Starting phenix.real_space_refine on Tue Sep 15 19:00:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6fml_4277/09_2026/6fml_4277.cif Found real_map, /net/cci-nas-00/data/ceres_data/6fml_4277/09_2026/6fml_4277.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6fml_4277/09_2026/6fml_4277.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6fml_4277/09_2026/6fml_4277.cif" model { file = "/net/cci-nas-00/data/ceres_data/6fml_4277/09_2026/6fml_4277.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6fml_4277/09_2026/6fml_4277.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6fml_4277/09_2026/6fml_4277.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6fml_4277/09_2026/6fml_4277.map" } resolution = 4.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 303 5.49 5 S 160 5.16 5 C 26392 2.51 5 N 7810 2.21 5 O 8795 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 43460 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3432 Classifications: {'peptide': 449} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 429} Chain: "B" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3352 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 419} Chain breaks: 1 Chain: "C" Number of atoms: 3511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3511 Classifications: {'peptide': 459} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 439} Chain: "D" Number of atoms: 3383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3383 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 14, 'TRANS': 424} Chain: "E" Number of atoms: 3396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3396 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 14, 'TRANS': 426} Chain breaks: 1 Chain: "F" Number of atoms: 3376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3376 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 14, 'TRANS': 422} Chain breaks: 1 Chain: "G" Number of atoms: 5964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5964 Classifications: {'peptide': 731} Link IDs: {'PTRANS': 33, 'TRANS': 697} Chain breaks: 1 Chain: "H" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 413 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'UNK:plan-1': 30} Unresolved non-hydrogen planarities: 30 Chain: "I" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 875 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain breaks: 1 Chain: "J" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2242 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 18, 'TRANS': 259} Chain breaks: 2 Chain: "J" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1601 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 10, 'TRANS': 214} Chain breaks: 3 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 58 Planarities with less than four sites: {'UNK:plan-1': 58} Unresolved non-hydrogen planarities: 58 Chain: "K" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2969 Classifications: {'DNA': 144} Link IDs: {'rna3p': 143} Chain: "L" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2935 Classifications: {'DNA': 144} Link IDs: {'rna3p': 143} Chain: "M" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 766 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "N" Number of atoms: 623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 623 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "O" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 764 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "P" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 728 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 787 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "R" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 635 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 791 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "T" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 724 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.20, per 1000 atoms: 0.21 Number of scatterers: 43460 At special positions: 0 Unit cell: (149.46, 177.02, 219.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 160 16.00 P 303 15.00 O 8795 8.00 N 7810 7.00 C 26392 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.75 Conformation dependent library (CDL) restraints added in 1.7 seconds 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8952 Finding SS restraints... Secondary structure from input PDB file: 200 helices and 50 sheets defined 49.2% alpha, 13.0% beta 102 base pairs and 215 stacking pairs defined. Time for finding SS restraints: 5.34 Creating SS restraints... Processing helix chain 'A' and resid 43 through 58 removed outlier: 3.825A pdb=" N ALA A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 89 removed outlier: 3.949A pdb=" N LEU A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 120 removed outlier: 3.550A pdb=" N VAL A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 183 Processing helix chain 'A' and resid 208 through 211 Processing helix chain 'A' and resid 241 through 250 Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 273 through 290 removed outlier: 3.845A pdb=" N ASN A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 308 Processing helix chain 'A' and resid 309 through 321 removed outlier: 3.907A pdb=" N TYR A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN A 317 " --> pdb=" O PHE A 313 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LYS A 318 " --> pdb=" O THR A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 357 removed outlier: 3.641A pdb=" N GLN A 357 " --> pdb=" O ASP A 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 354 through 357' Processing helix chain 'A' and resid 370 through 384 Processing helix chain 'A' and resid 388 through 402 Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.886A pdb=" N CYS A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 403 through 408' Processing helix chain 'A' and resid 411 through 421 removed outlier: 3.681A pdb=" N ILE A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 438 removed outlier: 3.703A pdb=" N ILE A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 452 removed outlier: 3.807A pdb=" N SER A 444 " --> pdb=" O ASP A 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 60 removed outlier: 3.525A pdb=" N ARG B 47 " --> pdb=" O GLN B 43 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N HIS B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 89 removed outlier: 3.844A pdb=" N LEU B 80 " --> pdb=" O GLY B 76 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY B 89 " --> pdb=" O SER B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 103 removed outlier: 3.738A pdb=" N TYR B 103 " --> pdb=" O SER B 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 100 through 103' Processing helix chain 'B' and resid 111 through 121 removed outlier: 3.521A pdb=" N ILE B 121 " --> pdb=" O PHE B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 241 through 250 Processing helix chain 'B' and resid 256 through 261 Processing helix chain 'B' and resid 273 through 290 removed outlier: 3.632A pdb=" N ARG B 277 " --> pdb=" O THR B 273 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS B 282 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 309 through 320 removed outlier: 4.733A pdb=" N TYR B 315 " --> pdb=" O GLU B 311 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN B 317 " --> pdb=" O PHE B 313 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS B 318 " --> pdb=" O THR B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 351 Processing helix chain 'B' and resid 352 through 357 removed outlier: 3.816A pdb=" N GLN B 357 " --> pdb=" O PRO B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 371 Processing helix chain 'B' and resid 372 through 384 Processing helix chain 'B' and resid 388 through 402 removed outlier: 3.721A pdb=" N ASP B 393 " --> pdb=" O ASP B 389 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG B 394 " --> pdb=" O ALA B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.746A pdb=" N CYS B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 420 removed outlier: 3.581A pdb=" N SER B 415 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE B 416 " --> pdb=" O ALA B 412 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL B 420 " --> pdb=" O ILE B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 438 removed outlier: 3.809A pdb=" N ILE B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 450 removed outlier: 3.556A pdb=" N SER B 444 " --> pdb=" O ASP B 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 59 Processing helix chain 'C' and resid 76 through 89 Processing helix chain 'C' and resid 98 through 102 removed outlier: 3.694A pdb=" N GLU C 101 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE C 102 " --> pdb=" O GLY C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 98 through 102' Processing helix chain 'C' and resid 108 through 120 removed outlier: 3.896A pdb=" N VAL C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU C 113 " --> pdb=" O LYS C 109 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N MET C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 185 Processing helix chain 'C' and resid 241 through 250 Processing helix chain 'C' and resid 258 through 263 Processing helix chain 'C' and resid 273 through 290 removed outlier: 3.708A pdb=" N ARG C 277 " --> pdb=" O THR C 273 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS C 286 " --> pdb=" O LYS C 282 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN C 289 " --> pdb=" O GLN C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 321 removed outlier: 3.706A pdb=" N PHE C 313 " --> pdb=" O ASP C 309 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR C 314 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS C 318 " --> pdb=" O THR C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 357 removed outlier: 4.021A pdb=" N GLN C 357 " --> pdb=" O PRO C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 384 Processing helix chain 'C' and resid 388 through 402 Processing helix chain 'C' and resid 403 through 408 removed outlier: 3.767A pdb=" N CYS C 407 " --> pdb=" O SER C 403 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 403 through 408' Processing helix chain 'C' and resid 411 through 422 Processing helix chain 'C' and resid 427 through 435 removed outlier: 3.683A pdb=" N ILE C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 451 removed outlier: 3.591A pdb=" N SER C 444 " --> pdb=" O ASP C 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 66 removed outlier: 3.750A pdb=" N GLY D 66 " --> pdb=" O MET D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 95 removed outlier: 3.736A pdb=" N GLY D 95 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 125 removed outlier: 3.698A pdb=" N LEU D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 185 removed outlier: 3.538A pdb=" N LYS D 183 " --> pdb=" O ASP D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 252 removed outlier: 3.734A pdb=" N ARG D 252 " --> pdb=" O VAL D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 285 removed outlier: 3.672A pdb=" N ARG D 272 " --> pdb=" O ARG D 268 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN D 274 " --> pdb=" O GLU D 270 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR D 277 " --> pdb=" O ASP D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 303 removed outlier: 3.506A pdb=" N MET D 302 " --> pdb=" O GLU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 315 removed outlier: 4.059A pdb=" N TYR D 310 " --> pdb=" O GLU D 306 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG D 313 " --> pdb=" O SER D 309 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU D 315 " --> pdb=" O ILE D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 377 removed outlier: 4.104A pdb=" N GLN D 368 " --> pdb=" O ASP D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 397 removed outlier: 3.835A pdb=" N GLU D 395 " --> pdb=" O LYS D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 415 removed outlier: 3.563A pdb=" N ALA D 401 " --> pdb=" O GLY D 397 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASN D 403 " --> pdb=" O ARG D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 432 Processing helix chain 'D' and resid 434 through 445 removed outlier: 4.028A pdb=" N ARG D 440 " --> pdb=" O ALA D 436 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER D 445 " --> pdb=" O PHE D 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 64 Processing helix chain 'E' and resid 83 through 93 Processing helix chain 'E' and resid 115 through 125 removed outlier: 3.504A pdb=" N ALA E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 185 removed outlier: 4.397A pdb=" N ALA E 180 " --> pdb=" O LYS E 176 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS E 183 " --> pdb=" O ASP E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 214 removed outlier: 5.361A pdb=" N ARG E 212 " --> pdb=" O ALA E 209 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR E 214 " --> pdb=" O SER E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 250 Processing helix chain 'E' and resid 257 through 262 Processing helix chain 'E' and resid 268 through 285 removed outlier: 3.916A pdb=" N ARG E 272 " --> pdb=" O ARG E 268 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA E 280 " --> pdb=" O ASN E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 303 Processing helix chain 'E' and resid 304 through 315 removed outlier: 3.564A pdb=" N PHE E 308 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR E 310 " --> pdb=" O GLU E 306 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ARG E 313 " --> pdb=" O SER E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 351 Processing helix chain 'E' and resid 362 through 378 removed outlier: 3.585A pdb=" N GLU E 377 " --> pdb=" O ARG E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 415 removed outlier: 3.794A pdb=" N GLU E 395 " --> pdb=" O LYS E 391 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N LEU E 398 " --> pdb=" O GLN E 394 " (cutoff:3.500A) removed outlier: 9.886A pdb=" N ARG E 399 " --> pdb=" O GLU E 395 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR E 400 " --> pdb=" O ALA E 396 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA E 401 " --> pdb=" O GLY E 397 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR E 406 " --> pdb=" O SER E 402 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU E 410 " --> pdb=" O THR E 406 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG E 415 " --> pdb=" O ILE E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 432 removed outlier: 4.310A pdb=" N ARG E 427 " --> pdb=" O GLU E 423 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS E 430 " --> pdb=" O GLN E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 444 Processing helix chain 'F' and resid 49 through 66 removed outlier: 3.658A pdb=" N GLN F 65 " --> pdb=" O GLU F 61 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY F 66 " --> pdb=" O MET F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.597A pdb=" N ALA F 87 " --> pdb=" O LYS F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 108 No H-bonds generated for 'chain 'F' and resid 106 through 108' Processing helix chain 'F' and resid 114 through 126 removed outlier: 3.954A pdb=" N ALA F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE F 123 " --> pdb=" O LEU F 119 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 185 removed outlier: 4.129A pdb=" N ASP F 179 " --> pdb=" O SER F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 211 No H-bonds generated for 'chain 'F' and resid 209 through 211' Processing helix chain 'F' and resid 243 through 250 Processing helix chain 'F' and resid 254 through 256 No H-bonds generated for 'chain 'F' and resid 254 through 256' Processing helix chain 'F' and resid 257 through 262 Processing helix chain 'F' and resid 268 through 285 removed outlier: 3.716A pdb=" N ARG F 272 " --> pdb=" O ARG F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 303 Processing helix chain 'F' and resid 304 through 315 removed outlier: 4.393A pdb=" N TYR F 310 " --> pdb=" O GLU F 306 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG F 313 " --> pdb=" O SER F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 345 Processing helix chain 'F' and resid 346 through 351 Processing helix chain 'F' and resid 362 through 377 removed outlier: 3.872A pdb=" N GLN F 368 " --> pdb=" O ASP F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 397 Processing helix chain 'F' and resid 397 through 402 Processing helix chain 'F' and resid 402 through 415 removed outlier: 4.610A pdb=" N THR F 406 " --> pdb=" O SER F 402 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR F 407 " --> pdb=" O ASN F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 432 Processing helix chain 'F' and resid 434 through 445 removed outlier: 3.854A pdb=" N VAL F 439 " --> pdb=" O PRO F 435 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG F 440 " --> pdb=" O ALA F 436 " (cutoff:3.500A) Processing helix chain 'G' and resid 973 through 989 Processing helix chain 'G' and resid 1002 through 1017 Processing helix chain 'G' and resid 1032 through 1044 Processing helix chain 'G' and resid 1055 through 1065 removed outlier: 3.696A pdb=" N LYS G1064 " --> pdb=" O LYS G1060 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE G1065 " --> pdb=" O VAL G1061 " (cutoff:3.500A) Processing helix chain 'G' and resid 1086 through 1092 Processing helix chain 'G' and resid 1092 through 1097 Processing helix chain 'G' and resid 1117 through 1125 Processing helix chain 'G' and resid 1143 through 1154 removed outlier: 4.085A pdb=" N PHE G1152 " --> pdb=" O ALA G1148 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET G1154 " --> pdb=" O LEU G1150 " (cutoff:3.500A) Processing helix chain 'G' and resid 1165 through 1180 removed outlier: 3.660A pdb=" N HIS G1175 " --> pdb=" O ASP G1171 " (cutoff:3.500A) Processing helix chain 'G' and resid 1186 through 1194 Processing helix chain 'G' and resid 1202 through 1208 removed outlier: 3.677A pdb=" N VAL G1206 " --> pdb=" O VAL G1202 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS G1208 " --> pdb=" O LYS G1204 " (cutoff:3.500A) Processing helix chain 'G' and resid 1223 through 1241 Processing helix chain 'G' and resid 1256 through 1270 Processing helix chain 'G' and resid 1271 through 1274 Processing helix chain 'G' and resid 1334 through 1345 removed outlier: 4.557A pdb=" N PHE G1338 " --> pdb=" O LEU G1334 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER G1340 " --> pdb=" O ALA G1336 " (cutoff:3.500A) Processing helix chain 'G' and resid 1352 through 1357 removed outlier: 3.713A pdb=" N SER G1357 " --> pdb=" O GLU G1353 " (cutoff:3.500A) Processing helix chain 'G' and resid 1365 through 1370 removed outlier: 3.560A pdb=" N LEU G1368 " --> pdb=" O PHE G1365 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG G1369 " --> pdb=" O THR G1366 " (cutoff:3.500A) Processing helix chain 'G' and resid 1374 through 1382 Processing helix chain 'G' and resid 1385 through 1394 removed outlier: 3.698A pdb=" N ARG G1389 " --> pdb=" O ASP G1385 " (cutoff:3.500A) Processing helix chain 'G' and resid 1402 through 1407 Processing helix chain 'G' and resid 1417 through 1421 Processing helix chain 'G' and resid 1429 through 1435 removed outlier: 3.753A pdb=" N VAL G1433 " --> pdb=" O ASN G1429 " (cutoff:3.500A) Processing helix chain 'G' and resid 1442 through 1447 removed outlier: 3.962A pdb=" N ASN G1447 " --> pdb=" O ARG G1443 " (cutoff:3.500A) Processing helix chain 'G' and resid 1447 through 1456 removed outlier: 3.643A pdb=" N VAL G1451 " --> pdb=" O ASN G1447 " (cutoff:3.500A) Processing helix chain 'G' and resid 1480 through 1491 removed outlier: 3.785A pdb=" N VAL G1484 " --> pdb=" O SER G1480 " (cutoff:3.500A) Processing helix chain 'G' and resid 1493 through 1502 removed outlier: 3.645A pdb=" N ARG G1497 " --> pdb=" O HIS G1493 " (cutoff:3.500A) Processing helix chain 'G' and resid 1504 through 1513 Processing helix chain 'G' and resid 1552 through 1569 Processing helix chain 'G' and resid 1578 through 1592 removed outlier: 3.924A pdb=" N ILE G1582 " --> pdb=" O MET G1578 " (cutoff:3.500A) Processing helix chain 'G' and resid 1604 through 1618 Processing helix chain 'G' and resid 1629 through 1632 Processing helix chain 'G' and resid 1651 through 1663 Processing helix chain 'G' and resid 1681 through 1702 removed outlier: 3.850A pdb=" N ARG G1685 " --> pdb=" O THR G1681 " (cutoff:3.500A) Processing helix chain 'H' and resid 385 through 413 Processing helix chain 'H' and resid 462 through 466 Processing helix chain 'H' and resid 470 through 475 removed outlier: 4.473A pdb=" N PHE H 474 " --> pdb=" O ALA H 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 20 Processing helix chain 'I' and resid 43 through 51 Processing helix chain 'I' and resid 190 through 199 Processing helix chain 'I' and resid 204 through 213 removed outlier: 4.189A pdb=" N LEU I 209 " --> pdb=" O GLY I 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 20 Processing helix chain 'J' and resid 45 through 50 Processing helix chain 'J' and resid 103 through 105 No H-bonds generated for 'chain 'J' and resid 103 through 105' Processing helix chain 'J' and resid 128 through 144 removed outlier: 3.948A pdb=" N HIS J 134 " --> pdb=" O ASP J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 179 Processing helix chain 'J' and resid 190 through 198 Processing helix chain 'J' and resid 234 through 250 removed outlier: 3.552A pdb=" N TYR J 250 " --> pdb=" O LEU J 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 259 through 271 removed outlier: 3.720A pdb=" N THR J 263 " --> pdb=" O ASN J 259 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP J 269 " --> pdb=" O HIS J 265 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS J 271 " --> pdb=" O VAL J 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 276 through 283 removed outlier: 3.991A pdb=" N ALA J 282 " --> pdb=" O ASP J 278 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY J 283 " --> pdb=" O ARG J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 294 removed outlier: 3.768A pdb=" N ARG J 293 " --> pdb=" O GLY J 289 " (cutoff:3.500A) Processing helix chain 'J' and resid 472 through 498 Processing helix chain 'J' and resid 505 through 519 Processing helix chain 'J' and resid 572 through 584 Processing helix chain 'J' and resid 607 through 614 removed outlier: 4.164A pdb=" N ALA J 611 " --> pdb=" O SER J 607 " (cutoff:3.500A) Processing helix chain 'J' and resid 623 through 628 removed outlier: 3.834A pdb=" N THR J 627 " --> pdb=" O SER J 623 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N HIS J 628 " --> pdb=" O GLN J 624 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 623 through 628' Processing helix chain 'J' and resid 634 through 639 removed outlier: 3.739A pdb=" N VAL J 639 " --> pdb=" O GLU J 635 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 642 No H-bonds generated for 'chain 'J' and resid 640 through 642' Processing helix chain 'J' and resid 645 through 650 removed outlier: 3.584A pdb=" N ILE J 649 " --> pdb=" O GLN J 645 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA J 650 " --> pdb=" O PRO J 646 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 645 through 650' Processing helix chain 'J' and resid 656 through 668 removed outlier: 3.763A pdb=" N ARG J 668 " --> pdb=" O ILE J 664 " (cutoff:3.500A) Processing helix chain 'J' and resid 678 through 683 removed outlier: 3.831A pdb=" N PHE J 682 " --> pdb=" O ALA J 678 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU J 683 " --> pdb=" O PRO J 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 678 through 683' Processing helix chain 'J' and resid 698 through 710 removed outlier: 3.504A pdb=" N LEU J 702 " --> pdb=" O PHE J 698 " (cutoff:3.500A) Processing helix chain 'J' and resid 726 through 736 removed outlier: 3.934A pdb=" N ALA J 732 " --> pdb=" O ALA J 728 " (cutoff:3.500A) Processing helix chain 'J' and resid 738 through 743 Processing helix chain 'J' and resid 748 through 755 removed outlier: 3.503A pdb=" N GLY J 755 " --> pdb=" O TYR J 751 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 55 Processing helix chain 'M' and resid 63 through 76 removed outlier: 3.528A pdb=" N PHE M 67 " --> pdb=" O ARG M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 114 Processing helix chain 'M' and resid 120 through 131 Processing helix chain 'N' and resid 25 through 29 Processing helix chain 'N' and resid 30 through 42 Processing helix chain 'N' and resid 49 through 76 removed outlier: 3.692A pdb=" N GLU N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 93 Processing helix chain 'O' and resid 17 through 21 Processing helix chain 'O' and resid 26 through 36 Processing helix chain 'O' and resid 46 through 73 Processing helix chain 'O' and resid 79 through 89 removed outlier: 3.513A pdb=" N LEU O 83 " --> pdb=" O ILE O 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 97 Processing helix chain 'O' and resid 112 through 116 Processing helix chain 'P' and resid 37 through 49 Processing helix chain 'P' and resid 55 through 84 Processing helix chain 'P' and resid 90 through 102 Processing helix chain 'P' and resid 104 through 122 removed outlier: 3.514A pdb=" N LYS P 108 " --> pdb=" O GLY P 104 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR P 122 " --> pdb=" O VAL P 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 57 removed outlier: 3.580A pdb=" N LEU Q 48 " --> pdb=" O GLY Q 44 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 76 removed outlier: 3.533A pdb=" N GLN Q 76 " --> pdb=" O ARG Q 72 " (cutoff:3.500A) Processing helix chain 'Q' and resid 85 through 114 removed outlier: 3.663A pdb=" N GLU Q 105 " --> pdb=" O VAL Q 101 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP Q 106 " --> pdb=" O GLY Q 102 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA Q 114 " --> pdb=" O CYS Q 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 132 Processing helix chain 'R' and resid 25 through 29 removed outlier: 3.644A pdb=" N ILE R 29 " --> pdb=" O ILE R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 42 Processing helix chain 'R' and resid 49 through 76 removed outlier: 3.688A pdb=" N GLU R 53 " --> pdb=" O LEU R 49 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP R 68 " --> pdb=" O ASN R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 94 removed outlier: 3.574A pdb=" N VAL R 86 " --> pdb=" O THR R 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 21 Processing helix chain 'S' and resid 26 through 36 Processing helix chain 'S' and resid 45 through 73 removed outlier: 4.609A pdb=" N VAL S 49 " --> pdb=" O ALA S 45 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU S 65 " --> pdb=" O GLU S 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 90 removed outlier: 3.507A pdb=" N ASN S 89 " --> pdb=" O LEU S 85 " (cutoff:3.500A) Processing helix chain 'S' and resid 90 through 97 Processing helix chain 'T' and resid 37 through 49 Processing helix chain 'T' and resid 55 through 84 Processing helix chain 'T' and resid 90 through 102 removed outlier: 3.519A pdb=" N ILE T 94 " --> pdb=" O THR T 90 " (cutoff:3.500A) Processing helix chain 'T' and resid 104 through 124 Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 97 removed outlier: 7.005A pdb=" N GLY A 66 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE A 362 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU A 68 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 233 through 240 Processing sheet with id=AA3, first strand: chain 'A' and resid 131 through 135 removed outlier: 3.926A pdb=" N GLY A 205 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR A 193 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG A 203 " --> pdb=" O TYR A 193 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU A 195 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N CYS A 201 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 143 Processing sheet with id=AA5, first strand: chain 'A' and resid 161 through 162 Processing sheet with id=AA6, first strand: chain 'A' and resid 336 through 338 Processing sheet with id=AA7, first strand: chain 'B' and resid 94 through 98 removed outlier: 6.483A pdb=" N CYS B 95 " --> pdb=" O PHE B 301 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASP B 303 " --> pdb=" O CYS B 95 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE B 97 " --> pdb=" O ASP B 303 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N VAL B 67 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY B 66 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ILE B 362 " --> pdb=" O GLY B 66 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU B 68 " --> pdb=" O ILE B 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 172 through 173 removed outlier: 3.626A pdb=" N LEU B 173 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU B 158 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU B 159 " --> pdb=" O MET B 139 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N MET B 139 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLY B 161 " --> pdb=" O THR B 137 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 221 