 " (cutoff:3.500A) Processing helix chain 'H' and resid 355 through 360 Processing helix chain 'H' and resid 422 through 430 Processing helix chain 'I' and resid 258 through 269 Processing helix chain 'I' and resid 271 through 276 Processing helix chain 'I' and resid 288 through 291 Processing helix chain 'I' and resid 293 through 310 removed outlier: 5.390A pdb=" N ILE I 299 " --> pdb=" O ASP I 295 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LEU I 300 " --> pdb=" O ASP I 296 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS I 308 " --> pdb=" O ASP I 304 " (cutoff:3.500A) Processing helix chain 'I' and resid 327 through 341 removed outlier: 3.543A pdb=" N SER I 332 " --> pdb=" O VAL I 328 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU I 333 " --> pdb=" O ASN I 329 " (cutoff:3.500A) Processing helix chain 'I' and resid 382 through 393 removed outlier: 3.552A pdb=" N LYS I 387 " --> pdb=" O ASP I 383 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS I 388 " --> pdb=" O GLU I 384 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS I 392 " --> pdb=" O CYS I 388 " (cutoff:3.500A) Processing helix chain 'I' and resid 422 through 430 Processing helix chain 'J' and resid 258 through 276 Proline residue: J 273 - end of helix Processing helix chain 'J' and resid 293 through 310 removed outlier: 5.562A pdb=" N ILE J 299 " --> pdb=" O ASP J 295 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N LEU J 300 " --> pdb=" O ASP J 296 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS J 308 " --> pdb=" O ASP J 304 " (cutoff:3.500A) Processing helix chain 'J' and resid 327 through 341 removed outlier: 3.614A pdb=" N ARG J 337 " --> pdb=" O GLU J 333 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER J 340 " --> pdb=" O LYS J 336 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG J 341 " --> pdb=" O ARG J 337 " (cutoff:3.500A) Processing helix chain 'J' and resid 355 through 360 removed outlier: 3.501A pdb=" N PHE J 359 " --> pdb=" O TYR J 355 " (cutoff:3.500A) Processing helix chain 'J' and resid 382 through 392 removed outlier: 3.687A pdb=" N LYS J 392 " --> pdb=" O CYS J 388 " (cutoff:3.500A) Processing helix chain 'J' and resid 422 through 430 Processing helix chain 'K' and resid 260 through 276 Proline residue: K 273 - end of helix Processing helix chain 'K' and resid 293 through 310 removed outlier: 5.199A pdb=" N ILE K 299 " --> pdb=" O ASP K 295 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU K 300 " --> pdb=" O ASP K 296 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS K 308 " --> pdb=" O ASP K 304 " (cutoff:3.500A) Processing helix chain 'K' and resid 327 through 341 removed outlier: 3.876A pdb=" N LEU K 331 " --> pdb=" O ASP K 327 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER K 332 " --> pdb=" O VAL K 328 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU K 333 " --> pdb=" O ASN K 329 " (cutoff:3.500A) Processing helix chain 'K' and resid 355 through 360 removed outlier: 3.564A pdb=" N PHE K 359 " --> pdb=" O TYR K 355 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN K 360 " --> pdb=" O PHE K 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 355 through 360' Processing helix chain 'K' and resid 382 through 392 removed outlier: 3.924A pdb=" N CYS K 388 " --> pdb=" O GLU K 384 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS K 392 " --> pdb=" O CYS K 388 " (cutoff:3.500A) Processing helix chain 'K' and resid 422 through 430 Processing helix chain 'L' and resid 258 through 270 removed outlier: 3.705A pdb=" N ASN L 269 " --> pdb=" O LYS L 265 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN L 270 " --> pdb=" O VAL L 266 " (cutoff:3.500A) Processing helix chain 'L' and resid 273 through 277 removed outlier: 3.771A pdb=" N ASN L 276 " --> pdb=" O PRO L 273 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE L 277 " --> pdb=" O SER L 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 273 through 277' Processing helix chain 'L' and resid 288 through 291 Processing helix chain 'L' and resid 293 through 310 removed outlier: 5.187A pdb=" N ILE L 299 " --> pdb=" O ASP L 295 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LEU L 300 " --> pdb=" O ASP L 296 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS L 308 " --> pdb=" O ASP L 304 " (cutoff:3.500A) Processing helix chain 'L' and resid 327 through 341 removed outlier: 3.793A pdb=" N GLU L 333 " --> pdb=" O ASN L 329 " (cutoff:3.500A) Processing helix chain 'L' and resid 355 through 361 Processing helix chain 'L' and resid 367 through 370 Processing helix chain 'L' and resid 382 through 392 removed outlier: 3.652A pdb=" N LYS L 392 " --> pdb=" O CYS L 388 " (cutoff:3.500A) Processing helix chain 'L' and resid 422 through 430 Processing helix chain 'M' and resid 20 through 27 removed outlier: 3.631A pdb=" N PHE M 24 " --> pdb=" O THR M 20 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 106 removed outlier: 4.007A pdb=" N LYS M 104 " --> pdb=" O ASP M 100 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE M 105 " --> pdb=" O ILE M 101 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE M 106 " --> pdb=" O LEU M 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 135 removed outlier: 3.677A pdb=" N PHE M 135 " --> pdb=" O GLY M 131 " (cutoff:3.500A) Processing helix chain 'M' and resid 148 through 162 Processing helix chain 'M' and resid 189 through 193 removed outlier: 3.665A pdb=" N GLU M 193 " --> pdb=" O SER M 190 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 199 Processing helix chain 'M' and resid 213 through 217 Processing helix chain 'M' and resid 218 through 226 removed outlier: 3.625A pdb=" N THR M 224 " --> pdb=" O GLU M 220 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU M 225 " --> pdb=" O GLU M 221 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE M 226 " --> pdb=" O LEU M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 233 through 253 Processing helix chain 'M' and resid 268 through 280 removed outlier: 3.784A pdb=" N VAL M 272 " --> pdb=" O ASN M 268 " (cutoff:3.500A) Processing helix chain 'M' and resid 304 through 309 removed outlier: 3.634A pdb=" N ILE M 307 " --> pdb=" O ASN M 304 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 347 Processing helix chain 'M' and resid 348 through 355 removed outlier: 3.537A pdb=" N LEU M 351 " --> pdb=" O ASP M 348 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU M 352 " --> pdb=" O LYS M 349 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N PHE M 353 " --> pdb=" O ARG M 350 " (cutoff:3.500A) Processing helix chain 'M' and resid 367 through 369 No H-bonds generated for 'chain 'M' and resid 367 through 369' Processing helix chain 'M' and resid 370 through 379 removed outlier: 3.581A pdb=" N GLN M 377 " --> pdb=" O ASP M 373 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE M 378 " --> pdb=" O ILE M 374 " (cutoff:3.500A) Processing helix chain 'M' and resid 396 through 398 No H-bonds generated for 'chain 'M' and resid 396 through 398' Processing helix chain 'M' and resid 399 through 424 Processing helix chain 'M' and resid 439 through 444 removed outlier: 4.183A pdb=" N TYR M 443 " --> pdb=" O GLU M 439 " (cutoff:3.500A) Processing helix chain 'M' and resid 452 through 466 removed outlier: 3.872A pdb=" N GLU M 460 " --> pdb=" O LYS M 456 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE M 462 " --> pdb=" O SER M 458 " (cutoff:3.500A) Processing helix chain 'M' and resid 479 through 483 Processing helix chain 'M' and resid 484 through 489 Processing helix chain 'M' and resid 501 through 512 Processing helix chain 'M' and resid 513 through 517 Processing helix chain 'M' and resid 518 through 526 removed outlier: 3.898A pdb=" N GLU M 521 " --> pdb=" O SER M 518 " (cutoff:3.500A) Proline residue: M 524 - end of helix Processing helix chain 'M' and resid 559 through 565 Processing helix chain 'M' and resid 574 through 581 removed outlier: 4.173A pdb=" N ARG M 581 " --> pdb=" O ILE M 577 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 27 Processing helix chain 'N' and resid 98 through 103 Processing helix chain 'N' and resid 131 through 135 Processing helix chain 'N' and resid 148 through 162 Processing helix chain 'N' and resid 189 through 193 Processing helix chain 'N' and resid 195 through 199 removed outlier: 3.581A pdb=" N ASP N 199 " --> pdb=" O LYS N 196 " (cutoff:3.500A) Processing helix chain 'N' and resid 213 through 217 Processing helix chain 'N' and resid 218 through 226 Processing helix chain 'N' and resid 233 through 253 Processing helix chain 'N' and resid 268 through 281 removed outlier: 3.630A pdb=" N VAL N 272 " --> pdb=" O ASN N 268 " (cutoff:3.500A) Processing helix chain 'N' and resid 335 through 348 Processing helix chain 'N' and resid 351 through 355 Processing helix chain 'N' and resid 367 through 369 No H-bonds generated for 'chain 'N' and resid 367 through 369' Processing helix chain 'N' and resid 370 through 378 Processing helix chain 'N' and resid 399 through 420 Processing helix chain 'N' and resid 439 through 443 Processing helix chain 'N' and resid 452 through 466 Processing helix chain 'N' and resid 479 through 483 Processing helix chain 'N' and resid 484 through 489 Processing helix chain 'N' and resid 501 through 512 Processing helix chain 'N' and resid 513 through 517 Processing helix chain 'N' and resid 518 through 526 removed outlier: 3.677A pdb=" N GLU N 521 " --> pdb=" O SER N 518 " (cutoff:3.500A) Proline residue: N 524 - end of helix Processing helix chain 'N' and resid 559 through 565 Processing helix chain 'N' and resid 572 through 583 removed outlier: 3.964A pdb=" N GLU N 583 " --> pdb=" O ARG N 579 " (cutoff:3.500A) Processing helix chain 'O' and resid 20 through 27 Processing helix chain 'O' and resid 98 through 106 Processing helix chain 'O' and resid 131 through 135 Processing helix chain 'O' and resid 148 through 162 removed outlier: 3.516A pdb=" N ALA O 152 " --> pdb=" O GLY O 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 187 through 192 removed outlier: 3.789A pdb=" N SER O 190 " --> pdb=" O GLU O 187 " (cutoff:3.500A) Processing helix chain 'O' and resid 195 through 199 Processing helix chain 'O' and resid 206 through 210 Processing helix chain 'O' and resid 213 through 217 removed outlier: 3.678A pdb=" N LEU O 216 " --> pdb=" O PRO O 213 " (cutoff:3.500A) Processing helix chain 'O' and resid 218 through 227 Processing helix chain 'O' and resid 233 through 253 removed outlier: 3.837A pdb=" N GLN O 237 " --> pdb=" O ASN O 233 " (cutoff:3.500A) Processing helix chain 'O' and resid 268 through 282 removed outlier: 3.761A pdb=" N VAL O 272 " --> pdb=" O ASN O 268 " (cutoff:3.500A) Processing helix chain 'O' and resid 304 through 310 removed outlier: 3.515A pdb=" N ILE O 307 " --> pdb=" O ASN O 304 " (cutoff:3.500A) Processing helix chain 'O' and resid 335 through 347 removed outlier: 3.548A pdb=" N SER O 340 " --> pdb=" O ASN O 336 " (cutoff:3.500A) Processing helix chain 'O' and resid 348 through 355 removed outlier: 3.891A pdb=" N GLU O 352 " --> pdb=" O LYS O 349 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N PHE O 353 " --> pdb=" O ARG O 350 " (cutoff:3.500A) Processing helix chain 'O' and resid 367 through 370 Processing helix chain 'O' and resid 371 through 379 removed outlier: 3.534A pdb=" N LEU O 375 " --> pdb=" O PHE O 371 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN O 377 " --> pdb=" O ASP O 373 " (cutoff:3.500A) Processing helix chain 'O' and resid 396 through 398 No H-bonds generated for 'chain 'O' and resid 396 through 398' Processing helix chain 'O' and resid 399 through 424 removed outlier: 3.925A pdb=" N GLN O 424 " --> pdb=" O LYS O 420 " (cutoff:3.500A) Processing helix chain 'O' and resid 440 through 443 Processing helix chain 'O' and resid 452 through 466 removed outlier: 3.687A pdb=" N ILE O 462 " --> pdb=" O SER O 458 " (cutoff:3.500A) Processing helix chain 'O' and resid 484 through 489 Processing helix chain 'O' and resid 501 through 512 removed outlier: 3.738A pdb=" N TYR O 507 " --> pdb=" O ASN O 503 " (cutoff:3.500A) Processing helix chain 'O' and resid 513 through 517 Processing helix chain 'O' and resid 518 through 523 removed outlier: 4.194A pdb=" N GLU O 521 " --> pdb=" O SER O 518 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE O 522 " --> pdb=" O ILE O 519 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU O 523 " --> pdb=" O SER O 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 518 through 523' Processing helix chain 'O' and resid 559 through 565 Processing helix chain 'O' and resid 572 through 582 Processing helix chain 'P' and resid 20 through 27 Processing helix chain 'P' and resid 98 through 103 removed outlier: 3.833A pdb=" N LEU P 102 " --> pdb=" O GLU P 98 " (cutoff:3.500A) Processing helix chain 'P' and resid 131 through 136 removed outlier: 3.533A pdb=" N SER P 136 " --> pdb=" O ASP P 132 " (cutoff:3.500A) Processing helix chain 'P' and resid 148 through 162 Processing helix chain 'P' and resid 195 through 199 Processing helix chain 'P' and resid 213 through 217 Processing helix chain 'P' and resid 218 through 227 Processing helix chain 'P' and resid 238 through 253 Processing helix chain 'P' and resid 268 through 278 removed outlier: 3.508A pdb=" N VAL P 272 " --> pdb=" O ASN P 268 " (cutoff:3.500A) Processing helix chain 'P' and resid 305 through 309 removed outlier: 3.523A pdb=" N PHE P 309 " --> pdb=" O GLN P 306 " (cutoff:3.500A) Processing helix chain 'P' and resid 336 through 347 Processing helix chain 'P' and resid 349 through 353 removed outlier: 3.701A pdb=" N GLU P 352 " --> pdb=" O LYS P 349 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE P 353 " --> pdb=" O ARG P 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 349 through 353' Processing helix chain 'P' and resid 367 through 371 Processing helix chain 'P' and resid 372 through 379 removed outlier: 3.938A pdb=" N PHE P 378 " --> pdb=" O ILE P 374 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET P 379 " --> pdb=" O LEU P 375 " (cutoff:3.500A) Processing helix chain 'P' and resid 396 through 398 No H-bonds generated for 'chain 'P' and resid 396 through 398' Processing helix chain 'P' and resid 399 through 424 removed outlier: 3.873A pdb=" N ARG P 409 " --> pdb=" O SER P 405 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN P 424 " --> pdb=" O LYS P 420 " (cutoff:3.500A) Processing helix chain 'P' and resid 440 through 443 Processing helix chain 'P' and resid 449 through 451 No H-bonds generated for 'chain 'P' and resid 449 through 451' Processing helix chain 'P' and resid 452 through 470 removed outlier: 3.507A pdb=" N LYS P 456 " --> pdb=" O PHE P 452 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG P 461 " --> pdb=" O LYS P 457 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE P 462 " --> pdb=" O SER P 458 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ARG P 467 " --> pdb=" O ALA P 463 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LYS P 468 " --> pdb=" O LYS P 464 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR P 469 " --> pdb=" O GLU P 465 " (cutoff:3.500A) Processing helix chain 'P' and resid 479 through 483 Processing helix chain 'P' and resid 484 through 489 Processing helix chain 'P' and resid 502 through 512 Processing helix chain 'P' and resid 518 through 526 removed outlier: 4.059A pdb=" N ILE P 522 " --> pdb=" O SER P 518 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU P 523 " --> pdb=" O ILE P 519 " (cutoff:3.500A) Proline residue: P 524 - end of helix No H-bonds generated for 'chain 'P' and resid 518 through 526' Processing helix chain 'P' and resid 559 through 565 Processing helix chain 'P' and resid 572 through 583 Processing helix chain 'Q' and resid 20 through 27 Processing helix chain 'Q' and resid 98 through 105 removed outlier: 3.546A pdb=" N LYS Q 104 " --> pdb=" O ASP Q 100 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE Q 105 " --> pdb=" O ILE Q 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 109 through 111 No H-bonds generated for 'chain 'Q' and resid 109 through 111' Processing helix chain 'Q' and resid 131 through 135 Processing helix chain 'Q' and resid 148 through 162 removed outlier: 3.851A pdb=" N ALA Q 152 " --> pdb=" O GLY Q 148 " (cutoff:3.500A) Processing helix chain 'Q' and resid 195 through 199 Processing helix chain 'Q' and resid 213 through 217 Processing helix chain 'Q' and resid 218 through 226 Processing helix chain 'Q' and resid 236 through 253 removed outlier: 3.595A pdb=" N GLN Q 240 " --> pdb=" O ASN Q 236 " (cutoff:3.500A) Processing helix chain 'Q' and resid 268 through 281 removed outlier: 3.505A pdb=" N VAL Q 272 " --> pdb=" O ASN Q 268 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU Q 281 " --> pdb=" O TYR Q 277 " (cutoff:3.500A) Processing helix chain 'Q' and resid 305 through 309 removed outlier: 3.516A pdb=" N PHE Q 309 " --> pdb=" O GLN Q 306 " (cutoff:3.500A) Processing helix chain 'Q' and resid 335 through 346 removed outlier: 3.617A pdb=" N LEU Q 339 " --> pdb=" O PHE Q 335 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER Q 340 " --> pdb=" O ASN Q 336 " (cutoff:3.500A) Processing helix chain 'Q' and resid 367 through 369 No H-bonds generated for 'chain 'Q' and resid 367 through 369' Processing helix chain 'Q' and resid 370 through 380 removed outlier: 3.983A pdb=" N ILE Q 374 " --> pdb=" O HIS Q 370 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE Q 378 " --> pdb=" O ILE Q 374 " (cutoff:3.500A) Processing helix chain 'Q' and resid 396 through 398 No H-bonds generated for 'chain 'Q' and resid 396 through 398' Processing helix chain 'Q' and resid 399 through 425 removed outlier: 3.779A pdb=" N GLN Q 424 " --> pdb=" O LYS Q 420 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS Q 425 " --> pdb=" O LEU Q 421 " (cutoff:3.500A) Processing helix chain 'Q' and resid 440 through 443 Processing helix chain 'Q' and resid 453 through 466 removed outlier: 3.604A pdb=" N ILE Q 462 " --> pdb=" O SER Q 458 " (cutoff:3.500A) Processing helix chain 'Q' and resid 484 through 489 Processing helix chain 'Q' and resid 501 