Starting phenix.real_space_refine on Sun Jul 5 16:18:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gtd_34250/07_2026/8gtd_34250.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gtd_34250/07_2026/8gtd_34250.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gtd_34250/07_2026/8gtd_34250.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gtd_34250/07_2026/8gtd_34250.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gtd_34250/07_2026/8gtd_34250.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gtd_34250/07_2026/8gtd_34250.map" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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: 3 Type Number sf(0) Gaussians C 14784 2.51 5 N 7392 2.21 5 O 7404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29580 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 1752 Classifications: {'peptide': 438} Incomplete info: {'backbone_only': 395} Link IDs: {'PTRANS': 25, 'TRANS': 412} Chain breaks: 2 Unresolved chain link angles: 25 Unresolved non-hydrogen bonds: 1705 Unresolved non-hydrogen angles: 2470 Unresolved non-hydrogen dihedrals: 1106 Unresolved non-hydrogen chiralities: 494 Planarities with less than four sites: {'TYR:plan': 8, 'ARG:plan': 40, 'ASP:plan': 27, 'PHE:plan': 19, 'GLU:plan': 29, 'HIS:plan': 8, 'GLN:plan1': 15, 'ASN:plan1': 12, 'TRP:plan': 9} Unresolved non-hydrogen planarities: 867 Chain: "M" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 713 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 165} Link IDs: {'PTRANS': 16, 'TRANS': 161} Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 683 Unresolved non-hydrogen angles: 1011 Unresolved non-hydrogen dihedrals: 430 Unresolved non-hydrogen chiralities: 219 Planarities with less than four sites: {'HIS:plan': 2, 'ASP:plan': 12, 'TRP:plan': 5, 'GLU:plan': 11, 'PHE:plan': 3, 'TYR:plan': 4, 'ARG:plan': 18, 'GLN:plan1': 3, 'PHE%COO:plan': 1} Unresolved non-hydrogen planarities: 316 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, N, O, P, Q, R, S, T, U, V, W, X Time building chain proxies: 3.68, per 1000 atoms: 0.12 Number of scatterers: 29580 At special positions: 0 Unit cell: (170.328, 170.328, 148.896, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 7404 8.00 N 7392 7.00 C 14784 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.61 Conformation dependent library (CDL) restraints added in 2.3 seconds 14592 Ramachandran restraints generated. 7296 Oldfield, 0 Emsley, 7296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 0 Finding SS restraints... Secondary structure from input PDB file: 228 helices and 84 sheets defined 46.1% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 50 through 73 removed outlier: 3.832A pdb=" N GLU A 54 " --> pdb=" O THR A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 88 Processing helix chain 'A' and resid 107 through 123 removed outlier: 4.099A pdb=" N GLY A 111 " --> pdb=" O ASP A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 151 Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 298 through 325 removed outlier: 4.277A pdb=" N ARG A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N LEU A 304 " --> pdb=" O THR A 300 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 317 " --> pdb=" O GLU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 347 removed outlier: 4.163A pdb=" N ASP A 344 " --> pdb=" O GLY A 340 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA A 345 " --> pdb=" O PRO A 341 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLN A 346 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE A 347 " --> pdb=" O ASP A 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 340 through 347' Processing helix chain 'A' and resid 377 through 394 Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 408 through 449 removed outlier: 3.588A pdb=" N PHE A 431 " --> pdb=" O GLN A 427 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS A 435 " --> pdb=" O PHE A 431 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP A 436 " --> pdb=" O GLU A 432 " (cutoff:3.500A) Proline residue: A 444 - end of helix Processing helix chain 'A' and resid 458 through 464 removed outlier: 4.077A pdb=" N PHE A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA A 464 " --> pdb=" O ASP A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 490 removed outlier: 3.527A pdb=" N ASP A 480 " --> pdb=" O ASN A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 503 removed outlier: 4.044A pdb=" N ILE A 498 " --> pdb=" O THR A 494 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS A 499 " --> pdb=" O ARG A 495 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG A 502 " --> pdb=" O ILE A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 523 removed outlier: 3.714A pdb=" N ASP A 522 " --> pdb=" O GLN A 518 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 27 removed outlier: 4.432A pdb=" N ASP M 27 " --> pdb=" O VAL M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 68 Processing helix chain 'M' and resid 112 through 130 removed outlier: 3.724A pdb=" N ARG M 116 " --> pdb=" O THR M 112 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR M 130 " --> pdb=" O GLU M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 167 Processing helix chain 'B' and resid 50 through 73 removed outlier: 3.832A pdb=" N GLU B 54 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 88 Processing helix chain 'B' and resid 107 through 123 removed outlier: 4.099A pdb=" N GLY B 111 " --> pdb=" O ASP B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 151 Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 239 through 241 No H-bonds generated for 'chain 'B' and resid 239 through 241' Processing helix chain 'B' and resid 298 through 325 removed outlier: 4.278A pdb=" N ARG B 303 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU B 304 " --> pdb=" O THR B 300 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 347 removed outlier: 4.163A pdb=" N ASP B 344 " --> pdb=" O GLY B 340 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA B 345 " --> pdb=" O PRO B 341 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLN B 346 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE B 347 " --> pdb=" O ASP B 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 340 through 347' Processing helix chain 'B' and resid 377 through 394 Processing helix chain 'B' and resid 396 through 401 Processing helix chain 'B' and resid 408 through 449 removed outlier: 3.589A pdb=" N PHE B 431 " --> pdb=" O GLN B 427 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS B 435 " --> pdb=" O PHE B 431 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP B 436 " --> pdb=" O GLU B 432 " (cutoff:3.500A) Proline residue: B 444 - end of helix Processing helix chain 'B' and resid 458 through 464 removed outlier: 4.079A pdb=" N PHE B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA B 464 " --> pdb=" O ASP B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 490 removed outlier: 3.527A pdb=" N ASP B 480 " --> pdb=" O ASN B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 503 removed outlier: 4.044A pdb=" N ILE B 498 " --> pdb=" O THR B 494 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS B 499 " --> pdb=" O ARG B 495 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG B 502 " --> pdb=" O ILE B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 523 removed outlier: 3.714A pdb=" N ASP B 522 " --> pdb=" O GLN B 518 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 27 removed outlier: 4.431A pdb=" N ASP N 27 " --> pdb=" O VAL N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 68 Processing helix chain 'N' and resid 112 through 130 removed outlier: 