through 222 removed outlier: 6.630A pdb=" N VAL B 222 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ARG B 206 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N CYS B 201 " --> pdb=" O GLU B 195 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N GLU B 195 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ARG B 203 " --> pdb=" O TYR B 193 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N TYR B 193 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY B 205 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ASP B 190 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 337 through 338 Processing sheet with id=AB2, first strand: chain 'C' and resid 299 through 303 removed outlier: 6.623A pdb=" N VAL C 67 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N GLY C 66 " --> pdb=" O LEU C 360 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ILE C 362 " --> pdb=" O GLY C 66 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU C 68 " --> pdb=" O ILE C 362 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 168 through 173 removed outlier: 6.490A pdb=" N LEU C 159 " --> pdb=" O MET C 139 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N MET C 139 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLY C 161 " --> pdb=" O THR C 137 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 202 through 206 removed outlier: 3.655A pdb=" N TYR C 193 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL C 191 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASP C 190 " --> pdb=" O VAL C 136 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 155 removed outlier: 5.226A pdb=" N VAL D 142 " --> pdb=" O LYS D 163 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LYS D 163 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY D 158 " --> pdb=" O MET D 173 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 155 removed outlier: 3.580A pdb=" N GLY D 140 " --> pdb=" O ILE D 192 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP D 190 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE D 191 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR D 202 " --> pdb=" O SER D 193 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 336 through 338 Processing sheet with id=AB8, first strand: chain 'D' and resid 100 through 104 removed outlier: 6.065A pdb=" N THR D 101 " --> pdb=" O PHE D 296 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ASP D 298 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU D 103 " --> pdb=" O ASP D 298 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU D 295 " --> pdb=" O ILE D 322 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 233 through 242 Processing sheet with id=AC1, first strand: chain 'D' and resid 331 through 333 Processing sheet with id=AC2, first strand: chain 'E' and resid 42 through 43 removed outlier: 4.014A pdb=" N SER E 43 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU E 46 " --> pdb=" O SER E 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 100 through 104 removed outlier: 6.634A pdb=" N THR E 101 " --> pdb=" O PHE E 296 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ASP E 298 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU E 103 " --> pdb=" O ASP E 298 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU E 295 " --> pdb=" O ILE E 324 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ALA E 326 " --> pdb=" O LEU E 295 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE E 297 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ALA E 72 " --> pdb=" O VAL E 354 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE E 356 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU E 74 " --> pdb=" O ILE E 356 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 233 through 242 removed outlier: 3.614A pdb=" N VAL E 237 " --> pdb=" O GLU E 133 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 141 through 147 removed outlier: 6.853A pdb=" N THR E 161 " --> pdb=" O VAL E 143 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ILE E 145 " --> pdb=" O LYS E 159 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS E 159 " --> pdb=" O ILE E 145 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 190 through 191 removed outlier: 3.677A pdb=" N GLY E 205 " --> pdb=" O ILE E 191 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 331 through 333 Processing sheet with id=AC8, first strand: chain 'F' and resid 42 through 43 removed outlier: 3.577A pdb=" N SER F 43 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU F 46 " --> pdb=" O SER F 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 100 through 104 removed outlier: 6.130A pdb=" N LEU F 295 " --> pdb=" O ILE F 324 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ALA F 326 " --> pdb=" O LEU F 295 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE F 297 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL F 73 " --> pdb=" O MET F 325 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 168 through 173 removed outlier: 7.785A pdb=" N GLN F 157 " --> pdb=" O ILE F 147 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ILE F 147 " --> pdb=" O GLN F 157 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LYS F 159 " --> pdb=" O ILE F 145 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ILE F 145 " --> pdb=" O LYS F 159 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N THR F 161 " --> pdb=" O VAL F 143 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS F 235 " --> pdb=" O SER F 135 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 223 through 224 removed outlier: 6.219A pdb=" N LEU F 224 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ARG F 206 " --> pdb=" O LEU F 224 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE F 191 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASP F 190 " --> pdb=" O VAL F 142 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 332 through 333 Processing sheet with id=AD4, first strand: chain 'G' and resid 1050 through 1051 removed outlier: 6.387A pdb=" N PHE G1024 " --> pdb=" O MET G1082 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N THR G1084 " --> pdb=" O PHE G1024 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL G1026 " --> pdb=" O THR G1084 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU G1025 " --> pdb=" O ILE G1105 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N GLN G1102 " --> pdb=" O ASN G1130 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU G1132 " --> pdb=" O GLN G1102 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N MET G1104 " --> pdb=" O LEU G1132 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 1213 through 1218 removed outlier: 3.860A pdb=" N ILE G1214 " --> pdb=" O VAL G1671 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG G1675 " --> pdb=" O ILE G1216 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL G1218 " --> pdb=" O ARG G1675 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 1283 through 1284 removed outlier: 6.805A pdb=" N PHE G1283 " --> pdb=" O SER G1470 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'G' and resid 1313 through 1314 removed outlier: 6.489A pdb=" N TYR G1313 " --> pdb=" O VAL G1477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'G' and resid 1575 through 1576 removed outlier: 3.501A pdb=" N SER G1627 " --> pdb=" O LEU G1599 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 80 through 82 removed outlier: 3.580A pdb=" N LEU J 185 " --> pdb=" O ILE J 746 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE J 746 " --> pdb=" O LEU J 185 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 96 through 101 removed outlier: 3.833A pdb=" N MET J 86 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG J 116 " --> pdb=" O MET J 86 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 203 through 208 Processing sheet with id=AE3, first strand: chain 'J' and resid 295 through 297 Processing sheet with id=AE4, first strand: chain 'J' and resid 686 through 688 removed outlier: 6.349A pdb=" N VAL J 686 " --> pdb=" O ARG J 719 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'M' and resid 83 through 84 removed outlier: 6.680A pdb=" N ARG M 83 " --> pdb=" O VAL N 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'M' and resid 118 through 119 Processing sheet with id=AE7, first strand: chain 'N' and resid 96 through 98 removed outlier: 6.549A pdb=" N THR N 96 " --> pdb=" O THR S 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'O' and resid 42 through 43 removed outlier: 7.646A pdb=" N ARG O 42 " --> pdb=" O ILE P 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'O' and resid 77 through 78 Processing sheet with id=AF1, first strand: chain 'O' and resid 100 through 102 Processing sheet with id=AF2, first strand: chain 'Q' and resid 83 through 84 removed outlier: 6.631A pdb=" N ARG Q 83 " --> pdb=" O VAL R 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'Q' and resid 118 through 119 Processing sheet with id=AF4, first strand: chain 'S' and resid 42 through 43 removed outlier: 7.431A pdb=" N ARG S 42 " --> pdb=" O ILE T 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'S' and resid 77 through 78 1672 hydrogen bonds defined for protein. 4845 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 255 hydrogen bonds 510 hydrogen bond angles 0 basepair planarities 102 basepair parallelities 215 stacking parallelities Total time for adding SS restraints: 13.49 Time building geometry restraints manager: 4.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 9269 1.33 - 1.45: 10737 1.45 - 1.57: 23915 1.57 - 1.69: 597 1.69 - 1.81: 277 Bond restraints: 44795 Sorted by residual: bond pdb=" C4 ATP J 801 " pdb=" C5 ATP J 801 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.69e+01 bond pdb=" C5 ATP J 801 " pdb=" C6 ATP J 801 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.15e+01 bond pdb=" CZ ARG J 112 " pdb=" NH1 ARG J 112 " ideal model delta sigma weight residual 1.323 1.411 -0.088 1.40e-02 5.10e+03 3.92e+01 bond pdb=" CG ARG J 112 " pdb=" CD ARG J 112 " ideal model delta sigma weight residual 1.520 1.350 0.170 3.00e-02 1.11e+03 3.20e+01 bond pdb=" C5 DG K 21 " pdb=" C6 DG K 21 " ideal model delta sigma weight residual 1.419 1.365 0.054 1.00e-02 1.00e+04 2.94e+01 ... (remaining 44790 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.13: 61372 4.13 - 8.26: 412 8.26 - 12.38: 34 12.38 - 16.51: 5 16.51 - 20.64: 3 Bond angle restraints: 61826 Sorted by residual: angle pdb=" PB ATP J 801 " pdb=" O3B ATP J 801 " pdb=" PG ATP J 801 " ideal model delta sigma weight residual 139.87 119.67 20.20 1.00e+00 1.00e+00 4.08e+02 angle pdb=" PA ATP J 801 " pdb=" O3A ATP J 801 " pdb=" PB ATP J 801 " ideal model delta sigma weight residual 136.83 119.30 17.53 1.00e+00 1.00e+00 3.07e+02 angle pdb=" C3' DA L 63 " pdb=" O3' DA L 63 " pdb=" P DT L 64 " ideal model delta sigma weight residual 119.70 129.30 -9.60 1.20e+00 6.94e-01 6.39e+01 angle pdb=" C5 ATP J 801 " pdb=" C4 ATP J 801 " pdb=" N3 ATP J 801 " ideal model delta sigma weight residual 126.80 119.35 7.45 1.00e+00 1.00e+00 5.56e+01 angle pdb=" OP1 DG K 23 " pdb=" P DG K 23 " pdb=" OP2 DG K 23 " ideal model delta sigma weight residual 120.00 99.36 20.64 3.00e+00 1.11e-01 4.73e+01 ... (remaining 61821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.57: 25126 35.57 - 71.14: 1293 71.14 - 106.71: 20 106.71 - 142.28: 11 142.28 - 177.84: 4 Dihedral angle restraints: 26454 sinusoidal: 12572 harmonic: 13882 Sorted by residual: dihedral pdb=" CA ILE G1701 " pdb=" C ILE G1701 " pdb=" N THR G1702 " pdb=" CA THR G1702 " ideal model delta harmonic sigma weight residual 180.00 136.34 43.66 0 5.00e+00 4.00e-02 7.62e+01 dihedral pdb=" CA THR G1550 " pdb=" C THR G1550 " pdb=" N ASP G1551 " pdb=" CA ASP G1551 " ideal model delta harmonic sigma weight residual -180.00 -140.04 -39.96 0 5.00e+00 4.00e-02 6.39e+01 dihedral pdb=" CA PHE G1548 " pdb=" C PHE G1548 " pdb=" N VAL G1549 " pdb=" CA VAL G1549 " ideal model delta harmonic sigma weight residual -180.00 -140.58 -39.42 0 5.00e+00 4.00e-02 6.22e+01 ... (remaining 26451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 6069 0.086 - 0.172: 916 0.172 - 0.259: 51 0.259 - 0.345: 3 0.345 - 0.431: 6 Chirality restraints: 7045 Sorted by residual: chirality pdb=" C3' DA L 63 " pdb=" C4' DA L 63 " pdb=" O3' DA L 63 " pdb=" C2' DA L 63 " both_signs ideal model delta sigma weight residual False -2.73 -2.30 -0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" CB ILE G1083 " pdb=" CA ILE G1083 " pdb=" CG1 ILE G1083 " pdb=" CG2 ILE G1083 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" CB ILE C 324 " pdb=" CA ILE C 324 " pdb=" CG1 ILE C 324 " pdb=" CG2 ILE C 324 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 7042 not shown) Planarity restraints: 6957 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP O 72 " -0.046 2.00e-02 2.50e+03 9.21e-02 8.48e+01 pdb=" CG ASP O 72 " 0.159 2.00e-02 2.50e+03 pdb=" OD1 ASP O 72 " -0.058 2.00e-02 2.50e+03 pdb=" OD2 ASP O 72 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP Q 77 " 0.043 2.00e-02 2.50e+03 8.52e-02 7.26e+01 pdb=" CG ASP Q 77 " -0.147 2.00e-02 2.50e+03 pdb=" OD1 ASP Q 77 " 0.056 2.00e-02 2.50e+03 pdb=" OD2 ASP Q 77 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE G1701 " -0.031 2.00e-02 2.50e+03 6.07e-02 3.69e+01 pdb=" C ILE G1701 " 0.105 2.00e-02 2.50e+03 pdb=" O ILE G1701 " -0.040 2.00e-02 2.50e+03 pdb=" N THR G1702 " -0.034 2.00e-02 2.50e+03 ... (remaining 6954 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 2384 2.71 - 3.26: 40372 3.26 - 3.81: 73434 3.81 - 4.35: 89469 4.35 - 4.90: 143427 Nonbonded interactions: 349086 Sorted by model distance: nonbonded pdb=" O SER C 100 " pdb=" OG1 THR F 116 " model vdw 2.165 3.040 nonbonded pdb=" OH TYR G1095 " pdb=" OP1 DG K 21 " model vdw 2.204 3.040 nonbonded pdb=" OE1 GLU E 245 " pdb=" OH TYR G1313 " model vdw 2.254 3.040 nonbonded pdb=" OD2 ASP B 256 " pdb=" OG SER B 259 " model vdw 2.264 3.040 nonbonded pdb=" NE2 HIS G1270 " pdb=" O VAL G1549 " model vdw 2.267 3.120 ... (remaining 349081 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 144 or resid 156 through 501)) selection = chain 'B' selection = (chain 'C' and (resid 14 through 144 or resid 156 through 501)) } ncs_group { reference = (chain 'D' and (resid 20 through 150 or resid 156 through 501)) selection = (chain 'E' and (resid 20 through 150 or resid 156 through 501)) selection = (chain 'F' and resid 20 through 501) } ncs_group { reference = (chain 'M' and (resid 40 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 58 or (resid 59 and (name N or nam \ e CA or name C or name O or name CB )) or resid 60 through 63 or (resid 64 and ( \ name N or name CA or