through 510 Processing helix chain 'Q' and resid 516 through 522 removed outlier: 3.578A pdb=" N ILE Q 522 " --> pdb=" O SER Q 518 " (cutoff:3.500A) Processing helix chain 'Q' and resid 559 through 565 Processing helix chain 'Q' and resid 572 through 582 Processing helix chain 'R' and resid 20 through 27 Processing helix chain 'R' and resid 98 through 107 Processing helix chain 'R' and resid 131 through 135 Processing helix chain 'R' and resid 148 through 162 Processing helix chain 'R' and resid 189 through 193 Processing helix chain 'R' and resid 195 through 199 Processing helix chain 'R' and resid 213 through 217 removed outlier: 3.596A pdb=" N LEU R 216 " --> pdb=" O PRO R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 224 Processing helix chain 'R' and resid 237 through 253 Processing helix chain 'R' and resid 268 through 278 Processing helix chain 'R' and resid 306 through 311 removed outlier: 4.294A pdb=" N ASN R 310 " --> pdb=" O GLN R 306 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU R 311 " --> pdb=" O ILE R 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 306 through 311' Processing helix chain 'R' and resid 335 through 347 removed outlier: 3.780A pdb=" N SER R 340 " --> pdb=" O ASN R 336 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG R 341 " --> pdb=" O ARG R 337 " (cutoff:3.500A) Processing helix chain 'R' and resid 351 through 355 removed outlier: 3.543A pdb=" N LEU R 355 " --> pdb=" O GLU R 352 " (cutoff:3.500A) Processing helix chain 'R' and resid 360 through 365 Processing helix chain 'R' and resid 367 through 369 No H-bonds generated for 'chain 'R' and resid 367 through 369' Processing helix chain 'R' and resid 370 through 379 removed outlier: 3.668A pdb=" N ILE R 374 " --> pdb=" O HIS R 370 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE R 378 " --> pdb=" O ILE R 374 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET R 379 " --> pdb=" O LEU R 375 " (cutoff:3.500A) Processing helix chain 'R' and resid 396 through 398 No H-bonds generated for 'chain 'R' and resid 396 through 398' Processing helix chain 'R' and resid 399 through 423 Processing helix chain 'R' and resid 424 through 426 No H-bonds generated for 'chain 'R' and resid 424 through 426' Processing helix chain 'R' and resid 449 through 451 No H-bonds generated for 'chain 'R' and resid 449 through 451' Processing helix chain 'R' and resid 452 through 465 removed outlier: 3.606A pdb=" N ILE R 462 " --> pdb=" O SER R 458 " (cutoff:3.500A) Processing helix chain 'R' and resid 479 through 483 Processing helix chain 'R' and resid 484 through 489 Processing helix chain 'R' and resid 501 through 512 Processing helix chain 'R' and resid 559 through 564 Processing helix chain 'R' and resid 572 through 581 removed outlier: 3.533A pdb=" N VAL R 576 " --> pdb=" O SER R 572 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 379 through 380 removed outlier: 6.628A pdb=" N PHE A 322 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ARG A 282 " --> pdb=" O CYS A 321 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ILE A 323 " --> pdb=" O ARG A 282 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N PHE A 284 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N TYR A 283 " --> pdb=" O TYR A 398 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N VAL A 400 " --> pdb=" O TYR A 283 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU A 397 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N LEU A 418 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE A 399 " --> pdb=" O LEU A 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 365 through 366 Processing sheet with id=AA3, first strand: chain 'B' and resid 345 through 346 removed outlier: 3.563A pdb=" N ILE B 378 " --> pdb=" O ILE B 346 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TYR B 283 " --> pdb=" O TYR B 398 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N VAL B 400 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU B 397 " --> pdb=" O GLU B 416 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU B 418 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ILE B 399 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 365 through 366 Processing sheet with id=AA5, first strand: chain 'C' and resid 345 through 346 removed outlier: 5.981A pdb=" N ILE C 346 " --> pdb=" O ILE C 378 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS C 321 " --> pdb=" O ARG C 282 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU C 397 " --> pdb=" O GLU C 416 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU C 418 " --> pdb=" O LEU C 397 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ILE C 399 " --> pdb=" O LEU C 418 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 349 through 350 removed outlier: 3.688A pdb=" N THR C 353 " --> pdb=" O ILE C 350 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 365 through 366 removed outlier: 3.935A pdb=" N TRP C 371 " --> pdb=" O ILE C 366 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 377 through 380 removed outlier: 6.219A pdb=" N PHE D 322 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS D 321 " --> pdb=" O ARG D 282 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TYR D 283 " --> pdb=" O TYR D 398 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL D 400 " --> pdb=" O TYR D 283 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE D 285 " --> pdb=" O VAL D 400 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU D 418 " --> pdb=" O LEU D 397 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ILE D 399 " --> pdb=" O LEU D 418 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 349 through 350 removed outlier: 3.968A pdb=" N THR D 353 " --> pdb=" O ILE D 350 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 365 through 366 Processing sheet with id=AB2, first strand: chain 'E' and resid 345 through 346 removed outlier: 5.762A pdb=" N ILE E 346 " --> pdb=" O ILE E 378 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N CYS E 380 " --> pdb=" O ILE E 346 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TYR E 283 " --> pdb=" O TYR E 398 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N VAL E 400 " --> pdb=" O TYR E 283 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE E 285 " --> pdb=" O VAL E 400 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU E 397 " --> pdb=" O GLU E 416 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LEU E 418 " --> pdb=" O LEU E 397 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE E 399 " --> pdb=" O LEU E 418 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 349 through 350 removed outlier: 3.618A pdb=" N THR E 353 " --> pdb=" O ILE E 350 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 365 through 366 Processing sheet with id=AB5, first strand: chain 'F' and resid 377 through 380 removed outlier: 7.142A pdb=" N ARG F 282 " --> pdb=" O CYS F 321 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ILE F 323 " --> pdb=" O ARG F 282 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE F 284 " --> pdb=" O ILE F 323 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N TYR F 283 " --> pdb=" O TYR F 398 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N VAL F 400 " --> pdb=" O TYR F 283 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ILE F 285 " --> pdb=" O VAL F 400 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU F 397 " --> pdb=" O GLU F 416 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU F 418 " --> pdb=" O LEU F 397 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ILE F 399 " --> pdb=" O LEU F 418 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 349 through 350 removed outlier: 3.758A pdb=" N THR F 353 " --> pdb=" O ILE F 350 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 365 through 366 Processing sheet with id=AB8, first strand: chain 'G' and resid 321 through 324 removed outlier: 6.108A pdb=" N TYR G 283 " --> pdb=" O TYR G 398 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL G 400 " --> pdb=" O TYR G 283 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE G 285 " --> pdb=" O VAL G 400 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU G 397 " --> pdb=" O GLU G 416 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LEU G 418 " --> pdb=" O LEU G 397 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE G 399 " --> pdb=" O LEU G 418 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 365 through 366 removed outlier: 3.931A pdb=" N TRP G 371 " --> pdb=" O ILE G 366 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 321 through 324 removed outlier: 6.299A pdb=" N TYR H 283 " --> pdb=" O TYR H 398 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 345 through 346 Processing sheet with id=AC3, first strand: chain 'I' and resid 345 through 346 removed outlier: 5.762A pdb=" N ILE I 346 " --> pdb=" O ILE I 378 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ARG I 282 " --> pdb=" O CYS I 321 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ILE I 323 " --> pdb=" O ARG I 282 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N PHE I 284 " --> pdb=" O ILE I 323 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N TYR I 283 " --> pdb=" O TYR I 398 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL I 400 " --> pdb=" O TYR I 283 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE I 285 " --> pdb=" O VAL I 400 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU I 397 " --> pdb=" O GLU I 416 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU I 418 " --> pdb=" O LEU I 397 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE I 399 " --> pdb=" O LEU I 418 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 365 through 366 Processing sheet with id=AC5, first strand: chain 'J' and resid 345 through 346 removed outlier: 6.615A pdb=" N LEU J 397 " --> pdb=" O GLU J 416 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N LEU J 418 " --> pdb=" O LEU J 397 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE J 399 " --> pdb=" O LEU J 418 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 365 through 366 Processing sheet with id=AC7, first strand: chain 'K' and resid 345 through 346 removed outlier: 5.949A pdb=" N ILE K 346 " --> pdb=" O ILE K 378 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG K 282 " --> pdb=" O CYS K 321 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ILE K 323 " --> pdb=" O ARG K 282 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N PHE K 284 " --> pdb=" O ILE K 323 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N TYR K 283 " --> pdb=" O TYR K 398 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL K 400 " --> pdb=" O TYR K 283 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE K 285 " --> pdb=" O VAL K 400 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 365 through 366 Processing sheet with id=AC9, first strand: chain 'L' and resid 345 through 346 removed outlier: 7.034A pdb=" N ARG L 282 " --> pdb=" O CYS L 321 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ILE L 323 " --> pdb=" O ARG L 282 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N PHE L 284 " --> pdb=" O ILE L 323 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU L 397 " --> pdb=" O GLU L 416 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU L 418 " --> pdb=" O LEU L 397 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE L 399 " --> pdb=" O LEU L 418 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 349 through 350 removed outlier: 3.679A pdb=" N THR L 353 " --> pdb=" O ILE L 350 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 365 through 366 Processing sheet with id=AD3, first strand: chain 'M' and resid 4 through 9 removed outlier: 6.528A pdb=" N LEU M 15 " --> pdb=" O ILE M 7 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 14 through 18 current: chain 'M' and resid 47 through 59 removed outlier: 6.560A pdb=" N LEU M 48 " --> pdb=" O VAL M 72 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR M 68 " --> pdb=" O GLN M 52 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ILE M 54 " --> pdb=" O ILE M 66 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ILE M 66 " --> pdb=" O ILE M 54 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE M 56 " --> pdb=" O ILE M 64 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE M 64 " --> pdb=" O ILE M 56 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR M 58 " --> pdb=" O GLU M 62 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLU M 62 " --> pdb=" O THR M 58 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 62 through 74 current: chain 'R' and resid 14 through 18 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 14 through 18 current: chain 'R' and resid 45 through 58 removed outlier: 6.519A pdb=" N PHE R 46 " --> pdb=" O ILE R 74 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE R 74 " --> pdb=" O PHE R 46 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU R 48 " --> pdb=" O VAL R 72 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR R 68 " --> pdb=" O GLN R 52 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ILE R 54 " --> pdb=" O ILE R 66 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE R 66 " --> pdb=" O ILE R 54 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE R 56 " --> pdb=" O ILE R 64 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE R 64 " --> pdb=" O ILE R 56 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU R 79 " --> pdb=" O LYS R 76 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 126 through 129 removed outlier: 5.907A pdb=" N PHE M 127 " --> pdb=" O LEU M 116 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN M 118 " --> pdb=" O LYS M 545 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA M 140 " --> pdb=" O ILE M 495 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE M 180 " --> pdb=" O VAL M 436 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N GLU M 438 " --> pdb=" O ILE M 180 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N PHE M 182 " --> pdb=" O GLU M 438 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE M 179 " --> pdb=" O SER M 388 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ILE M 390 " --> pdb=" O ILE M 179 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE M 181 " --> pdb=" O ILE M 390 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASN M 203 " --> pdb=" O ILE M 389 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASP M 391 " --> pdb=" O ASN M 203 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU M 205 " --> pdb=" O ASP M 391 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 163 through 164 Processing sheet with id=AD6, first strand: chain 'M' and resid 283 through 285 Processing sheet with id=AD7, first strand: chain 'N' and resid 79 through 81 removed outlier: 6.486A pdb=" N ILE N 64 " --> pdb=" O ILE N 56 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE N 56 " --> pdb=" O ILE N 64 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE N 66 " --> pdb=" O ILE N 54 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ILE N 54 " --> pdb=" O ILE N 66 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR N 68 " --> pdb=" O GLN N 52 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU N 48 " --> pdb=" O VAL N 72 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ILE N 74 " --> pdb=" O PHE N 46 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE N 46 " --> pdb=" O ILE N 74 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU N 15 " --> pdb=" O ILE N 7 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N PHE N 65 " --> pdb=" O ILE N 18 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 126 through 130 removed outlier: 4.276A pdb=" N GLY N 117 " --> pdb=" O PHE N 127 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU N 129 " --> pdb=" O HIS N 115 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N HIS N 115 " --> pdb=" O LEU N 129 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN N 118 " --> pdb=" O LYS N 545 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA N 140 " --> pdb=" O ILE N 495 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 203 through 205 removed outlier: 6.919A pdb=" N ASN N 203 " --> pdb=" O ILE N 389 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ASP N 391 " --> pdb=" O ASN N 203 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU N 205 " --> pdb=" O ASP N 391 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE N 179 " --> pdb=" O SER N 388 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE N 390 " --> pdb=" O ILE N 179 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE N 181 " --> pdb=" O ILE N 390 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE N 180 " --> pdb=" O VAL N 436 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 283 through 285 Processing sheet with id=AE2, first strand: chain 'O' and resid 4 through 9 removed outlier: 6.658A pdb=" N LEU O 15 " --> pdb=" O ILE O 7 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 14 through 18 current: chain 'O' and resid 45 through 57 removed outlier: 6.564A pdb=" N PHE O 46 " --> pdb=" O ILE O 74 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE O 74 " --> pdb=" O PHE O 46 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU O 48 " --> pdb=" O VAL O 72 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR O 68 " --> pdb=" O GLN O 52 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ILE O 54 " --> pdb=" O ILE O 66 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE O 66 " --> pdb=" O ILE O 54 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE O 56 " --> pdb=" O ILE O 64 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE O 64 " --> pdb=" O ILE O 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 79 through 82 current: chain 'Q' and resid 14 through 18 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 14 through 18 current: chain 'Q' and resid 45 through 55 removed outlier: 6.499A pdb=" N THR Q 68 " --> pdb=" O GLN Q 52 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE Q 54 " --> pdb=" O ILE Q 66 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE Q 66 " --> pdb=" O ILE Q 54 