Starting phenix.real_space_refine on Sun Oct 25 08:46:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/29jr_57214/10_2026/29jr_57214.cif Found real_map, /net/cci-nas-00/data/ceres_data/29jr_57214/10_2026/29jr_57214.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/29jr_57214/10_2026/29jr_57214.cif" } default_model = "/net/cci-nas-00/data/ceres_data/29jr_57214/10_2026/29jr_57214.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/29jr_57214/10_2026/29jr_57214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/29jr_57214/10_2026/29jr_57214.map" } resolution = 3.47 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= 0.006 sd= 0.055 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 12 5.49 5 S 74 5.16 5 C 9990 2.51 5 N 2851 2.21 5 O 3040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15967 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2455 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 11, 'TRANS': 315} Chain breaks: 2 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 2460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2460 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 9, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2515 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 10, 'TRANS': 320} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "D" Number of atoms: 2478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2478 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 6, 'ASP:plan': 3, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 78 Chain: "E" Number of atoms: 2479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2479 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 10, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 94 Planarities with less than four sites: {'GLU:plan': 15, 'ARG:plan': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 93 Chain: "F" Number of atoms: 2537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2537 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 53 Chain: "G" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 881 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain breaks: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 61 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 7, 'ASP:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 68 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} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" C1' ADP A 501 " occ=0.76 ... (25 atoms not shown) pdb=" PB ADP A 501 " occ=0.76 residue: pdb=" C1' ADP B 501 " occ=0.54 ... (25 atoms not shown) pdb=" PB ADP B 501 " occ=0.54 residue: pdb=" C1' ADP C 501 " occ=0.71 ... (25 atoms not shown) pdb=" PB ADP C 501 " occ=0.71 residue: pdb=" C1' ADP D 501 " occ=0.70 ... (25 atoms not shown) pdb=" PB ADP D 501 " occ=0.70 residue: pdb=" C1' ADP E 501 " occ=0.61 ... (25 atoms not shown) pdb=" PB ADP E 501 " occ=0.61 residue: pdb=" C1' ADP F 501 " occ=0.80 ... (25 atoms not shown) pdb=" PB ADP F 501 " occ=0.80 Time building chain proxies: 3.69, per 1000 atoms: 0.23 Number of scatterers: 15967 At special positions: 0 Unit cell: (107.95, 134.3, 135.15, 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 74 16.00 P 12 15.00 O 3040 8.00 N 2851 7.00 C 9990 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 761.7 milliseconds 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3896 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 24 sheets defined 54.7% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 11 through 16 removed outlier: 3.742A pdb=" N ILE A 15 " --> pdb=" O LYS A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 19 No H-bonds generated for 'chain 'A' and resid 17 through 19' Processing helix chain 'A' and resid 42 through 58 removed outlier: 3.533A pdb=" N GLU A 54 " --> pdb=" O GLY A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 88 removed outlier: 3.557A pdb=" N ALA A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 102 Processing helix chain 'A' and resid 107 through 119 removed outlier: 3.518A pdb=" N VAL A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.529A pdb=" N ARG A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 289 removed outlier: 3.503A pdb=" N ASN A 284 " --> pdb=" O ASN A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 307 Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.552A pdb=" N PHE A 312 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A 313 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU A 320 " --> pdb=" O HIS A 316 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER A 321 " --> pdb=" O ARG A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 350 Processing helix chain 'A' and resid 351 through 357 Processing helix chain 'A' and resid 367 through 383 removed outlier: 3.611A pdb=" N LYS A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN A 373 " --> pdb=" O GLN A 369 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS A 376 " --> pdb=" O LYS A 372 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR A 381 " --> pdb=" O ILE A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 401 removed outlier: 3.892A pdb=" N HIS A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 removed outlier: 3.701A pdb=" N GLN A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 421 Processing helix chain 'A' and resid 426 through 437 removed outlier: 3.602A pdb=" N GLU A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 452 removed outlier: 3.559A pdb=" N SER A 443 " --> pdb=" O ASP A 439 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 65 removed outlier: 3.826A pdb=" N ALA B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 95 removed outlier: 3.612A pdb=" N GLN B 92 " --> pdb=" O MET B 88 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 109 Processing helix chain 'B' and resid 114 through 125 Processing helix chain 'B' and resid 244 through 251 Processing helix chain 'B' and resid 269 through 286 removed outlier: 3.688A pdb=" N ARG B 273 " --> pdb=" O LYS B 269 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU B 274 " --> pdb=" O SER B 270 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN B 275 " --> pdb=" O GLU B 271 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU B 285 " --> pdb=" O ALA B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 304 removed outlier: 3.560A pdb=" N MET B 303 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 316 removed outlier: 3.592A pdb=" N PHE B 311 " --> pdb=" O GLU B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 352 removed outlier: 3.729A pdb=" N ASP B 352 " --> pdb=" O ILE B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 379 removed outlier: 3.583A pdb=" N GLN B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 397 removed outlier: 3.919A pdb=" N THR B 388 " --> pdb=" O GLU B 384 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL B 389 " --> pdb=" O ASP B 385 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG B 392 " --> pdb=" O THR B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 416 removed outlier: 3.674A pdb=" N ALA B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR B 407 " --> pdb=" O ILE B 403 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA B 408 " --> pdb=" O GLN B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 431 removed outlier: 3.625A pdb=" N SER B 431 " --> pdb=" O LYS B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 448 Processing helix chain 'C' and resid 49 through 65 removed outlier: 3.558A pdb=" N ARG C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 95 removed outlier: 3.704A pdb=" N GLY C 95 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 109 Processing helix chain 'C' and resid 114 through 126 removed outlier: 3.581A pdb=" N LEU C 119 " --> pdb=" O LYS C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 251 Processing helix chain 'C' and resid 269 through 286 removed outlier: 3.552A pdb=" N GLU C 285 " --> pdb=" O ALA C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 304 Processing helix chain 'C' and resid 305 through 316 removed outlier: 3.630A pdb=" N PHE C 309 " --> pdb=" O ASP C 305 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER C 310 " --> pdb=" O ILE C 306 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE C 311 " --> pdb=" O GLU C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 352 removed outlier: 4.043A pdb=" N ASP C 352 " --> pdb=" O ASP C 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 349 through 352' Processing helix chain 'C' and resid 363 through 379 Processing helix chain 'C' and resid 383 through 397 Processing helix chain 'C' and resid 398 through 416 removed outlier: 3.622A pdb=" N ILE C 403 " --> pdb=" O LEU C 399 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN C 404 " --> pdb=" O ARG C 400 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE C 406 " --> pdb=" O ALA C 402 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR C 407 " --> pdb=" O ILE