name C or name O or name CB )) or resid 65 through 134)) selection = (chain 'Q' and (resid 40 through 41 or (resid 42 and (name N or name CA or name \ C or name O or name CB )) or resid 43 through 82 or (resid 83 and (name N or nam \ e CA or name C or name O or name CB )) or resid 84 through 133 or (resid 134 and \ (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'N' and (resid 24 through 58 or (resid 59 and (name N or name CA or name \ C or name O or name CB )) or resid 60 through 76 or (resid 77 and (name N or nam \ e CA or name C or name O or name CB )) or resid 78 or (resid 79 and (name N or n \ ame CA or name C or name O or name CB )) or resid 80 through 102)) selection = (chain 'R' and (resid 24 through 43 or (resid 44 and (name N or name CA or name \ C or name O or name CB )) or resid 45 through 102)) } ncs_group { reference = (chain 'O' and (resid 16 through 74 or (resid 75 and (name N or name CA or name \ C or name O or name CB )) or resid 76 through 118)) selection = (chain 'S' and (resid 16 through 19 or (resid 20 through 21 and (name N or name \ CA or name C or name O or name CB )) or resid 22 through 34 or (resid 35 through \ 36 and (name N or name CA or name C or name O or name CB )) or resid 37 through \ 94 or (resid 95 and (name N or name CA or name C or name O or name CB )) or res \ id 96 through 118)) } ncs_group { reference = (chain 'P' and (resid 31 through 84 or (resid 85 and (name N or name CA or name \ C or name O or name CB )) or resid 86 through 125)) selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 46.530 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.110 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 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 : 0.009 0.170 44795 Z= 0.534 Angle : 1.046 20.639 61826 Z= 0.654 Chirality : 0.060 0.431 7045 Planarity : 0.008 0.092 6957 Dihedral : 16.637 177.844 17502 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.68 % Favored : 93.19 % Rotamer: Outliers : 0.13 % Allowed : 2.16 % Favored : 97.71 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.82 (0.10), residues: 4686 helix: -2.40 (0.08), residues: 2114 sheet: -2.26 (0.19), residues: 598 loop : -2.62 (0.12), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG O 88 TYR 0.074 0.004 TYR J 89 PHE 0.033 0.004 PHE G1576 TRP 0.030 0.003 TRP G1650 HIS 0.018 0.003 HIS B 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00948 / 0.53 (44795) covalent geometry : angle 1.04573 / 0.65 (61826) hydrogen bonds : bond 0.16146 / 10.80 ( 1915) hydrogen bonds : angle 6.71503 / 4.64 ( 5355) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1223 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1218 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.6285 (tmm) cc_final: 0.5666 (tmm) REVERT: A 85 SER cc_start: 0.9137 (p) cc_final: 0.8845 (t) REVERT: A 103 TYR cc_start: 0.7820 (m-80) cc_final: 0.7347 (m-80) REVERT: A 137 THR cc_start: 0.9304 (m) cc_final: 0.9099 (p) REVERT: A 155 ILE cc_start: 0.9418 (mt) cc_final: 0.9159 (tt) REVERT: A 177 ILE cc_start: 0.9396 (mt) cc_final: 0.9189 (mm) REVERT: A 309 ASP cc_start: 0.8669 (p0) cc_final: 0.8408 (p0) REVERT: A 359 LEU cc_start: 0.8760 (mt) cc_final: 0.8528 (mm) REVERT: A 416 ILE cc_start: 0.9256 (mm) cc_final: 0.9050 (mt) REVERT: B 100 SER cc_start: 0.9249 (m) cc_final: 0.8590 (t) REVERT: B 158 LEU cc_start: 0.7933 (tt) cc_final: 0.7217 (tt) REVERT: B 178 TYR cc_start: 0.7925 (t80) cc_final: 0.7699 (t80) REVERT: B 260 MET cc_start: 0.8437 (ptt) cc_final: 0.8194 (ptm) REVERT: B 261 MET cc_start: 0.8932 (mmp) cc_final: 0.8600 (mmm) REVERT: B 280 ILE cc_start: 0.9531 (mt) cc_final: 0.9249 (tt) REVERT: B 304 GLU cc_start: 0.8488 (mt-10) cc_final: 0.7959 (mt-10) REVERT: B 309 ASP cc_start: 0.7915 (p0) cc_final: 0.7507 (p0) REVERT: B 356 LEU cc_start: 0.8788 (tp) cc_final: 0.8577 (tt) REVERT: B 361 ILE cc_start: 0.9423 (mt) cc_final: 0.8861 (tt) REVERT: B 409 GLN cc_start: 0.7847 (mt0) cc_final: 0.7276 (mm-40) REVERT: C 8 ARG cc_start: 0.6893 (mtt180) cc_final: 0.6629 (mtt-85) REVERT: C 44 CYS cc_start: 0.7937 (m) cc_final: 0.6738 (t) REVERT: C 95 CYS cc_start: 0.8781 (t) cc_final: 0.8203 (m) REVERT: C 101 GLU cc_start: 0.7838 (tt0) cc_final: 0.7634 (tm-30) REVERT: C 110 THR cc_start: 0.8655 (p) cc_final: 0.8329 (p) REVERT: C 136 VAL cc_start: 0.7719 (t) cc_final: 0.7429 (t) REVERT: C 146 ASN cc_start: 0.9195 (m-40) cc_final: 0.8664 (p0) REVERT: C 159 LEU cc_start: 0.8878 (mp) cc_final: 0.8648 (tp) REVERT: C 160 ILE cc_start: 0.9207 (mt) cc_final: 0.8810 (mt) REVERT: C 197 ASN cc_start: 0.9326 (p0) cc_final: 0.9061 (p0) REVERT: C 364 THR cc_start: 0.8679 (m) cc_final: 0.8422 (p) REVERT: C 416 ILE cc_start: 0.8828 (mm) cc_final: 0.8536 (tt) REVERT: D 106 SER cc_start: 0.7964 (m) cc_final: 0.7321 (m) REVERT: D 107 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7356 (tm-30) REVERT: D 181 MET cc_start: 0.9334 (mmt) cc_final: 0.8724 (mmm) REVERT: D 247 ASP cc_start: 0.7893 (m-30) cc_final: 0.7575 (m-30) REVERT: D 253 THR cc_start: 0.8452 (m) cc_final: 0.8170 (m) REVERT: D 256 PHE cc_start: 0.6669 (m-80) cc_final: 0.6212 (m-80) REVERT: D 350 LEU cc_start: 0.8255 (mt) cc_final: 0.7899 (tp) REVERT: E 217 MET cc_start: 0.6572 (mmm) cc_final: 0.5466 (tpp) REVERT: E 307 CYS cc_start: 0.8479 (m) cc_final: 0.7987 (t) REVERT: E 369 ILE cc_start: 0.9268 (mt) cc_final: 0.8984 (mm) REVERT: E 407 THR cc_start: 0.8156 (m) cc_final: 0.7794 (t) REVERT: F 106 SER cc_start: 0.9287 (m) cc_final: 0.8047 (m) REVERT: F 112 GLU cc_start: 0.7819 (tt0) cc_final: 0.7584 (tt0) REVERT: F 138 MET cc_start: 0.8370 (ttp) cc_final: 0.8072 (ptm) REVERT: F 160 LEU cc_start: 0.8400 (tp) cc_final: 0.7970 (tt) REVERT: F 162 ILE cc_start: 0.7924 (pt) cc_final: 0.7616 (pt) REVERT: F 173 MET cc_start: 0.8092 (mtm) cc_final: 0.7727 (mpp) REVERT: F 179 ASP cc_start: 0.8728 (m-30) cc_final: 0.8220 (t70) REVERT: F 208 TYR cc_start: 0.7898 (m-80) cc_final: 0.7673 (m-80) REVERT: G 1033 LEU cc_start: 0.9015 (mt) cc_final: 0.8755 (tt) REVERT: G 1110 GLN cc_start: 0.8430 (pt0) cc_final: 0.8018 (tm-30) REVERT: G 1263 GLN cc_start: 0.6490 (tp-100) cc_final: 0.6273 (tp40) REVERT: G 1346 MET cc_start: 0.8264 (mmm) cc_final: 0.7884 (mmt) REVERT: G 1349 ILE cc_start: 0.9536 (pp) cc_final: 0.9250 (pp) REVERT: G 1694 GLU cc_start: 0.9281 (tt0) cc_final: 0.9022 (tm-30) REVERT: H 462 PRO cc_start: 0.8863 (Cg_exo) cc_final: 0.8060 (Cg_endo) REVERT: I 20 LEU cc_start: 0.9331 (mt) cc_final: 0.8497 (mm) REVERT: J 129 TRP cc_start: 0.7975 (m100) cc_final: 0.7690 (m100) REVERT: J 168 SER cc_start: 0.9524 (m) cc_final: 0.9322 (p) REVERT: J 284 TYR cc_start: 0.8564 (t80) cc_final: 0.8015 (t80) REVERT: M 64 LYS cc_start: 0.8703 (mmtm) cc_final: 0.8462 (mmtt) REVERT: M 67 PHE cc_start: 0.8448 (t80) cc_final: 0.6742 (t80) REVERT: M 113 HIS cc_start: 0.7682 (t70) cc_final: 0.5857 (t70) REVERT: N 49 LEU cc_start: 0.9184 (mt) cc_final: 0.8605 (mm) REVERT: N 81 VAL cc_start: 0.9035 (OUTLIER) cc_final: 0.8719 (p) REVERT: N 84 MET cc_start: 0.8254 (mmm) cc_final: 0.8014 (tpt) REVERT: O 25 PHE cc_start: 0.9291 (m-80) cc_final: 0.8595 (m-10) REVERT: O 27 VAL cc_start: 0.9014 (t) cc_final: 0.8510 (t) REVERT: P 59 MET cc_start: 0.9059 (tmm) cc_final: 0.8676 (tpp) REVERT: P 64 SER cc_start: 0.9645 (m) cc_final: 0.8912 (p) REVERT: P 80 LEU cc_start: 0.9577 (mt) cc_final: 0.9294 (tp) REVERT: P 93 GLU cc_start: 0.9264 (mp0) cc_final: 0.8990 (mp0) REVERT: Q 61 LEU cc_start: 0.8790 (mp) cc_final: 0.8130 (pt) REVERT: Q 62 ILE cc_start: 0.9013 (mt) cc_final: 0.8777 (mm) REVERT: Q 87 SER cc_start: 0.9248 (p) cc_final: 0.9046 (p) REVERT: Q 89 VAL cc_start: 0.9238 (t) cc_final: 0.9008 (p) REVERT: Q 100 LEU cc_start: 0.9514 (mt) cc_final: 0.9141 (pp) REVERT: R 37 LEU cc_start: 0.9473 (mt) cc_final: 0.8963 (mt) REVERT: R 43 VAL cc_start: 0.8294 (t) cc_final: 0.7417 (t) REVERT: R 60 VAL cc_start: 0.8477 (t) cc_final: 0.8203 (t) REVERT: R 84 MET cc_start: 0.8812 (mmm) cc_final: 0.8311 (tpp) REVERT: R 98 TYR cc_start: 0.8457 (m-10) cc_final: 0.7880 (m-10) REVERT: S 33 LEU cc_start: 0.9324 (mt) cc_final: 0.9007 (mt) REVERT: S 79 ILE cc_start: 0.8453 (pt) cc_final: 0.8159 (pt) REVERT: S 107 VAL cc_start: 0.8511 (m) cc_final: 0.8269 (t) REVERT: T 113 GLU cc_start: 0.8602 (mm-30) cc_final: 0.7818 (mt-10) outliers start: 5 outliers final: 1 residues processed: 1219 average time/residue: 0.2890 time to fit residues: 560.7913 Evaluate side-chains 634 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 632 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 30.0000 chunk 455 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 470 optimal weight: 5.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 HIS A 21 HIS A 60 HIS A 146 ASN A 237 GLN A 248 ASN B 28 ASN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN C 242 HIS C 446 ASN D 250 ASN D 274 GLN D 301 HIS D 394 GLN D 443 GLN D 452 ASN E 26 HIS E 92 GLN E 250 ASN E 394 GLN E 409 GLN F 24 HIS F 250 ASN ** F 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 964 GLN G 969 ASN ** G1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1130 ASN G1140 GLN G1191 HIS G1269 ASN G1402 HIS G1419 HIS G1570 HIS G1697 GLN I 19 GLN I 168 HIS I 199 ASN J 214 HIS ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 109 HIS Q 68 GLN Q 76 GLN R 25 ASN T 47 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.083461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.062782 restraints weight = 168188.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.064718 restraints weight = 99586.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.065477 restraints weight = 62761.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.065970 restraints weight = 48539.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.066216 restraints weight = 42781.179| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 44795 Z= 0.166 Angle : 0.713 10.678 61826 Z= 0.379 Chirality : 0.046 0.323 7045 Planarity : 0.006 0.065 6957 Dihedral : 21.327 177.024 8477 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.23 % Favored : 94.69 % Rotamer: Outliers : 0.13 % Allowed : 2.67 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.11), residues: 4686 helix: -0.92 (0.10), residues: 2126 sheet: -1.93 (0.20), residues: 595 loop : -2.22 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 95 TYR 0.032 0.002 TYR G1591 PHE 0.055 0.002 PHE G1158 TRP 0.028 0.002 TRP G1066 HIS 0.008 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (44795) covalent geometry : angle 0.71329 / 0.38 (61826) hydrogen bonds : bond 0.05157 / 3.51 ( 1915) hydrogen bonds : angle 5.20676 / 3.60 ( 5355) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 815 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 CYS cc_start: 0.8619 (m) cc_final: 0.8339 (m) REVERT: A 103 TYR cc_start: 0.7690 (m-80) cc_final: 0.7489 (m-80) REVERT: A 130 ASP cc_start: 0.8915 (m-30) cc_final: 0.7766 (p0) REVERT: A 190 ASP cc_start: 0.7875 (m-30) cc_final: 0.7617 (m-30) REVERT: A 278 MET cc_start: 0.8601 (tmm) cc_final: 0.8341 (tmm) REVERT: B 100 SER cc_start: 0.9200 (m) cc_final: 0.8581 (t) REVERT: B 158 LEU cc_start: 0.7826 (tt) cc_final: 0.7155 (tt) REVERT: B 178 TYR cc_start: 0.8145 (t80) cc_final: 0.7708 (t80) REVERT: B 248 ASN cc_start: 0.8499 (t0) cc_final: 0.8012 (t0) REVERT: B 261 MET cc_start: 0.8959 (mmp) cc_final: 0.8719 (tpp) REVERT: B 276 LEU cc_start: 0.8655 (tp) cc_final: 0.8395 (tt) REVERT: B 356 LEU cc_start: 0.8820 (tp) cc_final: 0.8606 (tt) REVERT: B 361 ILE cc_start: 0.9413 (mt) cc_final: 0.8793 (tt) REVERT: C 44 CYS cc_start: 0.7904 (m) cc_final: 0.6778 (t) REVERT: C 95 CYS cc_start: 0.8930 (t) cc_final: 0.8251 (m) REVERT: C 101 GLU cc_start: 0.7688 (tt0) cc_final: 0.7314 (tm-30) REVERT: C 216 LEU cc_start: 0.8948 (mt) cc_final: 0.8548 (mt) REVERT: C 261 MET cc_start: 0.7772 (mmt) cc_final: 0.7408 (mmt) REVERT: C 327 ILE cc_start: 0.9238 (tt) cc_final: 0.8961 (pt) REVERT: C 364 THR cc_start: 0.8879 (m) cc_final: 0.8634 (p) REVERT: C 416 ILE cc_start: 0.8894 (mm) cc_final: 0.8608 (tt) REVERT: D 46 LEU cc_start: 0.9089 (tp) cc_final: 0.8864 (tp) REVERT: D 113 MET cc_start: 0.8578 (ptt) cc_final: 0.8337 (ptt) REVERT: D 181 MET cc_start: 0.9290 (mmt) cc_final: 0.8778 (mmm) REVERT: D 247 ASP cc_start: 0.7957 (m-30) cc_final: 0.7684 (m-30) REVERT: D 325 MET cc_start: 0.8933 (ptp) cc_final: 0.8308 (ptp) REVERT: E 61 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8110 (tp30) REVERT: E 187 MET cc_start: 0.8697 (ttm) cc_final: 0.8312 (ttt) REVERT: E 217 MET cc_start: 0.6451 (mmm) cc_final: 0.5563 (tpp) REVERT: E 369 ILE cc_start: 0.9350 (mt) cc_final: 0.9013 (mm) REVERT: E 375 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8543 (tm-30) REVERT: E 407 THR cc_start: 0.8347 (m) cc_final: 0.7952 (t) REVERT: F 18 LEU cc_start: 0.8865 (mt) cc_final: 0.8466 (mm) REVERT: F 138 MET cc_start: 0.8469 (ttp) cc_final: 0.8089 (ptp) REVERT: F 160 LEU cc_start: 0.8448 (tp) cc_final: 0.7995 (tt) REVERT: F 162 ILE cc_start: 0.7978 (pt) cc_final: 0.7575 (pt) REVERT: F 173 MET cc_start: 0.8003 (mtm) cc_final: 0.7361 (mpp) REVERT: F 179 ASP cc_start: 0.8957 (m-30) cc_final: 0.8470 (t70) REVERT: G 1033 LEU cc_start: 0.9002 (mt) cc_final: 0.8801 (tt) REVERT: G 1050 LEU cc_start: 0.9297 (tp) cc_final: 0.9087 (tp) REVERT: G 1104 MET cc_start: 0.7810 (ttm) cc_final: 0.7294 (mtm) REVERT: G 1110 GLN cc_start: 0.8341 (pt0) cc_final: 0.7945 (tm-30) REVERT: G 1128 CYS cc_start: 0.4783 (m) cc_final: 0.3018 (m) REVERT: G 1143 MET cc_start: 0.8642 (mmp) cc_final: 0.8169 (mmp) REVERT: G 1198 MET cc_start: 0.8439 (tmm) cc_final: 0.8211 (tmm) REVERT: G 1262 MET cc_start: 0.8883 (mtp) cc_final: 0.8573 (mtp) REVERT: G 1349 ILE cc_start: 0.9478 (pt) cc_final: 0.9227 (pt) REVERT: G 1452 LYS cc_start: 0.8618 (tttt) cc_final: 0.8324 (tppt) REVERT: G 1491 MET cc_start: 0.8928 (mmp) cc_final: 0.8696 (mmp) REVERT: G 1591 TYR cc_start: 0.8130 (t80) cc_final: 0.7782 (t80) REVERT: G 1659 MET cc_start: 0.8977 (mtm) cc_final: 0.8758 (mtp) REVERT: G 1675 ARG cc_start: 0.7521 (mtm180) cc_final: 0.7306 (mtm180) REVERT: G 1694 GLU cc_start: 0.9305 (tt0) cc_final: 0.9029 (tm-30) REVERT: H 447 MET cc_start: 0.9103 (mmp) cc_final: 0.8830 (mmp) REVERT: J 129 TRP cc_start: 0.8087 (m100) cc_final: 0.7713 (m100) REVERT: J 168 SER cc_start: 0.9559 (m) cc_final: 0.9340 (p) REVERT: J 631 HIS cc_start: 0.8441 (m170) cc_final: 0.7872 (m170) REVERT: M 62 ILE cc_start: 0.8735 (tt) cc_final: 0.8531 (tt) REVERT: M 67 PHE cc_start: 0.8610 (t80) cc_final: 0.8306 (t80) REVERT: N 49 LEU cc_start: 0.9261 (mt) cc_final: 0.8666 (mm) REVERT: N 53 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8607 (mp0) REVERT: N 58 LEU cc_start: 0.9808 (tp) cc_final: 0.9602 (tp) REVERT: O 25 PHE cc_start: 0.9375 (m-80) cc_final: 0.8756 (m-10) REVERT: O 64 GLU cc_start: 0.9185 (tm-30) cc_final: 0.8788 (tm-30) REVERT: O 73 ASN cc_start: 0.8320 (m110) cc_final: 0.8078 (m110) REVERT: P 62 MET cc_start: 0.8477 (tpp) cc_final: 0.8012 (tpp) REVERT: P 64 SER cc_start: 0.9465 (m) cc_final: 0.9147 (p) REVERT: P 65 PHE cc_start: 0.9307 (t80) cc_final: 0.8984 (t80) REVERT: P 93 GLU cc_start: 0.9234 (mp0) cc_final: 0.8881 (mp0) REVERT: P 100 LEU cc_start: 0.9585 (mt) cc_final: 0.9195 (mm) REVERT: Q 89 VAL cc_start: 0.9377 (t) cc_final: 0.9174 (p) REVERT: Q 90 MET cc_start: 0.9128 (mmp) cc_final: 0.8847 (mmm) REVERT: Q 97 GLU cc_start: 0.9278 (pt0) cc_final: 0.9024 (pt0) REVERT: R 53 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8337 (pt0) REVERT: R 55 ARG cc_start: 0.8801 (mtt180) cc_final: 0.8190 (mtt180) REVERT: R 84 MET cc_start: 0.9040 (mmm) cc_final: 0.8417 (tpp) REVERT: R 97 LEU cc_start: 0.9159 (tt) cc_final: 0.8898 (tp) REVERT: R 98 TYR cc_start: 0.8515 (m-10) cc_final: 0.8215 (m-10) REVERT: S 30 VAL cc_start: 0.9567 (t) cc_final: 0.9347 (p) REVERT: S 89 ASN cc_start: 0.8066 (m-40) cc_final: 0.7568 (t0) REVERT: S 92 GLU cc_start: 0.8067 (pm20) cc_final: 0.7670 (mp0) REVERT: T 68 ASP cc_start: 0.8188 (t0) cc_final: 0.7928 (t70) REVERT: T 113 GLU cc_start: 0.8705 (mm-30) cc_final: 0.7977 (mt-10) outliers start: 5 outliers final: 1 residues processed: 817 average time/residue: 0.2592 time to fit residues: 351.8240 Evaluate side-chains 558 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 557 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 431 optimal weight: 10.0000 chunk 460 optimal weight: 0.0370 chunk 421 optimal weight: 5.9990 chunk 320 optimal weight: 0.9980 chunk 392 optimal weight: 50.0000 chunk 173 optimal weight: 0.9980 chunk 267 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 226 optimal weight: 9.9990 overall best weight: 1.4060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 ASN ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS B 398 HIS B 409 GLN C 10 ASN C 237 GLN D 146 GLN D 250 ASN E 368 GLN F 24 HIS F 250 ASN ** F 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 426 GLN ** G1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1269 ASN ** G1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1657 GLN I 19 GLN I 199 ASN J 262 GLN M 85 GLN S 31 HIS T 63 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.082395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.061211 restraints weight = 168858.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.062937 restraints weight = 93769.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.064119 restraints weight = 61033.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.064914 restraints weight = 44677.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.065459 restraints weight = 35950.941| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 44795 Z= 0.155 Angle : 0.677 11.826 61826 Z= 0.357 Chirality : 0.044 0.268 7045 Planarity : 0.005 0.059 6957 Dihedral : 21.364 177.105 8477 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.14 % Favored : 94.81 % Rotamer: Outliers : 0.08 % Allowed : 2.39 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.12), residues: 4686 helix: -0.43 (0.11), residues: 2137 sheet: -1.64 (0.21), residues: 588 loop : -2.01 (0.13), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 40 TYR 0.045 0.002 TYR G1103 PHE 0.022 0.002 PHE G1096 TRP 0.015 0.001 TRP G1066 HIS 0.013 0.001 HIS G1151 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 (44795) covalent geometry : angle 0.67732 / 0.36 (61826) hydrogen bonds : bond 0.04680 / 3.21 ( 1915) hydrogen bonds : angle 4.91616 / 3.39 ( 5355) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 689 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 CYS cc_start: 0.8579 (m) cc_final: 0.8215 (m) REVERT: A 62 MET cc_start: 0.6228 (tmm) cc_final: 0.6013 (tmm) REVERT: A 130 ASP cc_start: 0.8877 (m-30) cc_final: 0.7817 (p0) REVERT: A 278 MET cc_start: 0.8559 (tmm) cc_final: 0.7979 (tmm) REVERT: A 279 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7579 (mm-30) REVERT: A 328 VAL cc_start: 0.9195 (t) cc_final: 0.8885 (m) REVERT: B 62 MET cc_start: 0.6703 (ttp) cc_final: 0.5986 (ppp) REVERT: B 100 SER cc_start: 0.9248 (m) cc_final: 0.8708 (t) REVERT: B 158 LEU cc_start: 0.7882 (tt) cc_final: 0.7340 (tt) REVERT: B 178 TYR cc_start: 0.8172 (t80) cc_final: 0.7781 (t80) REVERT: B 248 ASN cc_start: 0.8586 (t0) cc_final: 0.7862 (t0) REVERT: B 261 MET cc_start: 0.9013 (mmp) cc_final: 0.8764 (tpp) REVERT: B 276 LEU cc_start: 0.8756 (tp) cc_final: 0.8516 (tt) REVERT: B 361 ILE cc_start: 0.9409 (mt) cc_final: 0.8837 (tt) REVERT: C 44 CYS cc_start: 0.8111 (m) cc_final: 0.6796 (t) REVERT: C 77 LYS cc_start: 0.8959 (mtmm) cc_final: 0.8367 (mtmm) REVERT: C 95 CYS cc_start: 0.8806 (t) cc_final: 0.8156 (m) REVERT: C 101 GLU cc_start: 0.7877 (tt0) cc_final: 0.7320 (tm-30) REVERT: C 159 LEU cc_start: 0.8972 (mp) cc_final: 0.8594 (mt) REVERT: C 179 GLU cc_start: 0.8368 (pm20) cc_final: 0.7367 (tp30) REVERT: C 216 LEU cc_start: 0.8825 (mt) cc_final: 0.8349 (mt) REVERT: C 261 MET cc_start: 0.7572 (mmt) cc_final: 0.7223 (mmt) REVERT: C 364 THR cc_start: 0.8873 (m) cc_final: 0.8614 (p) REVERT: D 30 LEU cc_start: 0.7760 (tt) cc_final: 0.7295 (tp) REVERT: D 181 MET cc_start: 0.9299 (mmt) cc_final: 0.8790 (mmm) REVERT: D 247 ASP cc_start: 0.8107 (m-30) cc_final: 0.7863 (m-30) REVERT: D 301 HIS cc_start: 0.8534 (p90) cc_final: 0.8217 (p90) REVERT: D 325 MET cc_start: 0.8914 (ptp) cc_final: 0.8321 (ptp) REVERT: E 187 MET cc_start: 0.8743 (ttm) cc_final: 0.8429 (ttt) REVERT: E 217 MET cc_start: 0.6479 (mmm) cc_final: 0.5543 (tpp) REVERT: E 369 ILE cc_start: 0.9323 (mt) cc_final: 0.8962 (mm) REVERT: E 407 THR cc_start: 0.8317 (m) cc_final: 0.7927 (t) REVERT: F 113 MET cc_start: 0.7160 (pmm) cc_final: 0.6890 (pmm) REVERT: F 173 MET cc_start: 0.8093 (mtm) cc_final: 0.7045 (mpp) REVERT: F 177 MET cc_start: 0.8358 (ttm) cc_final: 0.8116 (ttm) REVERT: F 179 ASP cc_start: 0.8845 (m-30) cc_final: 0.8501 (t70) REVERT: F 204 LEU cc_start: 0.9429 (mt) cc_final: 0.9163 (mp) REVERT: F 208 TYR cc_start: 0.7905 (m-80) cc_final: 0.7647 (m-80) REVERT: F 285 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7233 (mt-10) REVERT: F 400 TYR cc_start: 0.8592 (t80) cc_final: 0.7890 (t80) REVERT: G 1092 ASP cc_start: 0.8344 (t0) cc_final: 0.8106 (m-30) REVERT: G 1104 MET cc_start: 0.7674 (ttm) cc_final: 0.7163 (mtm) REVERT: G 1110 GLN cc_start: 0.8361 (pt0) cc_final: 0.7967 (tp40) REVERT: G 1128 CYS cc_start: 0.5052 (m) cc_final: 0.3135 (m) REVERT: G 1349 ILE cc_start: 0.9322 (pt) cc_final: 0.9114 (pt) REVERT: G 1576 PHE cc_start: 0.6864 (t80) cc_final: 0.6616 (t80) REVERT: G 1581 MET cc_start: 0.8444 (tpp) cc_final: 0.7866 (tmm) REVERT: G 1585 MET cc_start: 0.9443 (tpp) cc_final: 0.9238 (tpp) REVERT: G 1659 MET cc_start: 0.8936 (mtm) cc_final: 0.8679 (mtp) REVERT: G 1675 ARG cc_start: 0.7493 (mtm180) cc_final: 0.7264 (mtm180) REVERT: G 1694 GLU cc_start: 0.9248 (tt0) cc_final: 0.9004 (tm-30) REVERT: H 447 MET cc_start: 0.9032 (mmp) cc_final: 0.8686 (mmp) REVERT: J 168 SER cc_start: 0.9537 (m) cc_final: 0.9236 (p) REVERT: J 284 TYR cc_start: 0.8805 (t80) cc_final: 0.8437 (t80) REVERT: J 700 GLU cc_start: 0.8169 (mp0) cc_final: 0.7932 (mp0) REVERT: M 50 GLU cc_start: 0.9164 (mp0) cc_final: 0.8187 (mm-30) REVERT: M 67 PHE cc_start: 0.8664 (t80) cc_final: 0.8156 (t80) REVERT: N 46 ILE cc_start: 0.9337 (mp) cc_final: 0.8946 (mp) REVERT: N 84 MET cc_start: 0.8285 (tpt) cc_final: 0.7890 (tpp) REVERT: O 25 PHE cc_start: 0.9453 (m-80) cc_final: 0.8785 (m-10) REVERT: O 73 ASN cc_start: 0.8436 (m110) cc_final: 0.8186 (m110) REVERT: P 64 SER cc_start: 0.9495 (m) cc_final: 0.9281 (p) REVERT: P 66 VAL cc_start: 0.9258 (m) cc_final: 0.9037 (m) REVERT: P 69 ILE cc_start: 0.9636 (pt) cc_final: 0.9389 (pt) REVERT: P 93 GLU cc_start: 0.9210 (mp0) cc_final: 0.8883 (mp0) REVERT: P 100 LEU cc_start: 0.9678 (mt) cc_final: 0.9421 (mm) REVERT: Q 89 VAL cc_start: 0.9420 (t) cc_final: 0.9145 (p) REVERT: Q 90 MET cc_start: 0.9095 (mmp) cc_final: 0.8830 (mmm) REVERT: Q 94 GLU cc_start: 0.9317 (mm-30) cc_final: 0.8971 (mm-30) REVERT: Q 97 GLU cc_start: 0.9343 (pt0) cc_final: 0.8862 (mt-10) REVERT: R 55 ARG cc_start: 0.8750 (mtt180) cc_final: 0.8482 (mtt90) REVERT: R 84 MET cc_start: 0.9052 (mmm) cc_final: 0.8523 (tpp) REVERT: R 98 TYR cc_start: 0.8709 (m-10) cc_final: 0.8296 (m-10) REVERT: S 32 ARG cc_start: 0.8865 (tmm-80) cc_final: 0.8633 (ttp80) REVERT: S 78 ILE cc_start: 0.8351 (mm) cc_final: 0.8041 (mm) REVERT: S 89 ASN cc_start: 0.7998 (m-40) cc_final: 0.7637 (t0) REVERT: S 91 GLU cc_start: 0.8466 (mp0) cc_final: 0.8262 (mp0) REVERT: S 92 GLU cc_start: 0.8028 (pm20) cc_final: 0.7552 (mp0) REVERT: T 61 ILE cc_start: 0.8134 (mt) cc_final: 0.7909 (mt) REVERT: T 68 ASP cc_start: 0.8385 (t0) cc_final: 0.8046 (t70) REVERT: T 113 GLU cc_start: 0.8759 (mm-30) cc_final: 0.7973 (mt-10) outliers start: 3 outliers final: 1 residues processed: 691 average time/residue: 0.2424 time to fit residues: 284.2205 Evaluate side-chains 518 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 517 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 66 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 279 optimal weight: 4.9990 chunk 269 optimal weight: 7.9990 chunk 21 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 327 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 302 optimal weight: 7.9990 chunk 439 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 306 HIS B 409 GLN C 252 GLN D 49 GLN D 328 ASN F 250 ASN ** F 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1006 GLN ** G1141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1287 HIS ** G1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN ** J 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 84 GLN ** R 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 110 ASN T 63 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.081104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.060273 restraints weight = 170413.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.061821 restraints weight = 98829.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.062876 restraints weight = 66212.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.063598 restraints weight = 49796.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.064079 restraints weight = 40758.329| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 44795 Z= 0.174 Angle : 0.659 12.899 61826 Z= 0.348 Chirality : 0.044 0.261 7045 Planarity : 0.004 0.059 6957 Dihedral : 21.366 178.153 8477 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.36 % Favored : 94.58 % Rotamer: Outliers : 0.08 % Allowed : 2.39 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.12), residues: 4686 helix: -0.12 (0.11), residues: 2154 sheet: -1.56 (0.21), residues: 603 loop : -1.88 (0.14), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 95 TYR 0.026 0.002 TYR M 54 PHE 0.027 0.002 PHE A 40 TRP 0.023 0.002 TRP J 129 HIS 0.014 0.001 HIS F 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (44795) covalent geometry : angle 0.65910 / 0.35 (61826) hydrogen bonds : bond 0.04440 / 3.07 ( 1915) hydrogen bonds : angle 4.75499 / 3.29 ( 5355) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 657 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 CYS cc_start: 0.8631 (m) cc_final: 0.8260 (m) REVERT: A 62 MET cc_start: 0.6203 (tmm) cc_final: 0.5937 (tmm) REVERT: A 103 TYR cc_start: 0.8008 (m-80) cc_final: 0.7400 (m-80) REVERT: A 130 ASP cc_start: 0.8887 (m-30) cc_final: 0.7980 (p0) REVERT: A 278 MET cc_start: 0.8614 (tmm) cc_final: 0.8380 (tmm) REVERT: A 328 VAL cc_start: 0.9241 (t) cc_final: 0.8915 (m) REVERT: B 100 SER cc_start: 0.9292 (m) cc_final: 0.8770 (t) REVERT: B 158 LEU cc_start: 0.8067 (tt) cc_final: 0.7434 (tt) REVERT: B 178 TYR cc_start: 0.8217 (t80) cc_final: 0.7768 (t80) REVERT: B 248 ASN cc_start: 0.8484 (t0) cc_final: 0.7980 (t0) REVERT: B 261 MET cc_start: 0.9073 (mmp) cc_final: 0.8835 (tpp) REVERT: B 361 ILE cc_start: 0.9452 (mt) cc_final: 0.8874 (tt) REVERT: C 44 CYS cc_start: 0.7887 (m) cc_final: 0.6828 (t) REVERT: C 77 LYS cc_start: 0.9041 (mtmm) cc_final: 0.8334 (mtmm) REVERT: C 95 CYS cc_start: 0.8706 (t) cc_final: 0.8146 (m) REVERT: C 101 GLU cc_start: 0.7980 (tt0) cc_final: 0.7289 (tm-30) REVERT: C 159 LEU cc_start: 0.8927 (mp) cc_final: 0.8580 (mt) REVERT: C 216 LEU cc_start: 0.8793 (mt) cc_final: 0.8356 (mt) REVERT: D 113 MET cc_start: 0.8701 (ptt) cc_final: 0.8442 (ptt) REVERT: D 181 MET cc_start: 0.9266 (mmt) cc_final: 0.8807 (mmm) REVERT: D 247 ASP cc_start: 0.8178 (m-30) cc_final: 0.7940 (m-30) REVERT: D 312 ASN cc_start: 0.8636 (p0) cc_final: 0.8303 (p0) REVERT: D 325 MET cc_start: 0.8822 (ptp) cc_final: 0.8562 (ptp) REVERT: D 350 LEU cc_start: 0.8268 (mt) cc_final: 0.8047 (mt) REVERT: E 187 MET cc_start: 0.8764 (ttm) cc_final: 0.8557 (ttp) REVERT: E 217 MET cc_start: 0.6487 (mmm) cc_final: 0.5501 (tpp) REVERT: E 369 ILE cc_start: 0.9322 (mt) cc_final: 0.8930 (mm) REVERT: E 407 THR cc_start: 0.8350 (m) cc_final: 0.7915 (t) REVERT: F 160 LEU cc_start: 0.8203 (tp) cc_final: 0.7764 (tt) REVERT: F 162 ILE cc_start: 0.7737 (pt) cc_final: 0.7454 (pt) REVERT: F 173 MET cc_start: 0.8113 (mtm) cc_final: 0.7631 (mpp) REVERT: F 179 ASP cc_start: 0.8770 (m-30) cc_final: 0.8429 (t70) REVERT: F 190 ASP cc_start: 0.7459 (m-30) cc_final: 0.7113 (m-30) REVERT: F 400 TYR cc_start: 0.8683 (t80) cc_final: 0.8058 (t80) REVERT: G 1104 MET cc_start: 0.7674 (ttm) cc_final: 0.7170 (mtt) REVERT: G 1110 GLN cc_start: 0.8330 (pt0) cc_final: 0.7802 (tp-100) REVERT: G 1128 CYS cc_start: 0.5412 (m) cc_final: 0.3591 (m) REVERT: G 1491 MET cc_start: 0.8908 (mmp) cc_final: 0.8587 (mmp) REVERT: G 1496 MET cc_start: 0.8720 (mmm) cc_final: 0.8339 (mmm) REVERT: G 1659 MET cc_start: 0.8960 (mtm) cc_final: 0.8755 (mtp) REVERT: G 1675 ARG cc_start: 0.7520 (mtm180) cc_final: 0.7220 (mtm180) REVERT: G 1694 GLU cc_start: 0.9239 (tt0) cc_final: 0.8982 (tm-30) REVERT: H 447 MET cc_start: 0.9065 (mmp) cc_final: 0.8714 (mmp) REVERT: I 167 LYS cc_start: 0.8420 (ttpt) cc_final: 0.8093 (ptmt) REVERT: J 242 MET cc_start: 0.9516 (tpt) cc_final: 0.9289 (tpp) REVERT: J 284 TYR cc_start: 0.8821 (t80) cc_final: 0.8528 (t80) REVERT: M 50 GLU cc_start: 0.9418 (mp0) cc_final: 0.9181 (mp0) REVERT: M 67 PHE cc_start: 0.8678 (t80) cc_final: 0.8189 (t80) REVERT: N 39 ARG cc_start: 0.9110 (ttm170) cc_final: 0.8790 (ttm-80) REVERT: N 58 LEU cc_start: 0.9785 (tp) cc_final: 0.9535 (tp) REVERT: N 84 MET cc_start: 0.8523 (tpt) cc_final: 0.8259 (tpp) REVERT: O 25 PHE cc_start: 0.9541 (m-80) cc_final: 0.8791 (m-10) REVERT: O 64 GLU cc_start: 0.9249 (tp30) cc_final: 0.8920 (tp30) REVERT: O 73 ASN cc_start: 0.8426 (m110) cc_final: 0.8204 (m110) REVERT: O 78 ILE cc_start: 0.9526 (mm) cc_final: 0.9284 (tp) REVERT: P 65 PHE cc_start: 0.9198 (t80) cc_final: 0.8864 (t80) REVERT: P 69 ILE cc_start: 0.9666 (pt) cc_final: 0.9383 (pt) REVERT: P 93 GLU cc_start: 0.9220 (mp0) cc_final: 0.8954 (mp0) REVERT: Q 89 VAL cc_start: 0.9473 (t) cc_final: 0.9192 (p) REVERT: Q 90 MET cc_start: 0.9124 (mmp) cc_final: 0.8844 (mmm) REVERT: Q 97 GLU cc_start: 0.9289 (pt0) cc_final: 0.8936 (mt-10) REVERT: R 55 ARG cc_start: 0.8681 (mtt180) cc_final: 0.8402 (mtt90) REVERT: R 84 MET cc_start: 0.9099 (mmm) cc_final: 0.8550 (tpp) REVERT: S 78 ILE cc_start: 0.8552 (mm) cc_final: 0.8125 (mm) REVERT: S 89 ASN cc_start: 0.8031 (m-40) cc_final: 0.7688 (t0) REVERT: S 91 GLU cc_start: 0.8478 (mp0) cc_final: 0.8269 (mp0) REVERT: S 92 GLU cc_start: 0.8033 (pm20) cc_final: 0.7502 (mp0) REVERT: T 61 ILE cc_start: 0.8135 (mt) cc_final: 0.7885 (mt) REVERT: T 113 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8016 (pp20) outliers start: 3 outliers final: 1 residues processed: 658 average time/residue: 0.2339 time to fit residues: 260.2676 Evaluate side-chains 491 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 490 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 273 optimal weight: 0.0050 chunk 408 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 274 optimal weight: 6.9990 chunk 302 optimal weight: 1.9990 chunk 225 optimal weight: 8.9990 chunk 69 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 394 optimal weight: 50.0000 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN F 24 HIS F 250 ASN ** F 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1141 ASN ** G1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1404 GLN I 19 GLN ** J 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 49 HIS ** R 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 63 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.080685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.059348 restraints weight = 169786.