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 126 through 130 removed outlier: 3.616A pdb=" N GLY O 117 " --> pdb=" O PHE O 127 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU O 129 " --> pdb=" O HIS O 115 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N HIS O 115 " --> pdb=" O LEU O 129 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN O 118 " --> pdb=" O LYS O 545 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N PHE O 433 " --> pdb=" O SER O 472 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N MET O 474 " --> pdb=" O PHE O 433 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE O 435 " --> pdb=" O MET O 474 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL O 476 " --> pdb=" O ILE O 435 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N CYS O 437 " --> pdb=" O VAL O 476 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE O 180 " --> pdb=" O VAL O 436 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N GLU O 438 " --> pdb=" O ILE O 180 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE O 182 " --> pdb=" O GLU O 438 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE O 179 " --> pdb=" O SER O 388 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE O 390 " --> pdb=" O ILE O 179 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE O 181 " --> pdb=" O ILE O 390 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'O' and resid 283 through 285 Processing sheet with id=AE5, first strand: chain 'P' and resid 4 through 9 removed outlier: 6.708A pdb=" N LEU P 15 " --> pdb=" O ILE P 7 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 14 through 18 current: chain 'P' and resid 45 through 55 removed outlier: 3.500A pdb=" N GLY P 73 " --> pdb=" O LEU P 48 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL P 50 " --> pdb=" O PRO P 71 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLN P 52 " --> pdb=" O VAL P 69 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL P 69 " --> pdb=" O GLN P 52 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE P 54 " --> pdb=" O LEU P 67 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU P 67 " --> pdb=" O ILE P 54 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU P 79 " --> pdb=" O LYS P 76 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'P' and resid 126 through 130 removed outlier: 6.168A pdb=" N LEU P 129 " --> pdb=" O HIS P 115 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N HIS P 115 " --> pdb=" O LEU P 129 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN P 118 " --> pdb=" O LYS P 545 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER P 542 " --> pdb=" O VAL P 533 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE P 180 " --> pdb=" O VAL P 436 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLU P 438 " --> pdb=" O ILE P 180 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N PHE P 182 " --> pdb=" O GLU P 438 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE P 179 " --> pdb=" O SER P 388 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ILE P 390 " --> pdb=" O ILE P 179 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE P 181 " --> pdb=" O ILE P 390 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'P' and resid 163 through 164 Processing sheet with id=AE8, first strand: chain 'Q' and resid 126 through 130 removed outlier: 7.033A pdb=" N PHE Q 127 " --> pdb=" O LEU Q 116 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE Q 114 " --> pdb=" O LEU Q 129 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA Q 140 " --> pdb=" O ILE Q 495 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE Q 433 " --> pdb=" O SER Q 472 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N MET Q 474 " --> pdb=" O PHE Q 433 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE Q 435 " --> pdb=" O MET Q 474 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL Q 476 " --> pdb=" O ILE Q 435 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N CYS Q 437 " --> pdb=" O VAL Q 476 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE Q 179 " --> pdb=" O SER Q 388 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ILE Q 390 " --> pdb=" O ILE Q 179 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE Q 181 " --> pdb=" O ILE Q 390 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 163 through 164 Processing sheet with id=AF1, first strand: chain 'R' and resid 126 through 130 removed outlier: 7.027A pdb=" N PHE R 127 " --> pdb=" O LEU R 116 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER R 542 " --> pdb=" O VAL R 533 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA R 140 " --> pdb=" O ILE R 495 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE R 180 " --> pdb=" O VAL R 436 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N GLU R 438 " --> pdb=" O ILE R 180 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N PHE R 182 " --> pdb=" O GLU R 438 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE R 179 " --> pdb=" O SER R 388 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ILE R 390 " --> pdb=" O ILE R 179 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE R 181 " --> pdb=" O ILE R 390 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'R' and resid 163 through 164 1422 hydrogen bonds defined for protein. 3924 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: 11.48 Time building geometry restraints manager: 5.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 14938 1.34 - 1.46: 9228 1.46 - 1.58: 22538 1.58 - 1.69: 0 1.69 - 1.81: 186 Bond restraints: 46890 Sorted by residual: bond pdb=" N LYS P 295 " pdb=" CA LYS P 295 " ideal model delta sigma weight residual 1.454 1.497 -0.043 1.29e-02 6.01e+03 1.09e+01 bond pdb=" N SER P 297 " pdb=" CA SER P 297 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.29e-02 6.01e+03 8.62e+00 bond pdb=" N LEU P 296 " pdb=" CA LEU P 296 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.51e+00 bond pdb=" CA SER P 297 " pdb=" CB SER P 297 " ideal model delta sigma weight residual 1.530 1.497 0.034 1.69e-02 3.50e+03 3.97e+00 bond pdb=" N LEU P 301 " pdb=" CA LEU P 301 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.29e-02 6.01e+03 3.67e+00 ... (remaining 46885 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 62757 2.06 - 4.11: 444 4.11 - 6.17: 52 6.17 - 8.23: 7 8.23 - 10.28: 4 Bond angle restraints: 63264 Sorted by residual: angle pdb=" C THR M 570 " pdb=" N PRO M 571 " pdb=" CA PRO M 571 " ideal model delta sigma weight residual 119.84 125.79 -5.95 1.25e+00 6.40e-01 2.27e+01 angle pdb=" C SER Q 292 " pdb=" N LEU Q 293 " pdb=" CA LEU Q 293 " ideal model delta sigma weight residual 121.80 132.08 -10.28 2.44e+00 1.68e-01 1.78e+01 angle pdb=" C ASN P 304 " pdb=" N ARG P 305 " pdb=" CA ARG P 305 " ideal model delta sigma weight residual 121.54 129.37 -7.83 1.91e+00 2.74e-01 1.68e+01 angle pdb=" C ALA B 411 " pdb=" N ASP B 412 " pdb=" CA ASP B 412 " ideal model delta sigma weight residual 121.54 128.90 -7.36 1.91e+00 2.74e-01 1.48e+01 angle pdb=" N ILE N 450 " pdb=" CA ILE N 450 " pdb=" C ILE N 450 " ideal model delta sigma weight residual 112.96 109.38 3.58 1.00e+00 1.00e+00 1.28e+01 ... (remaining 63259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 25582 17.91 - 35.83: 2595 35.83 - 53.74: 338 53.74 - 71.65: 99 71.65 - 89.57: 24 Dihedral angle restraints: 28638 sinusoidal: 12030 harmonic: 16608 Sorted by residual: dihedral pdb=" CA ILE G 313 " pdb=" C ILE G 313 " pdb=" N LYS G 314 " pdb=" CA LYS G 314 " ideal model delta harmonic sigma weight residual 180.00 156.88 23.12 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA LYS N 349 " pdb=" C LYS N 349 " pdb=" N ARG N 350 " pdb=" CA ARG N 350 " ideal model delta harmonic sigma weight residual 180.00 159.03 20.97 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA SER G 379 " pdb=" C SER G 379 " pdb=" N CYS G 380 " pdb=" CA CYS G 380 " ideal model delta harmonic sigma weight residual 180.00 159.67 20.33 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 28635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 5883 0.056 - 0.112: 1016 0.112 - 0.168: 143 0.168 - 0.223: 0 0.223 - 0.279: 2 Chirality restraints: 7044 Sorted by residual: chirality pdb=" CB ILE Q 522 " pdb=" CA ILE Q 522 " pdb=" CG1 ILE Q 522 " pdb=" CG2 ILE Q 522 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA LEU P 301 " pdb=" N LEU P 301 " pdb=" C LEU P 301 " pdb=" CB LEU P 301 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA VAL K 272 " pdb=" N VAL K 272 " pdb=" C VAL K 272 " pdb=" CB VAL K 272 " both_signs ideal model delta sigma weight residual False 2.44 2.28 0.16 2.00e-01 2.50e+01 6.75e-01 ... (remaining 7041 not shown) Planarity restraints: 8154 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP M 568 " -0.015 2.00e-02 2.50e+03 1.23e-02 3.77e+00 pdb=" CG TRP M 568 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP M 568 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP M 568 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP M 568 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP M 568 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP M 568 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 568 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 568 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP M 568 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP P 383 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C ASP P 383 " -0.026 2.00e-02 2.50e+03 pdb=" O ASP P 383 " 0.010 2.00e-02 2.50e+03 pdb=" N ARG P 384 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER P 89 " -0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO P 90 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO P 90 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO P 90 " -0.020 5.00e-02 4.00e+02 ... (remaining 8151 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 4260 2.75 - 3.29: 43648 3.29 - 3.82: 72798 3.82 - 4.36: 90141 4.36 - 4.90: 157009 Nonbonded interactions: 367856 Sorted by model distance: nonbonded pdb=" OH TYR K 309 " pdb=" O LEU K 430 " model vdw 2.212 3.040 nonbonded pdb=" OH TYR J 309 " pdb=" O LEU J 430 " model vdw 2.213 3.040 nonbonded pdb=" OG1 THR O 260 " pdb=" ND2 ASN R 230 " model vdw 2.223 3.120 nonbonded pdb=" NH2 ARG C 267 " pdb=" OE1 GLU C 416 " model vdw 2.247 3.120 nonbonded pdb=" O SER N 144 " pdb=" OG SER N 147 " model vdw 2.248 3.040 ... (remaining 367851 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = (chain 'G' and resid 267 through 436) selection = (chain 'H' and resid 267 through 436) selection = (chain 'I' and resid 267 through 436) selection = (chain 'J' and resid 267 through 436) selection = (chain 'K' and resid 267 through 436) selection = (chain 'L' and resid 267 through 436) } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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: 0.010 Normalize map: mean=0, sd=1: 4.320 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: 0.050 Extract box with map and model: 0.730 Check model and map are aligned: 0.150 Set scattering table: 0.120 Process input model: 47.270 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 46890 Z= 0.088 Angle : 0.453 10.282 63264 Z= 0.243 Chirality : 0.043 0.279 7044 Planarity : 0.003 0.037 8154 Dihedral : 14.130 89.569 17826 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.36 % Favored : 95.41 % Rotamer: Outliers : 0.06 % Allowed : 0.04 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.11), residues: 5574 helix: 0.23 (0.13), residues: 1808 sheet: -0.27 (0.19), residues: 837 loop : -1.13 (0.11), residues: 2929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 569 TYR 0.017 0.001 TYR R 381 PHE 0.013 0.001 PHE Q 342 TRP 0.033 0.001 TRP M 568 HIS 0.004 0.000 HIS F 316 Details of bonding type rmsd covalent geometry : bond 0.00173 (46890) covalent geometry : angle 0.45301 (63264) hydrogen bonds : bond 0.22153 ( 1422) hydrogen bonds : angle 6.81725 ( 3924) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1167 residues out of total 5280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1164 time to evaluate : 1.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ASP cc_start: 0.8385 (t0) cc_final: 0.8184 (t0) REVERT: A 289 ASP cc_start: 0.7627 (m-30) cc_final: 0.7314 (m-30) REVERT: A 314 LYS cc_start: 0.8521 (ttmm) cc_final: 0.8120 (tttt) REVERT: A 342 ASN cc_start: 0.8612 (t0) cc_final: 0.8377 (m110) REVERT: A 368 LYS cc_start: 0.8184 (pttp) cc_final: 0.7435 (mppt) REVERT: A 384 GLU cc_start: 0.7276 (mm-30) cc_final: 0.6802 (mt-10) REVERT: A 387 LYS cc_start: 0.7631 (tptp) cc_final: 0.7278 (mttt) REVERT: A 424 ARG cc_start: 0.7097 (mmm160) cc_final: 0.6704 (mtp180) REVERT: A 433 LEU cc_start: 0.7303 (tp) cc_final: 0.6994 (tp) REVERT: B 287 ASP cc_start: 0.8268 (t0) cc_final: 0.7483 (t0) REVERT: B 296 ASP cc_start: 0.8511 (m-30) cc_final: 0.8147 (m-30) REVERT: B 300 LEU cc_start: 0.7786 (mt) cc_final: 0.7305 (mm) REVERT: B 342 ASN cc_start: 0.8221 (t0) cc_final: 0.7843 (t0) REVERT: B 387 LYS cc_start: 0.7874 (tttm) cc_final: 0.7526 (mtpt) REVERT: B 392 LYS cc_start: 0.7488 (ttpt) cc_final: 0.7254 (ttmt) REVERT: C 279 SER cc_start: 0.8618 (t) cc_final: 0.8360 (p) REVERT: C 296 ASP cc_start: 0.7933 (m-30) cc_final: 0.7628 (p0) REVERT: C 357 LYS cc_start: 0.8006 (mtpp) cc_final: 0.7439 (pttm) REVERT: C 373 GLU cc_start: 0.8238 (tt0) cc_final: 0.7995 (tt0) REVERT: C 382 SER cc_start: 0.7593 (m) cc_final: 0.7198 (p) REVERT: C 395 ASP cc_start: 0.8219 (m-30) cc_final: 0.7808 (m-30) REVERT: C 415 ILE cc_start: 0.8593 (mt) cc_final: 0.8320 (mm) REVERT: C 428 TYR cc_start: 0.8357 (t80) cc_final: 0.8062 (t80) REVERT: D 341 ARG cc_start: 0.7954 (mtt90) cc_final: 0.7563 (ttm170) REVERT: D 369 ASP cc_start: 0.8126 (m-30) cc_final: 0.7909 (t0) REVERT: E 274 SER cc_start: 0.8902 (m) cc_final: 0.8263 (p) REVERT: E 329 ASN cc_start: 0.8055 (m-40) cc_final: 0.7775 (m-40) REVERT: E 337 ARG cc_start: 0.7446 (mtp180) cc_final: 0.6955 (mtm-85) REVERT: E 419 GLU cc_start: 0.6700 (pm20) cc_final: 0.6495 (mp0) REVERT: F 269 ASN cc_start: 0.7744 (m-40) cc_final: 0.7516 (m-40) REVERT: F 337 ARG cc_start: 0.7375 (mtp180) cc_final: 0.6903 (mtm-85) REVERT: F 381 ASN cc_start: 0.8390 (p0) cc_final: 0.8151 (p0) REVERT: G 325 LYS cc_start: 0.8239 (tttp) cc_final: 0.7997 (tttt) REVERT: G 383 ASP cc_start: 0.6650 (p0) cc_final: 0.6424 (p0) REVERT: G 434 LYS cc_start: 0.8257 (tppp) cc_final: 0.7768 (mttm) REVERT: H 295 ASP cc_start: 0.8193 (t0) cc_final: 0.7110 (p0) REVERT: H 368 LYS cc_start: 0.8921 (mmtt) cc_final: 0.8539 (ptpp) REVERT: H 369 ASP cc_start: 0.6913 (t70) cc_final: 0.6594 (t0) REVERT: H 384 GLU cc_start: 0.7467 (pm20) cc_final: 0.7097 (pm20) REVERT: H 387 LYS cc_start: 0.7477 (mtmt) cc_final: 0.7139 (mmmm) REVERT: I 289 ASP cc_start: 0.8109 (m-30) cc_final: 0.7697 (m-30) REVERT: I 327 ASP cc_start: 0.7670 (m-30) cc_final: 0.7325 (t0) REVERT: I 343 ILE cc_start: 0.8043 (tt) cc_final: 0.7592 (mt) REVERT: I 357 LYS cc_start: 0.7807 (mmtm) cc_final: 0.7273 (ptmm) REVERT: I 365 ARG cc_start: 0.8525 (mtt-85) cc_final: 0.8106 (mtt90) REVERT: I 368 LYS cc_start: 0.8659 (mttt) cc_final: 0.8392 (ptmt) REVERT: I 416 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7300 (mm-30) REVERT: J 318 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8051 (mm-30) REVERT: J 329 ASN cc_start: 0.7397 (m110) cc_final: 0.6882 (t0) REVERT: J 344 GLN cc_start: 0.8348 (mm-40) cc_final: 0.8050 (mm-40) REVERT: J 369 ASP cc_start: 0.8206 (m-30) cc_final: 0.7987 (m-30) REVERT: K 265 LYS cc_start: 0.7268 (tttt) cc_final: 0.6965 (ttpp) REVERT: K 304 ASP cc_start: 0.8109 (m-30) cc_final: 0.7757 (m-30) REVERT: K 313 ILE cc_start: 0.8287 (pt) cc_final: 0.8082 (tt) REVERT: K 358 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7698 (mm-30) REVERT: K 368 LYS cc_start: 0.8554 (ttpt) cc_final: 0.8308 (mptt) REVERT: L 344 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7336 (mp10) REVERT: L 356 PHE cc_start: 0.8346 (t80) cc_final: 0.8121 (t80) REVERT: L 361 LYS cc_start: 0.8756 (ptpt) cc_final: 0.8281 (pttt) REVERT: L 407 LEU cc_start: 0.8581 (tp) cc_final: 0.8256 (tt) REVERT: M 100 ASP cc_start: 0.7936 (m-30) cc_final: 0.7604 (m-30) REVERT: M 122 ASN cc_start: 0.8432 (m-40) cc_final: 0.7727 (t0) REVERT: M 199 ASP cc_start: 0.8119 (t0) cc_final: 0.7679 (t70) REVERT: M 211 LYS cc_start: 0.7670 (mptt) cc_final: 0.7376 (mmtt) REVERT: M 239 SER cc_start: 0.8049 (t) cc_final: 0.7609 (p) REVERT: M 349 LYS cc_start: 0.7371 (mttt) cc_final: 0.6944 (ttpt) REVERT: M 439 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6464 (mp0) REVERT: M 453 LYS cc_start: 0.7901 (tttt) cc_final: 0.7302 (mmpt) REVERT: M 545 LYS cc_start: 0.7955 (tttt) cc_final: 0.7141 (tmtt) REVERT: M 554 ARG cc_start: 0.7450 (ttp-110) cc_final: 0.7219 (ttp-110) REVERT: N 55 LYS cc_start: 0.8208 (tttt) cc_final: 0.7768 (tptt) REVERT: N 112 LYS cc_start: 0.7728 (mttp) cc_final: 0.7398 (pttt) REVERT: N 133 LYS cc_start: 0.8542 (mttt) cc_final: 0.8091 (mtmt) REVERT: N 199 ASP cc_start: 0.8627 (t0) cc_final: 0.8300 (t0) REVERT: N 209 LYS cc_start: 0.8744 (mttt) cc_final: 0.8539 (mtmm) REVERT: N 242 LYS cc_start: 0.8303 (tttt) cc_final: 0.7734 (ttmm) REVERT: N 341 ARG cc_start: 0.6844 (mtm-85) cc_final: 0.5980 (ttt90) REVERT: N 383 ASP cc_start: 0.7612 (m-30) cc_final: 0.7357 (p0) REVERT: N 453 LYS cc_start: 0.7883 (tttt) cc_final: 0.7616 (mmtm) REVERT: N 517 ARG cc_start: 0.6380 (mmt180) cc_final: 0.6112 (mmt-90) REVERT: N 554 ARG cc_start: 0.7541 (ttp-110) cc_final: 0.7251 (mtm110) REVERT: N 582 LYS cc_start: 0.7024 (ttmm) cc_final: 0.6410 (tmmt) REVERT: O 79 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7696 (mp0) REVERT: O 98 GLU cc_start: 0.7404 (pt0) cc_final: 0.6899 (tp30) REVERT: O 104 LYS cc_start: 0.7917 (mttt) cc_final: 0.7609 (mtpt) REVERT: O 121 GLN cc_start: 0.5924 (tm-30) cc_final: 0.5610 (mp10) REVERT: O 123 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7616 (tp30) REVERT: O 167 ARG cc_start: 0.8166 (mtt90) cc_final: 0.7874 (mtp-110) REVERT: O 243 ARG cc_start: 0.7628 (ttt90) cc_final: 0.7258 (mtp-110) REVERT: O 349 LYS cc_start: 0.7804 (mmtp) cc_final: 0.7497 (tptp) REVERT: O 352 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7858 (mt-10) REVERT: O 453 LYS cc_start: 0.8013 (tttt) cc_final: 0.7333 (tptp) REVERT: O 461 ARG cc_start: 0.7043 (ttt180) cc_final: 0.6727 (ttm170) REVERT: O 479 ARG cc_start: 0.7725 (mmt180) cc_final: 0.7465 (mtp85) REVERT: O 498 ARG cc_start: 0.7938 (ttm170) cc_final: 0.7676 (ttm170) REVERT: O 545 LYS cc_start: 0.8315 (tmtt) cc_final: 0.8063 (tptp) REVERT: P 104 LYS cc_start: 0.7951 (mtmt) cc_final: 0.7509 (ttpp) REVERT: P 106 PHE cc_start: 0.8215 (m-80) cc_final: 0.7980 (m-80) REVERT: P 173 ASP cc_start: 0.7287 (t0) cc_final: 0.7016 (p0) REVERT: P 228 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6859 (mt-10) REVERT: P 295 LYS cc_start: 0.7092 (OUTLIER) cc_final: 0.6326 (ttmm) REVERT: P 296 LEU cc_start: 0.5824 (OUTLIER) cc_final: 0.5557 (pp) REVERT: P 330 PRO cc_start: 0.7913 (Cg_exo) cc_final: 0.7656 (Cg_endo) REVERT: P 552 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8358 (mp0) REVERT: P 562 LYS cc_start: 0.8794 (ptmm) cc_final: 0.8592 (ptmm) REVERT: P 569 ARG cc_start: 0.7829 (mmt-90) cc_final: 0.7515 (mmt180) REVERT: Q 81 PHE cc_start: 0.8104 (m-80) cc_final: 0.7735 (m-80) REVERT: Q 115 HIS cc_start: 0.8263 (m-70) cc_final: 0.7560 (t-90) REVERT: Q 256 PHE cc_start: 0.7107 (m-80) cc_final: 0.6855 (m-80) REVERT: Q 456 LYS cc_start: 0.8333 (mtpt) cc_final: 0.8005 (mtpt) REVERT: Q 457 LYS cc_start: 0.7540 (tttt) cc_final: 0.7283 (tttp) REVERT: Q 562 LYS cc_start: 0.8420 (tptt) cc_final: 0.7907 (ttpp) REVERT: R 41 GLU cc_start: 0.8323 (tt0) cc_final: 0.8072 (tt0) REVERT: R 115 HIS cc_start: 0.8186 (m-70) cc_final: 0.7363 (t70) REVERT: R 167 ARG cc_start: 0.7959 (mpt180) cc_final: 0.7590 (tpp80) REVERT: R 187 GLU cc_start: 0.7854 (pt0) cc_final: 0.7380 (pt0) REVERT: R 211 LYS cc_start: 0.8422 (mtmm) cc_final: 0.7927 (mmtm) REVERT: R 457 LYS cc_start: 0.7812 (tttm) cc_final: 0.7102 (mtpt) REVERT: R 485 ASP cc_start: 0.8649 (t70) cc_final: 0.8257 (t0) outliers start: 3 outliers final: 1 residues processed: 1167 average time/residue: 0.3016 time to fit residues: 571.0098 Evaluate side-chains 683 residues out of total 5280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 680 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 295 LYS Chi-restraints excluded: chain P residue 296 LEU Chi-restraints excluded: chain P residue 301 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 394 optimal weight: 3.9990 chunk 430 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 265 optimal weight: 3.9990 chunk 523 optimal weight: 10.0000 chunk 497 optimal weight: 0.7980 chunk 414 optimal weight: 9.9990 chunk 310 optimal weight: 5.9990 chunk 488 optimal weight: 3.9990 chunk 366 optimal weight: 2.9990 chunk 223 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN D 370 ASN H 270 GLN H 381 ASN M 248 ASN ** M 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 386 ASN N 82 GLN O 236 ASN O 370 HIS O 556 GLN P 70 GLN P 298 ASN P 310 ASN P 332 ASN P 370 HIS Q 503 ASN R 490 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.142122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.105380 restraints weight = 54464.089| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.59 r_work: 0.3042 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 46890 Z= 0.261 Angle : 0.640 10.394 63264 Z= 0.337 Chirality : 0.050 0.226 7044 Planarity : 0.004 0.063 8154 Dihedral : 4.843 58.724 6038 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.54 % Favored : 94.29 % Rotamer: Outliers : 1.52 % Allowed : 9.41 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.11), residues: 5574 helix: 0.03 (0.12), residues: 1860 sheet: -0.35 (0.19), residues: 767 loop : -1.29 (0.11), residues: 2947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 282 TYR 0.017 0.002 TYR L 355 PHE 0.021 0.002 PHE H 356 TRP 0.037 0.003 TRP N 580 HIS 0.011 0.001 HIS G 335 Details of bonding type rmsd covalent geometry : bond 0.00656 (46890) covalent geometry : angle 0.64041 (63264) hydrogen bonds : bond 0.05111 ( 1422) hydrogen bonds : angle 5.05469 ( 3924) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 5280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 652 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 ASN cc_start: 0.8689 (t0) cc_final: 0.8363 (m-40) REVERT: A 384 GLU cc_start: 0.7329 (mm-30) cc_final: 0.7026 (mt-10) REVERT: A 387 LYS cc_start: 0.7739 (tptp) cc_final: 0.7471 (mtmt) REVERT: B 296 ASP cc_start: 0.8412 (m-30) cc_final: 0.8133 (m-30) REVERT: B 300 LEU cc_start: 0.7997 (mt) cc_final: 0.7576 (mm) REVERT: B 311 SER cc_start: 0.9020 (OUTLIER) cc_final: 0.8656 (p) REVERT: B 342 ASN cc_start: 0.8436 (t0) cc_final: 0.8094 (t0) REVERT: B 387 LYS cc_start: 0.7822 (tttm) cc_final: 0.7518 (mtpt) REVERT: B 424 ARG cc_start: 0.7629 (mmm160) cc_final: 0.7231 (mtp85) REVERT: C 279 SER cc_start: 0.8855 (t) cc_final: 0.8638 (p) REVERT: C 296 ASP cc_start: 0.8052 (m-30) cc_final: 0.7659 (p0) REVERT: C 357 LYS cc_start: 0.8320 (mtpp) cc_final: 0.7856 (pttm) REVERT: C 416 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7314 (mm-30) REVERT: C 424 ARG cc_start: 0.7981 (mtp85) cc_final: 0.7765 (mtp85) REVERT: C 428 TYR cc_start: 0.8522 (t80) cc_final: 0.8309 (t80) REVERT: D 325 LYS cc_start: 0.8796 (ttpt) cc_final: 0.8518 (ttpt) REVERT: E 274 SER cc_start: 0.9094 (m) cc_final: 0.8623 (p) REVERT: E 419 GLU cc_start: 0.6897 (pm20) cc_final: 0.6600 (mp0) REVERT: F 269 ASN cc_start: 0.8214 (m-40) cc_final: 0.8008 (m-40) REVERT: F 337 ARG cc_start: 0.7822 (mtp180) cc_final: 0.7472 (mtm-85) REVERT: F 378 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.7962 (mp) REVERT: F 381 ASN cc_start: 0.8542 (p0) cc_final: 0.8226 (p0) REVERT: G 358 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8021 (mm-30) REVERT: G 362 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8187 (mm-30) REVERT: G 383 ASP cc_start: 0.7150 (p0) cc_final: 0.6852 (p0) REVERT: G 434 LYS cc_start: 0.8356 (tppp) cc_final: 0.7884 (mttt) REVERT: H 295 ASP cc_start: 0.8445 (t0) cc_final: 0.8085 (m-30) REVERT: H 362 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7520 (mp0) REVERT: H 368 LYS cc_start: 0.8982 (mmtt) cc_final: 0.8351 (ptpp) REVERT: I 289 ASP cc_start: 0.7951 (m-30) cc_final: 0.7604 (m-30) REVERT: I 357 LYS cc_start: 0.8055 (mmtm) cc_final: 0.7532 (ptmm) REVERT: I 365 ARG cc_start: 0.8780 (mtt-85) cc_final: 0.8433 (mtt90) REVERT: I 416 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7428 (mm-30) REVERT: J 272 VAL cc_start: 0.8354 (t) cc_final: 0.8115 (t) REVERT: K 265 LYS cc_start: 0.7107 (tttt) cc_final: 0.6741 (ttpp) REVERT: K 368 LYS cc_start: 0.8754 (ttpt) cc_final: 0.8438 (mptt) REVERT: L 265 LYS cc_start: 0.7402 (tptt) cc_final: 0.6924 (tttt) REVERT: L 333 GLU cc_start: 0.7758 (mp0) cc_final: 0.7476 (mp0) REVERT: L 344 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7725 (mp10) REVERT: L 361 LYS cc_start: 0.8605 (ptpt) cc_final: 0.8280 (pttt) REVERT: M 110 LYS cc_start: 0.6314 (tppp) cc_final: 0.5779 (mtmm) REVERT: M 113 ILE cc_start: 0.8309 (tp) cc_final: 0.8065 (tt) REVERT: M 199 ASP cc_start: 0.8288 (t0) cc_final: 0.8006 (t0) REVERT: M 211 LYS cc_start: 0.7887 (mptt) cc_final: 0.7618 (mmtt) REVERT: M 239 SER cc_start: 0.8032 (t) cc_final: 0.7442 (p) REVERT: M 343 GLU cc_start: 0.8190 (tt0) cc_final: 0.7818 (tt0) REVERT: M 439 GLU cc_start: 0.7477 (mm-30) cc_final: 0.6903 (mp0) REVERT: M 467 ARG cc_start: 0.7883 (mtp-110) cc_final: 0.7626 (ttt-90) REVERT: M 498 ARG cc_start: 0.8134 (ttp-170) cc_final: 0.7866 (ttm-80) REVERT: M 522 ILE cc_start: 0.7841 (tp) cc_final: 0.7600 (tp) REVERT: M 545 LYS cc_start: 0.8408 (tttt) cc_final: 0.7822 (tptp) REVERT: N 8 GLU cc_start: 0.8105 (tt0) cc_final: 0.7820 (tt0) REVERT: N 115 HIS cc_start: 0.7807 (m-70) cc_final: 0.6987 (t70) REVERT: N 133 LYS cc_start: 0.8582 (mttt) cc_final: 0.8193 (mttm) REVERT: N 199 ASP cc_start: 0.8505 (t0) cc_final: 0.8163 (t0) REVERT: N 242 LYS cc_start: 0.8085 (tttt) cc_final: 0.7715 (ttmt) REVERT: N 341 ARG cc_start: 0.6808 (mtm-85) cc_final: 0.6208 (ttt90) REVERT: N 383 ASP cc_start: 0.7828 (m-30) cc_final: 0.7546 (p0) REVERT: N 446 ARG cc_start: 0.8101 (ttm-80) cc_final: 0.7838 (ttm170) REVERT: N 453 LYS cc_start: 0.8050 (tttt) cc_final: 0.7775 (mmtm) REVERT: N 582 LYS cc_start: 0.7499 (ttmm) cc_final: 0.6797 (tmmt) REVERT: O 79 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7449 (mp0) REVERT: O 104 LYS cc_start: 0.8017 (mttt) cc_final: 0.7746 (mtpt) REVERT: O 109 GLU cc_start: 0.5562 (mp0) cc_final: 0.5228 (mm-30) REVERT: O 112 LYS cc_start: 0.6843 (pptt) cc_final: 0.6595 (pttt) REVERT: O 123 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7678 (tp30) REVERT: O 167 ARG cc_start: 0.8216 (mtt90) cc_final: 0.7651 (mtp-110) REVERT: O 243 ARG cc_start: 0.7666 (ttt90) cc_final: 0.7347 (mtp-110) REVERT: O 349 LYS cc_start: 0.7984 (mmtp) cc_final: 0.7620 (tptp) REVERT: O 461 ARG cc_start: 0.7181 (ttt180) cc_final: 0.6805 (ttp80) REVERT: O 510 ASN cc_start: 0.7725 (m-40) cc_final: 0.7517 (m-40) REVERT: P 1 MET cc_start: 0.7344 (mtt) cc_final: 0.7042 (mtt) REVERT: P 104 LYS cc_start: 0.8086 (mtmt) cc_final: 0.7789 (ttpp) REVERT: P 123 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7302 (mm-30) REVERT: P 173 ASP cc_start: 0.7686 (t0) cc_final: 0.6856 (p0) REVERT: P 402 ILE cc_start: 0.8124 (mt) cc_final: 0.7923 (mt) REVERT: P 562 LYS cc_start: 0.8898 (ptmm) cc_final: 0.8574 (pttp) REVERT: Q 115 HIS cc_start: 0.8415 (m-70) cc_final: 0.7539 (t70) REVERT: Q 562 LYS cc_start: 0.8630 (tptt) cc_final: 0.8053 (tmtt) REVERT: R 78 GLU cc_start: 0.7028 (mm-30) cc_final: 0.6814 (mm-30) REVERT: R 115 HIS cc_start: 0.8167 (m-70) cc_final: 0.7441 (t70) REVERT: R 167 ARG cc_start: 0.7945 (mpt180) cc_final: 0.7645 (tpp80) REVERT: R 187 GLU cc_start: 0.7941 (pt0) cc_final: 0.7595 (pt0) REVERT: R 457 LYS cc_start: 0.7824 (tttm) cc_final: 0.7113 (mtpt) REVERT: R 485 ASP cc_start: 0.8363 (t70) cc_final: 0.7950 (t0) outliers start: 80 outliers final: 57 residues processed: 704 average time/residue: 0.3106 time to fit residues: 350.0633 Evaluate side-chains 632 residues out of total 5280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 572 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 383 ASP Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 384 GLU Chi-restraints excluded: chain G residue 274 SER Chi-restraints excluded: chain G residue 369 ASP Chi-restraints excluded: chain G residue 378 ILE Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain H residue 274 SER Chi-restraints excluded: chain H residue 286 ILE Chi-restraints excluded: chain H residue 362 GLU Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 405 VAL Chi-restraints excluded: chain H residue 409 ASP Chi-restraints excluded: chain I residue 352 ASP Chi-restraints excluded: chain I residue 379 SER Chi-restraints excluded: chain I residue 407 LEU Chi-restraints excluded: chain J residue 281 SER Chi-restraints excluded: chain J residue 347 THR Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain L residue 313 ILE Chi-restraints excluded: chain L residue 400 VAL Chi-restraints excluded: chain L residue 434 LYS Chi-restraints excluded: chain M residue 385 SER Chi-restraints excluded: chain M residue 511 LEU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 99 ASP Chi-restraints excluded: chain N residue 511 LEU Chi-restraints excluded: chain O residue 370 HIS Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 126 SER Chi-restraints excluded: chain P residue 295 LYS Chi-restraints excluded: chain P residue 332 ASN Chi-restraints excluded: chain P residue 521 GLU Chi-restraints excluded: chain P residue 555 SER Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain Q residue 96 LEU Chi-restraints excluded: chain Q residue 108 ASN Chi-restraints excluded: chain Q residue 184 ILE Chi-restraints excluded: chain Q residue 311 GLU Chi-restraints excluded: chain Q residue 496 ASN Chi-restraints excluded: chain Q residue 536 ASP Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 184 ILE Chi-restraints excluded: chain R residue 227 ILE Chi-restraints excluded: chain R residue 502 ILE Chi-restraints excluded: chain R residue 577 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 518 optimal weight: 3.9990 chunk 260 optimal weight: 7.9990 chunk 470 optimal weight: 10.0000 chunk 297 optimal weight: 20.0000 chunk 363 optimal weight: 5.9990 chunk 143 optimal weight: 0.9980 chunk 325 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 551 optimal weight: 1.9990 chunk 442 optimal weight: 0.6980 chunk 382 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 ASN B 276 ASN ** H 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 330 ASN ** M 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 248 ASN O 370 HIS O 556 GLN P 332 ASN Q 45 ASN Q 503 ASN R 332 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.144187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.107915 restraints weight = 53894.693| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.57 r_work: 0.3080 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 46890 Z= 0.121 Angle : 0.497 9.986 63264 Z= 0.265 Chirality : 0.045 0.207 7044 Planarity : 0.003 0.035 8154 Dihedral : 4.440 57.217 6034 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.45 % Favored : 95.39 % Rotamer: Outliers : 1.57 % Allowed : 11.80 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.11), residues: 5574 helix: 0.34 (0.12), residues: 1923 sheet: -0.33 (0.19), residues: 767 loop : -1.31 (0.11), residues: 2884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 554 TYR 0.012 0.001 TYR N 507 PHE 0.019 0.001 PHE H 356 TRP 0.027 0.001 TRP N 580 HIS 0.009 0.001 HIS O 370 Details of bonding type rmsd covalent geometry : bond 0.00287 (46890) covalent geometry : angle 0.49676 (63264) hydrogen bonds : bond 0.03815 ( 1422) hydrogen bonds : angle 4.63963 ( 3924) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 5280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 606 time to evaluate : 1.836 Fit side-chains revert: symmetry clash REVERT: A 378 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.8790 (mp) REVERT: A 384 GLU cc_start: 0.7242 (mm-30) cc_final: 0.6941 (mt-10) REVERT: A 387 LYS cc_start: 0.7613 (tptp) cc_final: 0.7307 (mtpt) REVERT: A 424 ARG cc_start: 0.7457 (mtp180) cc_final: 0.7243 (mtp85) REVERT: A 428 TYR cc_start: 0.8434 (t80) cc_final: 0.8203 (t80) REVERT: B 296 ASP cc_start: 0.8395 (m-30) cc_final: 0.8117 (m-30) REVERT: B 342 ASN cc_start: 0.8394 (t0) cc_final: 0.8062 (t0) REVERT: B 378 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.8717 (mt) REVERT: B 387 LYS cc_start: 0.7839 (tttm) cc_final: 0.7533 (mtpt) REVERT: B 424 ARG cc_start: 0.7539 (mmm160) cc_final: 0.7068 (mtp85) REVERT: C 279 SER cc_start: 0.8803 (t) cc_final: 0.8562 (p) REVERT: C 296 ASP cc_start: 0.8041 (m-30) cc_final: 0.7666 (p0) REVERT: C 342 ASN cc_start: 0.8755 (m-40) cc_final: 0.8513 (m-40) REVERT: C 357 LYS cc_start: 0.8263 (mtpp) cc_final: 0.7856 (pttm) REVERT: C 416 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7215 (mm-30) REVERT: D 325 LYS cc_start: 0.8696 (ttpt) cc_final: 0.8401 (ttpt) REVERT: E 274 SER cc_start: 0.9082 (m) cc_final: 0.8564 (p) REVERT: E 337 ARG cc_start: 0.7908 (mtp180) cc_final: 0.7449 (mmm160) REVERT: E 419 GLU cc_start: 0.6823 (pm20) cc_final: 0.6514 (mp0) REVERT: F 337 ARG cc_start: 0.7698 (mtp180) cc_final: 0.7413 (mtm-85) REVERT: F 341 ARG cc_start: 0.8211 (tpp-160) cc_final: 0.7998 (tpp-160) REVERT: F 369 ASP cc_start: 0.8160 (t0) cc_final: 0.7946 (t0) REVERT: F 381 ASN cc_start: 0.8542 (p0) cc_final: 0.8218 (p0) REVERT: G 358 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7987 (mm-30) REVERT: G 362 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8297 (mm-30) REVERT: G 368 LYS cc_start: 0.7905 (mtmm) cc_final: 0.7651 (ptpp) REVERT: G 434 LYS cc_start: 0.8320 (tppp) cc_final: 0.7859 (mttt) REVERT: H 295 ASP cc_start: 0.8434 (t0) cc_final: 0.7996 (m-30) REVERT: H 297 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7671 (mt-10) REVERT: H 368 LYS cc_start: 0.8848 (mmtt) cc_final: 0.8428 (ptpp) REVERT: I 289 ASP cc_start: 0.7939 (m-30) cc_final: 0.7575 (m-30) REVERT: I 357 LYS cc_start: 0.8017 (mmtm) cc_final: 0.7533 (ptmm) REVERT: I 365 ARG cc_start: 0.8681 (mtt-85) cc_final: 0.8458 (mtt90) REVERT: I 425 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8658 (mt-10) REVERT: J 272 VAL cc_start: 0.8252 (t) cc_final: 0.7987 (t) REVERT: J 318 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8278 (mm-30) REVERT: K 265 LYS cc_start: 0.6972 (tttt) cc_final: 0.6617 (ttpp) REVERT: K 299 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8337 (mp) REVERT: K 368 LYS cc_start: 0.8737 (ttpt) cc_final: 0.8460 (mptt) REVERT: L 265 LYS cc_start: 0.7506 (tptt) cc_final: 0.7020 (tttt) REVERT: L 344 GLN cc_start: 0.8050 (mm-40) cc_final: 0.7718 (mp10) REVERT: L 361 LYS cc_start: 0.8555 (ptpt) cc_final: 0.8257 (pttt) REVERT: M 95 PHE cc_start: 0.8444 (m-80) cc_final: 0.8204 (m-80) REVERT: M 110 LYS cc_start: 0.6306 (tppp) cc_final: 0.5720 (mtmm) REVERT: M 199 ASP cc_start: 0.8276 (t0) cc_final: 0.8002 (t0) REVERT: M 211 LYS cc_start: 0.7773 (mptt) cc_final: 0.7491 (mmmt) REVERT: M 239 SER cc_start: 0.7986 (t) cc_final: 0.7347 (p) REVERT: M 343 GLU cc_start: 0.8090 (tt0) cc_final: 0.7798 (tt0) REVERT: M 439 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7153 (mt-10) REVERT: M 467 ARG cc_start: 0.7872 (mtp-110) cc_final: 0.7542 (ttt-90) REVERT: M 522 ILE cc_start: 0.7751 (tp) cc_final: 0.7528 (tp) REVERT: M 545 LYS cc_start: 0.8408 (tttt) cc_final: 0.7716 (tmtt) REVERT: N 55 LYS cc_start: 0.8625 (tttt) cc_final: 0.8305 (ttpp) REVERT: N 112 LYS cc_start: 0.7646 (mttm) cc_final: 0.7090 (pttt) REVERT: N 115 HIS cc_start: 0.7713 (m-70) cc_final: 0.7034 (t70) REVERT: N 133 LYS cc_start: 0.8468 (mttt) cc_final: 0.8102 (mtpp) REVERT: N 199 ASP cc_start: 0.8441 (t0) cc_final: 0.8087 (t0) REVERT: N 242 LYS cc_start: 0.8152 (tttt) cc_final: 0.7750 (ttmt) REVERT: N 341 ARG cc_start: 0.6722 (mtm-85) cc_final: 0.6061 (ttt90) REVERT: N 453 LYS cc_start: 0.8001 (tttt) cc_final: 0.7706 (mmtm) REVERT: N 522 ILE cc_start: 0.7752 (tp) cc_final: 0.7397 (mt) REVERT: N 580 TRP cc_start: 0.7126 (OUTLIER) cc_final: 0.5582 (t60) REVERT: N 582 LYS cc_start: 0.7560 (ttmm) cc_final: 0.6817 (tmmt) REVERT: O 79 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7423 (mp0) REVERT: O 104 LYS cc_start: 0.8008 (mttt) cc_final: 0.7718 (mmmt) REVERT: O 112 LYS cc_start: 0.6768 (pptt) cc_final: 0.6547 (pttt) REVERT: O 123 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7632 (tp30) REVERT: O 167 ARG cc_start: 0.8242 (mtt90) cc_final: 0.7655 (mtp-110) REVERT: O 243 ARG cc_start: 0.7477 (ttt90) cc_final: 0.7181 (mtp-110) REVERT: O 349 LYS cc_start: 0.8135 (mmtp) cc_final: 0.7805 (tptp) REVERT: O 352 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7633 (mt-10) REVERT: O 509 LYS cc_start: 0.8178 (mtpt) cc_final: 0.7605 (mttm) REVERT: O 578 MET cc_start: 0.7855 (ttt) cc_final: 0.7458 (tpp) REVERT: P 1 MET cc_start: 0.7089 (mtt) cc_final: 0.6775 (mtt) REVERT: P 104 LYS cc_start: 0.7987 (mtmt) cc_final: 0.7720 (ttpp) REVERT: P 106 PHE cc_start: 0.8536 (m-80) cc_final: 0.8221 (m-80) REVERT: P 173 ASP cc_start: 0.7581 (t0) cc_final: 0.6740 (p0) REVERT: P 295 LYS cc_start: 0.6951 (OUTLIER) cc_final: 0.6652 (tttm) REVERT: P 562 LYS cc_start: 0.8906 (ptmm) cc_final: 0.8563 (pttp) REVERT: Q 115 HIS cc_start: 0.8403 (m-70) cc_final: 0.7511 (t70) REVERT: Q 562 LYS cc_start: 0.8625 (tptt) cc_final: 0.8120 (tmtt) REVERT: R 8 GLU cc_start: 0.8475 (tt0) cc_final: 0.8179 (tt0) REVERT: R 107 SER cc_start: 0.7762 (t) cc_final: 0.7312 (m) REVERT: R 115 HIS cc_start: 0.8160 (m-70) cc_final: 0.7431 (t70) REVERT: R 165 ASP cc_start: 0.7429 (m-30) cc_final: 0.7178 (t0) REVERT: R 167 ARG cc_start: 0.7907 (mpt180) cc_final: 0.7617 (tpp80) REVERT: R 187 GLU cc_start: 0.7884 (pt0) cc_final: 0.7590 (pt0) REVERT: R 199 ASP cc_start: 0.7843 (t70) cc_final: 0.7606 (t0) REVERT: R 457 LYS cc_start: 0.7775 (tttm) cc_final: 0.7087 (mtpt) REVERT: R 485 ASP cc_start: 0.8353 (t70) cc_final: 0.8030 (t0) REVERT: R 562 LYS cc_start: 0.8418 (ttmt) cc_final: 0.8057 (ttpt) outliers start: 83 outliers final: 55 residues processed: 663 average time/residue: 0.3039 time to fit residues: 326.1723 Evaluate side-chains 627 residues out of total 5280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 567 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 356 PHE Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 384 GLU Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 286 ILE Chi-restraints excluded: chain H residue 289 ASP Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 405 VAL Chi-restraints excluded: chain H residue 409 ASP Chi-restraints excluded: chain I residue 272 VAL Chi-restraints excluded: chain I residue 379 SER Chi-restraints excluded: chain I residue 407 LEU Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain K residue 299 ILE Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain L residue 313 ILE Chi-restraints excluded: chain L residue 434 LYS Chi-restraints excluded: chain M residue 101 ILE Chi-restraints excluded: chain M residue 208 GLU Chi-restraints excluded: chain M residue 385 SER Chi-restraints excluded: chain M residue 558 ILE Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 74 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 99 ASP Chi-restraints excluded: chain N residue 580 TRP Chi-restraints excluded: chain O residue 402 ILE Chi-restraints excluded: chain O residue 478 GLN Chi-restraints excluded: chain O residue 540 ILE Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 101 ILE Chi-restraints excluded: chain P residue 295 LYS Chi-restraints excluded: chain P residue 521 GLU Chi-restraints excluded: chain Q residue 6 VAL Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain Q residue 108 ASN Chi-restraints excluded: chain Q residue 184 ILE Chi-restraints excluded: chain Q residue 193 GLU Chi-restraints excluded: chain Q residue 451 GLU Chi-restraints excluded: chain Q residue 496 ASN Chi-restraints excluded: chain Q residue 572 SER Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 184 ILE Chi-restraints excluded: chain R residue 379 MET Chi-restraints excluded: chain R residue 577 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 322 optimal weight: 7.9990 chunk 396 optimal weight: 6.9990 chunk 375 optimal weight: 8.9990 chunk 410 optimal weight: 0.9980 chunk 498 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 508 optimal weight: 0.0010 chunk 277 optimal weight: 0.7980 chunk 366 optimal weight: 0.9990 chunk 453 optimal weight: 1.9990 chunk 328 optimal weight: 0.0270 overall best weight: 0.5646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 GLN M 248 ASN ** M 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN O 370 HIS O 556 GLN P 298 ASN ** P 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.146030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.109909 restraints weight = 53933.841| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.57 r_work: 0.3111 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 46890 Z= 0.093 Angle : 0.462 9.970 63264 Z= 0.246 Chirality : 0.044 0.221 7044 Planarity : 0.003 0.036 8154 Dihedral : 4.224 59.504 6034 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.70 % Favored : 95.14 % Rotamer: Outliers : 1.50 % Allowed : 12.84 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.11), residues: 5574 helix: 0.55 (0.12), residues: 1920 sheet: -0.28 (0.19), residues: 769 loop : -1.24 (0.11), residues: 2885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 337 TYR 0.016 0.001 TYR B 391 PHE 0.015 0.001 PHE K 356 TRP 0.025 0.001 TRP N 580 HIS 0.004 0.000 HIS Q 235 Details of bonding type rmsd covalent geometry : bond 0.00209 (46890) covalent geometry : angle 0.46165 (63264) hydrogen bonds : bond 0.03191 ( 1422) hydrogen bonds : angle 4.40863 ( 3924) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 5280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 612 time to evaluate : 1.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 ASN cc_start: 0.8169 (t0) cc_final: 0.7765 (p0) REVERT: A 384 GLU cc_start: 0.7232 (mm-30) cc_final: 0.6975 (mt-10) REVERT: A 387 LYS cc_start: 0.7574 (tptp) cc_final: 0.7233 (mtpt) REVERT: B 296 ASP cc_start: 0.8412 (m-30) cc_final: 0.8125 (m-30) REVERT: B 311 SER cc_start: 0.8761 (OUTLIER) cc_final: 0.8443 (p) REVERT: B 342 ASN cc_start: 0.8381 (t0) cc_final: 0.8047 (t0) REVERT: B 387 LYS cc_start: 0.7861 (tttm) cc_final: 0.7561 (mtpt) REVERT: B 424 ARG cc_start: 0.7553 (mmm160) cc_final: 0.7102 (mtp85) REVERT: C 279 SER cc_start: 0.8784 (t) cc_final: 0.8529 (p) REVERT: C 280 ARG cc_start: 0.8226 (ttt90) cc_final: 0.8012 (ttt90) REVERT: C 296 ASP cc_start: 0.7991 (m-30) cc_final: 0.7633 (p0) REVERT: C 342 ASN cc_start: 0.8780 (m-40) cc_final: 0.8531 (m-40) REVERT: C 357 LYS cc_start: 0.8216 (mtpp) cc_final: 0.7831 (pttm) REVERT: C 416 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7228 (mm-30) REVERT: D 325 LYS cc_start: 0.8672 (ttpt) cc_final: 0.8381 (ttpt) REVERT: E 274 SER cc_start: 0.9055 (m) cc_final: 0.8524 (p) REVERT: E 419 GLU cc_start: 0.6909 (pm20) cc_final: 0.6474 (mp0) REVERT: F 337 ARG cc_start: 0.7664 (mtp180) cc_final: 0.7359 (mtm-85) REVERT: F 369 ASP cc_start: 0.8192 (t0) cc_final: 0.7878 (t0) REVERT: F 381 ASN cc_start: 0.8632 (p0) cc_final: 0.8270 (p0) REVERT: G 358 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7973 (mm-30) REVERT: G 362 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8260 (mm-30) REVERT: G 434 LYS cc_start: 0.8256 (tppp) cc_final: 0.7816 (mttm) REVERT: H 295 ASP cc_start: 0.8439 (t0) cc_final: 0.8003 (m-30) REVERT: H 368 LYS cc_start: 0.8873 (mmtt) cc_final: 0.8504 (ptpp) REVERT: I 289 ASP cc_start: 0.7947 (m-30) cc_final: 0.7571 (m-30) REVERT: I 357 LYS cc_start: 0.7981 (mmtm) cc_final: 0.7542 (ptmm) REVERT: I 365 ARG cc_start: 0.8621 (mtt-85) cc_final: 0.8403 (mtt90) REVERT: I 384 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7656 (mp0) REVERT: J 272 VAL cc_start: 0.8230 (t) cc_final: 0.7967 (t) REVERT: J 318 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8263 (mm-30) REVERT: J 362 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8233 (mt-10) REVERT: K 265 LYS cc_start: 0.6893 (tttt) cc_final: 0.6516 (ttpp) REVERT: K 299 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8375 (mp) REVERT: K 368 LYS cc_start: 0.8717 (ttpt) cc_final: 0.8446 (mptt) REVERT: L 265 LYS cc_start: 0.7423 (tptt) cc_final: 0.7062 (tttt) REVERT: L 344 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7658 (mp10) REVERT: L 361 LYS cc_start: 0.8523 (ptpt) cc_final: 0.8227 (pttt) REVERT: L 407 LEU cc_start: 0.8640 (tp) cc_final: 0.8345 (tt) REVERT: M 110 LYS cc_start: 0.6210 (tppp) cc_final: 0.5654 (mtmm) REVERT: M 199 ASP cc_start: 0.8273 (t0) cc_final: 0.8008 (t0) REVERT: M 211 LYS cc_start: 0.7745 (mptt) cc_final: 0.7434 (mmmt) REVERT: M 239 SER cc_start: 0.7973 (t) cc_final: 0.7330 (p) REVERT: M 343 GLU cc_start: 0.8081 (tt0) cc_final: 0.7755 (tt0) REVERT: M 467 ARG cc_start: 0.7850 (mtp-110) cc_final: 0.7526 (ttt-90) REVERT: M 522 ILE cc_start: 0.7688 (tp) cc_final: 0.7481 (tp) REVERT: M 545 LYS cc_start: 0.8420 (tttt) cc_final: 0.7712 (tmtt) REVERT: N 112 LYS cc_start: 0.7542 (mttm) cc_final: 0.7261 (pttt) REVERT: N 115 HIS cc_start: 0.7723 (m-70) cc_final: 0.7083 (t70) REVERT: N 167 ARG cc_start: 0.7982 (mtt90) cc_final: 0.7575 (mtm-85) REVERT: N 199 ASP cc_start: 0.8410 (t0) cc_final: 0.8066 (t0) REVERT: N 242 LYS cc_start: 0.8132 (tttt) cc_final: 0.7733 (ttmt) REVERT: N 341 ARG cc_start: 0.6821 (mtm-85) cc_final: 0.6199 (ttt90) REVERT: N 453 LYS cc_start: 0.7994 (tttt) cc_final: 0.7706 (mmtm) REVERT: N 522 ILE cc_start: 0.7750 (tp) cc_final: 0.7359 (mt) REVERT: N 580 TRP cc_start: 0.7074 (OUTLIER) cc_final: 0.5573 (t60) REVERT: N 582 LYS cc_start: 0.7456 (ttmm) cc_final: 0.6679 (tmmt) REVERT: O 64 ILE cc_start: 0.7841 (mt) cc_final: 0.7540 (mp) REVERT: O 79 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7403 (mp0) REVERT: O 104 LYS cc_start: 0.8017 (mttt) cc_final: 0.7719 (mmmt) REVERT: O 123 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7630 (tp30) REVERT: O 167 ARG cc_start: 0.8232 (mtt90) cc_final: 0.7659 (mtp-110) REVERT: O 243 ARG cc_start: 0.7471 (ttt90) cc_final: 0.7183 (mtp-110) REVERT: O 349 LYS cc_start: 0.8129 (mmtp) cc_final: 0.7600 (tptp) REVERT: O 352 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7451 (mt-10) REVERT: O 509 LYS cc_start: 0.8162 (mtpt) cc_final: 0.7591 (mttm) REVERT: O 578 MET cc_start: 0.7748 (ttt) cc_final: 0.7420 (tpp) REVERT: P 104 LYS cc_start: 0.8038 (mtmt) cc_final: 0.7703 (ttpp) REVERT: P 106 PHE cc_start: 0.8565 (m-80) cc_final: 0.8253 (m-80) REVERT: P 173 ASP cc_start: 0.7564 (t0) cc_final: 0.6733 (p0) REVERT: P 295 LYS cc_start: 0.6984 (OUTLIER) cc_final: 0.6774 (ttpp) REVERT: Q 115 HIS cc_start: 0.8385 (m-70) cc_final: 0.7487 (t70) REVERT: Q 336 ASN cc_start: 0.8045 (m-40) cc_final: 0.7797 (m110) REVERT: Q 562 LYS cc_start: 0.8587 (tptt) cc_final: 0.7997 (tmtt) REVERT: Q 572 SER cc_start: 0.7011 (p) cc_final: 0.6617 (t) REVERT: R 107 SER cc_start: 0.7619 (t) cc_final: 0.7262 (m) REVERT: R 115 HIS cc_start: 0.8167 (m-70) cc_final: 0.7417 (t70) REVERT: R 165 ASP cc_start: 0.7390 (m-30) cc_final: 0.7166 (t0) REVERT: R 167 ARG cc_start: 0.7940 (mpt180) cc_final: 0.7655 (tpp80) REVERT: R 187 GLU cc_start: 0.7882 (pt0) cc_final: 0.7558 (pt0) REVERT: R 199 ASP cc_start: 0.7807 (t70) cc_final: 0.7492 (t0) REVERT: R 457 LYS cc_start: 0.7689 (tttm) cc_final: 0.7052 (mtpt) REVERT: R 485 ASP cc_start: 0.8367 (t70) cc_final: 0.8021 (t0) REVERT: R 562 LYS cc_start: 0.8394 (ttmt) cc_final: 0.8032 (ttpt) outliers start: 79 outliers final: 62 residues processed: 661 average time/residue: 0.2758 time to fit residues: 296.1220 Evaluate side-chains 634 residues out of total 5280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 568 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 356 PHE Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 384 GLU Chi-restraints excluded: chain F residue 416 GLU Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 378 ILE Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 286 ILE Chi-restraints excluded: chain H residue 289 ASP Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 405 VAL Chi-restraints excluded: chain H residue 409 ASP Chi-restraints excluded: chain I residue 407 LEU Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain K residue 299 ILE Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain L residue 313 ILE Chi-restraints excluded: chain L residue 400 VAL Chi-restraints excluded: chain L residue 434 LYS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 208 GLU Chi-restraints excluded: chain M residue 248 ASN Chi-restraints excluded: chain M residue 385 SER Chi-restraints excluded: chain M residue 511 LEU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 99 ASP Chi-restraints excluded: chain N residue 296 LEU Chi-restraints excluded: chain N residue 511 LEU Chi-restraints excluded: chain N residue 580 TRP Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 370 HIS Chi-restraints excluded: chain O residue 478 GLN Chi-restraints excluded: chain O residue 540 ILE Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 6 VAL Chi-restraints excluded: chain P residue 101 ILE Chi-restraints excluded: chain P residue 126 SER Chi-restraints excluded: chain P residue 283 VAL Chi-restraints excluded: chain P residue 295 LYS Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 521 GLU Chi-restraints excluded: chain Q residue 6 VAL Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain Q residue 101 ILE Chi-restraints excluded: chain Q residue 108 ASN Chi-restraints excluded: chain Q residue 184 ILE Chi-restraints excluded: chain Q residue 193 GLU Chi-restraints excluded: chain Q residue 451 GLU Chi-restraints excluded: chain Q residue 496 ASN Chi-restraints excluded: chain R residue 21 LEU Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 184 ILE Chi-restraints excluded: chain R residue 577 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 241 optimal weight: 9.9990 chunk 48 optimal weight: 0.5980 chunk 365 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 383 optimal weight: 2.9990 chunk 496 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 228 optimal weight: 0.9990 chunk 182 optimal weight: 4.9990 chunk 430 optimal weight: 3.9990 chunk 342 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 360 ASN H 381 ASN M 248 ASN ** M 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN O 556 GLN ** P 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.143968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.109914 restraints weight = 53845.927| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.44 r_work: 0.3091 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 46890 Z= 0.132 Angle : 0.484 9.977 63264 Z= 0.256 Chirality : 0.045 0.220 7044 Planarity : 0.003 0.036 8154 Dihedral : 4.305 59.033 6034 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.88 % Favored : 94.96 % Rotamer: Outliers : 1.84 % Allowed : 12.99 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.11), residues: 5574 helix: 0.56 (0.12), residues: 1924 sheet: -0.32 (0.19), residues: 767 loop : -1.25 (0.11), residues: 2883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 337 TYR 0.014 0.001 TYR M 188 PHE 0.016 0.001 PHE N 95 TRP 0.028 0.002 TRP N 580 HIS 0.009 0.001 HIS G 335 Details of bonding type rmsd covalent geometry : bond 0.00321 (46890) covalent geometry : angle 0.48382 (63264) hydrogen bonds : bond 0.03466 ( 1422) hydrogen bonds : angle 4.40214 ( 3924) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 5280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 572 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.8815 (mp) REVERT: A 381 ASN cc_start: 0.8246 (t0) cc_final: 0.7737 (p0) REVERT: A 384 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6709 (mt-10) REVERT: A 387 LYS cc_start: 0.7625 (tptp) cc_final: 0.7266 (mtpt) REVERT: B 296 ASP cc_start: 0.8483 (m-30) cc_final: 0.8183 (m-30) REVERT: B 311 SER cc_start: 0.8808 (OUTLIER) cc_final: 0.8512 (p) REVERT: B 342 ASN cc_start: 0.8458 (t0) cc_final: 0.8073 (t0) REVERT: B 378 ILE cc_start: 0.9253 (OUTLIER) cc_final: 0.8744 (mt) REVERT: B 387 LYS cc_start: 0.7741 (tttm) cc_final: 0.7417 (mtpt) REVERT: B 424 ARG cc_start: 0.7486 (mmm160) cc_final: 0.7049 (mtp85) REVERT: C 279 SER cc_start: 0.8810 (t) cc_final: 0.8557 (p) REVERT: C 296 ASP cc_start: 0.8148 (m-30) cc_final: 0.7618 (p0) REVERT: C 342 ASN cc_start: 0.8880 (m-40) cc_final: 0.8627 (m-40) REVERT: C 357 LYS cc_start: 0.8268 (mtpp) cc_final: 0.7806 (pttm) REVERT: C 416 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7147 (mm-30) REVERT: D 325 LYS cc_start: 0.8698 (ttpt) cc_final: 0.8479 (ttpt) REVERT: E 274 SER cc_start: 0.9013 (m) cc_final: 0.8483 (p) REVERT: E 419 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6485 (mp0) REVERT: F 337 ARG cc_start: 0.7719 (mtp180) cc_final: 0.7271 (mtm-85) REVERT: F 369 ASP cc_start: 0.8371 (t0) cc_final: 0.8030 (t0) REVERT: F 381 ASN cc_start: 0.8699 (p0) cc_final: 0.8343 (p0) REVERT: G 358 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8074 (mm-30) REVERT: G 362 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8351 (mm-30) REVERT: G 434 LYS cc_start: 0.8372 (tppp) cc_final: 0.7756 (mttt) REVERT: H 368 LYS cc_start: 0.8865 (mmtt) cc_final: 0.8446 (ptpp) REVERT: H 432 MET cc_start: 0.8876 (mtm) cc_final: 0.8517 (mtm) REVERT: H 435 GLU cc_start: 0.6539 (mm-30) cc_final: 0.6112 (mp0) REVERT: I 289 ASP cc_start: 0.8082 (m-30) cc_final: 0.7645 (m-30) REVERT: I 357 LYS cc_start: 0.7976 (mmtm) cc_final: 0.7443 (ptmm) REVERT: I 365 ARG cc_start: 0.8734 (mtt-85) cc_final: 0.8493 (mtt90) REVERT: J 272 VAL cc_start: 0.8263 (t) cc_final: 0.7999 (t) REVERT: J 318 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8309 (mm-30) REVERT: J 362 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8461 (mt-10) REVERT: K 265 LYS cc_start: 0.6726 (tttt) cc_final: 0.6355 (ttpp) REVERT: K 299 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8487 (mp) REVERT: K 368 LYS cc_start: 0.8761 (ttpt) cc_final: 0.8422 (mptt) REVERT: L 265 LYS cc_start: 0.7448 (tptt) cc_final: 0.6924 (tttt) REVERT: L 307 ASP cc_start: 