C 403 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA C 408 " --> pdb=" O GLN C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 433 Processing helix chain 'C' and resid 435 through 443 Processing helix chain 'D' and resid 49 through 65 Processing helix chain 'D' and resid 82 through 95 Processing helix chain 'D' and resid 106 through 108 No H-bonds generated for 'chain 'D' and resid 106 through 108' Processing helix chain 'D' and resid 114 through 125 removed outlier: 3.553A pdb=" N ALA D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 251 Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 269 through 287 Processing helix chain 'D' and resid 300 through 304 Processing helix chain 'D' and resid 305 through 317 removed outlier: 3.688A pdb=" N GLU D 317 " --> pdb=" O ASN D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 363 through 378 removed outlier: 3.678A pdb=" N GLN D 369 " --> pdb=" O LYS D 365 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU D 376 " --> pdb=" O ARG D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 397 Processing helix chain 'D' and resid 398 through 416 removed outlier: 3.555A pdb=" N ALA D 402 " --> pdb=" O SER D 398 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE D 406 " --> pdb=" O ALA D 402 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR D 407 " --> pdb=" O ILE D 403 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 432 removed outlier: 3.614A pdb=" N ILE D 426 " --> pdb=" O GLN D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 448 removed outlier: 3.896A pdb=" N ASP D 448 " --> pdb=" O LYS D 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 65 removed outlier: 3.540A pdb=" N ARG E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG E 64 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU E 65 " --> pdb=" O GLU E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 95 removed outlier: 3.525A pdb=" N ALA E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY E 95 " --> pdb=" O ALA E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 109 Processing helix chain 'E' and resid 114 through 126 removed outlier: 3.523A pdb=" N SER E 126 " --> pdb=" O ALA E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 251 removed outlier: 3.790A pdb=" N ASN E 251 " --> pdb=" O ILE E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 286 removed outlier: 3.549A pdb=" N ARG E 273 " --> pdb=" O LYS E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 304 Processing helix chain 'E' and resid 305 through 318 removed outlier: 3.788A pdb=" N GLU E 317 " --> pdb=" O ASN E 313 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N SER E 318 " --> pdb=" O ARG E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 352 Processing helix chain 'E' and resid 363 through 378 Processing helix chain 'E' and resid 383 through 397 Processing helix chain 'E' and resid 398 through 416 removed outlier: 3.626A pdb=" N ILE E 406 " --> pdb=" O ALA E 402 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR E 407 " --> pdb=" O ILE E 403 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 432 removed outlier: 3.574A pdb=" N ILE E 426 " --> pdb=" O GLN E 422 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER E 431 " --> pdb=" O LYS E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 447 Processing helix chain 'F' and resid 18 through 23 Processing helix chain 'F' and resid 49 through 66 removed outlier: 3.663A pdb=" N VAL F 58 " --> pdb=" O ARG F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 95 removed outlier: 3.644A pdb=" N ALA F 93 " --> pdb=" O GLY F 89 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU F 94 " --> pdb=" O MET F 90 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 109 removed outlier: 3.543A pdb=" N PHE F 109 " --> pdb=" O SER F 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 106 through 109' Processing helix chain 'F' and resid 114 through 124 Processing helix chain 'F' and resid 244 through 252 removed outlier: 3.625A pdb=" N ILE F 250 " --> pdb=" O GLU F 246 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN F 251 " --> pdb=" O ILE F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 286 removed outlier: 3.552A pdb=" N GLU F 286 " --> pdb=" O GLU F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 304 Processing helix chain 'F' and resid 305 through 316 Processing helix chain 'F' and resid 347 through 352 removed outlier: 3.616A pdb=" N ASP F 352 " --> pdb=" O ILE F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 378 Processing helix chain 'F' and resid 383 through 397 removed outlier: 3.515A pdb=" N TYR F 387 " --> pdb=" O SER F 383 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR F 388 " --> pdb=" O GLU F 384 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL F 389 " --> pdb=" O ASP F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 416 removed outlier: 3.595A pdb=" N ILE F 406 " --> pdb=" O ALA F 402 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA F 408 " --> pdb=" O GLN F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 433 removed outlier: 3.583A pdb=" N ILE F 426 " --> pdb=" O GLN F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 447 removed outlier: 3.844A pdb=" N THR F 440 " --> pdb=" O GLU F 436 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR F 446 " --> pdb=" O TYR F 442 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN F 447 " --> pdb=" O MET F 443 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 112 Processing helix chain 'G' and resid 117 through 127 removed outlier: 3.650A pdb=" N LEU G 126 " --> pdb=" O ALA G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 135 removed outlier: 3.551A pdb=" N GLY G 132 " --> pdb=" O GLY G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 142 removed outlier: 4.038A pdb=" N GLY G 142 " --> pdb=" O VAL G 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 139 through 142' Processing helix chain 'G' and resid 143 through 153 removed outlier: 3.673A pdb=" N ASP G 153 " --> pdb=" O VAL G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 161 through 172 Processing helix chain 'G' and resid 175 through 182 Processing helix chain 'G' and resid 184 through 202 Processing helix chain 'G' and resid 223 through 240 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 97 removed outlier: 6.715A pdb=" N CYS A 94 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ASP A 302 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N MET A 96 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL A 66 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N SER A 331 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU A 68 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 67 " --> pdb=" O MET A 359 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE A 360 " --> pdb=" O LEU B 434 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 236 through 239 Processing sheet with id=AA4, first strand: chain 'A' and resid 336 through 337 Processing sheet with id=AA5, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.573A pdb=" N SER B 43 " --> pdb=" O MET B 46 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 104 removed outlier: 6.392A pdb=" N THR B 101 " --> pdb=" O PHE B 297 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ASP B 299 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE B 103 " --> pdb=" O ASP B 299 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ALA B 72 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N VAL B 357 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU B 74 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 240 through 243 removed outlier: 3.521A pdb=" N GLU B 290 " --> pdb=" O ARG B 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 332 through 334 Processing sheet with id=AA9, first strand: chain 'C' and resid 42 through 43 Processing sheet with id=AB1, first strand: chain 'C' and resid 100 through 104 removed outlier: 6.526A pdb=" N THR C 101 " --> pdb=" O PHE C 297 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ASP C 299 " --> pdb=" O THR C 101 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE C 103 " --> pdb=" O ASP C 299 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL C 73 " --> pdb=" O MET C 326 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N THR C 328 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE C 75 " --> pdb=" O THR C 328 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA C 72 " --> pdb=" O LEU C 355 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N VAL C 357 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU C 74 " --> pdb=" O VAL C 357 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE C 356 " --> pdb=" O LEU D 434 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 240 through 243 Processing sheet with id=AB3, first strand: chain 'C' and resid 332 through 334 Processing sheet with id=AB4, first strand: chain 'D' and resid 42 through 43 