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.060995 restraints weight = 95390.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.062110 restraints weight = 62707.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.062873 restraints weight = 46452.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.063318 restraints weight = 37697.016| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 44795 Z= 0.163 Angle : 0.644 9.315 61826 Z= 0.340 Chirality : 0.044 0.275 7045 Planarity : 0.004 0.055 6957 Dihedral : 21.356 178.444 8477 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.12 % Favored : 94.81 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.12), residues: 4686 helix: 0.09 (0.11), residues: 2150 sheet: -1.43 (0.20), residues: 619 loop : -1.83 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG R 39 TYR 0.035 0.002 TYR G1103 PHE 0.028 0.002 PHE O 25 TRP 0.014 0.001 TRP G1066 HIS 0.010 0.001 HIS G1151 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (44795) covalent geometry : angle 0.64439 / 0.34 (61826) hydrogen bonds : bond 0.04272 / 2.95 ( 1915) hydrogen bonds : angle 4.60964 / 3.19 ( 5355) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 639 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 CYS cc_start: 0.8802 (m) cc_final: 0.7670 (t) REVERT: A 130 ASP cc_start: 0.8875 (m-30) cc_final: 0.8011 (p0) REVERT: A 278 MET cc_start: 0.8740 (tmm) cc_final: 0.8436 (tmm) REVERT: A 279 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7993 (mm-30) REVERT: A 328 VAL cc_start: 0.9207 (t) cc_final: 0.8835 (m) REVERT: B 100 SER cc_start: 0.9255 (m) cc_final: 0.8786 (t) REVERT: B 248 ASN cc_start: 0.8777 (t0) cc_final: 0.8238 (t0) REVERT: B 261 MET cc_start: 0.9131 (mmp) cc_final: 0.8885 (tpp) REVERT: B 361 ILE cc_start: 0.9476 (mt) cc_final: 0.8877 (tt) REVERT: C 44 CYS cc_start: 0.7889 (m) cc_final: 0.6800 (t) REVERT: C 77 LYS cc_start: 0.9047 (mtmm) cc_final: 0.8407 (mtmm) REVERT: C 95 CYS cc_start: 0.8659 (t) cc_final: 0.8138 (m) REVERT: C 101 GLU cc_start: 0.7955 (tt0) cc_final: 0.7229 (tm-30) REVERT: C 139 MET cc_start: 0.8564 (mmm) cc_final: 0.8180 (mmm) REVERT: C 146 ASN cc_start: 0.9323 (m-40) cc_final: 0.8789 (p0) REVERT: C 159 LEU cc_start: 0.8938 (mp) cc_final: 0.8622 (mt) REVERT: C 197 ASN cc_start: 0.9307 (p0) cc_final: 0.8978 (p0) REVERT: D 46 LEU cc_start: 0.9246 (tp) cc_final: 0.9028 (tp) REVERT: D 179 ASP cc_start: 0.8457 (m-30) cc_final: 0.8203 (m-30) REVERT: D 181 MET cc_start: 0.9276 (mmt) cc_final: 0.8835 (mmm) REVERT: D 247 ASP cc_start: 0.8218 (m-30) cc_final: 0.7951 (m-30) REVERT: D 301 HIS cc_start: 0.8722 (p90) cc_final: 0.8451 (p90) REVERT: D 350 LEU cc_start: 0.8381 (mt) cc_final: 0.8165 (mt) REVERT: E 187 MET cc_start: 0.8804 (ttm) cc_final: 0.8531 (ttm) REVERT: E 217 MET cc_start: 0.6694 (mmm) cc_final: 0.5805 (tpp) REVERT: E 295 LEU cc_start: 0.9281 (tp) cc_final: 0.9051 (tp) REVERT: E 369 ILE cc_start: 0.9333 (mt) cc_final: 0.8912 (mm) REVERT: E 407 THR cc_start: 0.8356 (m) cc_final: 0.7997 (t) REVERT: F 160 LEU cc_start: 0.8359 (tp) cc_final: 0.7969 (tt) REVERT: F 162 ILE cc_start: 0.7737 (pt) cc_final: 0.7479 (pt) REVERT: F 173 MET cc_start: 0.8117 (mtm) cc_final: 0.7720 (mpp) REVERT: F 179 ASP cc_start: 0.8726 (m-30) cc_final: 0.8414 (t70) REVERT: F 190 ASP cc_start: 0.7612 (m-30) cc_final: 0.7394 (m-30) REVERT: F 400 TYR cc_start: 0.8820 (t80) cc_final: 0.8167 (t80) REVERT: G 1092 ASP cc_start: 0.8545 (t0) cc_final: 0.8137 (m-30) REVERT: G 1099 MET cc_start: 0.7655 (mtt) cc_final: 0.7436 (mtt) REVERT: G 1104 MET cc_start: 0.7502 (ttm) cc_final: 0.7155 (mtt) REVERT: G 1110 GLN cc_start: 0.8376 (pt0) cc_final: 0.7832 (tp-100) REVERT: G 1128 CYS cc_start: 0.5562 (m) cc_final: 0.3461 (m) REVERT: G 1143 MET cc_start: 0.8873 (mmp) cc_final: 0.7979 (mmm) REVERT: G 1349 ILE cc_start: 0.9420 (pt) cc_final: 0.9215 (pt) REVERT: G 1491 MET cc_start: 0.8918 (mmp) cc_final: 0.8456 (mmp) REVERT: G 1496 MET cc_start: 0.8788 (mmm) cc_final: 0.8503 (mmm) REVERT: G 1578 MET cc_start: 0.8483 (mpp) cc_final: 0.8014 (mtm) REVERT: G 1610 ASP cc_start: 0.8342 (m-30) cc_final: 0.8138 (m-30) REVERT: G 1659 MET cc_start: 0.8999 (mtm) cc_final: 0.8781 (mtp) REVERT: G 1675 ARG cc_start: 0.7497 (mtm180) cc_final: 0.7157 (mtp180) REVERT: G 1694 GLU cc_start: 0.9248 (tt0) cc_final: 0.8980 (tm-30) REVERT: H 447 MET cc_start: 0.9045 (mmp) cc_final: 0.8612 (mmp) REVERT: I 167 LYS cc_start: 0.8384 (ttpt) cc_final: 0.7983 (ptmt) REVERT: I 169 TYR cc_start: 0.8133 (m-10) cc_final: 0.7792 (m-10) REVERT: J 242 MET cc_start: 0.9513 (tpt) cc_final: 0.9271 (tpp) REVERT: M 67 PHE cc_start: 0.8701 (t80) cc_final: 0.8193 (t80) REVERT: N 59 LYS cc_start: 0.9559 (ptmm) cc_final: 0.9109 (pttm) REVERT: N 63 GLU cc_start: 0.9496 (pt0) cc_final: 0.9243 (pt0) REVERT: O 25 PHE cc_start: 0.9320 (m-80) cc_final: 0.8768 (m-80) REVERT: O 73 ASN cc_start: 0.8416 (m110) cc_final: 0.8209 (m110) REVERT: O 78 ILE cc_start: 0.9553 (mm) cc_final: 0.9198 (tp) REVERT: P 93 GLU cc_start: 0.9195 (mp0) cc_final: 0.8985 (mp0) REVERT: P 100 LEU cc_start: 0.9297 (mm) cc_final: 0.8986 (mm) REVERT: Q 50 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8579 (mm-30) REVERT: Q 97 GLU cc_start: 0.9334 (pt0) cc_final: 0.8941 (mt-10) REVERT: Q 99 TYR cc_start: 0.8782 (t80) cc_final: 0.8576 (t80) REVERT: R 55 ARG cc_start: 0.8742 (mtt180) cc_final: 0.8456 (mtt90) REVERT: R 84 MET cc_start: 0.9143 (mmm) cc_final: 0.8526 (tpp) REVERT: S 78 ILE cc_start: 0.8678 (mm) cc_final: 0.8107 (mm) REVERT: S 89 ASN cc_start: 0.8107 (m-40) cc_final: 0.7880 (t0) REVERT: S 92 GLU cc_start: 0.8014 (pm20) cc_final: 0.7527 (mp0) REVERT: T 61 ILE cc_start: 0.8185 (mt) cc_final: 0.7978 (mt) REVERT: T 113 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8186 (pp20) outliers start: 0 outliers final: 0 residues processed: 639 average time/residue: 0.2488 time to fit residues: 270.1932 Evaluate side-chains 474 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 474 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 431 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 chunk 389 optimal weight: 40.0000 chunk 160 optimal weight: 3.9990 chunk 467 optimal weight: 9.9990 chunk 262 optimal weight: 0.0050 chunk 337 optimal weight: 9.9990 chunk 443 optimal weight: 10.0000 chunk 336 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 HIS ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 HIS D 49 GLN D 368 GLN E 92 GLN F 250 ASN ** F 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 403 ASN ** G1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN ** J 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 25 ASN ** N 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 63 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.079437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.058353 restraints weight = 170395.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.059855 restraints weight = 99222.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.060874 restraints weight = 66841.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.061590 restraints weight = 50384.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.062065 restraints weight = 41364.954| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 44795 Z= 0.197 Angle : 0.666 9.778 61826 Z= 0.351 Chirality : 0.044 0.267 7045 Planarity : 0.004 0.062 6957 Dihedral : 21.388 178.937 8477 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.61 % Favored : 94.32 % Rotamer: Outliers : 0.05 % Allowed : 1.83 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.12), residues: 4686 helix: 0.19 (0.11), residues: 2165 sheet: -1.39 (0.21), residues: 619 loop : -1.81 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G1201 TYR 0.025 0.002 TYR A 193 PHE 0.024 0.002 PHE P 65 TRP 0.015 0.001 TRP J 129 HIS 0.010 0.001 HIS G1151 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.20 (44795) covalent geometry : angle 0.66603 / 0.35 (61826) hydrogen bonds : bond 0.04360 / 3.02 ( 1915) hydrogen bonds : angle 4.59692 / 3.18 ( 5355) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 604 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 CYS cc_start: 0.8831 (m) cc_final: 0.7800 (t) REVERT: A 62 MET cc_start: 0.6153 (tmm) cc_final: 0.5430 (tmm) REVERT: A 130 ASP cc_start: 0.8894 (m-30) cc_final: 0.7967 (p0) REVERT: A 278 MET cc_start: 0.8626 (tmm) cc_final: 0.8343 (tmm) REVERT: B 100 SER cc_start: 0.9258 (m) cc_final: 0.8797 (t) REVERT: B 248 ASN cc_start: 0.8794 (t0) cc_final: 0.8226 (t0) REVERT: B 361 ILE cc_start: 0.9517 (mt) cc_final: 0.8928 (tt) REVERT: C 44 CYS cc_start: 0.7850 (m) cc_final: 0.7391 (m) REVERT: C 77 LYS cc_start: 0.9029 (mtmm) cc_final: 0.8387 (mtmm) REVERT: C 95 CYS cc_start: 0.8529 (t) cc_final: 0.8160 (m) REVERT: C 101 GLU cc_start: 0.7932 (tt0) cc_final: 0.7038 (tm-30) REVERT: C 146 ASN cc_start: 0.9350 (m-40) cc_final: 0.8798 (p0) REVERT: C 159 LEU cc_start: 0.8991 (mp) cc_final: 0.8755 (mt) REVERT: C 197 ASN cc_start: 0.9350 (p0) cc_final: 0.9030 (p0) REVERT: C 261 MET cc_start: 0.8167 (tpp) cc_final: 0.7862 (mmt) REVERT: C 327 ILE cc_start: 0.8886 (pt) cc_final: 0.8635 (pt) REVERT: D 30 LEU cc_start: 0.8148 (tt) cc_final: 0.7788 (tp) REVERT: D 46 LEU cc_start: 0.9250 (tp) cc_final: 0.8914 (tp) REVERT: D 113 MET cc_start: 0.8799 (ptt) cc_final: 0.8511 (ptt) REVERT: D 134 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7240 (tm-30) REVERT: D 179 ASP cc_start: 0.8507 (m-30) cc_final: 0.8246 (m-30) REVERT: D 181 MET cc_start: 0.9270 (mmt) cc_final: 0.8838 (mmm) REVERT: D 223 PHE cc_start: 0.8466 (t80) cc_final: 0.8253 (t80) REVERT: D 247 ASP cc_start: 0.8344 (m-30) cc_final: 0.8071 (m-30) REVERT: D 301 HIS cc_start: 0.8819 (p90) cc_final: 0.8543 (p90) REVERT: E 88 MET cc_start: 0.8806 (mmp) cc_final: 0.8529 (tpt) REVERT: E 217 MET cc_start: 0.6846 (mmm) cc_final: 0.5979 (tpp) REVERT: E 407 THR cc_start: 0.8432 (m) cc_final: 0.8044 (t) REVERT: E 442 VAL cc_start: 0.9074 (t) cc_final: 0.8761 (p) REVERT: F 160 LEU cc_start: 0.8461 (tp) cc_final: 0.8091 (tt) REVERT: F 173 MET cc_start: 0.8077 (mtm) cc_final: 0.7623 (mpp) REVERT: F 179 ASP cc_start: 0.8761 (m-30) cc_final: 0.8502 (t70) REVERT: F 190 ASP cc_start: 0.7961 (m-30) cc_final: 0.7707 (m-30) REVERT: F 400 TYR cc_start: 0.8917 (t80) cc_final: 0.8323 (t80) REVERT: G 1099 MET cc_start: 0.7756 (mtt) cc_final: 0.7500 (mtt) REVERT: G 1104 MET cc_start: 0.7620 (ttm) cc_final: 0.7414 (ttp) REVERT: G 1110 GLN cc_start: 0.8492 (pt0) cc_final: 0.8136 (tp40) REVERT: G 1128 CYS cc_start: 0.5600 (m) cc_final: 0.5173 (m) REVERT: G 1143 MET cc_start: 0.8966 (mmp) cc_final: 0.8136 (mmm) REVERT: G 1349 ILE cc_start: 0.9397 (pt) cc_final: 0.9155 (pt) REVERT: G 1496 MET cc_start: 0.8852 (mmm) cc_final: 0.8225 (mmm) REVERT: G 1501 PHE cc_start: 0.8524 (m-80) cc_final: 0.7906 (m-10) REVERT: G 1576 PHE cc_start: 0.7019 (t80) cc_final: 0.6261 (t80) REVERT: G 1578 MET cc_start: 0.8468 (mpp) cc_final: 0.8109 (mtm) REVERT: G 1675 ARG cc_start: 0.7483 (mtm180) cc_final: 0.7142 (mtp180) REVERT: G 1694 GLU cc_start: 0.9244 (tt0) cc_final: 0.8929 (tm-30) REVERT: H 447 MET cc_start: 0.9064 (mmp) cc_final: 0.8631 (mmp) REVERT: I 167 LYS cc_start: 0.8412 (ttpt) cc_final: 0.7933 (ptmt) REVERT: I 169 TYR cc_start: 0.8191 (m-10) cc_final: 0.7727 (m-10) REVERT: J 242 MET cc_start: 0.9517 (tpt) cc_final: 0.9266 (tpp) REVERT: J 768 PHE cc_start: 0.7333 (t80) cc_final: 0.7025 (t80) REVERT: M 50 GLU cc_start: 0.9655 (mp0) cc_final: 0.9309 (mp0) REVERT: M 67 PHE cc_start: 0.8693 (t80) cc_final: 0.7444 (t80) REVERT: N 31 LYS cc_start: 0.9763 (mmtt) cc_final: 0.9501 (mmmt) REVERT: N 59 LYS cc_start: 0.9562 (ptmm) cc_final: 0.9349 (ptmm) REVERT: N 63 GLU cc_start: 0.9527 (pt0) cc_final: 0.9123 (pt0) REVERT: N 84 MET cc_start: 0.8988 (mmp) cc_final: 0.8707 (tpp) REVERT: O 25 PHE cc_start: 0.9282 (m-80) cc_final: 0.8779 (m-80) REVERT: O 41 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7776 (mm-30) REVERT: O 73 ASN cc_start: 0.8442 (m110) cc_final: 0.8236 (m110) REVERT: O 78 ILE cc_start: 0.9567 (mm) cc_final: 0.9233 (tp) REVERT: P 65 PHE cc_start: 0.9345 (t80) cc_final: 0.9109 (t80) REVERT: P 93 GLU cc_start: 0.9205 (mp0) cc_final: 0.8989 (mp0) REVERT: Q 50 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8674 (mm-30) REVERT: Q 97 GLU cc_start: 0.9305 (pt0) cc_final: 0.8976 (mt-10) REVERT: R 55 ARG cc_start: 0.8780 (mtt90) cc_final: 0.8304 (mmt90) REVERT: R 84 MET cc_start: 0.9170 (mmm) cc_final: 0.8887 (tpp) REVERT: S 78 ILE cc_start: 0.8747 (mm) cc_final: 0.8363 (mm) REVERT: S 92 GLU cc_start: 0.8130 (pm20) cc_final: 0.7626 (mp0) REVERT: T 113 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8316 (pp20) outliers start: 2 outliers final: 1 residues processed: 606 average time/residue: 0.2413 time to fit residues: 251.7926 Evaluate side-chains 460 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 459 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 383 optimal weight: 40.0000 chunk 185 optimal weight: 0.7980 chunk 366 optimal weight: 0.6980 chunk 392 optimal weight: 50.0000 chunk 169 optimal weight: 1.9990 chunk 334 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 190 optimal weight: 0.9990 chunk 395 optimal weight: 30.0000 chunk 312 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 ASN ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN ** G1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1404 GLN I 19 GLN ** I 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 93 GLN ** N 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 ASN ** P 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 75 HIS ** 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 = 0.3512 r_free = 0.3512 target = 0.080522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.059625 restraints weight = 169550.