3.725A pdb=" N ARG N 116 " --> pdb=" O THR N 112 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR N 130 " --> pdb=" O GLU N 126 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 167 Processing helix chain 'C' and resid 50 through 73 removed outlier: 3.831A pdb=" N GLU C 54 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 88 Processing helix chain 'C' and resid 107 through 123 removed outlier: 4.100A pdb=" N GLY C 111 " --> pdb=" O ASP C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 151 Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 239 through 241 No H-bonds generated for 'chain 'C' and resid 239 through 241' Processing helix chain 'C' and resid 298 through 325 removed outlier: 4.278A pdb=" N ARG C 303 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU C 304 " --> pdb=" O THR C 300 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR C 317 " --> pdb=" O GLU C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 347 removed outlier: 4.163A pdb=" N ASP C 344 " --> pdb=" O GLY C 340 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA C 345 " --> pdb=" O PRO C 341 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLN C 346 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE C 347 " --> pdb=" O ASP C 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 340 through 347' Processing helix chain 'C' and resid 377 through 394 Processing helix chain 'C' and resid 396 through 401 Processing helix chain 'C' and resid 408 through 449 removed outlier: 3.587A pdb=" N PHE C 431 " --> pdb=" O GLN C 427 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS C 435 " --> pdb=" O PHE C 431 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASP C 436 " --> pdb=" O GLU C 432 " (cutoff:3.500A) Proline residue: C 444 - end of helix Processing helix chain 'C' and resid 458 through 464 removed outlier: 4.077A pdb=" N PHE C 462 " --> pdb=" O LYS C 458 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA C 464 " --> pdb=" O ASP C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 490 removed outlier: 3.527A pdb=" N ASP C 480 " --> pdb=" O ASN C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 503 removed outlier: 4.044A pdb=" N ILE C 498 " --> pdb=" O THR C 494 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS C 499 " --> pdb=" O ARG C 495 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG C 502 " --> pdb=" O ILE C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 523 removed outlier: 3.714A pdb=" N ASP C 522 " --> pdb=" O GLN C 518 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 27 removed outlier: 4.432A pdb=" N ASP O 27 " --> pdb=" O VAL O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 68 Processing helix chain 'O' and resid 112 through 130 removed outlier: 3.725A pdb=" N ARG O 116 " --> pdb=" O THR O 112 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR O 130 " --> pdb=" O GLU O 126 " (cutoff:3.500A) Processing helix chain 'O' and resid 147 through 167 Processing helix chain 'D' and resid 50 through 73 removed outlier: 3.832A pdb=" N GLU D 54 " --> pdb=" O THR D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 88 Processing helix chain 'D' and resid 107 through 123 removed outlier: 4.100A pdb=" N GLY D 111 " --> pdb=" O ASP D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 151 Processing helix chain 'D' and resid 221 through 225 Processing helix chain 'D' and resid 239 through 241 No H-bonds generated for 'chain 'D' and resid 239 through 241' Processing helix chain 'D' and resid 298 through 325 removed outlier: 4.277A pdb=" N ARG D 303 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU D 304 " --> pdb=" O THR D 300 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR D 317 " --> pdb=" O GLU D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 347 removed outlier: 4.163A pdb=" N ASP D 344 " --> pdb=" O GLY D 340 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA D 345 " --> pdb=" O PRO D 341 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLN D 346 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE D 347 " --> pdb=" O ASP D 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 340 through 347' Processing helix chain 'D' and resid 377 through 394 Processing helix chain 'D' and resid 396 through 401 Processing helix chain 'D' and resid 408 through 449 removed outlier: 3.587A pdb=" N PHE D 431 " --> pdb=" O GLN D 427 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS D 435 " --> pdb=" O PHE D 431 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP D 436 " --> pdb=" O GLU D 432 " (cutoff:3.500A) Proline residue: D 444 - end of helix Processing helix chain 'D' and resid 458 through 464 removed outlier: 4.077A pdb=" N PHE D 462 " --> pdb=" O LYS D 458 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA D 464 " --> pdb=" O ASP D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 490 removed outlier: 3.526A pdb=" N ASP D 480 " --> pdb=" O ASN D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 503 removed outlier: 4.044A pdb=" N ILE D 498 " --> pdb=" O THR D 494 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS D 499 " --> pdb=" O ARG D 495 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG D 502 " --> pdb=" O ILE D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 523 removed outlier: 3.714A pdb=" N ASP D 522 " --> pdb=" O GLN D 518 " (cutoff:3.500A) Processing helix chain 'P' and resid 23 through 27 removed outlier: 4.432A pdb=" N ASP P 27 " --> pdb=" O VAL P 24 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 68 Processing helix chain 'P' and resid 112 through 130 removed outlier: 3.724A pdb=" N ARG P 116 " --> pdb=" O THR P 112 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR P 130 " --> pdb=" O GLU P 126 " (cutoff:3.500A) Processing helix chain 'P' and resid 147 through 167 Processing helix chain 'E' and resid 50 through 73 removed outlier: 3.831A pdb=" N GLU E 54 " --> pdb=" O THR E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 88 Processing helix chain 'E' and resid 107 through 123 removed outlier: 4.099A pdb=" N GLY E 111 " --> pdb=" O ASP E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 151 Processing helix chain 'E' and resid 221 through 225 Processing helix chain 'E' and resid 239 through 241 No H-bonds generated for 'chain 'E' and resid 239 through 241' Processing helix chain 'E' and resid 298 through 325 removed outlier: 4.278A pdb=" N ARG E 303 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU E 304 " --> pdb=" O THR E 300 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR E 317 " --> pdb=" O GLU E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 347 removed outlier: 4.164A pdb=" N ASP E 344 " --> pdb=" O GLY E 340 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA E 345 " --> pdb=" O PRO E 341 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLN E 346 " --> pdb=" O GLU E 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE E 347 " --> pdb=" O ASP E 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 340 through 347' Processing helix chain 'E' and resid 377 through 394 Processing helix chain 'E' and resid 396 through 401 Processing helix chain 'E' and resid 408 through 449 removed outlier: 3.587A pdb=" N PHE E 431 " --> pdb=" O GLN E 427 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS E 435 " --> pdb=" O PHE E 431 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP E 436 " --> pdb=" O GLU E 432 " (cutoff:3.500A) Proline residue: E 444 - end of helix Processing helix chain 'E' and resid 458 through 464 removed outlier: 4.078A pdb=" N PHE E 462 " --> pdb=" O LYS E 458 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA E 464 " --> pdb=" O ASP