removed outlier: 3.749A pdb=" N SER D 43 " --> pdb=" O MET D 46 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET D 46 " --> pdb=" O SER D 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 100 through 104 removed outlier: 6.077A pdb=" N LEU D 296 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ALA D 327 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE D 298 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE D 356 " --> pdb=" O LEU E 434 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 240 through 243 Processing sheet with id=AB7, first strand: chain 'D' and resid 332 through 334 Processing sheet with id=AB8, first strand: chain 'E' and resid 42 through 43 Processing sheet with id=AB9, first strand: chain 'E' and resid 100 through 104 removed outlier: 3.575A pdb=" N THR E 328 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR E 359 " --> pdb=" O ALA E 76 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 240 through 243 Processing sheet with id=AC2, first strand: chain 'E' and resid 332 through 334 removed outlier: 3.663A pdb=" N THR E 333 " --> pdb=" O SER E 342 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AC4, first strand: chain 'F' and resid 100 through 104 removed outlier: 6.517A pdb=" N THR F 101 " --> pdb=" O PHE F 297 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ASP F 299 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE F 103 " --> pdb=" O ASP F 299 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU F 296 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ALA F 327 " --> pdb=" O LEU F 296 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE F 298 " --> pdb=" O ALA F 327 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL F 73 " --> pdb=" O MET F 326 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N THR F 328 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE F 75 " --> pdb=" O THR F 328 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA F 72 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL F 357 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU F 74 " --> pdb=" O VAL F 357 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'F' and resid 240 through 243 removed outlier: 3.891A pdb=" N ILE F 292 " --> pdb=" O GLY F 128 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 332 through 334 removed outlier: 3.646A pdb=" N SER F 342 " --> pdb=" O THR F 333 " (cutoff:3.500A) 783 hydrogen bonds defined for protein. 2268 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.28 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5410 1.34 - 1.46: 2375 1.46 - 1.58: 8242 1.58 - 1.69: 18 1.69 - 1.81: 131 Bond restraints: 16176 Sorted by residual: bond pdb=" C4 ADP E 501 " pdb=" C5 ADP E 501 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" C4 ADP C 501 " pdb=" C5 ADP C 501 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" C4 ADP F 501 " pdb=" C5 ADP F 501 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C4 ADP A 501 " pdb=" C5 ADP A 501 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C4 ADP B 501 " pdb=" C5 ADP B 501 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 ... (remaining 16171 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 20634 2.49 - 4.98: 1161 4.98 - 7.47: 85 7.47 - 9.96: 22 9.96 - 12.45: 11 Bond angle restraints: 21913 Sorted by residual: angle pdb=" N GLN B 447 " pdb=" CA GLN B 447 " pdb=" C GLN B 447 " ideal model delta sigma weight residual 111.03 117.07 -6.04 1.11e+00 8.12e-01 2.96e+01 angle pdb=" N ILE C 426 " pdb=" CA ILE C 426 " pdb=" C ILE C 426 " ideal model delta sigma weight residual 110.42 105.43 4.99 9.60e-01 1.09e+00 2.71e+01 angle pdb=" C SER D 114 " pdb=" N LYS D 115 " pdb=" CA LYS D 115 " ideal model delta sigma weight residual 120.38 113.65 6.73 1.37e+00 5.33e-01 2.41e+01 angle pdb=" CA THR C 440 " pdb=" CB THR C 440 " pdb=" OG1 THR C 440 " ideal model delta sigma weight residual 109.60 102.32 7.28 1.50e+00 4.44e-01 2.36e+01 angle pdb=" CA GLY E 256 " pdb=" C GLY E 256 " pdb=" O GLY E 256 " ideal model delta sigma weight residual 122.29 118.48 3.81 8.10e-01 1.52e+00 2.21e+01 ... (remaining 21908 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.72: 9341 28.72 - 57.45: 439 57.45 - 86.17: 61 86.17 - 114.90: 4 114.90 - 143.62: 3 Dihedral angle restraints: 9848 sinusoidal: 3815 harmonic: 6033 Sorted by residual: dihedral pdb=" CD ARG C 314 " pdb=" NE ARG C 314 " pdb=" CZ ARG C 314 " pdb=" NH1 ARG C 314 " ideal model delta sinusoidal sigma weight residual 0.00 76.19 -76.19 1 1.00e+01 1.00e-02 7.31e+01 dihedral pdb=" O2A ADP A 501 " pdb=" O3A ADP A 501 " pdb=" PA ADP A 501 " pdb=" PB ADP A 501 " ideal model delta sinusoidal sigma weight residual 300.00 156.38 143.62 1 2.00e+01 2.50e-03 4.33e+01 dihedral pdb=" O1B ADP A 501 " pdb=" O3A ADP A 501 " pdb=" PB ADP A 501 " pdb=" PA ADP A 501 " ideal model delta sinusoidal sigma weight residual 300.00 172.07 127.93 1 2.00e+01 2.50e-03 3.88e+01 ... (remaining 9845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1784 0.061 - 0.122: 605 0.122 - 0.184: 176 0.184 - 0.245: 59 0.245 - 0.306: 8 Chirality restraints: 2632 Sorted by residual: chirality pdb=" CA ILE B 370 " pdb=" N ILE B 370 " pdb=" C ILE B 370 " pdb=" CB ILE B 370 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA VAL B 357 " pdb=" N VAL B 357 " pdb=" C VAL B 357 " pdb=" CB VAL B 357 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA ILE F 127 " pdb=" N ILE F 127 " pdb=" C ILE F 127 " pdb=" CB ILE F 127 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 2629 not shown) Planarity restraints: 2789 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 314 " -1.042 9.50e-02 1.11e+02 4.67e-01 1.32e+02 pdb=" NE ARG C 314 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG C 314 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG C 314 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG C 314 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 353 " -0.557 9.50e-02 1.11e+02 2.50e-01 3.81e+01 pdb=" NE ARG D 353 " 0.033 2.00e-02 2.50e+03 pdb=" CZ ARG D 353 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG D 353 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D 353 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 336 " 0.543 9.50e-02 1.11e+02 2.44e-01 3.63e+01 pdb=" NE ARG C 336 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG C 336 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG C 336 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 336 " 0.017 2.00e-02 2.50e+03 ... (remaining 2786 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 147 2.60 - 3.17: 14178 3.17 - 3.75: 23117 3.75 - 4.32: 30745 4.32 - 4.90: 51095 Nonbonded interactions: 119282 Sorted by model distance: nonbonded pdb=" CE1 HIS A 316 " pdb=" OD2 ASP A 353 " model vdw 2.022 3.260 nonbonded pdb=" CD1 ILE A 3 " pdb=" OH TYR A 286 " model vdw 2.029 3.460 nonbonded pdb=" CD2 LEU A 122 " pdb=" CD2 LEU A 294 " model vdw 2.097 3.880 nonbonded pdb=" CD2 LEU B 60 " pdb=" CG MET B 90 " model vdw 2.122 3.860 nonbonded pdb=" OD1 ASN C 313 " pdb=" NH2 ARG C 353 " model vdw 2.191 3.120 ... (remaining 119277 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 'B' and (resid 19 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 64 or (resid 65 and (name N or nam \ e CA or name C or name O or name CB )) or resid 66 through 245 or (resid 246 and \ (name N or name CA or name C or name O or name CB )) or resid 247 through 256 o \ r (resid 257 through 260 and (name N or name CA or name C or name O or name CB ) \ ) or resid 261 or (resid 262 and (name N or name CA or name C or name O or name \ CB )) or resid 263 or (resid 264 and (name N or name CA or name C or name O or n \ ame CB )) or resid 265 through 266 or (resid 267 and (name N or name CA or name \ C or name O or name CB )) or resid 268 through 270 or (resid 271 and (name N or \ name CA or name C or name O or name CB )) or resid 272 through 284 or (resid 285 \ through 286 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 87 through 299 or (resid 300 and (name N or name CA or name C or name O or name \ CB )) or resid 301 through 316 or (resid 317 and (name N or name CA or name C or \ name O or name CB )) or resid 318 through 351 or (resid 352 and (name N or name \ CA or name C or name O or name CB )) or resid 353 through 363 or (resid 364 and \ (name N or name CA or name C or name O or name CB )) or resid 365 or (resid 366 \ and (name N or name CA or name C or name O or name CB )) or resid 367 through 3 \ 75 or (resid 376 through 379 and (name N or name CA or name C or name O or name \ CB )) or resid 380 or (resid 381 and (name N or name CA or name C or name O or n \ ame CB )) or resid 382 through 395 or (resid 396 and (name N or name CA or name \ C or name O or name CB )) or resid 397 through 413 or (resid 414 through 415 and \ (name N or name CA or name C or name O or name CB )) or resid 416 or (resid 417 \ and (name N or name CA or name C or name O or name CB )) or resid 418 through 4 \ 19 or (resid 420 and (name N or name CA or name C or name O or name CB )) or res \ id 421 through 442 or (resid 443 and (name N or name CA or name C or name O or n \ ame CB )) or resid 501)) selection = (chain 'C' and ((resid 19 through 22 and (name N or name CA or name C or name O \ or name CB )) or resid 23 through 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB )) or resid 30 through 37 or (resid 38 and (name N or na \ me CA or name C or name O or name CB )) or resid 39 through 64 or (resid 65 and \ (name N or name CA or name C or name O or name CB )) or resid 66 through 238 or \ resid 240 through 252 or (resid 253 through 255 and (name N or name CA or name C \ or name O or name CB )) or resid 256 through 266 or (resid 267 and (name N or n \ ame CA or name C or name O or name CB )) or resid 268 through 270 or (resid 271 \ and (name N or name CA or name C or name O or name CB )) or resid 272 through 27 \ 8 or (resid 279 and (name N or name CA or name C or name O or name CB )) or resi \ d 280 through 281 or (resid 282 and (name N or name CA or name C or name O or na \ me CB )) or resid 283 through 284 or (resid 285 through 286 and (name N or name \ CA or name C or name O or name CB )) or resid 287 or (resid 288 through 289 and \ (name N or name CA or name C or name O or name CB )) or resid 290 through 299 or \ (resid 300 and (name N or name CA or name C or name O or name CB )) or resid 30 \ 1 through 316 or (resid 317 and (name N or name CA or name C or name O or name C \ B )) or resid 318 through 351 or (resid 352 and (name N or name CA or name C or \ name O or name CB )) or resid 353 through 365 or (resid 366 and (name N or name \ CA or name C or name O or name CB )) or resid 367 through 375 or (resid 376 thro \ ugh 379 and (name N or name CA or name C or name O or name CB )) or resid 380 or \ (resid 381 and (name N or name CA or name C or name O or name CB )) or resid 38 \ 2 through 395 or (resid 396 and (name N or name CA or name C or name O or name C \ B )) or resid 397 through 413 or (resid 414 through 415 and (name N or name CA o \ r name C or name O or name CB )) or resid 416 or (resid 417 and (name N or name \ CA or name C or name O or name CB )) or resid 418 through 419 or (resid 420 and \ (name N or name CA or name C or name O or name CB )) or resid 421 through 442 or \ (resid 443 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 1)) selection = (chain 'D' and ((resid 19 through 22 and (name N or name CA or name C or name O \ or name CB )) or resid 23 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 64 or (resid 65 and (name N or na \ me CA or name C or name O or name CB )) or resid 66 through 131 or (resid 132 an \ d (name N or name CA or name C or name O or name CB )) or resid 239 through 245 \ or (resid 246 and (name N or name CA or name C or name O or name CB )) or resid \ 247 through 253 or (resid 254 through 255 and (name N or name CA or name C or na \ me O or name CB )) or resid 256 or (resid 257 through 260 and (name N or name CA \ or name C or name O or name CB )) or resid 261 or (resid 262 and (name N or nam \ e CA or name C or name O or name CB )) or resid 263 through 270 or (resid 271 an \ d (name N or name CA or name C or name O or name CB )) or resid 272 through 278 \ or (resid 279 and (name N or name CA or name C or name O or name CB )) or resid \ 280 through 281 or (resid 282 and (name N or name CA or name C or name O or name \ CB )) or resid 283 through 284 or (resid 285 through 286 and (name N or name CA \ or name C or name O or name CB )) or resid 287 through 299 or (resid 300 and (n \ ame N or name CA or name C or name O or name CB )) or resid 301 through 351 or ( \ resid 352 and (name N or name CA or name C or name O or name CB )) or resid 353 \ through 363 or (resid 364 and (name N or name CA or name C or name O or name CB \ )) or resid 365 or (resid 366 and (name N or name CA or name C or name O or name \ CB )) or resid 367 through 375 or (resid 376 through 379 and (name N or name CA \ or name C or name O or name CB )) or resid 380 or (resid 381 and (name N or nam \ e CA or name C or name O or name CB )) or resid 382 through 442 or (resid 443 an \ d (name N or name CA or name C or name O or name CB )) or resid 501)) selection = (chain 'E' and ((resid 19 through 22 and (name N or name CA or name C or name O \ or name CB )) or resid 23 through 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB )) or resid 30 through 37 or (resid 38 and (name N or na \ me CA or name C or name O or name CB )) or resid 39 through 132 or resid 239 thr \ ough 252 or (resid 253 through 255 and (name N or name CA or name C or name O or \ name CB )) or resid 256 or (resid 257 through 260 and (name N or name CA or nam \ e C or name O or name CB )) or resid 261 or (resid 262 and (name N or name CA or \ name C or name O or name CB )) or resid 263 or (resid 264 and (name N or name C \ A or name C or name O or name CB )) or resid 265 through 266 or (resid 267 and ( \ name N or name CA or name C or name O or name CB )) or resid 268 through 299 or \ (resid 300 and (name N or name CA or name C or name O or name CB )) or resid 301 \ through 316 or (resid 317 and (name N or name CA or name C or name O or name CB \ )) or resid 318 through 375 or (resid 376 through 379 and (name N or name CA or \ name C or name O or name CB )) or resid 380 through 413 or (resid 414 through 4 \ 15 and (name N or name CA or name C or name O or name CB )) or resid 416 through \ 442 or (resid 443 and (name N or name CA or name C or name O or name CB )) or r \ esid 501)) selection = (chain 'F' and ((resid 19 through 22 and (name N or name CA or name C or name O \ or name CB )) or resid 23 through 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB )) or resid 30 through 132 or resid 239 through 245 or ( \ resid 246 and (name N or name CA or name C or name O or name CB )) or resid 247 \ through 253 or (resid 254 through 255 and (name N or name CA or name C or name O \ or name CB )) or resid 256 or (resid 257 through 260 and (name N or name CA or \ name C or name O or name CB )) or resid 261 or (resid 262 and (name N or name CA \ or name C or name O or name CB )) or resid 263 or (resid 264 and (name N or nam \ e CA or name C or name O or name CB )) or resid 265 through 266 or (resid 267 an \ d (name N or name CA or name C or name O or name CB )) or resid 268 through 270 \ or (resid 271 and (name N or name CA or name C or name O or name CB )) or resid \ 272 through 278 or (resid 279 and (name N or name CA or name C or name O or name \ CB )) or resid 280 through 316 or (resid 317 and (name N or name CA or name C o \ r name O or name CB )) or resid 318 through 351 or (resid 352 and (name N or nam \ e CA or name C or name O or name CB )) or resid 353 through 363 or (resid 364 an \ d (name N or name CA or name C or name O or name CB )) or resid 365 or (resid 36 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 367 through \ 376 or (resid 377 through 379 and (name N or name CA or name C or name O or name \ CB )) or resid 380 or (resid 381 and (name N or name CA or name C or name O or \ name CB )) or resid 382 through 395 or (resid 396 and (name N or name CA or name \ C or name O or name CB )) or resid 397 through 413 or (resid 414 through 415 an \ d (name N or name CA or name C or name O or name CB )) or resid 416 through 443 \ or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.54 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 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: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.670 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 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 : 0.012 0.832 16177 Z= 0.950 Angle : 1.223 12.454 21913 Z= 0.854 Chirality : 0.072 0.306 2632 Planarity : 0.020 0.467 2789 Dihedral : 15.852 143.621 5952 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.64 % Allowed : 16.19 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.17), residues: 2081 helix: -0.51 (0.15), residues: 1049 sheet: 0.25 (0.33), residues: 270 loop : -1.25 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 160 TYR 0.012 0.002 TYR B 446 PHE 0.019 0.002 PHE G 176 TRP 0.009 0.001 TRP B 283 HIS 0.006 0.001 HIS E 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00991 / 0.69 (16176) covalent geometry : angle 1.22311 / 0.85 (21913) hydrogen bonds : bond 0.26423 / 18.17 ( 783) hydrogen bonds : angle 7.80460 / 5.47 ( 2268) Misc. bond : bond 0.83236 / 43.81 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 441 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.6781 (pttt) cc_final: 0.6245 (mmtt) REVERT: A 31 LEU cc_start: 0.6880 (mp) cc_final: 0.6656 (mp) REVERT: A 53 VAL cc_start: 0.7281 (t) cc_final: 0.6990 (m) REVERT: A 86 GLU cc_start: 0.8699 (tp30) cc_final: 0.8242 (mm-30) REVERT: A 359 MET cc_start: 0.7869 (mtp) cc_final: 0.7565 (mtp) REVERT: A 364 MET cc_start: 