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.061157 restraints weight = 98104.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.062196 restraints weight = 65829.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.062928 restraints weight = 49530.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.063414 restraints weight = 40496.976| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 44795 Z= 0.133 Angle : 0.630 13.293 61826 Z= 0.331 Chirality : 0.043 0.268 7045 Planarity : 0.004 0.058 6957 Dihedral : 21.349 178.063 8477 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.74 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.12), residues: 4686 helix: 0.26 (0.11), residues: 2162 sheet: -1.29 (0.20), residues: 629 loop : -1.75 (0.14), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG S 32 TYR 0.028 0.002 TYR A 193 PHE 0.032 0.001 PHE M 67 TRP 0.016 0.001 TRP J 129 HIS 0.010 0.001 HIS G1151 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (44795) covalent geometry : angle 0.63040 / 0.33 (61826) hydrogen bonds : bond 0.04056 / 2.82 ( 1915) hydrogen bonds : angle 4.42694 / 3.06 ( 5355) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 617 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 CYS cc_start: 0.8780 (m) cc_final: 0.7728 (t) REVERT: A 62 MET cc_start: 0.6224 (tmm) cc_final: 0.5668 (tmm) REVERT: A 85 SER cc_start: 0.9254 (t) cc_final: 0.9048 (p) REVERT: A 130 ASP cc_start: 0.8839 (m-30) cc_final: 0.7810 (p0) REVERT: A 278 MET cc_start: 0.8507 (tmm) cc_final: 0.8227 (tmm) REVERT: B 100 SER cc_start: 0.9329 (m) cc_final: 0.8809 (t) REVERT: B 361 ILE cc_start: 0.9510 (mt) cc_final: 0.8904 (tt) REVERT: C 95 CYS cc_start: 0.8591 (t) cc_final: 0.8191 (m) REVERT: C 101 GLU cc_start: 0.7960 (tt0) cc_final: 0.6999 (tm-30) REVERT: C 146 ASN cc_start: 0.9376 (m-40) cc_final: 0.8817 (p0) REVERT: C 159 LEU cc_start: 0.9040 (mp) cc_final: 0.8767 (tp) REVERT: C 197 ASN cc_start: 0.9331 (p0) cc_final: 0.9027 (p0) REVERT: C 327 ILE cc_start: 0.8819 (pt) cc_final: 0.8563 (pt) REVERT: D 46 LEU cc_start: 0.9297 (tp) cc_final: 0.9021 (tp) REVERT: D 113 MET cc_start: 0.8671 (ptt) cc_final: 0.8403 (ptt) REVERT: D 160 LEU cc_start: 0.9256 (tp) cc_final: 0.8998 (tt) REVERT: D 179 ASP cc_start: 0.8494 (m-30) cc_final: 0.8215 (m-30) REVERT: D 181 MET cc_start: 0.9294 (mmt) cc_final: 0.8842 (mmm) REVERT: D 247 ASP cc_start: 0.8256 (m-30) cc_final: 0.7944 (m-30) REVERT: D 301 HIS cc_start: 0.8847 (p90) cc_final: 0.8604 (p90) REVERT: E 88 MET cc_start: 0.8790 (mmp) cc_final: 0.8406 (tpt) REVERT: E 217 MET cc_start: 0.6845 (mmm) cc_final: 0.5912 (tpp) REVERT: E 407 THR cc_start: 0.8432 (m) cc_final: 0.7984 (t) REVERT: E 442 VAL cc_start: 0.9060 (t) cc_final: 0.8771 (p) REVERT: F 160 LEU cc_start: 0.8575 (tp) cc_final: 0.8153 (tt) REVERT: F 173 MET cc_start: 0.7792 (mtm) cc_final: 0.7425 (mtm) REVERT: F 179 ASP cc_start: 0.8788 (m-30) cc_final: 0.8498 (m-30) REVERT: F 400 TYR cc_start: 0.8922 (t80) cc_final: 0.8395 (t80) REVERT: G 1104 MET cc_start: 0.7609 (ttm) cc_final: 0.7363 (ttp) REVERT: G 1110 GLN cc_start: 0.8484 (pt0) cc_final: 0.8110 (tp40) REVERT: G 1128 CYS cc_start: 0.5403 (m) cc_final: 0.4937 (m) REVERT: G 1143 MET cc_start: 0.8921 (mmp) cc_final: 0.8050 (mmm) REVERT: G 1240 MET cc_start: 0.3880 (mtt) cc_final: 0.2895 (mtt) REVERT: G 1262 MET cc_start: 0.8932 (mmm) cc_final: 0.7703 (mmm) REVERT: G 1496 MET cc_start: 0.8938 (mmm) cc_final: 0.8313 (mmm) REVERT: G 1501 PHE cc_start: 0.8506 (m-80) cc_final: 0.7996 (m-10) REVERT: G 1578 MET cc_start: 0.8563 (mpp) cc_final: 0.7985 (mtp) REVERT: G 1659 MET cc_start: 0.9115 (mtp) cc_final: 0.8786 (mtp) REVERT: G 1675 ARG cc_start: 0.7429 (mtm180) cc_final: 0.7099 (mtp180) REVERT: G 1694 GLU cc_start: 0.9333 (tt0) cc_final: 0.8995 (pt0) REVERT: H 447 MET cc_start: 0.9083 (mmp) cc_final: 0.8598 (mmp) REVERT: I 167 LYS cc_start: 0.8387 (ttpt) cc_final: 0.8143 (ptmt) REVERT: I 169 TYR cc_start: 0.8150 (m-10) cc_final: 0.7692 (m-80) REVERT: J 242 MET cc_start: 0.9573 (tpt) cc_final: 0.9287 (tpp) REVERT: J 768 PHE cc_start: 0.7384 (t80) cc_final: 0.7092 (t80) REVERT: M 50 GLU cc_start: 0.9631 (mp0) cc_final: 0.9250 (mp0) REVERT: N 31 LYS cc_start: 0.9788 (mmtt) cc_final: 0.9545 (mmmt) REVERT: N 59 LYS cc_start: 0.9567 (ptmm) cc_final: 0.9080 (pttm) REVERT: N 63 GLU cc_start: 0.9532 (pt0) cc_final: 0.9230 (pt0) REVERT: N 84 MET cc_start: 0.8979 (mmp) cc_final: 0.8688 (tpp) REVERT: O 25 PHE cc_start: 0.9284 (m-80) cc_final: 0.8673 (m-80) REVERT: O 41 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7983 (mm-30) REVERT: O 59 THR cc_start: 0.9586 (p) cc_final: 0.9297 (p) REVERT: O 61 GLU cc_start: 0.8723 (mp0) cc_final: 0.8353 (mp0) REVERT: O 64 GLU cc_start: 0.9197 (tp30) cc_final: 0.8931 (tp30) REVERT: O 73 ASN cc_start: 0.8452 (m110) cc_final: 0.8234 (m110) REVERT: O 78 ILE cc_start: 0.9603 (mm) cc_final: 0.9218 (tp) REVERT: O 83 LEU cc_start: 0.9773 (tp) cc_final: 0.9512 (pp) REVERT: P 69 ILE cc_start: 0.9590 (pt) cc_final: 0.9255 (pt) REVERT: P 93 GLU cc_start: 0.9166 (mp0) cc_final: 0.8933 (mp0) REVERT: P 100 LEU cc_start: 0.9110 (mm) cc_final: 0.8827 (mm) REVERT: Q 50 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8744 (mm-30) REVERT: Q 90 MET cc_start: 0.9299 (mmp) cc_final: 0.9068 (mmm) REVERT: Q 97 GLU cc_start: 0.9355 (pt0) cc_final: 0.9032 (mt-10) REVERT: R 55 ARG cc_start: 0.8737 (mtt90) cc_final: 0.8425 (mtt90) REVERT: R 84 MET cc_start: 0.9139 (mmm) cc_final: 0.8875 (tpp) REVERT: S 78 ILE cc_start: 0.8695 (mm) cc_final: 0.8137 (mm) REVERT: S 79 ILE cc_start: 0.8665 (pt) cc_final: 0.8463 (pt) REVERT: S 91 GLU cc_start: 0.7838 (pm20) cc_final: 0.7540 (pp20) REVERT: S 92 GLU cc_start: 0.8135 (pm20) cc_final: 0.7721 (pm20) REVERT: T 113 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8330 (pp20) outliers start: 0 outliers final: 0 residues processed: 617 average time/residue: 0.2424 time to fit residues: 257.0445 Evaluate side-chains 470 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 470 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 390 optimal weight: 40.0000 chunk 5 optimal weight: 6.9990 chunk 435 optimal weight: 40.0000 chunk 302 optimal weight: 6.9990 chunk 333 optimal weight: 0.9990 chunk 398 optimal weight: 40.0000 chunk 144 optimal weight: 0.9990 chunk 316 optimal weight: 4.9990 chunk 237 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN E 49 GLN F 24 HIS F 250 ASN ** F 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1364 ASN I 19 GLN ** I 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 63 ASN ** P 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 75 HIS T 63 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.078853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.057887 restraints weight = 171810.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.059381 restraints weight = 99835.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.060404 restraints weight = 67132.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.061100 restraints weight = 50598.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.061570 restraints weight = 41663.941| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 44795 Z= 0.186 Angle : 0.662 9.711 61826 Z= 0.348 Chirality : 0.044 0.242 7045 Planarity : 0.004 0.060 6957 Dihedral : 21.370 178.953 8477 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.44 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.12), residues: 4686 helix: 0.37 (0.11), residues: 2154 sheet: -1.22 (0.20), residues: 639 loop : -1.73 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 92 TYR 0.028 0.002 TYR A 193 PHE 0.024 0.002 PHE G1096 TRP 0.018 0.002 TRP J 129 HIS 0.009 0.001 HIS G1151 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.19 (44795) covalent geometry : angle 0.66238 / 0.35 (61826) hydrogen bonds : bond 0.04224 / 2.93 ( 1915) hydrogen bonds : angle 4.47434 / 3.10 ( 5355) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 588 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 CYS cc_start: 0.8672 (m) cc_final: 0.7694 (t) REVERT: A 62 MET cc_start: 0.6142 (tmm) cc_final: 0.5623 (tmm) REVERT: A 130 ASP cc_start: 0.8862 (m-30) cc_final: 0.7990 (p0) REVERT: A 278 MET cc_start: 0.8531 (tmm) cc_final: 0.8266 (tmm) REVERT: B 100 SER cc_start: 0.9314 (m) cc_final: 0.8839 (t) REVERT: B 361 ILE cc_start: 0.9533 (mt) cc_final: 0.8956 (tt) REVERT: C 77 LYS cc_start: 0.9033 (mtmm) cc_final: 0.8355 (mtmm) REVERT: C 95 CYS cc_start: 0.8358 (t) cc_final: 0.8091 (m) REVERT: C 101 GLU cc_start: 0.7921 (tt0) cc_final: 0.7015 (tm-30) REVERT: C 159 LEU cc_start: 0.9004 (mp) cc_final: 0.8717 (tp) REVERT: C 197 ASN cc_start: 0.9342 (p0) cc_final: 0.9007 (p0) REVERT: C 261 MET cc_start: 0.8086 (tpp) cc_final: 0.7630 (mmt) REVERT: D 46 LEU cc_start: 0.9218 (tp) cc_final: 0.8929 (tp) REVERT: D 113 MET cc_start: 0.8827 (ptt) cc_final: 0.8498 (ptt) REVERT: D 179 ASP cc_start: 0.8507 (m-30) cc_final: 0.8246 (m-30) REVERT: D 181 MET cc_start: 0.9236 (mmt) cc_final: 0.8831 (mmm) REVERT: D 247 ASP cc_start: 0.8344 (m-30) cc_final: 0.8039 (m-30) REVERT: E 88 MET cc_start: 0.8762 (mmp) cc_final: 0.8545 (tpt) REVERT: E 217 MET cc_start: 0.6873 (mmm) cc_final: 0.6059 (tpp) REVERT: E 407 THR cc_start: 0.8483 (m) cc_final: 0.7978 (t) REVERT: E 442 VAL cc_start: 0.9022 (t) cc_final: 0.8685 (p) REVERT: F 138 MET cc_start: 0.8326 (tmm) cc_final: 0.8120 (tmm) REVERT: F 160 LEU cc_start: 0.8514 (tp) cc_final: 0.8213 (tt) REVERT: F 173 MET cc_start: 0.8104 (mtm) cc_final: 0.7631 (mpp) REVERT: F 179 ASP cc_start: 0.8672 (m-30) cc_final: 0.8347 (m-30) REVERT: F 190 ASP cc_start: 0.8082 (m-30) cc_final: 0.7557 (m-30) REVERT: F 202 THR cc_start: 0.9198 (t) cc_final: 0.8944 (p) REVERT: F 400 TYR cc_start: 0.9158 (t80) cc_final: 0.8529 (t80) REVERT: G 1104 MET cc_start: 0.7489 (ttm) cc_final: 0.7266 (ttp) REVERT: G 1110 GLN cc_start: 0.8408 (pt0) cc_final: 0.8075 (tp40) REVERT: G 1128 CYS cc_start: 0.5744 (m) cc_final: 0.5257 (m) REVERT: G 1143 MET cc_start: 0.9044 (mmp) cc_final: 0.8146 (mmm) REVERT: G 1262 MET cc_start: 0.8969 (mmm) cc_final: 0.8726 (mmm) REVERT: G 1403 MET cc_start: 0.8581 (mmt) cc_final: 0.8228 (mmm) REVERT: G 1496 MET cc_start: 0.8789 (mmm) cc_final: 0.8469 (mmm) REVERT: G 1576 PHE cc_start: 0.7134 (t80) cc_final: 0.6227 (t80) REVERT: G 1578 MET cc_start: 0.8573 (mpp) cc_final: 0.8051 (mtm) REVERT: G 1610 ASP cc_start: 0.8289 (m-30) cc_final: 0.8063 (m-30) REVERT: G 1675 ARG cc_start: 0.7474 (mtm180) cc_final: 0.7126 (mtp180) REVERT: G 1694 GLU cc_start: 0.9230 (tt0) cc_final: 0.8928 (tm-30) REVERT: H 447 MET cc_start: 0.9051 (mmp) cc_final: 0.8642 (mmp) REVERT: I 167 LYS cc_start: 0.8247 (ttpt) cc_final: 0.7797 (ptmt) REVERT: I 169 TYR cc_start: 0.8079 (m-10) cc_final: 0.7651 (m-10) REVERT: J 158 MET cc_start: 0.8309 (ttm) cc_final: 0.7757 (ttm) REVERT: J 242 MET cc_start: 0.9520 (tpt) cc_final: 0.9290 (tpp) REVERT: J 768 PHE cc_start: 0.7354 (t80) cc_final: 0.7010 (t80) REVERT: M 97 GLU cc_start: 0.9176 (pp20) cc_final: 0.8975 (pp20) REVERT: M 105 GLU cc_start: 0.9296 (tm-30) cc_final: 0.9083 (tm-30) REVERT: M 113 HIS cc_start: 0.7468 (t70) cc_final: 0.6096 (t70) REVERT: N 31 LYS cc_start: 0.9795 (mmtt) cc_final: 0.9552 (mmmt) REVERT: N 59 LYS cc_start: 0.9567 (ptmm) cc_final: 0.9265 (ptmm) REVERT: N 63 GLU cc_start: 0.9495 (pt0) cc_final: 0.9046 (pt0) REVERT: N 84 MET cc_start: 0.8941 (mmp) cc_final: 0.8709 (tpp) REVERT: O 25 PHE cc_start: 0.9286 (m-80) cc_final: 0.8703 (m-80) REVERT: O 38 ASN cc_start: 0.8474 (m110) cc_final: 0.8262 (m110) REVERT: O 41 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7963 (mm-30) REVERT: O 73 ASN cc_start: 0.8475 (m110) cc_final: 0.8271 (m110) REVERT: O 75 LYS cc_start: 0.7661 (mmtp) cc_final: 0.7410 (mmmm) REVERT: O 78 ILE cc_start: 0.9546 (mm) cc_final: 0.9233 (tp) REVERT: O 83 LEU cc_start: 0.9732 (tp) cc_final: 0.9502 (pp) REVERT: P 93 GLU cc_start: 0.9190 (mp0) cc_final: 0.8964 (mp0) REVERT: Q 50 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8705 (mm-30) REVERT: Q 77 ASP cc_start: 0.8963 (t70) cc_final: 0.8748 (t70) REVERT: Q 90 MET cc_start: 0.9276 (mmp) cc_final: 0.9034 (mmp) REVERT: Q 122 LYS cc_start: 0.9149 (mppt) cc_final: 0.8520 (ptmt) REVERT: R 22 LEU cc_start: 0.4128 (tp) cc_final: 0.3899 (tt) REVERT: R 55 ARG cc_start: 0.8807 (mtt90) cc_final: 0.8352 (mmt90) REVERT: R 84 MET cc_start: 0.9213 (mmm) cc_final: 0.8831 (tpp) REVERT: S 91 GLU cc_start: 0.7891 (pm20) cc_final: 0.7663 (pp20) outliers start: 0 outliers final: 0 residues processed: 588 average time/residue: 0.2416 time to fit residues: 245.5824 Evaluate side-chains 459 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 459 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 154 optimal weight: 1.9990 chunk 285 optimal weight: 7.9990 chunk 148 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 467 optimal weight: 5.9990 chunk 253 optimal weight: 6.9990 chunk 309 optimal weight: 0.9980 chunk 452 optimal weight: 8.9990 chunk 293 optimal weight: 3.9990 chunk 386 optimal weight: 50.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 ASN A 146 ASN ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN C 446 ASN D 452 ASN F 24 HIS F 250 ASN F 328 ASN ** G1161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN ** I 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.078284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.057302 restraints weight = 171161.