0.7913 (m-30) cc_final: 0.7496 (m-30) REVERT: L 344 GLN cc_start: 0.8162 (mm-40) cc_final: 0.7648 (mt0) REVERT: L 361 LYS cc_start: 0.8358 (ptpt) cc_final: 0.8081 (pttt) REVERT: L 407 LEU cc_start: 0.8623 (tp) cc_final: 0.8308 (tt) REVERT: M 110 LYS cc_start: 0.5959 (tppp) cc_final: 0.5377 (mtmm) REVERT: M 113 ILE cc_start: 0.8196 (tt) cc_final: 0.7938 (tp) REVERT: M 199 ASP cc_start: 0.8441 (t0) cc_final: 0.8191 (t0) REVERT: M 211 LYS cc_start: 0.7870 (mptt) cc_final: 0.7540 (mmmt) REVERT: M 239 SER cc_start: 0.7851 (t) cc_final: 0.7219 (p) REVERT: M 343 GLU cc_start: 0.8309 (tt0) cc_final: 0.7952 (tt0) REVERT: M 467 ARG cc_start: 0.7998 (mtp-110) cc_final: 0.7535 (ttt-90) REVERT: M 545 LYS cc_start: 0.8437 (tttt) cc_final: 0.7671 (tmtt) REVERT: N 101 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7622 (mt) REVERT: N 112 LYS cc_start: 0.7415 (mttm) cc_final: 0.6994 (pttt) REVERT: N 115 HIS cc_start: 0.7930 (m-70) cc_final: 0.7156 (t70) REVERT: N 167 ARG cc_start: 0.7931 (mtt90) cc_final: 0.7452 (mtm-85) REVERT: N 199 ASP cc_start: 0.8534 (t0) cc_final: 0.8123 (t0) REVERT: N 242 LYS cc_start: 0.7968 (tttt) cc_final: 0.7599 (ttmt) REVERT: N 341 ARG cc_start: 0.6949 (mtm-85) cc_final: 0.6194 (ttt90) REVERT: N 363 ASN cc_start: 0.7200 (m-40) cc_final: 0.6804 (t0) REVERT: N 453 LYS cc_start: 0.8030 (tttt) cc_final: 0.7646 (mmtm) REVERT: N 522 ILE cc_start: 0.7696 (tp) cc_final: 0.7301 (mt) REVERT: N 580 TRP cc_start: 0.7155 (OUTLIER) cc_final: 0.5601 (t60) REVERT: N 582 LYS cc_start: 0.7344 (ttmm) cc_final: 0.6575 (tmmt) REVERT: O 64 ILE cc_start: 0.7832 (mt) cc_final: 0.7503 (mp) REVERT: O 79 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7418 (mp0) REVERT: O 104 LYS cc_start: 0.7858 (mttt) cc_final: 0.7553 (mmmt) REVERT: O 123 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7646 (tp30) REVERT: O 167 ARG cc_start: 0.8246 (mtt90) cc_final: 0.7492 (mtp-110) REVERT: O 243 ARG cc_start: 0.7611 (ttt90) cc_final: 0.7288 (mtp-110) REVERT: O 349 LYS cc_start: 0.8184 (mmtp) cc_final: 0.7513 (tptp) REVERT: O 352 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7593 (mt-10) REVERT: O 509 LYS cc_start: 0.8062 (mtpt) cc_final: 0.7469 (mttm) REVERT: O 558 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7627 (mt) REVERT: O 578 MET cc_start: 0.7824 (ttt) cc_final: 0.7387 (tpp) REVERT: P 104 LYS cc_start: 0.8067 (mtmt) cc_final: 0.7668 (ttpp) REVERT: P 173 ASP cc_start: 0.7656 (t0) cc_final: 0.6652 (p0) REVERT: P 228 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7221 (tm-30) REVERT: P 295 LYS cc_start: 0.6818 (OUTLIER) cc_final: 0.6457 (tttm) REVERT: P 296 LEU cc_start: 0.5447 (OUTLIER) cc_final: 0.5238 (pp) REVERT: P 446 ARG cc_start: 0.8225 (ttm-80) cc_final: 0.7719 (ttm-80) REVERT: P 457 LYS cc_start: 0.8598 (tttt) cc_final: 0.8016 (tptt) REVERT: Q 115 HIS cc_start: 0.8469 (m-70) cc_final: 0.7428 (t70) REVERT: Q 233 ASN cc_start: 0.6700 (m-40) cc_final: 0.6432 (m-40) REVERT: Q 336 ASN cc_start: 0.7936 (m-40) cc_final: 0.7674 (m-40) REVERT: Q 562 LYS cc_start: 0.8583 (tptt) cc_final: 0.7945 (tmtt) REVERT: Q 572 SER cc_start: 0.6828 (OUTLIER) cc_final: 0.6457 (t) REVERT: R 78 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7208 (mm-30) REVERT: R 107 SER cc_start: 0.7582 (t) cc_final: 0.7217 (m) REVERT: R 115 HIS cc_start: 0.8309 (m-70) cc_final: 0.7343 (t70) REVERT: R 165 ASP cc_start: 0.7716 (m-30) cc_final: 0.7286 (t0) REVERT: R 167 ARG cc_start: 0.7885 (mpt180) cc_final: 0.7565 (tpp80) REVERT: R 187 GLU cc_start: 0.8027 (pt0) cc_final: 0.7692 (pt0) REVERT: R 457 LYS cc_start: 0.7811 (tttm) cc_final: 0.7125 (mtpt) REVERT: R 485 ASP cc_start: 0.8451 (t70) cc_final: 0.8051 (t0) outliers start: 97 outliers final: 72 residues processed: 633 average time/residue: 0.2663 time to fit residues: 274.5477 Evaluate side-chains 642 residues out of total 5280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 558 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 356 PHE Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 419 GLU Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 384 GLU Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 378 ILE Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 286 ILE Chi-restraints excluded: chain H residue 289 ASP Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 405 VAL Chi-restraints excluded: chain H residue 409 ASP Chi-restraints excluded: chain I residue 272 VAL Chi-restraints excluded: chain I residue 379 SER Chi-restraints excluded: chain I residue 407 LEU Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain K residue 299 ILE Chi-restraints excluded: chain K residue 313 ILE Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain L residue 313 ILE Chi-restraints excluded: chain L residue 400 VAL Chi-restraints excluded: chain L residue 434 LYS Chi-restraints excluded: chain M residue 6 VAL Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 101 ILE Chi-restraints excluded: chain M residue 208 GLU Chi-restraints excluded: chain M residue 301 LEU Chi-restraints excluded: chain M residue 511 LEU Chi-restraints excluded: chain M residue 558 ILE Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 74 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 99 ASP Chi-restraints excluded: chain N residue 101 ILE Chi-restraints excluded: chain N residue 296 LEU Chi-restraints excluded: chain N residue 511 LEU Chi-restraints excluded: chain N residue 580 TRP Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 478 GLN Chi-restraints excluded: chain O residue 540 ILE Chi-restraints excluded: chain O residue 558 ILE Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 6 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 101 ILE Chi-restraints excluded: chain P residue 228 GLU Chi-restraints excluded: chain P residue 283 VAL Chi-restraints excluded: chain P residue 295 LYS Chi-restraints excluded: chain P residue 296 LEU Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 521 GLU Chi-restraints excluded: chain Q residue 6 VAL Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain Q residue 101 ILE Chi-restraints excluded: chain Q residue 108 ASN Chi-restraints excluded: chain Q residue 184 ILE Chi-restraints excluded: chain Q residue 193 GLU Chi-restraints excluded: chain Q residue 356 LEU Chi-restraints excluded: chain Q residue 451 GLU Chi-restraints excluded: chain Q residue 496 ASN Chi-restraints excluded: chain Q residue 572 SER Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 184 ILE Chi-restraints excluded: chain R residue 577 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 322 optimal weight: 4.9990 chunk 406 optimal weight: 6.9990 chunk 324 optimal weight: 3.9990 chunk 129 optimal weight: 0.4980 chunk 245 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 216 optimal weight: 4.9990 chunk 219 optimal weight: 0.7980 chunk 329 optimal weight: 3.9990 chunk 326 optimal weight: 0.0000 chunk 488 optimal weight: 5.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN H 381 ASN M 248 ASN ** M 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN O 370 HIS O 386 ASN O 556 GLN ** P 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.142446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.108412 restraints weight = 53943.477| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.48 r_work: 0.3065 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 46890 Z= 0.157 Angle : 0.506 9.983 63264 Z= 0.268 Chirality : 0.045 0.203 7044 Planarity : 0.003 0.035 8154 Dihedral : 4.427 55.055 6034 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.20 % Favored : 94.65 % Rotamer: Outliers : 2.23 % Allowed : 13.41 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.11), residues: 5574 helix: 0.53 (0.12), residues: 1932 sheet: -0.38 (0.19), residues: 766 loop : -1.29 (0.11), residues: 2876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 337 TYR 0.014 0.001 TYR F 355 PHE 0.020 0.001 PHE F 356 TRP 0.029 0.002 TRP N 580 HIS 0.009 0.001 HIS G 335 Details of bonding type rmsd covalent geometry : bond 0.00387 (46890) covalent geometry : angle 0.50568 (63264) hydrogen bonds : bond 0.03663 ( 1422) hydrogen bonds : angle 4.42699 ( 3924) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 5280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 571 time to evaluate : 1.574 Fit side-chains revert: symmetry clash REVERT: A 378 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.8812 (mp) REVERT: A 381 ASN cc_start: 0.8309 (t0) cc_final: 0.7750 (p0) REVERT: A 384 GLU cc_start: 0.7071 (mm-30) cc_final: 0.6725 (mt-10) REVERT: A 387 LYS cc_start: 0.7705 (tptp) cc_final: 0.7300 (mtpt) REVERT: B 296 ASP cc_start: 0.8520 (m-30) cc_final: 0.8219 (m-30) REVERT: B 311 SER cc_start: 0.8814 (OUTLIER) cc_final: 0.8503 (p) REVERT: B 342 ASN cc_start: 0.8334 (t0) cc_final: 0.8053 (t0) REVERT: B 350 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8623 (mt) REVERT: B 378 ILE cc_start: 0.9252 (OUTLIER) cc_final: 0.8747 (mt) REVERT: B 387 LYS cc_start: 0.7730 (tttm) cc_final: 0.7402 (mtpt) REVERT: B 424 ARG cc_start: 0.7496 (mmm160) cc_final: 0.7077 (mtp85) REVERT: C 279 SER cc_start: 0.8827 (t) cc_final: 0.8575 (p) REVERT: C 296 ASP cc_start: 0.8201 (m-30) cc_final: 0.7629 (p0) REVERT: C 342 ASN cc_start: 0.8850 (m-40) cc_final: 0.8567 (m-40) REVERT: C 357 LYS cc_start: 0.8296 (mtpp) cc_final: 0.7804 (pttm) REVERT: C 416 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7582 (mm-30) REVERT: D 325 LYS cc_start: 0.8675 (ttpt) cc_final: 0.8459 (ttpt) REVERT: E 274 SER cc_start: 0.8999 (m) cc_final: 0.8468 (p) REVERT: E 341 ARG cc_start: 0.7824 (mtt-85) cc_final: 0.7531 (mtp85) REVERT: E 419 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6472 (mp0) REVERT: F 337 ARG cc_start: 0.7674 (mtp180) cc_final: 0.7237 (mtm-85) REVERT: F 369 ASP cc_start: 0.8404 (t0) cc_final: 0.8053 (t0) REVERT: F 378 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8080 (mp) REVERT: F 381 ASN cc_start: 0.8675 (p0) cc_final: 0.8319 (p0) REVERT: G 333 GLU cc_start: 0.7727 (pt0) cc_final: 0.7462 (mm-30) REVERT: G 358 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8126 (mm-30) REVERT: G 362 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8378 (mm-30) REVERT: G 368 LYS cc_start: 0.8182 (ptpp) cc_final: 0.7544 (ptmm) REVERT: G 434 LYS cc_start: 0.8405 (tppp) cc_final: 0.7813 (mttm) REVERT: H 368 LYS cc_start: 0.8884 (mmtt) cc_final: 0.8426 (ptpp) REVERT: H 387 LYS cc_start: 0.7558 (mtpt) cc_final: 0.7223 (mmmm) REVERT: H 435 GLU cc_start: 0.6607 (mm-30) cc_final: 0.6178 (mp0) REVERT: I 289 ASP cc_start: 0.8081 (m-30) cc_final: 0.7647 (m-30) REVERT: I 357 LYS cc_start: 0.7972 (mmtm) cc_final: 0.7425 (ptmm) REVERT: I 365 ARG cc_start: 0.8750 (mtt-85) cc_final: 0.8494 (mtt90) REVERT: J 272 VAL cc_start: 0.8260 (OUTLIER) cc_final: 0.7998 (t) REVERT: K 265 LYS cc_start: 0.6704 (tttt) cc_final: 0.6368 (ttpp) REVERT: K 299 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8432 (mp) REVERT: K 318 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.6986 (mt-10) REVERT: K 368 LYS cc_start: 0.8775 (ttpt) cc_final: 0.8424 (mptt) REVERT: L 265 LYS cc_start: 0.7489 (tptt) cc_final: 0.6901 (ttmm) REVERT: L 307 ASP cc_start: 0.7942 (m-30) cc_final: 0.7551 (m-30) REVERT: L 344 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7638 (mt0) REVERT: L 361 LYS cc_start: 0.8400 (ptpt) cc_final: 0.8114 (pttt) REVERT: L 407 LEU cc_start: 0.8637 (tp) cc_final: 0.8324 (tt) REVERT: M 110 LYS cc_start: 0.5872 (tppp) cc_final: 0.5285 (mtmm) REVERT: M 113 ILE cc_start: 0.8410 (tt) cc_final: 0.8132 (tp) REVERT: M 199 ASP cc_start: 0.8448 (t0) cc_final: 0.8170 (t0) REVERT: M 211 LYS cc_start: 0.7880 (mptt) cc_final: 0.7548 (mmmt) REVERT: M 239 SER cc_start: 0.7908 (t) cc_final: 0.7268 (p) REVERT: M 343 GLU cc_start: 0.8128 (tt0) cc_final: 0.7879 (tt0) REVERT: M 467 ARG cc_start: 0.7996 (mtp-110) cc_final: 0.7582 (ttt-90) REVERT: M 545 LYS cc_start: 0.8447 (tttt) cc_final: 0.7831 (tptp) REVERT: N 55 LYS cc_start: 0.8786 (tttt) cc_final: 0.8472 (ttpp) REVERT: N 101 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7617 (mt) REVERT: N 115 HIS cc_start: 0.8015 (m-70) cc_final: 0.7207 (t70) REVERT: N 165 ASP cc_start: 0.7837 (t0) cc_final: 0.7432 (t0) REVERT: N 199 ASP cc_start: 0.8498 (t0) cc_final: 0.8083 (t0) REVERT: N 242 LYS cc_start: 0.7940 (tttt) cc_final: 0.7571 (ttmt) REVERT: N 341 ARG cc_start: 0.6926 (mtm-85) cc_final: 0.6169 (ttt90) REVERT: N 363 ASN cc_start: 0.7206 (m-40) cc_final: 0.6824 (t0) REVERT: N 453 LYS cc_start: 0.8056 (tttt) cc_final: 0.7602 (mmtm) REVERT: N 522 ILE cc_start: 0.7731 (tp) cc_final: 0.7319 (mt) REVERT: N 580 TRP cc_start: 0.7213 (OUTLIER) cc_final: 0.5759 (t60) REVERT: N 582 LYS cc_start: 0.7373 (ttmm) cc_final: 0.6588 (tmmt) REVERT: O 64 ILE cc_start: 0.7833 (mt) cc_final: 0.7517 (mp) REVERT: O 79 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7347 (mp0) REVERT: O 104 LYS cc_start: 0.7869 (mttt) cc_final: 0.7568 (mmmt) REVERT: O 109 GLU cc_start: 0.5513 (mm-30) cc_final: 0.5259 (mp0) REVERT: O 123 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7667 (tp30) REVERT: O 167 ARG cc_start: 0.8241 (mtt90) cc_final: 0.7554 (mtp-110) REVERT: O 184 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.8045 (mm) REVERT: O 243 ARG cc_start: 0.7600 (ttt90) cc_final: 0.7260 (mtp-110) REVERT: O 349 LYS cc_start: 0.8208 (mmtp) cc_final: 0.7679 (tptp) REVERT: O 352 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7776 (mt-10) REVERT: O 509 LYS cc_start: 0.8043 (mtpt) cc_final: 0.7552 (mttt) REVERT: O 578 MET cc_start: 0.7801 (ttt) cc_final: 0.7384 (tpp) REVERT: P 104 LYS cc_start: 0.7994 (mtmt) cc_final: 0.7680 (ttpp) REVERT: P 173 ASP cc_start: 0.7678 (t0) cc_final: 0.6928 (p0) REVERT: P 228 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7194 (tm-30) REVERT: P 295 LYS cc_start: 0.6961 (OUTLIER) cc_final: 0.6676 (ttpp) REVERT: P 296 LEU cc_start: 0.5393 (OUTLIER) cc_final: 0.5099 (pp) REVERT: P 457 LYS cc_start: 0.8573 (tttt) cc_final: 0.8032 (ttmm) REVERT: Q 115 HIS cc_start: 0.8468 (m-70) cc_final: 0.7315 (t-170) REVERT: Q 233 ASN cc_start: 0.6825 (m-40) cc_final: 0.6619 (m-40) REVERT: Q 336 ASN cc_start: 0.7952 (m-40) cc_final: 0.7668 (m-40) REVERT: Q 562 LYS cc_start: 0.8593 (tptt) cc_final: 0.8015 (tmtt) REVERT: Q 572 SER cc_start: 0.6728 (OUTLIER) cc_final: 0.6392 (t) REVERT: R 78 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7231 (mm-30) REVERT: R 107 SER cc_start: 0.7621 (t) cc_final: 0.7295 (m) REVERT: R 115 HIS cc_start: 0.8301 (m-70) cc_final: 0.7330 (t70) REVERT: R 165 ASP cc_start: 0.7757 (m-30) cc_final: 0.7312 (t0) REVERT: R 167 ARG cc_start: 0.7913 (mpt180) cc_final: 0.7600 (tpp80) REVERT: R 187 GLU cc_start: 0.8050 (pt0) cc_final: 0.7826 (pt0) REVERT: R 457 LYS cc_start: 0.7891 (tttm) cc_final: 0.7212 (mtpt) REVERT: R 485 ASP cc_start: 0.8452 (t70) cc_final: 0.8081 (t0) outliers start: 118 outliers final: 85 residues processed: 644 average time/residue: 0.2700 time to fit residues: 281.9463 Evaluate side-chains 655 residues out of total 5280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 554 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 356 PHE Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 419 GLU Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 384 GLU Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 369 ASP Chi-restraints excluded: chain G residue 378 ILE Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 274 SER Chi-restraints excluded: chain H residue 286 ILE Chi-restraints excluded: chain H residue 289 ASP Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 405 VAL Chi-restraints excluded: chain H residue 409 ASP Chi-restraints excluded: chain I residue 272 VAL Chi-restraints excluded: chain I residue 379 SER Chi-restraints excluded: chain I residue 407 LEU Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain K residue 299 ILE Chi-restraints excluded: chain K residue 313 ILE Chi-restraints excluded: chain K residue 318 GLU Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain L residue 313 ILE Chi-restraints excluded: chain L residue 400 VAL Chi-restraints excluded: chain L residue 434 LYS Chi-restraints excluded: chain M residue 6 VAL Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 101 ILE Chi-restraints excluded: chain M residue 208 GLU Chi-restraints excluded: chain M residue 301 LEU Chi-restraints excluded: chain M residue 511 LEU Chi-restraints excluded: chain M residue 558 ILE Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 74 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 99 ASP Chi-restraints excluded: chain N residue 101 ILE Chi-restraints excluded: chain N residue 285 ASN Chi-restraints excluded: chain N residue 296 LEU Chi-restraints excluded: chain N residue 356 LEU Chi-restraints excluded: chain N residue 511 LEU Chi-restraints excluded: chain N residue 580 TRP Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 184 ILE Chi-restraints excluded: chain O residue 370 HIS Chi-restraints excluded: chain O residue 402 ILE Chi-restraints excluded: chain O residue 540 ILE Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 6 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 101 ILE Chi-restraints excluded: chain P residue 126 SER Chi-restraints excluded: chain P residue 228 GLU Chi-restraints excluded: chain P residue 283 VAL Chi-restraints excluded: chain P residue 295 LYS Chi-restraints excluded: chain P residue 296 LEU Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 521 GLU Chi-restraints excluded: chain P residue 555 SER Chi-restraints excluded: chain Q residue 6 VAL Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain Q residue 101 ILE Chi-restraints excluded: chain Q residue 108 ASN Chi-restraints excluded: chain Q residue 184 ILE Chi-restraints excluded: chain Q residue 193 GLU Chi-restraints excluded: chain Q residue 356 LEU Chi-restraints excluded: chain Q residue 451 GLU Chi-restraints excluded: chain Q residue 496 ASN Chi-restraints excluded: chain Q residue 572 SER Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 184 ILE Chi-restraints excluded: chain R residue 260 THR Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 577 ILE