0.7991 (mtm) cc_final: 0.7430 (mmm) REVERT: A 441 LYS cc_start: 0.7835 (tptm) cc_final: 0.7501 (tttt) REVERT: B 290 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6675 (pt0) REVERT: B 377 GLU cc_start: 0.8714 (tp30) cc_final: 0.8281 (tm-30) REVERT: B 396 GLU cc_start: 0.8044 (tp30) cc_final: 0.6944 (tt0) REVERT: B 446 TYR cc_start: 0.7162 (t80) cc_final: 0.6934 (t80) REVERT: C 88 MET cc_start: 0.7395 (tpt) cc_final: 0.7134 (tpt) REVERT: C 107 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7357 (tm-30) REVERT: C 113 MET cc_start: 0.6934 (ptt) cc_final: 0.6330 (ptt) REVERT: C 299 ASP cc_start: 0.6517 (t0) cc_final: 0.6221 (t0) REVERT: C 300 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7249 (mm-30) REVERT: D 67 LYS cc_start: 0.6615 (mmtt) cc_final: 0.6409 (mmtp) REVERT: D 78 GLN cc_start: 0.7354 (mp10) cc_final: 0.7099 (mt0) REVERT: D 81 THR cc_start: 0.6573 (t) cc_final: 0.6252 (p) REVERT: D 257 PHE cc_start: 0.6546 (p90) cc_final: 0.6272 (p90) REVERT: D 269 LYS cc_start: 0.7809 (mmtt) cc_final: 0.7537 (mmtt) REVERT: D 384 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7726 (tm-30) REVERT: E 413 CYS cc_start: 0.6241 (t) cc_final: 0.6009 (t) REVERT: E 416 ARG cc_start: 0.6721 (ttp-110) cc_final: 0.6463 (tmm-80) REVERT: E 422 GLN cc_start: 0.7494 (mm-40) cc_final: 0.7029 (mm110) REVERT: F 67 LYS cc_start: 0.8150 (mtpp) cc_final: 0.7670 (mtmm) REVERT: F 395 LEU cc_start: 0.7891 (tt) cc_final: 0.7577 (mt) REVERT: F 406 ILE cc_start: 0.7844 (mt) cc_final: 0.7516 (mm) outliers start: 43 outliers final: 18 residues processed: 468 average time/residue: 0.1545 time to fit residues: 101.1380 Evaluate side-chains 275 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 256 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: [98, 194, 107, 10, 66, 130, 124, 103, 200, 77, 122] chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 20 HIS A 247 ASN ** A 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 HIS C 25 HIS ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 240 HIS D 240 HIS D 251 ASN F 27 HIS ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.118476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.086764 restraints weight = 28389.093| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.37 r_work: 0.2931 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2937 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16177 Z= 0.187 Angle : 0.648 7.641 21913 Z= 0.321 Chirality : 0.044 0.167 2632 Planarity : 0.004 0.059 2789 Dihedral : 7.635 156.184 2375 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.17 % Allowed : 16.25 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.18), residues: 2081 helix: 0.74 (0.16), residues: 1102 sheet: 0.56 (0.32), residues: 278 loop : -1.25 (0.21), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 64 TYR 0.021 0.001 TYR G 120 PHE 0.016 0.002 PHE G 176 TRP 0.010 0.001 TRP B 283 HIS 0.006 0.001 HIS A 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (16176) covalent geometry : angle 0.64829 / 0.32 (21913) hydrogen bonds : bond 0.04448 / 3.02 ( 783) hydrogen bonds : angle 4.50605 / 3.16 ( 2268) Misc. bond : bond 0.00081 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 259 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 7 LYS cc_start: 0.7762 (pttt) cc_final: 0.7452 (mmtp) REVERT: A 86 GLU cc_start: 0.8937 (tp30) cc_final: 0.8661 (tp30) REVERT: A 357 ARG cc_start: 0.7928 (mmm-85) cc_final: 0.7504 (mtt90) REVERT: B 269 LYS cc_start: 0.9132 (tptp) cc_final: 0.8652 (mtpp) REVERT: B 377 GLU cc_start: 0.8902 (tp30) cc_final: 0.8544 (tm-30) REVERT: B 396 GLU cc_start: 0.8823 (tp30) cc_final: 0.8010 (tt0) REVERT: C 88 MET cc_start: 0.8859 (tpt) cc_final: 0.8467 (tpt) REVERT: C 107 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8551 (tp30) REVERT: D 78 GLN cc_start: 0.8135 (mp10) cc_final: 0.7927 (mt0) REVERT: D 269 LYS cc_start: 0.7863 (mmtt) cc_final: 0.7520 (mptt) REVERT: D 300 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8545 (mm-30) REVERT: D 356 ILE cc_start: 0.9419 (mm) cc_final: 0.9184 (mm) REVERT: E 46 MET cc_start: 0.9162 (mmm) cc_final: 0.8899 (mmm) REVERT: E 251 ASN cc_start: 0.7694 (m-40) cc_final: 0.7411 (m-40) REVERT: E 414 ARG cc_start: 0.8786 (tmm160) cc_final: 0.8479 (ttp80) REVERT: E 415 LYS cc_start: 0.8309 (tppt) cc_final: 0.7871 (tppt) REVERT: F 411 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8846 (tt) REVERT: F 441 GLN cc_start: 0.8142 (tm-30) cc_final: 0.7814 (tt0) REVERT: G 121 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8402 (mm-40) REVERT: G 194 LEU cc_start: 0.7538 (tt) cc_final: 0.7130 (mt) outliers start: 68 outliers final: 33 residues processed: 312 average time/residue: 0.1194 time to fit residues: 55.8916 Evaluate side-chains 250 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 215 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 413 CYS Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 342 SER Chi-restraints excluded: chain D residue 366 ASP Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 240 HIS Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 399 LEU Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain G residue 121 GLN Chi-restraints excluded: chain G residue 138 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: [146, 164, 178, 82, 136, 135, 190, 26, 23, 143, 34] chunk 146 optimal weight: 10.0000 chunk 164 optimal weight: 0.8980 chunk 178 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 chunk 190 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 420 ASN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 240 HIS C 302 HIS C 404 GLN D 251 ASN D 277 ASN ** E 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.115261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.084715 restraints weight = 28530.468| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.28 r_work: 0.2864 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16177 Z= 0.228 Angle : 0.633 7.791 21913 Z= 0.314 Chirality : 0.044 0.165 2632 Planarity : 0.004 0.041 2789 Dihedral : 7.421 172.671 2358 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.60 % Allowed : 18.70 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.18), residues: 2081 helix: 1.07 (0.16), residues: 1101 sheet: 0.67 (0.31), residues: 276 loop : -1.30 (0.21), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 378 TYR 0.019 0.001 TYR G 120 PHE 0.011 0.002 PHE D 433 TRP 0.005 0.001 TRP C 283 HIS 0.006 0.001 HIS A 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.23 (16176) covalent geometry : angle 0.63326 / 0.31 (21913) hydrogen bonds : bond 0.05355 / 3.65 ( 783) hydrogen bonds : angle 4.42873 / 3.11 ( 2268) Misc. bond : bond 0.00082 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 221 time to evaluate : 0.609 Fit side-chains REVERT: A 7 LYS cc_start: 0.7755 (pttt) cc_final: 0.7394 (mmtm) REVERT: A 86 GLU cc_start: 0.9055 (tp30) cc_final: 0.8778 (tp30) REVERT: A 306 MET cc_start: 0.9357 (tpp) cc_final: 0.8799 (mmt) REVERT: B 269 LYS cc_start: 0.9100 (tptp) cc_final: 0.8505 (mtpp) REVERT: B 314 ARG cc_start: 0.8794 (ttm-80) cc_final: 0.8505 (mtp85) REVERT: B 377 GLU cc_start: 0.8954 (tp30) cc_final: 0.8518 (tm-30) REVERT: B 396 GLU cc_start: 0.8792 (tp30) cc_final: 0.8144 (tt0) REVERT: C 248 ASP cc_start: 0.8593 (p0) cc_final: 0.8336 (p0) REVERT: C 441 GLN cc_start: 0.8477 (tp40) cc_final: 0.8004 (tt0) REVERT: C 442 TYR cc_start: 0.7528 (m-80) cc_final: 0.7293 (m-80) REVERT: D 67 LYS cc_start: 0.8294 (mmtp) cc_final: 0.8043 (mmtp) REVERT: D 126 SER cc_start: 0.9547 (m) cc_final: 0.9271 (t) REVERT: D 258 LEU cc_start: 0.9376 (mt) cc_final: 0.9115 (mt) REVERT: D 269 LYS cc_start: 0.7958 (mmtt) cc_final: 0.7611 (mptt) REVERT: D 405 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8852 (mp) REVERT: E 251 ASN cc_start: 0.8371 (m-40) cc_final: 0.8090 (m-40) REVERT: E 415 LYS cc_start: 0.8226 (tppt) cc_final: 0.7811 (tppt) REVERT: F 14 ARG cc_start: 0.8451 (ttp-170) cc_final: 0.8197 (ttp-170) REVERT: F 276 ILE cc_start: 0.9105 (mm) cc_final: 0.8823 (mt) REVERT: F 441 GLN cc_start: 0.8391 (tm-30) cc_final: 0.8183 (tm-30) REVERT: G 121 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8480 (mm-40) REVERT: G 176 PHE cc_start: 0.8456 (t80) cc_final: 0.7691 (t80) REVERT: G 191 CYS cc_start: 0.8628 (p) cc_final: 0.8158 (p) REVERT: G 195 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.7627 (m-10) outliers start: 75 outliers final: 48 residues processed: 280 average time/residue: 0.1262 time to fit residues: 52.3709 Evaluate side-chains 247 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 196 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 413 CYS Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 413 CYS Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 375 CYS Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 240 HIS Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 399 LEU Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 