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.058761 restraints weight = 99931.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.059762 restraints weight = 67680.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.060449 restraints weight = 51294.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.060906 restraints weight = 42319.156| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 44795 Z= 0.192 Angle : 0.672 9.282 61826 Z= 0.354 Chirality : 0.044 0.264 7045 Planarity : 0.004 0.061 6957 Dihedral : 21.392 178.466 8477 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.42 % Favored : 94.52 % Rotamer: Outliers : 0.03 % Allowed : 0.61 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.12), residues: 4686 helix: 0.38 (0.11), residues: 2151 sheet: -1.22 (0.21), residues: 635 loop : -1.73 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 92 TYR 0.034 0.002 TYR A 193 PHE 0.030 0.002 PHE N 61 TRP 0.016 0.002 TRP J 129 HIS 0.011 0.001 HIS E 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 (44795) covalent geometry : angle 0.67242 / 0.35 (61826) hydrogen bonds : bond 0.04230 / 2.95 ( 1915) hydrogen bonds : angle 4.50000 / 3.12 ( 5355) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 571 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 CYS cc_start: 0.8720 (m) cc_final: 0.8268 (m) REVERT: A 62 MET cc_start: 0.6249 (tmm) cc_final: 0.5741 (tmm) REVERT: A 130 ASP cc_start: 0.8806 (m-30) cc_final: 0.7963 (p0) REVERT: A 278 MET cc_start: 0.8535 (tmm) cc_final: 0.8287 (tmm) REVERT: A 279 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7876 (mm-30) REVERT: B 100 SER cc_start: 0.9314 (m) cc_final: 0.8861 (t) REVERT: B 248 ASN cc_start: 0.8405 (t0) cc_final: 0.7765 (t0) REVERT: B 361 ILE cc_start: 0.9529 (mt) cc_final: 0.8955 (tt) REVERT: B 406 TYR cc_start: 0.8987 (t80) cc_final: 0.8730 (t80) REVERT: C 77 LYS cc_start: 0.8998 (mtmm) cc_final: 0.8341 (mtmm) REVERT: C 101 GLU cc_start: 0.7774 (tt0) cc_final: 0.6912 (tm-30) REVERT: C 146 ASN cc_start: 0.9189 (m-40) cc_final: 0.8821 (p0) REVERT: C 159 LEU cc_start: 0.9036 (mp) cc_final: 0.8754 (tp) REVERT: C 197 ASN cc_start: 0.9356 (p0) cc_final: 0.9025 (p0) REVERT: D 46 LEU cc_start: 0.9212 (tp) cc_final: 0.8928 (tp) REVERT: D 113 MET cc_start: 0.8856 (ptt) cc_final: 0.8535 (ptt) REVERT: D 179 ASP cc_start: 0.8527 (m-30) cc_final: 0.8255 (m-30) REVERT: D 181 MET cc_start: 0.9218 (mmt) cc_final: 0.8777 (mmm) REVERT: D 247 ASP cc_start: 0.8254 (m-30) cc_final: 0.7968 (m-30) REVERT: E 88 MET cc_start: 0.8777 (mmp) cc_final: 0.8532 (tpt) REVERT: E 217 MET cc_start: 0.6948 (mmm) cc_final: 0.6060 (tpp) REVERT: E 442 VAL cc_start: 0.9071 (t) cc_final: 0.8735 (p) REVERT: F 138 MET cc_start: 0.8319 (tmm) cc_final: 0.8051 (tmm) REVERT: F 160 LEU cc_start: 0.8585 (tp) cc_final: 0.8342 (tt) REVERT: F 173 MET cc_start: 0.8139 (mtm) cc_final: 0.7677 (mpp) REVERT: F 190 ASP cc_start: 0.8172 (m-30) cc_final: 0.7756 (m-30) REVERT: F 202 THR cc_start: 0.9258 (t) cc_final: 0.8948 (p) REVERT: F 400 TYR cc_start: 0.9104 (t80) cc_final: 0.8526 (t80) REVERT: G 1014 LEU cc_start: 0.9041 (tp) cc_final: 0.8772 (tp) REVERT: G 1110 GLN cc_start: 0.8407 (pt0) cc_final: 0.8119 (tp40) REVERT: G 1128 CYS cc_start: 0.5674 (m) cc_final: 0.5112 (m) REVERT: G 1143 MET cc_start: 0.9041 (mmp) cc_final: 0.8191 (mmm) REVERT: G 1192 MET cc_start: 0.8982 (ptp) cc_final: 0.8746 (ppp) REVERT: G 1496 MET cc_start: 0.8840 (mmm) cc_final: 0.8578 (mmm) REVERT: G 1578 MET cc_start: 0.8446 (mpp) cc_final: 0.7863 (mtm) REVERT: G 1675 ARG cc_start: 0.7495 (mtm180) cc_final: 0.7158 (mtp180) REVERT: H 447 MET cc_start: 0.9041 (mmp) cc_final: 0.8640 (mmp) REVERT: I 169 TYR cc_start: 0.8003 (m-10) cc_final: 0.7595 (m-10) REVERT: I 188 TYR cc_start: 0.8384 (p90) cc_final: 0.8122 (p90) REVERT: J 242 MET cc_start: 0.9526 (tpt) cc_final: 0.9278 (tpp) REVERT: M 67 PHE cc_start: 0.8580 (t80) cc_final: 0.8144 (t80) REVERT: M 105 GLU cc_start: 0.9270 (tm-30) cc_final: 0.9054 (tm-30) REVERT: M 113 HIS cc_start: 0.7515 (t70) cc_final: 0.6228 (t70) REVERT: N 31 LYS cc_start: 0.9806 (mmtt) cc_final: 0.9570 (mmmt) REVERT: N 59 LYS cc_start: 0.9563 (ptmm) cc_final: 0.9259 (ptmm) REVERT: N 63 GLU cc_start: 0.9480 (pt0) cc_final: 0.9027 (pt0) REVERT: N 84 MET cc_start: 0.8943 (mmp) cc_final: 0.8720 (tpp) REVERT: N 98 TYR cc_start: 0.8609 (m-80) cc_final: 0.8036 (m-80) REVERT: O 25 PHE cc_start: 0.9305 (m-80) cc_final: 0.8888 (m-10) REVERT: O 38 ASN cc_start: 0.8543 (m110) cc_final: 0.8103 (m110) REVERT: O 41 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8108 (mm-30) REVERT: O 61 GLU cc_start: 0.8674 (mp0) cc_final: 0.8152 (mp0) REVERT: O 73 ASN cc_start: 0.8504 (m110) cc_final: 0.8300 (m110) REVERT: O 78 ILE cc_start: 0.9532 (mm) cc_final: 0.9221 (tp) REVERT: O 83 LEU cc_start: 0.9739 (tp) cc_final: 0.9531 (pp) REVERT: P 40 TYR cc_start: 0.8827 (m-80) cc_final: 0.8502 (m-80) REVERT: Q 90 MET cc_start: 0.9277 (mmp) cc_final: 0.9017 (mmm) REVERT: Q 97 GLU cc_start: 0.9322 (tt0) cc_final: 0.9026 (pt0) REVERT: Q 122 LYS cc_start: 0.9204 (mppt) cc_final: 0.8656 (ptmt) REVERT: R 55 ARG cc_start: 0.8832 (mtt90) cc_final: 0.8362 (mmt90) REVERT: R 84 MET cc_start: 0.9214 (mmm) cc_final: 0.8826 (tpp) REVERT: S 91 GLU cc_start: 0.8064 (pm20) cc_final: 0.7717 (pp20) REVERT: S 92 GLU cc_start: 0.8131 (pm20) cc_final: 0.7856 (pm20) outliers start: 1 outliers final: 0 residues processed: 571 average time/residue: 0.2416 time to fit residues: 237.9983 Evaluate side-chains 426 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 426 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 170 optimal weight: 0.9990 chunk 459 optimal weight: 9.9990 chunk 230 optimal weight: 0.9990 chunk 202 optimal weight: 1.9990 chunk 320 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 212 optimal weight: 8.9990 chunk 293 optimal weight: 6.9990 chunk 382 optimal weight: 50.0000 chunk 76 optimal weight: 4.9990 chunk 407 optimal weight: 0.4980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN D 250 ASN F 24 HIS F 250 ASN ** G1161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1263 GLN G1593 ASN I 19 GLN ** I 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 HIS ** P 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.079224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.058367 restraints weight = 171296.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.059873 restraints weight = 99032.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.060873 restraints weight = 66470.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.061590 restraints weight = 50227.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.062064 restraints weight = 41238.591| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 44795 Z= 0.137 Angle : 0.646 10.343 61826 Z= 0.338 Chirality : 0.043 0.435 7045 Planarity : 0.004 0.060 6957 Dihedral : 21.349 177.860 8477 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.78 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.12), residues: 4686 helix: 0.48 (0.11), residues: 2142 sheet: -1.16 (0.21), residues: 633 loop : -1.67 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG P 92 TYR 0.027 0.002 TYR A 193 PHE 0.027 0.001 PHE Q 104 TRP 0.017 0.001 TRP J 129 HIS 0.010 0.001 HIS G1151 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (44795) covalent geometry : angle 0.64593 / 0.34 (61826) hydrogen bonds : bond 0.03999 / 2.78 ( 1915) hydrogen bonds : angle 4.34316 / 3.00 ( 5355) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 581 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 CYS cc_start: 0.8659 (m) cc_final: 0.8193 (m) REVERT: A 62 MET cc_start: 0.6136 (tmm) cc_final: 0.5571 (tmm) REVERT: A 130 ASP cc_start: 0.8800 (m-30) cc_final: 0.7962 (p0) REVERT: A 278 MET cc_start: 0.8511 (tmm) cc_final: 0.8253 (tmm) REVERT: B 100 SER cc_start: 0.9287 (m) cc_final: 0.8864 (t) REVERT: B 248 ASN cc_start: 0.8378 (t0) cc_final: 0.7735 (t0) REVERT: B 361 ILE cc_start: 0.9507 (mt) cc_final: 0.8917 (tt) REVERT: C 77 LYS cc_start: 0.8963 (mtmm) cc_final: 0.8282 (mtmm) REVERT: C 101 GLU cc_start: 0.7617 (tt0) cc_final: 0.6777 (tm-30) REVERT: C 146 ASN cc_start: 0.9176 (m-40) cc_final: 0.8791 (p0) REVERT: C 159 LEU cc_start: 0.9002 (mp) cc_final: 0.8732 (tp) REVERT: C 197 ASN cc_start: 0.9309 (p0) cc_final: 0.8963 (p0) REVERT: C 311 GLU cc_start: 0.8379 (tm-30) cc_final: 0.7879 (tm-30) REVERT: C 327 ILE cc_start: 0.8869 (pt) cc_final: 0.8602 (pt) REVERT: D 46 LEU cc_start: 0.9195 (tp) cc_final: 0.8893 (tp) REVERT: D 113 MET cc_start: 0.8834 (ptt) cc_final: 0.8496 (ptt) REVERT: D 177 MET cc_start: 0.8723 (mmt) cc_final: 0.8502 (mmm) REVERT: D 179 ASP cc_start: 0.8495 (m-30) cc_final: 0.8240 (m-30) REVERT: D 181 MET cc_start: 0.9185 (mmt) cc_final: 0.8748 (mmm) REVERT: D 247 ASP cc_start: 0.8222 (m-30) cc_final: 0.7898 (m-30) REVERT: D 301 HIS cc_start: 0.8955 (p90) cc_final: 0.8730 (p90) REVERT: E 88 MET cc_start: 0.8792 (mmp) cc_final: 0.8467 (tpt) REVERT: E 173 MET cc_start: 0.7619 (ptp) cc_final: 0.7345 (ptp) REVERT: E 217 MET cc_start: 0.6897 (mmm) cc_final: 0.5970 (tpp) REVERT: E 407 THR cc_start: 0.8355 (m) cc_final: 0.7818 (t) REVERT: E 442 VAL cc_start: 0.9032 (t) cc_final: 0.8692 (p) REVERT: F 160 LEU cc_start: 0.8587 (tp) cc_final: 0.8371 (tt) REVERT: F 173 MET cc_start: 0.8074 (mtm) cc_final: 0.7728 (mpp) REVERT: F 190 ASP cc_start: 0.8174 (m-30) cc_final: 0.7697 (m-30) REVERT: F 202 THR cc_start: 0.9245 (t) cc_final: 0.8970 (p) REVERT: F 400 TYR cc_start: 0.9043 (t80) cc_final: 0.8288 (t80) REVERT: G 972 LEU cc_start: 0.7119 (mt) cc_final: 0.6800 (mm) REVERT: G 1014 LEU cc_start: 0.8962 (tp) cc_final: 0.8706 (tp) REVERT: G 1067 ASP cc_start: 0.6341 (m-30) cc_final: 0.6017 (m-30) REVERT: G 1110 GLN cc_start: 0.8338 (pt0) cc_final: 0.8070 (tp40) REVERT: G 1143 MET cc_start: 0.8959 (mmp) cc_final: 0.8150 (mmm) REVERT: G 1192 MET cc_start: 0.9001 (ptp) cc_final: 0.8762 (ppp) REVERT: G 1240 MET cc_start: 0.3271 (mtt) cc_final: 0.2124 (mtt) REVERT: G 1491 MET cc_start: 0.8820 (mmp) cc_final: 0.8454 (mmp) REVERT: G 1496 MET cc_start: 0.8764 (mmm) cc_final: 0.8491 (mmm) REVERT: G 1610 ASP cc_start: 0.8252 (m-30) cc_final: 0.8029 (m-30) REVERT: G 1675 ARG cc_start: 0.7412 (mtm180) cc_final: 0.7119 (mtp180) REVERT: H 447 MET cc_start: 0.8984 (mmp) cc_final: 0.8580 (mmp) REVERT: I 169 TYR cc_start: 0.8163 (m-10) cc_final: 0.7788 (m-10) REVERT: J 242 MET cc_start: 0.9515 (tpt) cc_final: 0.9173 (tpp) REVERT: J 768 PHE cc_start: 0.7504 (t80) cc_final: 0.7189 (t80) REVERT: M 67 PHE cc_start: 0.8609 (t80) cc_final: 0.8251 (t80) REVERT: M 97 GLU cc_start: 0.9190 (pp20) cc_final: 0.8977 (pp20) REVERT: M 105 GLU cc_start: 0.9293 (tm-30) cc_final: 0.9064 (tm-30) REVERT: M 113 HIS cc_start: 0.7465 (t70) cc_final: 0.6172 (t70) REVERT: N 58 LEU cc_start: 0.9796 (tp) cc_final: 0.9570 (tp) REVERT: N 59 LYS cc_start: 0.9544 (ptmm) cc_final: 0.9267 (ptmm) REVERT: N 63 GLU cc_start: 0.9456 (pt0) cc_final: 0.8987 (pt0) REVERT: N 84 MET cc_start: 0.8907 (mmp) cc_final: 0.8659 (tpp) REVERT: N 98 TYR cc_start: 0.8521 (m-80) cc_final: 0.7959 (m-80) REVERT: O 25 PHE cc_start: 0.9255 (m-80) cc_final: 0.8802 (m-80) REVERT: O 38 ASN cc_start: 0.8492 (m110) cc_final: 0.8039 (m110) REVERT: O 41 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8107 (mm-30) REVERT: O 61 GLU cc_start: 0.8757 (mp0) cc_final: 0.8192 (mp0) REVERT: O 64 GLU cc_start: 0.9136 (tp30) cc_final: 0.8857 (tp30) REVERT: O 73 ASN cc_start: 0.8478 (m110) cc_final: 0.8267 (m110) REVERT: O 78 ILE cc_start: 0.9520 (mm) cc_final: 0.9203 (tp) REVERT: O 83 LEU cc_start: 0.9754 (tp) cc_final: 0.9535 (pp) REVERT: P 40 TYR cc_start: 0.8760 (m-80) cc_final: 0.8511 (m-80) REVERT: P 100 LEU cc_start: 0.9136 (mm) cc_final: 0.8791 (mm) REVERT: Q 90 MET cc_start: 0.9249 (mmp) cc_final: 0.8983 (mmm) REVERT: Q 97 GLU cc_start: 0.9339 (tt0) cc_final: 0.8997 (pt0) REVERT: Q 122 LYS cc_start: 0.9185 (mppt) cc_final: 0.8660 (ptmt) REVERT: R 55 ARG cc_start: 0.8826 (mtt90) cc_final: 0.8376 (mmt90) REVERT: R 84 MET cc_start: 0.9208 (mmm) cc_final: 0.8768 (tpp) REVERT: S 91 GLU cc_start: 0.8082 (pm20) cc_final: 0.7753 (pp20) REVERT: S 92 GLU cc_start: 0.8104 (pm20) cc_final: 0.7789 (pm20) REVERT: T 76 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8761 (mm-30) REVERT: T 113 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8168 (mt-10) outliers start: 0 outliers final: 0 residues processed: 581 average time/residue: 0.2400 time to fit residues: 241.4473 Evaluate side-chains 441 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 441 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 59 optimal weight: 0.7980 chunk 297 optimal weight: 0.8980 chunk 127 optimal weight: 8.9990 chunk 139 optimal weight: 7.9990 chunk 264 optimal weight: 9.9990 chunk 416 optimal weight: 2.9990 chunk 278 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 216 optimal weight: 4.9990 chunk 340 optimal weight: 4.9990 chunk 375 optimal weight: 40.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN D 250 ASN F 24 HIS F 250 ASN G1034 HIS G1127 HIS ** G1161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN ** I 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 84 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 = 0.3451 r_free = 0.3451 target = 0.077550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.056563 restraints weight = 172685.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.058001 restraints weight = 100704.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.058988 restraints weight = 68013.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.059660 restraints weight = 51619.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.060044 restraints weight = 42676.464| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 44795 Z= 0.203 Angle : 0.687 10.155 61826 Z= 0.360 Chirality : 0.044 0.223 7045 Planarity : 0.004 0.061 6957 Dihedral : 21.366 178.454 8477 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.68 % Favored : 94.26 % Rotamer: Outliers : 0.03 % Allowed : 0.15 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.12), residues: 4686 helix: 0.42 (0.11), residues: 2149 sheet: -1.19 (0.20), residues: 637 loop : -1.71 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG N 92 TYR 0.030 0.002 TYR A 193 PHE 0.029 0.002 PHE M 104 TRP 0.021 0.002 TRP G1101 HIS 0.008 0.001 HIS G1151 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 (44795) covalent geometry : angle 0.68744 / 0.36 (61826) hydrogen bonds : bond 0.04237 / 2.96 ( 1915) hydrogen bonds : angle 4.46806 / 3.10 ( 5355) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8083.27 seconds wall clock time: 140 minutes 26.91 seconds (8426.91 seconds total)