Chi-restraints excluded: chain R residue 578 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 521 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 316 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 542 optimal weight: 6.9990 chunk 297 optimal weight: 0.5980 chunk 220 optimal weight: 5.9990 chunk 553 optimal weight: 1.9990 chunk 227 optimal weight: 6.9990 chunk 242 optimal weight: 0.0070 chunk 392 optimal weight: 2.9990 overall best weight: 1.3204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN C 270 GLN M 248 ASN ** M 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN O 556 GLN ** P 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.143024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.109058 restraints weight = 53711.190| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.45 r_work: 0.3082 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 46890 Z= 0.133 Angle : 0.492 9.971 63264 Z= 0.261 Chirality : 0.045 0.226 7044 Planarity : 0.003 0.035 8154 Dihedral : 4.378 47.197 6034 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.75 % Favored : 95.10 % Rotamer: Outliers : 2.10 % Allowed : 14.05 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.11), residues: 5574 helix: 0.58 (0.12), residues: 1933 sheet: -0.42 (0.19), residues: 769 loop : -1.30 (0.11), residues: 2872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 267 TYR 0.015 0.001 TYR B 391 PHE 0.025 0.001 PHE K 356 TRP 0.027 0.002 TRP N 580 HIS 0.019 0.001 HIS O 370 Details of bonding type rmsd covalent geometry : bond 0.00325 (46890) covalent geometry : angle 0.49162 (63264) hydrogen bonds : bond 0.03463 ( 1422) hydrogen bonds : angle 4.37854 ( 3924) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 5280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 577 time to evaluate : 2.203 Fit side-chains revert: symmetry clash REVERT: A 337 ARG cc_start: 0.7880 (mmm-85) cc_final: 0.7662 (mtt90) REVERT: A 378 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.8833 (mp) REVERT: A 381 ASN cc_start: 0.8314 (t0) cc_final: 0.7746 (p0) REVERT: A 384 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6738 (mt-10) REVERT: A 387 LYS cc_start: 0.7719 (tptp) cc_final: 0.7318 (mtpt) REVERT: B 296 ASP cc_start: 0.8536 (m-30) cc_final: 0.8240 (m-30) REVERT: B 311 SER cc_start: 0.8812 (OUTLIER) cc_final: 0.8513 (p) REVERT: B 342 ASN cc_start: 0.8427 (t0) cc_final: 0.8036 (t0) REVERT: B 350 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8608 (mt) REVERT: B 378 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.8732 (mt) REVERT: B 387 LYS cc_start: 0.7744 (tttm) cc_final: 0.7420 (mtpt) REVERT: B 424 ARG cc_start: 0.7506 (mmm160) cc_final: 0.7096 (mtp85) REVERT: C 279 SER cc_start: 0.8824 (t) cc_final: 0.8578 (p) REVERT: C 280 ARG cc_start: 0.8218 (ttt90) cc_final: 0.7913 (ttt90) REVERT: C 296 ASP cc_start: 0.8226 (m-30) cc_final: 0.7640 (p0) REVERT: C 357 LYS cc_start: 0.8290 (mtpp) cc_final: 0.7808 (pttm) REVERT: C 416 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7547 (mm-30) REVERT: E 274 SER cc_start: 0.9001 (m) cc_final: 0.8467 (p) REVERT: E 419 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6474 (mp0) REVERT: F 337 ARG cc_start: 0.7679 (mtp180) cc_final: 0.7253 (mtm-85) REVERT: F 369 ASP cc_start: 0.8423 (t0) cc_final: 0.8075 (t0) REVERT: F 378 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8070 (mp) REVERT: F 381 ASN cc_start: 0.8701 (p0) cc_final: 0.8343 (p0) REVERT: G 333 GLU cc_start: 0.7737 (pt0) cc_final: 0.7476 (mm-30) REVERT: G 362 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8361 (mm-30) REVERT: G 368 LYS cc_start: 0.8172 (ptpp) cc_final: 0.7553 (ptmm) REVERT: G 434 LYS cc_start: 0.8413 (tppp) cc_final: 0.7802 (mttm) REVERT: H 368 LYS cc_start: 0.8901 (mmtt) cc_final: 0.8488 (ptpp) REVERT: H 387 LYS cc_start: 0.7600 (mtpt) cc_final: 0.7324 (mmmm) REVERT: H 432 MET cc_start: 0.8836 (mtm) cc_final: 0.8503 (mtm) REVERT: H 435 GLU cc_start: 0.6523 (mm-30) cc_final: 0.6137 (mp0) REVERT: I 289 ASP cc_start: 0.8077 (m-30) cc_final: 0.7641 (m-30) REVERT: I 357 LYS cc_start: 0.7973 (mmtm) cc_final: 0.7436 (ptmm) REVERT: I 365 ARG cc_start: 0.8743 (mtt-85) cc_final: 0.8487 (mtt90) REVERT: J 272 VAL cc_start: 0.8331 (OUTLIER) cc_final: 0.8070 (t) REVERT: K 265 LYS cc_start: 0.6686 (tttt) cc_final: 0.6366 (ttpp) REVERT: K 299 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8466 (mp) REVERT: K 318 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7009 (mt-10) REVERT: K 368 LYS cc_start: 0.8785 (ttpt) cc_final: 0.8429 (mptt) REVERT: K 369 ASP cc_start: 0.8480 (t0) cc_final: 0.8273 (t0) REVERT: L 265 LYS cc_start: 0.7565 (tptt) cc_final: 0.7012 (ttmm) REVERT: L 307 ASP cc_start: 0.7887 (m-30) cc_final: 0.7496 (m-30) REVERT: L 344 GLN cc_start: 0.8136 (mm-40) cc_final: 0.7645 (mt0) REVERT: L 361 LYS cc_start: 0.8407 (ptpt) cc_final: 0.8104 (pttt) REVERT: L 407 LEU cc_start: 0.8630 (tp) cc_final: 0.8316 (tt) REVERT: M 110 LYS cc_start: 0.5921 (tppp) cc_final: 0.5318 (mtmm) REVERT: M 113 ILE cc_start: 0.8448 (tt) cc_final: 0.8160 (tp) REVERT: M 199 ASP cc_start: 0.8445 (t0) cc_final: 0.8202 (t0) REVERT: M 211 LYS cc_start: 0.7898 (mptt) cc_final: 0.7539 (mmmt) REVERT: M 239 SER cc_start: 0.7928 (t) cc_final: 0.7293 (p) REVERT: M 343 GLU cc_start: 0.8128 (tt0) cc_final: 0.7867 (tt0) REVERT: M 467 ARG cc_start: 0.7988 (mtp-110) cc_final: 0.7526 (ttt-90) REVERT: M 545 LYS cc_start: 0.8442 (tttt) cc_final: 0.7829 (tptp) REVERT: N 8 GLU cc_start: 0.8431 (tt0) cc_final: 0.8217 (tt0) REVERT: N 55 LYS cc_start: 0.8789 (tttt) cc_final: 0.8483 (ttpp) REVERT: N 101 ILE cc_start: 0.8005 (OUTLIER) cc_final: 0.7595 (mt) REVERT: N 112 LYS cc_start: 0.7288 (ttmm) cc_final: 0.6661 (tttp) REVERT: N 115 HIS cc_start: 0.8002 (m-70) cc_final: 0.7242 (t70) REVERT: N 165 ASP cc_start: 0.7899 (t0) cc_final: 0.7519 (t0) REVERT: N 199 ASP cc_start: 0.8503 (t0) cc_final: 0.8077 (t0) REVERT: N 242 LYS cc_start: 0.7978 (tttt) cc_final: 0.7610 (ttmt) REVERT: N 341 ARG cc_start: 0.6867 (mtm-85) cc_final: 0.6167 (ttt90) REVERT: N 363 ASN cc_start: 0.7274 (m-40) cc_final: 0.6911 (t0) REVERT: N 453 LYS cc_start: 0.8051 (tttt) cc_final: 0.7597 (mmtm) REVERT: N 522 ILE cc_start: 0.7691 (tp) cc_final: 0.7290 (mt) REVERT: N 580 TRP cc_start: 0.7168 (OUTLIER) cc_final: 0.5718 (t60) REVERT: N 582 LYS cc_start: 0.7389 (ttmm) cc_final: 0.6598 (tmmt) REVERT: O 64 ILE cc_start: 0.7846 (mt) cc_final: 0.7496 (mp) REVERT: O 79 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7342 (mp0) REVERT: O 104 LYS cc_start: 0.7868 (mttt) cc_final: 0.7573 (mmmt) REVERT: O 123 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7725 (tp30) REVERT: O 167 ARG cc_start: 0.8262 (mtt90) cc_final: 0.7582 (mtp-110) REVERT: O 184 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.8029 (mm) REVERT: O 243 ARG cc_start: 0.7638 (ttt90) cc_final: 0.7305 (mtp-110) REVERT: O 349 LYS cc_start: 0.8221 (mmtp) cc_final: 0.7756 (tptp) REVERT: O 352 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7837 (mt-10) REVERT: O 509 LYS cc_start: 0.8067 (mtpt) cc_final: 0.7504 (mttt) REVERT: O 558 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7527 (mt) REVERT: O 578 MET cc_start: 0.7809 (ttt) cc_final: 0.7387 (tpp) REVERT: P 104 LYS cc_start: 0.8063 (mtmt) cc_final: 0.7670 (ttpp) REVERT: P 173 ASP cc_start: 0.7665 (t0) cc_final: 0.6914 (p0) REVERT: P 228 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7176 (tm-30) REVERT: P 295 LYS cc_start: 0.6944 (OUTLIER) cc_final: 0.6728 (ttpp) REVERT: P 296 LEU cc_start: 0.5514 (OUTLIER) cc_final: 0.5254 (pp) REVERT: P 446 ARG cc_start: 0.8231 (ttm-80) cc_final: 0.7828 (ttm-80) REVERT: P 457 LYS cc_start: 0.8574 (tttt) cc_final: 0.8048 (ttmm) REVERT: Q 115 HIS cc_start: 0.8456 (m-70) cc_final: 0.7332 (t-170) REVERT: Q 233 ASN cc_start: 0.6824 (m-40) cc_final: 0.6610 (m-40) REVERT: Q 336 ASN cc_start: 0.7971 (m-40) cc_final: 0.7689 (m-40) REVERT: Q 562 LYS cc_start: 0.8584 (tptt) cc_final: 0.7957 (tmtt) REVERT: Q 572 SER cc_start: 0.6761 (OUTLIER) cc_final: 0.6429 (t) REVERT: R 78 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7259 (mm-30) REVERT: R 107 SER cc_start: 0.7582 (t) cc_final: 0.7279 (m) REVERT: R 115 HIS cc_start: 0.8307 (m-70) cc_final: 0.7347 (t70) REVERT: R 165 ASP cc_start: 0.7770 (m-30) cc_final: 0.7319 (t0) REVERT: R 167 ARG cc_start: 0.7921 (mpt180) cc_final: 0.7612 (tpp80) REVERT: R 187 GLU cc_start: 0.8045 (pt0) cc_final: 0.7819 (pt0) REVERT: R 457 LYS cc_start: 0.7872 (tttm) cc_final: 0.7199 (mtpt) REVERT: R 485 ASP cc_start: 0.8449 (t70) cc_final: 0.8088 (t0) outliers start: 111 outliers final: 84 residues processed: 647 average time/residue: 0.2162 time to fit residues: 228.7921 Evaluate side-chains 666 residues out of total 5280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 565 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 356 PHE Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 419 GLU Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 384 GLU Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 378 ILE Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 274 SER Chi-restraints excluded: chain H residue 286 ILE Chi-restraints excluded: chain H residue 289 ASP Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 405 VAL Chi-restraints excluded: chain H residue 409 ASP Chi-restraints excluded: chain I residue 272 VAL Chi-restraints excluded: chain I residue 281 SER Chi-restraints excluded: chain I residue 379 SER Chi-restraints excluded: chain I residue 407 LEU Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain K residue 299 ILE Chi-restraints excluded: chain K residue 313 ILE Chi-restraints excluded: chain K residue 318 GLU Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain L residue 313 ILE Chi-restraints excluded: chain L residue 400 VAL Chi-restraints excluded: chain L residue 434 LYS Chi-restraints excluded: chain M residue 6 VAL Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 101 ILE Chi-restraints excluded: chain M residue 208 GLU Chi-restraints excluded: chain M residue 511 LEU Chi-restraints excluded: chain M residue 558 ILE Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 74 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 99 ASP Chi-restraints excluded: chain N residue 101 ILE Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 296 LEU Chi-restraints excluded: chain N residue 356 LEU Chi-restraints excluded: chain N residue 511 LEU Chi-restraints excluded: chain N residue 580 TRP Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain O residue 184 ILE Chi-restraints excluded: chain O residue 255 GLU Chi-restraints excluded: chain O residue 393 SER Chi-restraints excluded: chain O residue 402 ILE Chi-restraints excluded: chain O residue 478 GLN Chi-restraints excluded: chain O residue 540 ILE Chi-restraints excluded: chain O residue 558 ILE Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 6 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 101 ILE Chi-restraints excluded: chain P residue 228 GLU Chi-restraints excluded: chain P residue 283 VAL Chi-restraints excluded: chain P residue 295 LYS Chi-restraints excluded: chain P residue 296 LEU Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 521 GLU Chi-restraints excluded: chain P residue 555 SER Chi-restraints excluded: chain Q residue 6 VAL Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain Q residue 101 ILE Chi-restraints excluded: chain Q residue 108 ASN Chi-restraints excluded: chain Q residue 184 ILE Chi-restraints excluded: chain Q residue 193 GLU Chi-restraints excluded: chain Q residue 356 LEU Chi-restraints excluded: chain Q residue 451 GLU Chi-restraints excluded: chain Q residue 496 ASN Chi-restraints excluded: chain Q residue 572 SER Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 184 ILE Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 577 ILE Chi-restraints excluded: chain R residue 578 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 2 optimal weight: 2.9990 chunk 534 optimal weight: 10.0000 chunk 337 optimal weight: 0.8980 chunk 494 optimal weight: 9.9990 chunk 148 optimal weight: 0.0270 chunk 463 optimal weight: 4.9990 chunk 200 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 466 optimal weight: 6.9990 chunk 215 optimal weight: 0.9980 chunk 440 optimal weight: 4.9990 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 248 ASN ** M 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 370 HIS O 556 GLN ** P 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.143232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.109379 restraints weight = 53814.345| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.46 r_work: 0.3083 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 46890 Z= 0.124 Angle : 0.483 10.757 63264 Z= 0.256 Chirality : 0.044 0.217 7044 Planarity : 0.003 0.035 8154 Dihedral : 4.287 46.437 6034 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.97 % Favored : 94.89 % Rotamer: Outliers : 2.22 % Allowed : 14.36 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.11), residues: 5574 helix: 0.62 (0.12), residues: 1933 sheet: -0.43 (0.19), residues: 769 loop : -1.28 (0.11), residues: 2872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 579 TYR 0.020 0.001 TYR B 391 PHE 0.023 0.001 PHE K 356 TRP 0.026 0.001 TRP N 580 HIS 0.006 0.001 HIS G 335 Details of bonding type rmsd covalent geometry : bond 0.00300 (46890) covalent geometry : angle 0.48295 (63264) hydrogen bonds : bond 0.03315 ( 1422) hydrogen bonds : angle 4.32242 ( 3924) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 5280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 585 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.8828 (mp) REVERT: A 381 ASN cc_start: 0.8275 (t0) cc_final: 0.7689 (p0) REVERT: A 384 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6701 (mt-10) REVERT: A 387 LYS cc_start: 0.7692 (tptp) cc_final: 0.7274 (mtpt) REVERT: B 296 ASP cc_start: 0.8536 (m-30) cc_final: 0.8230 (m-30) REVERT: B 311 SER cc_start: 0.8809 (OUTLIER) cc_final: 0.8494 (p) REVERT: B 342 ASN cc_start: 0.8423 (t0) cc_final: 0.8023 (t0) REVERT: B 350 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8575 (mt) REVERT: B 378 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8704 (mt) REVERT: B 387 LYS cc_start: 0.7783 (tttm) cc_final: 0.7394 (mtpt) REVERT: B 424 ARG cc_start: 0.7479 (mmm160) cc_final: 0.7082 (mtp85) REVERT: C 279 SER cc_start: 0.8809 (t) cc_final: 0.8557 (p) REVERT: C 296 ASP cc_start: 0.8229 (m-30) cc_final: 0.7639 (p0) REVERT: C 357 LYS cc_start: 0.8268 (mtpp) cc_final: 0.7788 (pttm) REVERT: E 274 SER cc_start: 0.8987 (m) cc_final: 0.8427 (p) REVERT: E 307 ASP cc_start: 0.8363 (p0) cc_final: 0.8154 (p0) REVERT: E 381 ASN cc_start: 0.8756 (t0) cc_final: 0.8438 (t0) REVERT: E 419 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6457 (mp0) REVERT: F 337 ARG cc_start: 0.7614 (mtp180) cc_final: 0.7199 (mtm-85) REVERT: F 369 ASP cc_start: 0.8373 (t0) cc_final: 0.8014 (t0) REVERT: F 378 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8053 (mp) REVERT: F 381 ASN cc_start: 0.8675 (p0) cc_final: 0.8306 (p0) REVERT: G 333 GLU cc_start: 0.7734 (pt0) cc_final: 0.7463 (mm-30) REVERT: G 362 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8359 (mm-30) REVERT: G 368 LYS cc_start: 0.8169 (ptpp) cc_final: 0.7544 (ptmm) REVERT: G 416 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7502 (mt-10) REVERT: G 434 LYS cc_start: 0.8407 (tppp) cc_final: 0.7770 (mttt) REVERT: H 368 LYS cc_start: 0.8899 (mmtt) cc_final: 0.8470 (ptpp) REVERT: H 387 LYS cc_start: 0.7694 (mtpt) cc_final: 0.7307 (mmmm) REVERT: H 432 MET cc_start: 0.8817 (mtm) cc_final: 0.8561 (mtm) REVERT: H 435 GLU cc_start: 0.6609 (mm-30) cc_final: 0.6192 (mp0) REVERT: I 289 ASP cc_start: 0.8079 (m-30) cc_final: 0.7641 (m-30) REVERT: I 357 LYS cc_start: 0.7952 (mmtm) cc_final: 0.7419 (ptmm) REVERT: I 365 ARG cc_start: 0.8723 (mtt-85) cc_final: 0.8478 (mtt90) REVERT: J 272 VAL cc_start: 0.8315 (OUTLIER) cc_final: 0.8055 (t) REVERT: J 297 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7684 (mt-10) REVERT: J 318 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8250 (mm-30) REVERT: K 265 LYS cc_start: 0.6613 (tttt) cc_final: 0.6311 (ttpp) REVERT: K 299 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8450 (mp) REVERT: K 318 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.6998 (mt-10) REVERT: K 368 LYS cc_start: 0.8787 (ttpt) cc_final: 0.8427 (mptt) REVERT: L 265 LYS cc_start: 0.7586 (tptt) cc_final: 0.7141 (ttpt) REVERT: L 307 ASP cc_start: 0.7868 (m-30) cc_final: 0.7487 (m-30) REVERT: L 344 GLN cc_start: 0.8158 (mm-40) cc_final: 0.7634 (mt0) REVERT: L 361 LYS cc_start: 0.8412 (ptpt) cc_final: 0.8100 (pttt) REVERT: L 407 LEU cc_start: 0.8614 (tp) cc_final: 0.8310 (tt) REVERT: M 41 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8212 (tm-30) REVERT: M 95 PHE cc_start: 0.8534 (m-80) cc_final: 0.8282 (m-80) REVERT: M 110 LYS cc_start: 0.5805 (tppp) cc_final: 0.5201 (mtmm) REVERT: M 113 ILE cc_start: 0.8445 (tt) cc_final: 0.8160 (tp) REVERT: M 199 ASP cc_start: 0.8437 (t0) cc_final: 0.8193 (t0) REVERT: M 211 LYS cc_start: 0.7886 (mptt) cc_final: 0.7514 (mmmt) REVERT: M 239 SER cc_start: 0.7876 (t) cc_final: 0.7185 (p) REVERT: M 343 GLU cc_start: 0.8118 (tt0) cc_final: 0.7835 (tt0) REVERT: M 467 ARG cc_start: 0.7970 (mtp-110) cc_final: 0.7507 (ttt-90) REVERT: M 545 LYS cc_start: 0.8443 (tttt) cc_final: 0.7840 (tptp) REVERT: N 55 LYS cc_start: 0.8781 (tttt) cc_final: 0.8469 (ttpp) REVERT: N 101 ILE cc_start: 0.7994 (OUTLIER) cc_final: 0.7584 (mt) REVERT: N 112 LYS cc_start: 0.7221 (ttmm) cc_final: 0.6869 (tttm) REVERT: N 115 HIS cc_start: 0.8064 (m-70) cc_final: 0.7157 (t70) REVERT: N 165 ASP cc_start: 0.7887 (t0) cc_final: 0.7513 (t0) REVERT: N 199 ASP cc_start: 0.8491 (t0) cc_final: 0.8064 (t0) REVERT: N 242 LYS cc_start: 0.7949 (tttt) cc_final: 0.7590 (ttmt) REVERT: N 341 ARG cc_start: 0.6811 (mtm-85) cc_final: 0.6086 (ttt90) REVERT: N 363 ASN cc_start: 0.7294 (m-40) cc_final: 0.6895 (t0) REVERT: N 453 LYS cc_start: 0.8051 (tttt) cc_final: 0.7593 (mmtm) REVERT: N 522 ILE cc_start: 0.7701 (tp) cc_final: 0.7312 (mt) REVERT: N 580 TRP cc_start: 