121 GLN Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 195 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: [153, 37, 27, 38, 73, 6, 68, 191, 136, 175, 56] chunk 153 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 191 optimal weight: 0.9990 chunk 136 optimal weight: 7.9990 chunk 175 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 302 HIS ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 ASN D 277 ASN E 78 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.117927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.087641 restraints weight = 27995.592| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.26 r_work: 0.2935 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16177 Z= 0.098 Angle : 0.529 7.105 21913 Z= 0.253 Chirality : 0.040 0.140 2632 Planarity : 0.003 0.040 2789 Dihedral : 6.631 156.211 2357 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.94 % Allowed : 19.93 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.19), residues: 2081 helix: 1.50 (0.16), residues: 1101 sheet: 0.83 (0.31), residues: 276 loop : -1.10 (0.21), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 416 TYR 0.020 0.001 TYR G 120 PHE 0.025 0.001 PHE C 261 TRP 0.002 0.000 TRP E 283 HIS 0.003 0.000 HIS A 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (16176) covalent geometry : angle 0.52912 / 0.25 (21913) hydrogen bonds : bond 0.03196 / 2.15 ( 783) hydrogen bonds : angle 3.70869 / 2.61 ( 2268) Misc. bond : bond 0.00016 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 229 time to evaluate : 0.616 Fit side-chains REVERT: A 7 LYS cc_start: 0.7747 (pttt) cc_final: 0.7398 (mmtm) REVERT: A 86 GLU cc_start: 0.8948 (tp30) cc_final: 0.8529 (tp30) REVERT: B 269 LYS cc_start: 0.9052 (tptp) cc_final: 0.8478 (mtpp) REVERT: B 314 ARG cc_start: 0.8760 (ttm-80) cc_final: 0.8544 (mtp85) REVERT: B 377 GLU cc_start: 0.8966 (tp30) cc_final: 0.8485 (tm-30) REVERT: B 396 GLU cc_start: 0.8736 (tp30) cc_final: 0.8141 (tt0) REVERT: C 54 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7722 (ttp80) REVERT: C 88 MET cc_start: 0.8983 (tpt) cc_final: 0.7969 (tpp) REVERT: C 248 ASP cc_start: 0.8564 (p0) cc_final: 0.8213 (p0) REVERT: C 441 GLN cc_start: 0.8378 (tp40) cc_final: 0.7917 (tt0) REVERT: C 442 TYR cc_start: 0.7558 (m-80) cc_final: 0.7340 (m-80) REVERT: D 67 LYS cc_start: 0.8097 (mmtp) cc_final: 0.7603 (mmtp) REVERT: D 78 GLN cc_start: 0.8205 (mp10) cc_final: 0.7933 (mt0) REVERT: D 81 THR cc_start: 0.8104 (t) cc_final: 0.7870 (p) REVERT: D 126 SER cc_start: 0.9520 (m) cc_final: 0.9256 (t) REVERT: D 258 LEU cc_start: 0.9356 (mt) cc_final: 0.9095 (mt) REVERT: D 269 LYS cc_start: 0.7774 (mmtt) cc_final: 0.7448 (mptt) REVERT: E 78 GLN cc_start: 0.8044 (mp-120) cc_final: 0.7781 (mm-40) REVERT: E 251 ASN cc_start: 0.8321 (m-40) cc_final: 0.7970 (m-40) REVERT: E 320 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8141 (mmm) REVERT: F 276 ILE cc_start: 0.8963 (mm) cc_final: 0.8653 (mt) REVERT: G 121 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8456 (mm110) REVERT: G 176 PHE cc_start: 0.8351 (t80) cc_final: 0.7652 (t80) REVERT: G 191 CYS cc_start: 0.8609 (p) cc_final: 0.8154 (p) REVERT: G 195 PHE cc_start: 0.7701 (OUTLIER) cc_final: 0.7455 (m-10) outliers start: 48 outliers final: 28 residues processed: 263 average time/residue: 0.1361 time to fit residues: 52.2757 Evaluate side-chains 241 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 209 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 413 CYS Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 375 CYS Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 320 MET Chi-restraints excluded: chain E residue 399 LEU Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain G residue 121 GLN Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 195 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: [15, 174, 43, 103, 179, 77, 10, 35, 21, 8, 200] chunk 15 optimal weight: 6.9990 chunk 174 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 179 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 8 optimal weight: 0.0870 chunk 200 optimal weight: 0.0270 overall best weight: 1.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN A 280 ASN B 78 GLN C 49 GLN D 251 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.118184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.087463 restraints weight = 28108.059| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.31 r_work: 0.2909 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16177 Z= 0.121 Angle : 0.538 6.618 21913 Z= 0.257 Chirality : 0.041 0.181 2632 Planarity : 0.003 0.036 2789 Dihedral : 5.922 107.996 2355 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.00 % Allowed : 20.11 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.19), residues: 2081 helix: 1.63 (0.16), residues: 1102 sheet: 0.86 (0.31), residues: 276 loop : -1.04 (0.21), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 64 TYR 0.020 0.001 TYR G 120 PHE 0.009 0.001 PHE F 257 TRP 0.004 0.001 TRP E 283 HIS 0.003 0.001 HIS A 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (16176) covalent geometry : angle 0.53765 / 0.26 (21913) hydrogen bonds : bond 0.03514 / 2.39 ( 783) hydrogen bonds : angle 3.67129 / 2.59 ( 2268) Misc. bond : bond 0.00023 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 214 time to evaluate : 0.616 Fit side-chains REVERT: A 86 GLU cc_start: 0.8997 (tp30) cc_final: 0.8721 (tp30) REVERT: B 269 LYS cc_start: 0.9073 (tptp) cc_final: 0.8458 (mtpp) REVERT: B 314 ARG cc_start: 0.8760 (ttm-80) cc_final: 0.8533 (mtp85) REVERT: B 377 GLU cc_start: 0.8968 (tp30) cc_final: 0.8491 (tm-30) REVERT: B 396 GLU cc_start: 0.8775 (tp30) cc_final: 0.8167 (tt0) REVERT: C 54 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7904 (ttp80) REVERT: C 251 ASN cc_start: 0.8262 (m-40) cc_final: 0.8028 (t0) REVERT: C 441 GLN cc_start: 0.8309 (tp40) cc_final: 0.7869 (tt0) REVERT: C 442 TYR cc_start: 0.7574 (m-80) cc_final: 0.7331 (m-80) REVERT: D 67 LYS cc_start: 0.8083 (mmtp) cc_final: 0.7816 (mmtp) REVERT: D 78 GLN cc_start: 0.8268 (mp10) cc_final: 0.8004 (mt0) REVERT: D 81 THR cc_start: 0.8201 (t) cc_final: 0.7940 (p) REVERT: D 126 SER cc_start: 0.9521 (m) cc_final: 0.9272 (t) REVERT: D 258 LEU cc_start: 0.9357 (mt) cc_final: 0.9071 (mt) REVERT: D 269 LYS cc_start: 0.7757 (mmtt) cc_final: 0.7410 (mptt) REVERT: E 251 ASN cc_start: 0.8499 (m-40) cc_final: 0.8152 (m-40) REVERT: E 320 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8152 (mmm) REVERT: F 276 ILE cc_start: 0.9007 (mm) cc_final: 0.8714 (mt) REVERT: G 121 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8588 (mm-40) REVERT: G 170 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8148 (mp) REVERT: G 176 PHE cc_start: 0.8397 (t80) cc_final: 0.7750 (t80) REVERT: G 191 CYS cc_start: 0.8656 (p) cc_final: 0.8216 (p) REVERT: G 195 PHE cc_start: 0.7685 (OUTLIER) cc_final: 0.7407 (m-10) outliers start: 49 outliers final: 32 residues processed: 248 average time/residue: 0.1245 time to fit residues: 46.2911 Evaluate side-chains 238 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 201 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 413 CYS Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 375 CYS Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 320 MET Chi-restraints excluded: chain E residue 399 LEU Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 121 GLN Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 195 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: [35, 178, 141, 122, 206, 135, 166, 26, 16, 88, 172] chunk 35 optimal weight: 0.9990 chunk 178 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 206 optimal weight: 40.0000 chunk 135 optimal weight: 0.5980 chunk 166 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 172 optimal weight: 7.