E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 490 removed outlier: 3.527A pdb=" N ASP E 480 " --> pdb=" O ASN E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 503 removed outlier: 4.044A pdb=" N ILE E 498 " --> pdb=" O THR E 494 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS E 499 " --> pdb=" O ARG E 495 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG E 502 " --> pdb=" O ILE E 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 523 removed outlier: 3.715A pdb=" N ASP E 522 " --> pdb=" O GLN E 518 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 27 removed outlier: 4.432A pdb=" N ASP Q 27 " --> pdb=" O VAL Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 68 Processing helix chain 'Q' and resid 112 through 130 removed outlier: 3.724A pdb=" N ARG Q 116 " --> pdb=" O THR Q 112 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR Q 130 " --> pdb=" O GLU Q 126 " (cutoff:3.500A) Processing helix chain 'Q' and resid 147 through 167 Processing helix chain 'F' and resid 50 through 73 removed outlier: 3.832A pdb=" N GLU F 54 " --> pdb=" O THR F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 88 Processing helix chain 'F' and resid 107 through 123 removed outlier: 4.099A pdb=" N GLY F 111 " --> pdb=" O ASP F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 151 Processing helix chain 'F' and resid 221 through 225 Processing helix chain 'F' and resid 239 through 241 No H-bonds generated for 'chain 'F' and resid 239 through 241' Processing helix chain 'F' and resid 298 through 325 removed outlier: 4.277A pdb=" N ARG F 303 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU F 304 " --> pdb=" O THR F 300 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR F 317 " --> pdb=" O GLU F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 347 removed outlier: 4.163A pdb=" N ASP F 344 " --> pdb=" O GLY F 340 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA F 345 " --> pdb=" O PRO F 341 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLN F 346 " --> pdb=" O GLU F 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE F 347 " --> pdb=" O ASP F 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 340 through 347' Processing helix chain 'F' and resid 377 through 394 Processing helix chain 'F' and resid 396 through 401 Processing helix chain 'F' and resid 408 through 449 removed outlier: 3.587A pdb=" N PHE F 431 " --> pdb=" O GLN F 427 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS F 435 " --> pdb=" O PHE F 431 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP F 436 " --> pdb=" O GLU F 432 " (cutoff:3.500A) Proline residue: F 444 - end of helix Processing helix chain 'F' and resid 458 through 464 removed outlier: 4.078A pdb=" N PHE F 462 " --> pdb=" O LYS F 458 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA F 464 " --> pdb=" O ASP F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 490 removed outlier: 3.526A pdb=" N ASP F 480 " --> pdb=" O ASN F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 503 removed outlier: 4.044A pdb=" N ILE F 498 " --> pdb=" O THR F 494 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS F 499 " --> pdb=" O ARG F 495 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG F 502 " --> pdb=" O ILE F 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 505 through 523 removed outlier: 3.715A pdb=" N ASP F 522 " --> pdb=" O GLN F 518 " (cutoff:3.500A) Processing helix chain 'R' and resid 23 through 27 removed outlier: 4.431A pdb=" N ASP R 27 " --> pdb=" O VAL R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 68 Processing helix chain 'R' and resid 112 through 130 removed outlier: 3.724A pdb=" N ARG R 116 " --> pdb=" O THR R 112 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR R 130 " --> pdb=" O GLU R 126 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 167 Processing helix chain 'G' and resid 50 through 73 removed outlier: 3.831A pdb=" N GLU G 54 " --> pdb=" O THR G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 88 Processing helix chain 'G' and resid 107 through 123 removed outlier: 4.100A pdb=" N GLY G 111 " --> pdb=" O ASP G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 151 Processing helix chain 'G' and resid 221 through 225 Processing helix chain 'G' and resid 239 through 241 No H-bonds generated for 'chain 'G' and resid 239 through 241' Processing helix chain 'G' and resid 298 through 325 removed outlier: 4.278A pdb=" N ARG G 303 " --> pdb=" O ALA G 299 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU G 304 " --> pdb=" O THR G 300 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR G 317 " --> pdb=" O GLU G 313 " (cutoff:3.500A) Processing helix chain 'G' and resid 340 through 347 removed outlier: 4.163A pdb=" N ASP G 344 " --> pdb=" O GLY G 340 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA G 345 " --> pdb=" O PRO G 341 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLN G 346 " --> pdb=" O GLU G 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE G 347 " --> pdb=" O ASP G 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 340 through 347' Processing helix chain 'G' and resid 377 through 394 Processing helix chain 'G' and resid 396 through 401 Processing helix chain 'G' and resid 408 through 449 removed outlier: 3.587A pdb=" N PHE G 431 " --> pdb=" O GLN G 427 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS G 435 " --> pdb=" O PHE G 431 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP G 436 " --> pdb=" O GLU G 432 " (cutoff:3.500A) Proline residue: G 444 - end of helix Processing helix chain 'G' and resid 458 through 464 removed outlier: 4.078A pdb=" N PHE G 462 " --> pdb=" O LYS G 458 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA G 464 " --> pdb=" O ASP G 460 " (cutoff:3.500A) Processing helix chain 'G' and resid 476 through 490 removed outlier: 3.527A pdb=" N ASP G 480 " --> pdb=" O ASN G 476 " (cutoff:3.500A) Processing helix chain 'G' and resid 494 through 503 removed outlier: 4.044A pdb=" N ILE G 498 " --> pdb=" O THR G 494 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS G 499 " --> pdb=" O ARG G 495 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG G 502 " --> pdb=" O ILE G 498 " (cutoff:3.500A) Processing helix chain 'G' and resid 505 through 523 removed outlier: 3.715A pdb=" N ASP G 522 " --> pdb=" O GLN G 518 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 27 removed outlier: 4.432A pdb=" N ASP S 27 " --> pdb=" O VAL S 24 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 68 Processing helix chain 'S' and resid 112 through 130 removed outlier: 3.725A pdb=" N ARG S 116 " --> pdb=" O THR S 112 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR S 130 " --> pdb=" O GLU S 126 " (cutoff:3.500A) Processing helix chain 'S' and resid 147 through 167 Processing helix chain 'H' and resid 50 through 73 removed outlier: 3.832A pdb=" N GLU H 54 " --> pdb=" O THR H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 88 Processing helix chain 'H' and resid 107 through 123 removed outlier: 4.099A pdb=" N GLY H 111 " --> pdb=" O ASP H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 151 Processing helix chain 'H' and resid 221 through 225 Processing helix chain 'H' and resid 239 through 241 No H-bonds generated for 'chain 'H' and resid 239 through 241' Processing helix chain 'H' and resid 298 through 325 removed outlier: 4.277A pdb=" N ARG H 303 " --> pdb=" O ALA H 299 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU H 304 " --> pdb=" O THR H 300 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR H 317 " --> pdb=" O GLU H 313 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 347 removed outlier: 4.163A pdb=" N ASP H 344 " --> pdb=" O GLY H 340 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA H 345 " --> pdb=" O PRO H 341 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLN H 346 " --> pdb=" O GLU H 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE H 347 " --> pdb=" O ASP H 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 340 through 347' Processing helix chain 'H' and resid 377 through 394 Processing helix chain 'H' and resid 396 through 401 Processing helix chain 'H' and resid 408 through 449 removed outlier: 3.589A pdb=" N PHE H 431 " --> pdb=" O GLN H 427 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS H 435 " --> pdb=" O PHE H 431 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP H 436 " --> pdb=" O GLU H 432 " (cutoff:3.500A) Proline residue: H 444 - end of helix Processing helix chain 'H' and resid 458 through 464 removed outlier: 4.078A pdb=" N PHE H 462 " --> pdb=" O LYS H 458 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA H 464 " --> pdb=" O ASP H 460 " (cutoff:3.500A) Processing helix chain 'H' and resid 476 through 490 removed outlier: 3.526A pdb=" N ASP H 480 " --> pdb=" O ASN H 476 " (cutoff:3.500A) Processing helix chain 'H' and resid 494 through 503 removed outlier: 4.044A pdb=" N ILE H 498 " --> pdb=" O THR H 494 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS H 499 " --> pdb=" O ARG H 495 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG H 502 " --> pdb=" O ILE H 498 " (cutoff:3.500A) Processing helix chain 'H' and resid 505 through 523 removed outlier: 3.714A pdb=" N ASP H 522 " --> pdb=" O GLN H 518 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 27 removed outlier: 4.432A pdb=" N ASP T 27 " --> pdb=" O VAL T 24 " (cutoff:3.500A) Processing helix chain 'T' and resid 63 through 68 Processing helix chain 'T' and resid 112 through 130 removed outlier: 3.725A pdb=" N ARG T 116 " --> pdb=" O THR T 112 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR T 130 " --> pdb=" O GLU T 126 " (cutoff:3.500A) Processing helix chain 'T' and resid 147 through 167 Processing helix chain 'I' and resid 50 through 73 removed outlier: 3.831A pdb=" N GLU I 54 " --> pdb=" O THR I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 88 Processing helix chain 'I' and resid 107 through 123 removed outlier: 4.100A pdb=" N GLY I 111 " --> pdb=" O ASP I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 151 Processing helix chain 'I' and resid 221 through 225 Processing helix chain 'I' and resid 239 through 241 No H-bonds generated for 'chain 'I' and resid 239 through 241' Processing helix chain 'I' and resid 298 through 325 removed outlier: 4.278A pdb=" N ARG I 303 " --> pdb=" O ALA I 299 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU I 304 " --> pdb=" O THR I 300 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR I 317 " --> pdb=" O GLU I 313 " (cutoff:3.500A) Processing helix chain 'I' and resid 340 through 347 removed outlier: 4.163A pdb=" N ASP I 344 " --> pdb=" O GLY I 340 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA I 345 " --> pdb=" O PRO I 341 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLN I 346 " --> pdb=" O GLU I 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE I 347 " --> pdb=" O ASP I 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 340 through 347' Processing helix chain 'I' and resid 377 through 394 Processing helix chain 'I' and resid 396 through 401 Processing helix chain 'I' and resid 408 through 449 removed outlier: 3.587A pdb=" N PHE I 431 " --> pdb=" O GLN I 427 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS I 435 " --> pdb=" O PHE I 431 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASP I 436 " --> pdb=" O GLU I 432 " (cutoff:3.500A) Proline residue: I 444 - end of helix Processing helix chain 'I' and resid 458 through 464 removed outlier: 4.077A pdb=" N PHE I 462 " --> pdb=" O LYS I 458 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA I 464 " --> pdb=" O ASP I 460 " (cutoff:3.500A) Processing helix chain 'I' and resid 476 through 490 removed outlier: 3.527A pdb=" N ASP I 480 " --> pdb=" O ASN I 476 " (cutoff:3.500A) Processing helix chain 'I' and resid 494 through 503 removed outlier: 4.044A pdb=" N ILE I 498 " --> pdb=" O THR I 494 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS I 499 " --> pdb=" O ARG I 495 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG I 502 " --> pdb=" O ILE I 498 " (cutoff:3.500A) Processing helix chain 'I' and resid 505 through 523 removed outlier: 3.714A pdb=" N ASP I 522 " --> pdb=" O GLN I 518 " (cutoff:3.500A) Processing helix chain 'U' and resid 23 through 27 removed outlier: 4.432A pdb=" N ASP U 27 " --> pdb=" O VAL U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 63 through 68 Processing helix chain 'U' and resid 112 through 130 removed outlier: 3.725A pdb=" N ARG U 116 " --> pdb=" O THR U 112 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR U 130 " --> pdb=" O GLU U 126 " (cutoff:3.500A) Processing helix chain 'U' and resid 147 through 167 Processing helix chain 'J' and resid 50 through 73 removed outlier: 3.832A pdb=" N GLU J 54 " --> pdb=" O THR J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 88 Processing helix chain 'J' and resid 107 through 123 removed outlier: 4.099A pdb=" N GLY J 111 " --> pdb=" O ASP J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 151 Processing helix chain 'J' and resid 221 through 225 Processing helix chain 'J' and resid 239 through 241 No H-bonds generated for 'chain 'J' and resid 239 through 241' Processing helix chain 'J' and resid 298 through 325 removed outlier: 4.277A pdb=" N ARG J 303 " --> pdb=" O ALA J 299 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU J 304 " --> pdb=" O THR J 300 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR J 317 " --> pdb=" O GLU J 313 " (cutoff:3.500A) Processing helix chain 'J' and resid 340 through 347 removed outlier: 4.163A pdb=" N ASP J 344 " --> pdb=" O GLY J 340 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA J 345 " --> pdb=" O PRO J 341 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLN J 346 " --> pdb=" O GLU J 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE J 347 " --> pdb=" O ASP J 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 340 through 347' Processing helix chain 'J' and resid 377 through 394 Processing helix chain 'J' and resid 396 through 401 Processing helix chain 'J' and resid 408 through 449 removed outlier: 3.587A pdb=" N PHE J 431 " --> pdb=" O GLN J 427 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS J 435 " --> pdb=" O PHE J 431 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP J 436 " --> pdb=" O GLU J 432 " (cutoff:3.500A) Proline residue: J 444 - end of helix Processing helix chain 'J' and resid 458 through 464 removed outlier: 4.077A pdb=" N PHE J 462 " --> pdb=" O LYS J 458 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA J 464 " --> pdb=" O ASP J 460 " (cutoff:3.500A) Processing helix chain 'J' and resid 476 through 490 removed outlier: 3.526A pdb=" N ASP J 480 " --> pdb=" O ASN J 476 " (cutoff:3.500A) Processing helix chain 'J' and resid 494 through 503 removed outlier: 4.044A pdb=" N ILE J 498 " --> pdb=" O THR J 494 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS J 499 " --> pdb=" O ARG J 495 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG J 502 " --> pdb=" O ILE J 498 " (cutoff:3.500A) Processing helix chain 'J' and resid 505 through 523 removed outlier: 3.714A pdb=" N ASP J 522 " --> pdb=" O GLN J 518 " (cutoff:3.500A) Processing helix chain 'V' and resid 23 through 27 removed outlier: 4.432A pdb=" N ASP V 27 " --> pdb=" O VAL V 24 " (cutoff:3.500A) Processing helix