0.7128 (OUTLIER) cc_final: 0.5627 (t60) REVERT: N 582 LYS cc_start: 0.7393 (ttmm) cc_final: 0.6583 (tmmt) REVERT: O 64 ILE cc_start: 0.7839 (mt) cc_final: 0.7495 (mp) REVERT: O 79 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7327 (mp0) REVERT: O 86 MET cc_start: 0.6793 (tpp) cc_final: 0.6576 (tpp) REVERT: O 104 LYS cc_start: 0.7854 (mttt) cc_final: 0.7560 (mmmt) REVERT: O 123 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7739 (tp30) REVERT: O 167 ARG cc_start: 0.8236 (mtt90) cc_final: 0.7549 (mtp-110) REVERT: O 184 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.7978 (mm) REVERT: O 243 ARG cc_start: 0.7587 (ttt90) cc_final: 0.7254 (mtp-110) REVERT: O 349 LYS cc_start: 0.8234 (mmtp) cc_final: 0.7763 (tptp) REVERT: O 352 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7925 (mt-10) REVERT: O 509 LYS cc_start: 0.8031 (mtpt) cc_final: 0.7517 (mttt) REVERT: O 578 MET cc_start: 0.7800 (ttt) cc_final: 0.7367 (tpp) REVERT: P 104 LYS cc_start: 0.8055 (mtmt) cc_final: 0.7672 (ttpp) REVERT: P 446 ARG cc_start: 0.8231 (ttm-80) cc_final: 0.7827 (ttm-80) REVERT: P 457 LYS cc_start: 0.8570 (tttt) cc_final: 0.8020 (ttmm) REVERT: Q 115 HIS cc_start: 0.8438 (m-70) cc_final: 0.7419 (t70) REVERT: Q 233 ASN cc_start: 0.6785 (m-40) cc_final: 0.6565 (m-40) REVERT: Q 336 ASN cc_start: 0.7908 (m-40) cc_final: 0.7624 (m-40) REVERT: Q 562 LYS cc_start: 0.8576 (tptt) cc_final: 0.7936 (tmtt) REVERT: Q 572 SER cc_start: 0.6755 (OUTLIER) cc_final: 0.6424 (t) REVERT: R 8 GLU cc_start: 0.8710 (tt0) cc_final: 0.8487 (tt0) REVERT: R 78 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7257 (mm-30) REVERT: R 107 SER cc_start: 0.7543 (t) cc_final: 0.7279 (m) REVERT: R 115 HIS cc_start: 0.8318 (m-70) cc_final: 0.7359 (t-170) REVERT: R 165 ASP cc_start: 0.7808 (m-30) cc_final: 0.7331 (t0) REVERT: R 167 ARG cc_start: 0.7905 (mpt180) cc_final: 0.7597 (tpp80) REVERT: R 187 GLU cc_start: 0.8040 (pt0) cc_final: 0.7812 (pt0) REVERT: R 457 LYS cc_start: 0.7807 (tttm) cc_final: 0.7134 (mtpt) REVERT: R 485 ASP cc_start: 0.8453 (t70) cc_final: 0.8019 (t0) outliers start: 117 outliers final: 89 residues processed: 659 average time/residue: 0.1889 time to fit residues: 204.4254 Evaluate side-chains 664 residues out of total 5280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 562 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 356 PHE Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 419 GLU Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 384 GLU Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 378 ILE Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 286 ILE Chi-restraints excluded: chain H residue 289 ASP Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 405 VAL Chi-restraints excluded: chain I residue 272 VAL Chi-restraints excluded: chain I residue 281 SER Chi-restraints excluded: chain I residue 379 SER Chi-restraints excluded: chain I residue 407 LEU Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain K residue 299 ILE Chi-restraints excluded: chain K residue 313 ILE Chi-restraints excluded: chain K residue 318 GLU Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain L residue 313 ILE Chi-restraints excluded: chain L residue 400 VAL Chi-restraints excluded: chain L residue 434 LYS Chi-restraints excluded: chain M residue 6 VAL Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 101 ILE Chi-restraints excluded: chain M residue 208 GLU Chi-restraints excluded: chain M residue 511 LEU Chi-restraints excluded: chain M residue 558 ILE Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 74 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 99 ASP Chi-restraints excluded: chain N residue 101 ILE Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 285 ASN Chi-restraints excluded: chain N residue 296 LEU Chi-restraints excluded: chain N residue 356 LEU Chi-restraints excluded: chain N residue 511 LEU Chi-restraints excluded: chain N residue 580 TRP Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain O residue 184 ILE Chi-restraints excluded: chain O residue 370 HIS Chi-restraints excluded: chain O residue 393 SER Chi-restraints excluded: chain O residue 402 ILE Chi-restraints excluded: chain O residue 478 GLN Chi-restraints excluded: chain O residue 540 ILE Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 6 VAL Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 101 ILE Chi-restraints excluded: chain P residue 126 SER Chi-restraints excluded: chain P residue 228 GLU Chi-restraints excluded: chain P residue 283 VAL Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 521 GLU Chi-restraints excluded: chain P residue 555 SER Chi-restraints excluded: chain Q residue 6 VAL Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain Q residue 101 ILE Chi-restraints excluded: chain Q residue 108 ASN Chi-restraints excluded: chain Q residue 184 ILE Chi-restraints excluded: chain Q residue 193 GLU Chi-restraints excluded: chain Q residue 369 GLU Chi-restraints excluded: chain Q residue 451 GLU Chi-restraints excluded: chain Q residue 496 ASN Chi-restraints excluded: chain Q residue 572 SER Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 184 ILE Chi-restraints excluded: chain R residue 260 THR Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 502 ILE Chi-restraints excluded: chain R residue 577 ILE Chi-restraints excluded: chain R residue 578 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 480 optimal weight: 5.9990 chunk 192 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 365 optimal weight: 0.9990 chunk 546 optimal weight: 0.0470 chunk 126 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 99 optimal weight: 0.0670 chunk 528 optimal weight: 20.0000 chunk 8 optimal weight: 3.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 381 ASN M 248 ASN ** M 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 248 ASN N 319 ASN O 556 GLN P 236 ASN Q 310 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.145716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.112071 restraints weight = 53655.816| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.39 r_work: 0.3117 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 46890 Z= 0.090 Angle : 0.457 10.133 63264 Z= 0.244 Chirality : 0.044 0.212 7044 Planarity : 0.003 0.034 8154 Dihedral : 4.067 45.042 6030 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.22 % Favored : 95.64 % Rotamer: Outliers : 1.67 % Allowed : 14.89 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.11), residues: 5574 helix: 0.76 (0.13), residues: 1922 sheet: -0.35 (0.19), residues: 776 loop : -1.20 (0.11), residues: 2876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 446 TYR 0.018 0.001 TYR R 277 PHE 0.024 0.001 PHE H 356 TRP 0.025 0.001 TRP O 580 HIS 0.034 0.001 HIS O 370 Details of bonding type rmsd covalent geometry : bond 0.00201 (46890) covalent geometry : angle 0.45735 (63264) hydrogen bonds : bond 0.02872 ( 1422) hydrogen bonds : angle 4.19166 ( 3924) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11148 Ramachandran restraints generated. 5574 Oldfield, 0 Emsley, 5574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 5280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 598 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ASP cc_start: 0.8161 (m-30) cc_final: 0.7823 (m-30) REVERT: A 378 ILE cc_start: 0.9310 (OUTLIER) cc_final: 0.8849 (mp) REVERT: A 381 ASN cc_start: 0.8274 (t0) cc_final: 0.7687 (p0) REVERT: A 384 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6816 (mt-10) REVERT: A 387 LYS cc_start: 0.7634 (tptp) cc_final: 0.7162 (mtpt) REVERT: B 296 ASP cc_start: 0.8532 (m-30) cc_final: 0.8214 (m-30) REVERT: B 311 SER cc_start: 0.8775 (OUTLIER) cc_final: 0.8501 (p) REVERT: B 342 ASN cc_start: 0.8397 (t0) cc_final: 0.7975 (t0) REVERT: B 350 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8633 (mt) REVERT: B 378 ILE cc_start: 0.9262 (OUTLIER) cc_final: 0.8745 (mt) REVERT: B 387 LYS cc_start: 0.7851 (tttm) cc_final: 0.7475 (mtpt) REVERT: B 424 ARG cc_start: 0.7561 (mmm160) cc_final: 0.7096 (mtp85) REVERT: C 279 SER cc_start: 0.8820 (t) cc_final: 0.8555 (p) REVERT: C 296 ASP cc_start: 0.8224 (m-30) cc_final: 0.7633 (p0) REVERT: C 341 ARG cc_start: 0.8126 (mmt90) cc_final: 0.7810 (mtp85) REVERT: C 357 LYS cc_start: 0.8290 (mtpp) cc_final: 0.7853 (pttm) REVERT: C 416 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8124 (mm-30) REVERT: D 304 ASP cc_start: 0.8379 (p0) cc_final: 0.8149 (p0) REVERT: E 274 SER cc_start: 0.9067 (m) cc_final: 0.8483 (p) REVERT: E 381 ASN cc_start: 0.8640 (t0) cc_final: 0.8384 (t0) REVERT: E 419 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6488 (mp0) REVERT: F 337 ARG cc_start: 0.7636 (mtp180) cc_final: 0.7282 (mtm-85) REVERT: F 369 ASP cc_start: 0.8435 (t0) cc_final: 0.8098 (t0) REVERT: F 378 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8071 (mp) REVERT: G 333 GLU cc_start: 0.7806 (pt0) cc_final: 0.7552 (mm-30) REVERT: G 362 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8447 (mm-30) REVERT: G 368 LYS cc_start: 0.8237 (ptpp) cc_final: 0.7600 (ptmm) REVERT: G 416 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7789 (mt-10) REVERT: G 434 LYS cc_start: 0.8324 (tppp) cc_final: 0.7776 (mttt) REVERT: H 368 LYS cc_start: 0.8914 (mmtt) cc_final: 0.8496 (ptpp) REVERT: H 387 LYS cc_start: 0.7664 (mtpt) cc_final: 0.7313 (mmmm) REVERT: H 435 GLU cc_start: 0.6392 (mm-30) cc_final: 0.6120 (mp0) REVERT: I 289 ASP cc_start: 0.8097 (m-30) cc_final: 0.7659 (m-30) REVERT: I 329 ASN cc_start: 0.7987 (m-40) cc_final: 0.7308 (m-40) REVERT: I 357 LYS cc_start: 0.7978 (mmtm) cc_final: 0.7474 (ptmm) REVERT: I 365 ARG cc_start: 0.8687 (mtt-85) cc_final: 0.8473 (mtt90) REVERT: J 272 VAL cc_start: 0.8407 (OUTLIER) cc_final: 0.8139 (t) REVERT: J 318 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8283 (mm-30) REVERT: L 265 LYS cc_start: 0.7629 (tptt) cc_final: 0.7148 (ttmm) REVERT: L 307 ASP cc_start: 0.7960 (m-30) cc_final: 0.7535 (m-30) REVERT: L 361 LYS cc_start: 0.8451 (ptpt) cc_final: 0.8144 (pttt) REVERT: L 407 LEU cc_start: 0.8570 (tp) cc_final: 0.8307 (tt) REVERT: M 41 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8264 (tm-30) REVERT: M 48 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8402 (mm) REVERT: M 110 LYS cc_start: 0.5843 (tppp) cc_final: 0.5240 (mtmm) REVERT: M 113 ILE cc_start: 0.8469 (tt) cc_final: 0.8198 (tp) REVERT: M 199 ASP cc_start: 0.8445 (t0) cc_final: 0.8215 (t0) REVERT: M 211 LYS cc_start: 0.7847 (mptt) cc_final: 0.7505 (mmtt) REVERT: M 239 SER cc_start: 0.7983 (t) cc_final: 0.7305 (p) REVERT: M 343 GLU cc_start: 0.8199 (tt0) cc_final: 0.7915 (tt0) REVERT: M 467 ARG cc_start: 0.7970 (mtp-110) cc_final: 0.7532 (ttt-90) REVERT: M 545 LYS cc_start: 0.8505 (tttt) cc_final: 0.7925 (tptp) REVERT: N 112 LYS cc_start: 0.7246 (ttmm) cc_final: 0.6897 (tttm) REVERT: N 115 HIS cc_start: 0.8069 (m-70) cc_final: 0.7310 (t70) REVERT: N 165 ASP cc_start: 0.7920 (t0) cc_final: 0.7571 (t0) REVERT: N 199 ASP cc_start: 0.8481 (t0) cc_final: 0.8087 (t0) REVERT: N 242 LYS cc_start: 0.8065 (tttt) cc_final: 0.7603 (ttmt) REVERT: N 341 ARG cc_start: 0.6881 (mtm-85) cc_final: 0.6218 (ttt90) REVERT: N 363 ASN cc_start: 0.7369 (m-40) cc_final: 0.6992 (t0) REVERT: N 453 LYS cc_start: 0.8068 (tttt) cc_final: 0.7660 (mmtm) REVERT: N 486 THR cc_start: 0.8924 (m) cc_final: 0.8605 (p) REVERT: N 522 ILE cc_start: 0.7802 (tp) cc_final: 0.7370 (mt) REVERT: N 580 TRP cc_start: 0.7016 (OUTLIER) cc_final: 0.5588 (t60) REVERT: N 582 LYS cc_start: 0.7492 (ttmm) cc_final: 0.6671 (tmmt) REVERT: O 79 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7409 (mp0) REVERT: O 86 MET cc_start: 0.6755 (tpp) cc_final: 0.6518 (tpp) REVERT: O 104 LYS cc_start: 0.7935 (mttt) cc_final: 0.7636 (mmmt) REVERT: O 123 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7865 (tp30) REVERT: O 167 ARG cc_start: 0.8335 (mtt90) cc_final: 0.7606 (mtp-110) REVERT: O 184 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7881 (mm) REVERT: O 243 ARG cc_start: 0.7619 (ttt90) cc_final: 0.7311 (mtp-110) REVERT: O 349 LYS cc_start: 0.8270 (mmtp) cc_final: 0.7785 (tptp) REVERT: O 352 GLU cc_start: 0.8245 (mt-10) cc_final: 0.8007 (mt-10) REVERT: O 509 LYS cc_start: 0.8098 (mtpt) cc_final: 0.7616 (mttt) REVERT: O 558 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7644 (mt) REVERT: O 578 MET cc_start: 0.7879 (ttt) cc_final: 0.7493 (tpp) REVERT: P 104 LYS cc_start: 0.8063 (mtmt) cc_final: 0.7704 (ttpp) REVERT: P 173 ASP cc_start: 0.7705 (t0) cc_final: 0.7004 (p0) REVERT: P 446 ARG cc_start: 0.8214 (ttm-80) cc_final: 0.7814 (ttm-80) REVERT: P 457 LYS cc_start: 0.8669 (tttt) cc_final: 0.8158 (tptt) REVERT: Q 115 HIS cc_start: 0.8461 (m-70) cc_final: 0.7524 (t70) REVERT: Q 233 ASN cc_start: 0.6695 (m-40) cc_final: 0.6481 (m-40) REVERT: Q 336 ASN cc_start: 0.7992 (m-40) cc_final: 0.7719 (m-40) REVERT: Q 562 LYS cc_start: 0.8642 (tptt) cc_final: 0.8021 (tmtt) REVERT: Q 572 SER cc_start: 0.6760 (OUTLIER) cc_final: 0.6434 (t) REVERT: R 78 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7223 (mm-30) REVERT: R 115 HIS cc_start: 0.8367 (m-70) cc_final: 0.7453 (t-170) REVERT: R 165 ASP cc_start: 0.7817 (m-30) cc_final: 0.7365 (t0) REVERT: R 167 ARG cc_start: 0.7944 (mpt180) cc_final: 0.7694 (tpp80) REVERT: R 187 GLU cc_start: 0.8013 (pt0) cc_final: 0.7794 (pt0) REVERT: R 457 LYS cc_start: 0.7892 (tttm) cc_final: 0.7227 (mtpt) REVERT: R 485 ASP cc_start: 0.8422 (t70) cc_final: 0.8140 (t0) outliers start: 88 outliers final: 67 residues processed: 655 average time/residue: 0.1867 time to fit residues: 202.1968 Evaluate side-chains 646 residues out of total 5280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 567 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 356 PHE Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 419 GLU Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 384 GLU Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 378 ILE Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 286 ILE Chi-restraints excluded: chain H residue 289 ASP Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 405 VAL Chi-restraints excluded: chain I residue 272 VAL Chi-restraints excluded: chain I residue 407 LEU Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain L residue 313 ILE Chi-restraints excluded: chain L residue 400 VAL Chi-restraints excluded: chain L residue 434 LYS Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 101 ILE Chi-restraints excluded: chain M residue 511 LEU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 74 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 ASP Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 296 LEU Chi-restraints excluded: chain N residue 356 LEU Chi-restraints excluded: chain N residue 511 LEU Chi-restraints excluded: chain N residue 580 TRP Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain O residue 184 ILE Chi-restraints excluded: chain O residue 255 GLU Chi-restraints excluded: chain O residue 393 SER Chi-restraints excluded: chain O residue 402 ILE Chi-restraints excluded: chain O residue 540 ILE Chi-restraints excluded: chain O residue 558 ILE Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 6 VAL Chi-restraints excluded: chain P residue 101 ILE Chi-restraints excluded: chain P residue 126 SER Chi-restraints excluded: chain P residue 228 GLU Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 521 GLU Chi-restraints excluded: chain Q residue 6 VAL Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain Q residue 101 ILE Chi-restraints excluded: chain Q residue 108 ASN Chi-restraints excluded: chain Q residue 184 ILE Chi-restraints excluded: chain Q residue 193 GLU Chi-restraints excluded: chain Q residue 451 GLU Chi-restraints excluded: chain Q residue 496 ASN Chi-restraints excluded: chain Q residue 572 SER Chi-restraints excluded: chain R residue 25 GLU Chi-restraints excluded: chain R residue 184 ILE Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 502 ILE Chi-restraints excluded: chain R residue 577 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.2198 > 50: distance: 44 - 50: 35.245 distance: 45 - 79: 29.522 distance: 50 - 51: 11.303 distance: 51 - 52: 62.268 distance: 51 - 54: 12.241 distance: 52 - 53: 41.092 distance: 52 - 61: 45.757 distance: 53 - 90: 67.149 distance: 54 - 55: 11.931 distance: 55 - 56: 45.820 distance: 55 - 57: 48.194 distance: 57 - 59: 39.613 distance: 59 - 60: 39.002 distance: 61 - 62: 51.337 distance: 62 - 63: 17.895 distance: 62 - 65: 19.276 distance: 63 - 70: 39.677 distance: 65 - 66: 55.501 distance: 67 - 68: 28.799 distance: 68 - 69: 40.760 distance: 70 - 71: 27.983 distance: 71 - 72: 40.964 distance: 71 - 74: 25.865 distance: 72 - 73: 57.034 distance: 72 - 79: 3.686 distance: 76 - 77: 4.156 distance: 76 - 78: 52.128 distance: 79 - 80: 34.547 distance: 80 - 81: 19.734 distance: 80 - 83: 39.622 distance: 81 - 82: 21.675 distance: 81 - 90: 43.847 distance: 84 - 85: 41.099 distance: 84 - 86: 55.738 distance: 85 - 87: 40.416 distance: 86 - 88: 40.434 distance: 87 - 89: 39.348 distance: 91 - 92: 41.187 distance: 91 - 94: 40.758 distance: 92 - 93: 38.895 distance: 92 - 98: 39.596 distance: 94 - 95: 56.212 distance: 95 - 96: 40.987 distance: 98 - 99: 20.752 distance: 99 - 100: 44.243 distance: 99 - 102: 24.224 distance: 100 - 101: 40.494 distance: 102 - 103: 38.515 distance: 104 - 105: 39.798 distance: 107 - 108: 56.342 distance: 108 - 109: 40.517 distance: 108 - 111: 39.827 distance: 109 - 110: 40.852 distance: 109 - 116: 19.627 distance: 112 - 113: 21.900 distance: 113 - 114: 44.653 distance: 113 - 115: 19.692 distance: 116 - 117: 39.211 distance: 116 - 122: 44.815 distance: 117 - 120: 39.846 distance: 118 - 119: 39.090 distance: 118 - 123: 38.764 distance: 120 - 121: 40.531 distance: 121 - 122: 39.177 distance: 123 - 124: 40.892 distance: 124 - 125: 40.067 distance: 124 - 127: 56.926 distance: 125 - 126: 12.904 distance: 125 - 132: 6.065 distance: 129 - 130: 40.204 distance: 130 - 131: 40.731 distance: 132 - 133: 40.620 distance: 133 - 134: 40.306 distance: 134 - 143: 35.078 distance: 136 - 137: 38.470 distance: 138 - 139: 39.454 distance: 140 - 141: 39.271 distance: 140 - 142: 40.159