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 450 GLN D 251 ASN D 302 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.116409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.086018 restraints weight = 28217.201| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.27 r_work: 0.2917 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16177 Z= 0.114 Angle : 0.533 8.537 21913 Z= 0.252 Chirality : 0.041 0.194 2632 Planarity : 0.003 0.039 2789 Dihedral : 5.665 90.432 2355 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.31 % Allowed : 20.42 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.19), residues: 2081 helix: 1.71 (0.16), residues: 1105 sheet: 0.93 (0.30), residues: 273 loop : -0.99 (0.21), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 64 TYR 0.024 0.001 TYR D 430 PHE 0.008 0.001 PHE F 257 TRP 0.005 0.001 TRP E 283 HIS 0.003 0.000 HIS A 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (16176) covalent geometry : angle 0.53341 / 0.25 (21913) hydrogen bonds : bond 0.03226 / 2.19 ( 783) hydrogen bonds : angle 3.57514 / 2.52 ( 2268) Misc. bond : bond 0.00006 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 213 time to evaluate : 0.491 Fit side-chains REVERT: A 86 GLU cc_start: 0.8979 (tp30) cc_final: 0.8707 (tp30) REVERT: B 269 LYS cc_start: 0.9022 (tptp) cc_final: 0.8427 (mtpp) REVERT: B 314 ARG cc_start: 0.8759 (ttm-80) cc_final: 0.8440 (mtp85) REVERT: B 396 GLU cc_start: 0.8764 (tp30) cc_final: 0.8184 (tt0) REVERT: C 54 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7798 (ttp80) REVERT: C 441 GLN cc_start: 0.8229 (tp40) cc_final: 0.7831 (tt0) REVERT: C 442 TYR cc_start: 0.7521 (m-80) cc_final: 0.7266 (m-80) REVERT: D 65 GLU cc_start: 0.8823 (tp30) cc_final: 0.8336 (tm-30) REVERT: D 78 GLN cc_start: 0.8237 (mp10) cc_final: 0.7943 (mt0) REVERT: D 126 SER cc_start: 0.9524 (m) cc_final: 0.9271 (t) REVERT: D 258 LEU cc_start: 0.9351 (mt) cc_final: 0.9059 (mt) REVERT: D 269 LYS cc_start: 0.7728 (mmtt) cc_final: 0.7390 (mptt) REVERT: D 405 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8841 (mp) REVERT: E 46 MET cc_start: 0.9145 (mmm) cc_final: 0.8791 (mmm) REVERT: E 251 ASN cc_start: 0.8626 (m-40) cc_final: 0.8284 (m-40) REVERT: F 14 ARG cc_start: 0.8522 (ttp-170) cc_final: 0.8212 (ttt180) REVERT: F 257 PHE cc_start: 0.7441 (t80) cc_final: 0.7196 (t80) REVERT: F 276 ILE cc_start: 0.8985 (mm) cc_final: 0.8693 (mt) REVERT: G 121 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8616 (mm-40) REVERT: G 170 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8189 (mp) REVERT: G 176 PHE cc_start: 0.8417 (t80) cc_final: 0.7776 (t80) REVERT: G 191 CYS cc_start: 0.8689 (p) cc_final: 0.8251 (p) REVERT: G 195 PHE cc_start: 0.7678 (OUTLIER) cc_final: 0.7374 (m-10) outliers start: 54 outliers final: 38 residues processed: 252 average time/residue: 0.1233 time to fit residues: 46.5449 Evaluate side-chains 250 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 207 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 413 CYS Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 375 CYS Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 399 LEU Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 121 GLN Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 195 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: [154, 116, 18, 53, 117, 133, 61, 14, 199, 191, 169] chunk 154 optimal weight: 0.3980 chunk 116 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 133 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 199 optimal weight: 0.0370 chunk 191 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 overall best weight: 0.6462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 251 ASN D 251 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.120934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.090411 restraints weight = 27855.702| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.30 r_work: 0.2958 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16177 Z= 0.087 Angle : 0.518 9.211 21913 Z= 0.242 Chirality : 0.040 0.188 2632 Planarity : 0.003 0.040 2789 Dihedral : 5.320 80.086 2355 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.94 % Allowed : 21.58 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.19), residues: 2081 helix: 1.89 (0.16), residues: 1107 sheet: 1.05 (0.30), residues: 272 loop : -0.74 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 416 TYR 0.022 0.001 TYR D 430 PHE 0.006 0.001 PHE C 297 TRP 0.004 0.000 TRP E 283 HIS 0.003 0.000 HIS D 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.09 (16176) covalent geometry : angle 0.51771 / 0.24 (21913) hydrogen bonds : bond 0.02547 / 1.72 ( 783) hydrogen bonds : angle 3.31650 / 2.33 ( 2268) Misc. bond : bond 0.00019 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 226 time to evaluate : 0.611 Fit side-chains REVERT: A 86 GLU cc_start: 0.8975 (tp30) cc_final: 0.8593 (tp30) REVERT: B 269 LYS cc_start: 0.8953 (tptp) cc_final: 0.8686 (mmmt) REVERT: B 314 ARG cc_start: 0.8765 (ttm-80) cc_final: 0.8460 (mtp85) REVERT: B 396 GLU cc_start: 0.8745 (tp30) cc_final: 0.8185 (tt0) REVERT: C 54 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7743 (ttp80) REVERT: C 97 ASP cc_start: 0.8527 (p0) cc_final: 0.8299 (p0) REVERT: C 107 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8461 (tp30) REVERT: C 441 GLN cc_start: 0.8133 (tp40) cc_final: 0.7787 (tt0) REVERT: C 442 TYR cc_start: 0.7568 (m-80) cc_final: 0.7335 (m-80) REVERT: D 65 GLU cc_start: 0.8748 (tp30) cc_final: 0.8111 (tm-30) REVERT: D 67 LYS cc_start: 0.8040 (mmtp) cc_final: 0.7321 (mttm) REVERT: D 126 SER cc_start: 0.9507 (m) cc_final: 0.9272 (t) REVERT: D 258 LEU cc_start: 0.9312 (mt) cc_final: 0.9032 (mt) REVERT: D 269 LYS cc_start: 0.7690 (mmtt) cc_final: 0.7385 (mptt) REVERT: E 251 ASN cc_start: 0.8531 (m-40) cc_final: 0.8193 (m-40) REVERT: E 320 MET cc_start: 0.8689 (mmm) cc_final: 0.8196 (mpp) REVERT: E 414 ARG cc_start: 0.8725 (tmm160) cc_final: 0.8491 (ttp-170) REVERT: E 415 LYS cc_start: 0.8019 (tptp) cc_final: 0.7777 (tppt) REVERT: F 14 ARG cc_start: 0.8523 (ttp-170) cc_final: 0.8200 (ttp-170) REVERT: F 107 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8324 (tm-30) REVERT: F 257 PHE cc_start: 0.7486 (t80) cc_final: 0.7155 (t80) REVERT: F 368 LYS cc_start: 0.9067 (tttt) cc_final: 0.8835 (ttmt) REVERT: G 120 TYR cc_start: 0.7513 (t80) cc_final: 0.7221 (t80) REVERT: G 121 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8674 (mm-40) REVERT: G 170 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8212 (mp) REVERT: G 176 PHE cc_start: 0.8392 (t80) cc_final: 0.7775 (t80) REVERT: G 191 CYS cc_start: 0.8666 (p) cc_final: 0.8248 (p) REVERT: G 195 PHE cc_start: 0.7571 (OUTLIER) cc_final: 0.7227 (m-10) outliers start: 48 outliers final: 28 residues processed: 259 average time/residue: 0.1185 time to fit residues: 46.1398 Evaluate side-chains 239 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 375 CYS Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 399 LEU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain G residue 121 GLN Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 195 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: [74, 186, 10, 110, 26, 177, 201, 62, 70, 25, 172] chunk 74 optimal weight: 8.9990 chunk 186 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 chunk 201 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 172 optimal weight: 7.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 240 HIS C 251 ASN D 251 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.113729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.083421 restraints weight = 28323.127| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.23 r_work: 0.2855 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.5266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 16177 Z= 0.224 Angle : 0.622 9.627 21913 Z= 0.301 Chirality : 0.044 0.226 2632 Planarity : 0.004 0.045 2789 Dihedral : 5.796 73.731 2355 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.68 % Allowed : 21.77 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.19), residues: 2081 helix: 1.67 (0.16), residues: 1100 sheet: 0.75 (0.30), residues: 277 loop : -1.08 (0.21), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 378 TYR 0.025 0.002 TYR G 120 PHE 0.012 0.001 PHE F 261 TRP 0.008 0.001 TRP C 283 HIS 0.004 0.001 HIS D 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.22 (16176) covalent geometry : angle 0.62232 / 0.30 (21913) hydrogen bonds : bond 0.04495 / 3.08 ( 783) hydrogen bonds : angle 4.01552 / 2.83 ( 2268) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 193 time to evaluate : 0.588 Fit side-chains REVERT: A 86 GLU cc_start: 0.9004 (tp30) cc_final: 0.8730 (tp30) REVERT: B 269 LYS cc_start: 0.8942 (tptp) cc_final: 0.8432 (mtpp) REVERT: B 314 ARG cc_start: 0.8720 (ttm-80) cc_final: 0.8469 (mtp85) REVERT: C 54 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7945 (ttp80) REVERT: C 441 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7860 (tt0) REVERT: C 442 TYR cc_start: 0.7484 (m-80) cc_final: 0.7255 (m-80) REVERT: D 65 GLU cc_start: 0.8931 (tp30) cc_final: 0.8448 (tm-30) REVERT: D 67 LYS cc_start: 0.8231 (mmtp) cc_final: 0.7598 (mttm) REVERT: D 126 SER cc_start: 0.9540 (m) cc_final: 0.9262 (t) REVERT: D 258 LEU cc_start: 0.9310 (mt) cc_final: 0.9018 (mt) REVERT: D 269 LYS cc_start: 0.7823 (mmtt) cc_final: 0.7495 (mptt) REVERT: D 405 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8907 (mp) REVERT: E 251 ASN cc_start: 0.8725 (m-40) cc_final: 0.8386 (m-40) REVERT: E 320 MET cc_start: 0.8811 (mmm) cc_final: 0.8335 (mpp) REVERT: E 427 LYS cc_start: 0.8711 (ptpt) cc_final: 0.8473 (mptt) REVERT: F 14 ARG cc_start: 0.8585 (ttp-170) cc_final: 0.8297 (ttp80) REVERT: F 276 ILE cc_start: 0.9036 (mm) cc_final: 0.8811 (mt) REVERT: F 441 GLN cc_start: 0.8140 (tm-30) cc_final: 0.7909 (tt0) REVERT: G 121 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8662 (mm-40) REVERT: G 170 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8200 (mp) REVERT: G 176 PHE cc_start: 