chain 'V' and resid 63 through 68 Processing helix chain 'V' and resid 112 through 130 removed outlier: 3.724A pdb=" N ARG V 116 " --> pdb=" O THR V 112 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR V 130 " --> pdb=" O GLU V 126 " (cutoff:3.500A) Processing helix chain 'V' and resid 147 through 167 Processing helix chain 'K' and resid 50 through 73 removed outlier: 3.831A pdb=" N GLU K 54 " --> pdb=" O THR K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 88 Processing helix chain 'K' and resid 107 through 123 removed outlier: 4.099A pdb=" N GLY K 111 " --> pdb=" O ASP K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 151 Processing helix chain 'K' and resid 221 through 225 Processing helix chain 'K' and resid 239 through 241 No H-bonds generated for 'chain 'K' and resid 239 through 241' Processing helix chain 'K' and resid 298 through 325 removed outlier: 4.278A pdb=" N ARG K 303 " --> pdb=" O ALA K 299 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU K 304 " --> pdb=" O THR K 300 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR K 317 " --> pdb=" O GLU K 313 " (cutoff:3.500A) Processing helix chain 'K' and resid 340 through 347 removed outlier: 4.164A pdb=" N ASP K 344 " --> pdb=" O GLY K 340 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA K 345 " --> pdb=" O PRO K 341 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLN K 346 " --> pdb=" O GLU K 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE K 347 " --> pdb=" O ASP K 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 340 through 347' Processing helix chain 'K' and resid 377 through 394 Processing helix chain 'K' and resid 396 through 401 Processing helix chain 'K' and resid 408 through 449 removed outlier: 3.587A pdb=" N PHE K 431 " --> pdb=" O GLN K 427 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS K 435 " --> pdb=" O PHE K 431 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP K 436 " --> pdb=" O GLU K 432 " (cutoff:3.500A) Proline residue: K 444 - end of helix Processing helix chain 'K' and resid 458 through 464 removed outlier: 4.078A pdb=" N PHE K 462 " --> pdb=" O LYS K 458 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA K 464 " --> pdb=" O ASP K 460 " (cutoff:3.500A) Processing helix chain 'K' and resid 476 through 490 removed outlier: 3.527A pdb=" N ASP K 480 " --> pdb=" O ASN K 476 " (cutoff:3.500A) Processing helix chain 'K' and resid 494 through 503 removed outlier: 4.044A pdb=" N ILE K 498 " --> pdb=" O THR K 494 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS K 499 " --> pdb=" O ARG K 495 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG K 502 " --> pdb=" O ILE K 498 " (cutoff:3.500A) Processing helix chain 'K' and resid 505 through 523 removed outlier: 3.715A pdb=" N ASP K 522 " --> pdb=" O GLN K 518 " (cutoff:3.500A) Processing helix chain 'W' and resid 23 through 27 removed outlier: 4.432A pdb=" N ASP W 27 " --> pdb=" O VAL W 24 " (cutoff:3.500A) Processing helix chain 'W' and resid 63 through 68 Processing helix chain 'W' and resid 112 through 130 removed outlier: 3.724A pdb=" N ARG W 116 " --> pdb=" O THR W 112 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR W 130 " --> pdb=" O GLU W 126 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 167 Processing helix chain 'L' and resid 50 through 73 removed outlier: 3.832A pdb=" N GLU L 54 " --> pdb=" O THR L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 88 Processing helix chain 'L' and resid 107 through 123 removed outlier: 4.099A pdb=" N GLY L 111 " --> pdb=" O ASP L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 135 through 151 Processing helix chain 'L' and resid 221 through 225 Processing helix chain 'L' and resid 239 through 241 No H-bonds generated for 'chain 'L' and resid 239 through 241' Processing helix chain 'L' and resid 298 through 325 removed outlier: 4.277A pdb=" N ARG L 303 " --> pdb=" O ALA L 299 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU L 304 " --> pdb=" O THR L 300 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR L 317 " --> pdb=" O GLU L 313 " (cutoff:3.500A) Processing helix chain 'L' and resid 340 through 347 removed outlier: 4.163A pdb=" N ASP L 344 " --> pdb=" O GLY L 340 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA L 345 " --> pdb=" O PRO L 341 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLN L 346 " --> pdb=" O GLU L 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE L 347 " --> pdb=" O ASP L 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 340 through 347' Processing helix chain 'L' and resid 377 through 394 Processing helix chain 'L' and resid 396 through 401 Processing helix chain 'L' and resid 408 through 449 removed outlier: 3.587A pdb=" N PHE L 431 " --> pdb=" O GLN L 427 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS L 435 " --> pdb=" O PHE L 431 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP L 436 " --> pdb=" O GLU L 432 " (cutoff:3.500A) Proline residue: L 444 - end of helix Processing helix chain 'L' and resid 458 through 464 removed outlier: 4.078A pdb=" N PHE L 462 " --> pdb=" O LYS L 458 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA L 464 " --> pdb=" O ASP L 460 " (cutoff:3.500A) Processing helix chain 'L' and resid 476 through 490 removed outlier: 3.526A pdb=" N ASP L 480 " --> pdb=" O ASN L 476 " (cutoff:3.500A) Processing helix chain 'L' and resid 494 through 503 removed outlier: 4.044A pdb=" N ILE L 498 " --> pdb=" O THR L 494 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS L 499 " --> pdb=" O ARG L 495 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG L 502 " --> pdb=" O ILE L 498 " (cutoff:3.500A) Processing helix chain 'L' and resid 505 through 523 removed outlier: 3.715A pdb=" N ASP L 522 " --> pdb=" O GLN L 518 " (cutoff:3.500A) Processing helix chain 'X' and resid 23 through 27 removed outlier: 4.431A pdb=" N ASP X 27 " --> pdb=" O VAL X 24 " (cutoff:3.500A) Processing helix chain 'X' and resid 63 through 68 Processing helix chain 'X' and resid 112 through 130 removed outlier: 3.724A pdb=" N ARG X 116 " --> pdb=" O THR X 112 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR X 130 " --> pdb=" O GLU X 126 " (cutoff:3.500A) Processing helix chain 'X' and resid 147 through 167 Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 96 removed outlier: 3.585A pdb=" N ARG A 94 " --> pdb=" O ARG A 468 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 216 through 220 removed outlier: 4.496A pdb=" N PHE A 154 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 243 through 245 removed outlier: 3.612A pdb=" N ALA A 253 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET A 256 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N SER A 258 " --> pdb=" O ARG A 271 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ARG A 271 " --> pdb=" O SER A 258 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 327 through 328 Processing sheet with id=AA5, first strand: chain 'M' and resid 10 through 12 Processing sheet with id=AA6, first strand: chain 'M' and resid 80 through 83 Processing sheet with id=AA7, first strand: chain 'M' and resid 137 through 138 removed outlier: 3.617A pdb=" N SER M 137 " --> pdb=" O SER N 142 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 141 through 142 removed outlier: 3.593A pdb=" N SER X 137 " --> pdb=" O SER M 142 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 94 through 96 removed outlier: 3.585A pdb=" N ARG B 94 " --> pdb=" O ARG B 468 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 216 through 220 removed outlier: 4.496A pdb=" N PHE B 154 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 243 through 245 removed outlier: 3.612A pdb=" N ALA B 253 " --> pdb=" O GLU B 244 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET B 256 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N SER B 258 " --> pdb=" O ARG B 271 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ARG B 271 " --> pdb=" O SER B 258 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 327 through 328 Processing sheet with id=AB4, first strand: chain 'N' and resid 10 through 12 Processing sheet with id=AB5, first strand: chain 'N' and resid 80 through 83 Processing sheet with id=AB6, first strand: chain 'N' and resid 137 through 138 removed outlier: 3.588A pdb=" N SER N 137 " --> pdb=" O SER O 142 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 94 through 96 removed outlier: 3.586A pdb=" N ARG C 94 " --> pdb=" O ARG C 468 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 216 through 220 removed outlier: 4.496A pdb=" N PHE C 154 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 243 through 245 removed outlier: 3.613A pdb=" N ALA C 253 " --> pdb=" O GLU C 244 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET C 256 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N SER C 258 " --> pdb=" O ARG C 271 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ARG C 271 " --> pdb=" O SER C 258 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 327 through 328 Processing sheet with id=AC2, first strand: chain 'O' and resid 10 through 12 Processing sheet with id=AC3, first strand: chain 'O' and resid 80 through 83 Processing sheet with id=AC4, first strand: chain 'O' and resid 137 through 138 removed outlier: 3.596A pdb=" N SER O 137 " --> pdb=" O SER P 142 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 94 through 96 removed outlier: 3.585A pdb=" N ARG D 94 " --> pdb=" O ARG D 468 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 216 through 220 removed outlier: 4.495A pdb=" N PHE D 154 " --> pdb=" O ILE D 220 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 243 through 245 removed outlier: 3.612A pdb=" N ALA D 253 " --> pdb=" O GLU D 244 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET D 256 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N SER D 258 " --> pdb=" O ARG D 271 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ARG D 271 " --> pdb=" O SER D 258 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 327 through 328 Processing sheet with id=AC9, first strand: chain 'P' and resid 10 through 12 Processing sheet with id=AD1, first strand: chain 'P' and resid 80 through 83 Processing sheet with id=AD2, first strand: chain 'P' and resid 137 through 138 removed outlier: 3.597A pdb=" N SER P 137 " --> pdb=" O SER Q 142 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 94 through 96 removed outlier: 3.585A pdb=" N ARG E 94 " --> pdb=" O ARG E 468 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 216 through 220 removed outlier: 4.496A pdb=" N PHE E 154 " --> pdb=" O ILE E 220 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 243 through 245 removed outlier: 3.612A pdb=" N ALA E 253 " --> pdb=" O GLU E 244 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET E 256 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N SER E 258 " --> pdb=" O ARG E 271 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ARG E 271 " --> pdb=" O SER E 258 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 327 through 328 Processing sheet with id=AD7, first strand: chain 'Q' and resid 10 through 12 Processing sheet with id=AD8, first strand: chain 'Q' and resid 80 through 83 Processing sheet with id=AD9, first strand: chain 'Q' and resid 137 through 138 removed outlier: 3.595A pdb=" N SER Q 137 " --> pdb=" O SER R 142 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 94 through 96 removed outlier: 3.585A pdb=" N ARG F 94 " --> pdb=" O ARG F 468 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 216 through 220 removed outlier: 4.495A pdb=" N PHE F 154 " --> pdb=" O ILE F 220 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 243 through 245 removed outlier: 3.612A pdb=" N ALA F 253 " --> pdb=" O GLU F 244 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET F 256 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N SER F 258 " --> pdb=" O ARG F 271 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ARG F 271 " --> pdb=" O SER F 258 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 327 through 328 Processing sheet with id=AE5, first strand: chain 'R' and resid 10 through 12 Processing sheet with id=AE6, first strand: chain 'R' and resid 80 through 83 Processing sheet with id=AE7, first strand: chain 'R' and resid 137 through 138 removed outlier: 3.596A pdb=" N SER R 137 " --> pdb=" O SER S 142 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 94 through 96 removed outlier: 3.585A pdb=" N ARG G 94 " --> pdb=" O ARG G 468 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 216 through 220 removed outlier: 4.495A pdb=" N PHE G 154 " --> pdb=" O ILE G 220 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 243 through 245 removed outlier: 3.612A pdb=" N ALA G 253 " --> pdb=" O GLU G 244 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET G 256 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N SER G 258 " --> pdb=" O ARG G 271 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ARG G 271 " --> pdb=" O SER G 258 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 327 through 328 Processing sheet with id=AF3, first strand: chain 'S' and resid 10 through 12 Processing sheet with id=AF4, first strand: chain 'S' and resid 80 through 83 Processing sheet with id=AF5, first strand: chain 'S' and resid 137 through 138 removed outlier: 3.596A pdb=" N SER S 137 " --> pdb=" O SER T 142 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 94 through 96 removed outlier: 3.585A pdb=" N ARG H 94 " --> pdb=" O ARG H 468 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 216 through 220 removed outlier: 4.495A pdb=" N PHE H 154 " --> pdb=" O ILE H 220 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 243 through 245 removed outlier: 3.612A pdb=" N ALA H 253 " --> pdb=" O GLU H 244 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET H 256 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N SER H 258 " --> pdb=" O ARG H 271 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ARG H 271 " --> pdb=" O SER H 258 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 327 through 328 Processing sheet with id=AG1, first strand: chain 'T' and resid 10 through 12 Processing sheet with id=AG2, first strand: chain 'T' and resid 80 through 83 Processing sheet with id=AG3, first strand: chain 'T' and resid 137 through 138 removed outlier: 3.596A pdb=" N SER T 137 " --> pdb=" O SER U 142 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 94 through 96 removed outlier: 3.586A pdb=" N ARG I 94 " --> pdb=" O ARG I 468 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 216 through 220 removed outlier: 4.496A pdb=" N PHE I 154 " --> pdb=" O ILE I 220 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 243 through 245 removed outlier: 3.613A pdb=" N ALA I 253 " --> pdb=" O GLU I 244 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET I 256 " --> pdb=" O LEU I 273 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N SER I 258 " --> pdb=" O ARG I 271 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ARG I 271 " --> pdb=" O SER I 258 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 327 through 328 Processing sheet with id=AG8, first strand: chain 'U' and resid 10 through 12 Processing sheet with id=AG9, first strand: chain 'U' and resid 80 through 83 Processing sheet with id=AH1, first strand: chain 'U' and