0.8543 (t80) cc_final: 0.7863 (t80) REVERT: G 191 CYS cc_start: 0.8734 (p) cc_final: 0.8280 (p) REVERT: G 195 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.7310 (m-10) outliers start: 60 outliers final: 44 residues processed: 243 average time/residue: 0.1240 time to fit residues: 45.2075 Evaluate side-chains 242 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 192 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 413 CYS Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 375 CYS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 399 LEU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 121 GLN Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 195 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: [15, 113, 79, 29, 177, 184, 89, 167, 19, 174, 34] chunk 15 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 177 optimal weight: 9.9990 chunk 184 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 167 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 174 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 240 HIS C 251 ASN D 251 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.115687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.085591 restraints weight = 28169.330| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.52 r_work: 0.2881 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.5386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16177 Z= 0.136 Angle : 0.555 10.792 21913 Z= 0.263 Chirality : 0.041 0.182 2632 Planarity : 0.003 0.044 2789 Dihedral : 5.606 70.931 2355 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.88 % Allowed : 22.44 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.19), residues: 2081 helix: 1.78 (0.16), residues: 1104 sheet: 0.83 (0.30), residues: 276 loop : -1.02 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 64 TYR 0.022 0.001 TYR G 120 PHE 0.019 0.001 PHE F 257 TRP 0.002 0.000 TRP C 283 HIS 0.003 0.001 HIS A 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (16176) covalent geometry : angle 0.55482 / 0.26 (21913) hydrogen bonds : bond 0.03425 / 2.32 ( 783) hydrogen bonds : angle 3.65849 / 2.58 ( 2268) Misc. bond : bond 0.00014 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 201 time to evaluate : 0.648 Fit side-chains REVERT: A 86 GLU cc_start: 0.9012 (tp30) cc_final: 0.8742 (tp30) REVERT: B 269 LYS cc_start: 0.8896 (tptp) cc_final: 0.8452 (mtpp) REVERT: B 314 ARG cc_start: 0.8707 (ttm-80) cc_final: 0.8494 (mtp85) REVERT: B 396 GLU cc_start: 0.8799 (tp30) cc_final: 0.8256 (tt0) REVERT: C 97 ASP cc_start: 0.8434 (p0) cc_final: 0.8089 (p0) REVERT: C 441 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7827 (tt0) REVERT: D 65 GLU cc_start: 0.8911 (tp30) cc_final: 0.8346 (tm-30) REVERT: D 67 LYS cc_start: 0.8224 (mmtp) cc_final: 0.7516 (mttm) REVERT: D 126 SER cc_start: 0.9532 (m) cc_final: 0.9260 (t) REVERT: D 258 LEU cc_start: 0.9315 (mt) cc_final: 0.9018 (mt) REVERT: D 269 LYS cc_start: 0.7660 (mmtt) cc_final: 0.7334 (mptt) REVERT: E 251 ASN cc_start: 0.8663 (m-40) cc_final: 0.8305 (m-40) REVERT: E 320 MET cc_start: 0.8821 (mmm) cc_final: 0.8306 (mpp) REVERT: E 427 LYS cc_start: 0.8683 (ptpt) cc_final: 0.8446 (mmtm) REVERT: F 14 ARG cc_start: 0.8626 (ttp-170) cc_final: 0.8348 (ttp80) REVERT: F 276 ILE cc_start: 0.8997 (mm) cc_final: 0.8771 (mt) REVERT: G 170 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8191 (mp) REVERT: G 176 PHE cc_start: 0.8538 (t80) cc_final: 0.7874 (t80) REVERT: G 191 CYS cc_start: 0.8726 (p) cc_final: 0.8282 (p) REVERT: G 195 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.7285 (m-10) outliers start: 47 outliers final: 37 residues processed: 238 average time/residue: 0.1270 time to fit residues: 44.9190 Evaluate side-chains 235 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 413 CYS Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 375 CYS Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 399 LEU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 195 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: [20, 63, 143, 149, 14, 88, 74, 84, 136, 202, 101] chunk 20 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 202 optimal weight: 20.0000 chunk 101 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 240 HIS D 251 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.117746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.087264 restraints weight = 28169.784| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 3.30 r_work: 0.2901 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16177 Z= 0.121 Angle : 0.550 11.076 21913 Z= 0.260 Chirality : 0.041 0.188 2632 Planarity : 0.003 0.044 2789 Dihedral : 5.456 67.869 2355 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.51 % Allowed : 22.93 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.19), residues: 2081 helix: 1.84 (0.16), residues: 1106 sheet: 0.97 (0.30), residues: 269 loop : -0.97 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 339 TYR 0.023 0.001 TYR G 120 PHE 0.007 0.001 PHE F 261 TRP 0.002 0.000 TRP C 283 HIS 0.004 0.001 HIS A 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (16176) covalent geometry : angle 0.55046 / 0.26 (21913) hydrogen bonds : bond 0.03209 / 2.18 ( 783) hydrogen bonds : angle 3.53187 / 2.49 ( 2268) Misc. bond : bond 0.00018 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 197 time to evaluate : 0.508 Fit side-chains REVERT: A 86 GLU cc_start: 0.8991 (tp30) cc_final: 0.8720 (tp30) REVERT: B 269 LYS cc_start: 0.8853 (tptp) cc_final: 0.8456 (mtpp) REVERT: B 314 ARG cc_start: 0.8702 (ttm-80) cc_final: 0.8482 (mtp85) REVERT: B 396 GLU cc_start: 0.8781 (tp30) cc_final: 0.8261 (tt0) REVERT: C 97 ASP cc_start: 0.8432 (p0) cc_final: 0.8085 (p0) REVERT: C 107 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8523 (tp30) REVERT: C 441 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7801 (tt0) REVERT: D 65 GLU cc_start: 0.8794 (tp30) cc_final: 0.8321 (tm-30) REVERT: D 67 LYS cc_start: 0.8232 (mmtp) cc_final: 0.7512 (mttm) REVERT: D 126 SER cc_start: 0.9523 (m) cc_final: 0.9268 (t) REVERT: D 258 LEU cc_start: 0.9299 (mt) cc_final: 0.9001 (mt) REVERT: D 269 LYS cc_start: 0.7688 (mmtt) cc_final: 0.7367 (mptt) REVERT: D 392 ARG cc_start: 0.8173 (ttt180) cc_final: 0.7653 (ttt-90) REVERT: E 251 ASN cc_start: 0.8686 (m-40) cc_final: 0.8344 (m-40) REVERT: E 320 MET cc_start: 0.8822 (mmm) cc_final: 0.8478 (mpp) REVERT: E 427 LYS cc_start: 0.8709 (ptpt) cc_final: 0.8423 (mmtm) REVERT: F 14 ARG cc_start: 0.8635 (ttp-170) cc_final: 0.8337 (ttp80) REVERT: F 276 ILE cc_start: 0.8981 (mm) cc_final: 0.8751 (mt) REVERT: G 170 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8202 (mp) REVERT: G 176 PHE cc_start: 0.8544 (t80) cc_final: 0.7933 (t80) REVERT: G 191 CYS cc_start: 0.8728 (p) cc_final: 0.8287 (p) REVERT: G 195 PHE cc_start: 0.7564 (OUTLIER) cc_final: 0.7188 (m-10) outliers start: 41 outliers final: 36 residues processed: 228 average time/residue: 0.1183 time to fit residues: 40.6093 Evaluate side-chains 235 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 196 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 286 TYR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 413 CYS Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 375 CYS Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 399 LEU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 195 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: [54, 61, 91, 35, 108, 202, 98, 27, 84, 28, 106] chunk 54 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 202 optimal weight: 20.0000 chunk 98 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 chunk 84 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 106 optimal weight: 10.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 240 HIS D 251 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.114023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.083442 restraints weight = 28237.449| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 3.27 r_work: 0.2857 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16177 Z= 0.186 Angle : 0.589 10.751 21913 Z= 0.283 Chirality : 0.042 0.188 2632 Planarity : 0.004 0.047 2789 Dihedral : 5.664 71.713 2355 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.13 % Allowed : 22.62 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.19), residues: 2081 helix: 1.72 (0.16), residues: 1105 sheet: 0.79 (0.30), residues: 276 loop : -1.08 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 64 TYR 0.024 0.001 TYR G 120 PHE 0.027 0.001 PHE F 257 TRP 0.005 0.001 TRP C 283 HIS 0.004 0.001 HIS D 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (16176) covalent geometry : angle 0.58872 / 0.28 (21913) hydrogen bonds : bond 0.03969 / 2.71 ( 783) hydrogen bonds : angle 3.81394 / 2.69 ( 2268) Misc. bond : bond 0.00015 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3539.17 seconds wall clock time: 61 minutes 20.49 seconds (3680.49 seconds total)