resid 137 through 138 removed outlier: 3.596A pdb=" N SER U 137 " --> pdb=" O SER V 142 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 94 through 96 removed outlier: 3.585A pdb=" N ARG J 94 " --> pdb=" O ARG J 468 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 216 through 220 removed outlier: 4.495A pdb=" N PHE J 154 " --> pdb=" O ILE J 220 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'J' and resid 243 through 245 removed outlier: 3.612A pdb=" N ALA J 253 " --> pdb=" O GLU J 244 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET J 256 " --> pdb=" O LEU J 273 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N SER J 258 " --> pdb=" O ARG J 271 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ARG J 271 " --> pdb=" O SER J 258 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'J' and resid 327 through 328 Processing sheet with id=AH6, first strand: chain 'V' and resid 10 through 12 Processing sheet with id=AH7, first strand: chain 'V' and resid 80 through 83 Processing sheet with id=AH8, first strand: chain 'V' and resid 137 through 138 removed outlier: 3.597A pdb=" N SER V 137 " --> pdb=" O SER W 142 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'K' and resid 94 through 96 removed outlier: 3.585A pdb=" N ARG K 94 " --> pdb=" O ARG K 468 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'K' and resid 216 through 220 removed outlier: 4.496A pdb=" N PHE K 154 " --> pdb=" O ILE K 220 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'K' and resid 243 through 245 removed outlier: 3.612A pdb=" N ALA K 253 " --> pdb=" O GLU K 244 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET K 256 " --> pdb=" O LEU K 273 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N SER K 258 " --> pdb=" O ARG K 271 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ARG K 271 " --> pdb=" O SER K 258 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'K' and resid 327 through 328 Processing sheet with id=AI4, first strand: chain 'W' and resid 10 through 12 Processing sheet with id=AI5, first strand: chain 'W' and resid 80 through 83 Processing sheet with id=AI6, first strand: chain 'W' and resid 137 through 138 removed outlier: 3.596A pdb=" N SER W 137 " --> pdb=" O SER X 142 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'L' and resid 94 through 96 removed outlier: 3.585A pdb=" N ARG L 94 " --> pdb=" O ARG L 468 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'L' and resid 216 through 220 removed outlier: 4.495A pdb=" N PHE L 154 " --> pdb=" O ILE L 220 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'L' and resid 243 through 245 removed outlier: 3.612A pdb=" N ALA L 253 " --> pdb=" O GLU L 244 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET L 256 " --> pdb=" O LEU L 273 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N SER L 258 " --> pdb=" O ARG L 271 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ARG L 271 " --> pdb=" O SER L 258 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'L' and resid 327 through 328 Processing sheet with id=AJ2, first strand: chain 'X' and resid 10 through 12 Processing sheet with id=AJ3, first strand: chain 'X' and resid 80 through 83 2604 hydrogen bonds defined for protein. 7488 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: 7.57 Time building geometry restraints manager: 4.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.22: 1615 1.22 - 1.31: 5849 1.31 - 1.39: 7296 1.39 - 1.48: 7403 1.48 - 1.57: 7369 Bond restraints: 29532 Sorted by residual: bond pdb=" C ILE E 147 " pdb=" O ILE E 147 " ideal model delta sigma weight residual 1.237 1.137 0.100 1.13e-02 7.83e+03 7.85e+01 bond pdb=" C ILE K 147 " pdb=" O ILE K 147 " ideal model delta sigma weight residual 1.237 1.137 0.100 1.13e-02 7.83e+03 7.85e+01 bond pdb=" C ILE C 147 " pdb=" O ILE C 147 " ideal model delta sigma weight residual 1.237 1.137 0.100 1.13e-02 7.83e+03 7.84e+01 bond pdb=" C ILE I 147 " pdb=" O ILE I 147 " ideal model delta sigma weight residual 1.237 1.137 0.100 1.13e-02 7.83e+03 7.84e+01 bond pdb=" C ILE G 147 " pdb=" O ILE G 147 " ideal model delta sigma weight residual 1.237 1.137 0.100 1.13e-02 7.83e+03 7.80e+01 ... (remaining 29527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 31652 2.67 - 5.34: 3866 5.34 - 8.02: 902 8.02 - 10.69: 328 10.69 - 13.36: 92 Bond angle restraints: 36840 Sorted by residual: angle pdb=" N ILE P 143 " pdb=" CA ILE P 143 " pdb=" C ILE P 143 " ideal model delta sigma weight residual 110.72 123.10 -12.38 1.01e+00 9.80e-01 1.50e+02 angle pdb=" N ILE V 143 " pdb=" CA ILE V 143 " pdb=" C ILE V 143 " ideal model delta sigma weight residual 110.72 123.08 -12.36 1.01e+00 9.80e-01 1.50e+02 angle pdb=" N ILE X 143 " pdb=" CA ILE X 143 " pdb=" C ILE X 143 " ideal model delta sigma weight residual 110.72 123.08 -12.36 1.01e+00 9.80e-01 1.50e+02 angle pdb=" N ILE R 143 " pdb=" CA ILE R 143 " pdb=" C ILE R 143 " ideal model delta sigma weight residual 110.72 123.08 -12.36 1.01e+00 9.80e-01 1.50e+02 angle pdb=" N ILE W 143 " pdb=" CA ILE W 143 " pdb=" C ILE W 143 " ideal model delta sigma weight residual 110.72 123.07 -12.35 1.01e+00 9.80e-01 1.50e+02 ... (remaining 36835 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 15.90: 7296 15.90 - 31.78: 48 31.78 - 47.67: 0 47.67 - 63.56: 0 63.56 - 79.45: 12 Dihedral angle restraints: 7356 sinusoidal: 12 harmonic: 7344 Sorted by residual: dihedral pdb=" CA PRO E 130 " pdb=" C PRO E 130 " pdb=" N CYS E 131 " pdb=" CA CYS E 131 " ideal model delta harmonic sigma weight residual 180.00 152.02 27.98 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA PRO L 130 " pdb=" C PRO L 130 " pdb=" N CYS L 131 " pdb=" CA CYS L 131 " ideal model delta harmonic sigma weight residual 180.00 152.03 27.97 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA PRO F 130 " pdb=" C PRO F 130 " pdb=" N CYS F 131 " pdb=" CA CYS F 131 " ideal model delta harmonic sigma weight residual 180.00 152.03 27.97 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 7353 not shown) Chirality restraints: 0 Planarity restraints: 7356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE H 147 " -0.026 2.00e-02 2.50e+03 5.04e-02 2.54e+01 pdb=" C ILE H 147 " 0.087 2.00e-02 2.50e+03 pdb=" O ILE H 147 " -0.032 2.00e-02 2.50e+03 pdb=" N ALA H 148 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 147 " 0.026 2.00e-02 2.50e+03 5.04e-02 2.54e+01 pdb=" C ILE E 147 " -0.087 2.00e-02 2.50e+03 pdb=" O ILE E 147 " 0.032 2.00e-02 2.50e+03 pdb=" N ALA E 148 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE K 147 " -0.026 2.00e-02 2.50e+03 5.04e-02 2.54e+01 pdb=" C ILE K 147 " 0.087 2.00e-02 2.50e+03 pdb=" O ILE K 147 " -0.032 2.00e-02 2.50e+03 pdb=" N ALA K 148 " -0.029 2.00e-02 2.50e+03 ... (remaining 7353 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 12788 2.81 - 3.33: 24269 3.33 - 3.85: 35855 3.85 - 4.38: 34622 4.38 - 4.90: 51011 Nonbonded interactions: 158545 Sorted by model distance: nonbonded pdb=" O ASP N 109 " pdb=" O GLU O 41 " model vdw 2.285 3.040 nonbonded pdb=" O GLU M 41 " pdb=" O ASP X 109 " model vdw 2.291 3.040 nonbonded pdb=" O ASP T 109 " pdb=" O GLU U 41 " model vdw 2.296 3.040 nonbonded pdb=" O ASP V 109 " pdb=" O GLU W 41 " model vdw 2.296 3.040 nonbonded pdb=" O ASP P 109 " pdb=" O GLU Q 41 " model vdw 2.296 3.040 ... (remaining 158540 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: 0.21 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } pdb_interpretation.ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.400 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 29.330 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4371 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 : 0.014 0.108 29532 Z= 1.139 Angle : 2.156 13.358 36840 Z= 1.601 Chirality : 0.000 0.000 0 Planarity : 0.008 0.050 7356 Dihedral : 5.493 79.451 7356 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 1.64 % Allowed : 8.39 % Favored : 89.97 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: 0.41 (0.10), residues: 7296 helix: 2.98 (0.09), residues: 2976 sheet: -0.17 (0.18), residues: 804 loop : -2.22 (0.09), residues: 3516 Details of bonding type rmsd/Z covalent geometry : bond 0.01423 / 1.14 (29532) covalent geometry : angle 2.15645 / 1.60 (36840) hydrogen bonds : bond 0.22966 / 18.17 ( 2604) hydrogen bonds : angle 6.84787 / 5.53 ( 7488) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14592 Ramachandran restraints generated. 7296 Oldfield, 0 Emsley, 7296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14592 Ramachandran restraints generated. 7296 Oldfield, 0 Emsley, 7296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.070 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0101 time to fit residues: 0.3098 Evaluate side-chains 12 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.071 Evaluate side-chains 1 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.029 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0044 time to fit residues: 0.0517 Evaluate side-chains 1 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 394 optimal weight: 40.0000 chunk 430 optimal weight: 40.0000 chunk 41 optimal weight: 50.0000 chunk 265 optimal weight: 40.0000 chunk 523 optimal weight: 9.9990 chunk 497 optimal weight: 50.0000 chunk 414 optimal weight: 50.0000 chunk 310 optimal weight: 50.0000 chunk 488 optimal weight: 50.0000 chunk 366 optimal weight: 0.0030 chunk 597 optimal weight: 0.8980 overall best weight: 18.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.097647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.089065 restraints weight = 8426.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.087605 restraints weight = 18882.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.088150 restraints weight = 17951.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.087999 restraints weight = 16477.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.088048 restraints weight = 14499.972| |-----------------------------------------------------------------------------| r_work (final): 0.3094 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.098471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.085327 restraints weight = 3256.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.082743 restraints weight = 5056.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.082942 restraints weight = 4434.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.082945 restraints weight = 4128.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.083321 restraints weight = 4110.567| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4909 moved from start: 0.7030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29532 Z= 0.267 Angle : 0.715 6.416 36840 Z= 0.444 Chirality : 0.000 0.000 0 Planarity : 0.004 0.020 7356 Dihedral : 6.138 29.268 7356 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 0.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.91 % Favored : 92.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -0.35 (0.10), residues: 7296 helix: 2.39 (0.09), residues: 2880 sheet: -0.69 (0.17), residues: 948 loop : -2.57 (0.10), residues: 3468 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.27 (29532) covalent geometry : angle 0.71481 / 0.44 (36840) hydrogen bonds : bond 0.06256 / 4.95 ( 2604) hydrogen bonds : angle 5.40176 / 4.43 ( 7488) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14592 Ramachandran restraints generated. 7296 Oldfield, 0 Emsley, 7296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14592 Ramachandran restraints generated. 7296 Oldfield, 0 Emsley, 7296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.050 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0088 time to fit residues: 0.2931 Evaluate side-chains 12 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.071 Evaluate side-chains 1 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.029 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0043 time to fit residues: 0.0502 Evaluate side-chains 1 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 33 optimal weight: 40.0000 chunk 248 optimal weight: 50.0000 chunk 499 optimal weight: 50.0000 chunk 618 optimal weight: 50.0000 chunk 325 optimal weight: 30.0000 chunk 569 optimal weight: 50.0000 chunk 201 optimal weight: 30.0000 chunk 0 optimal weight: 50.0000 chunk 44 optimal weight: 50.0000 chunk 63 optimal weight: 40.0000 chunk 137 optimal weight: 50.0000 overall best weight: 38.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.085050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.076713 restraints weight = 8653.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.076043 restraints weight = 16729.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.076291 restraints weight = 16853.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.076105 restraints weight = 13971.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.076153 restraints weight = 15244.975| |-----------------------------------------------------------------------------| r_work (final): 0.2869 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.084272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.071472 restraints weight = 3445.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.071470 restraints weight = 3435.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.071470 restraints weight = 3454.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.071470 restraints weight = 3454.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.071470 restraints weight = 3454.739| |-----------------------------------------------------------------------------| r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5019 moved from start: 0.9089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 29532 Z= 0.365 Angle : 0.852 8.151 36840 Z= 0.546 Chirality : 0.000 0.000 0 Planarity : 0.004 0.018 7356 Dihedral : 6.626 25.023 7356 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.49 % Allowed : 11.68 % Favored : 87.83 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -1.01 (0.10), residues: 7296 helix: 1.81 (0.09), residues: 2892 sheet: -1.11 (0.18), residues: 888 loop : -2.88 (0.10), residues: 3516 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.36 (29532) covalent geometry : angle 0.85198 / 0.55 (36840) hydrogen bonds : bond 0.08257 / 6.57 ( 2604) hydrogen bonds : angle 6.05474 / 4.95 ( 7488) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14592 Ramachandran restraints generated. 7296 Oldfield, 0 Emsley, 7296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14592 Ramachandran restraints generated. 7296 Oldfield, 0 Emsley, 7296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.071 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0088 time to fit residues: 0.2941 Evaluate side-chains 12 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.061 Evaluate side-chains 1 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.030 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0044 time to fit residues: 0.0525 Evaluate side-chains 1 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 353 optimal weight: 50.0000 chunk 339 optimal weight: 50.0000 chunk 173 optimal weight: 50.0000 chunk 91 optimal weight: 50.0000 chunk 573 optimal weight: 40.0000 chunk 282 optimal weight: 50.0000 chunk 469 optimal weight: 50.0000 chunk 6 optimal weight: 50.0000 chunk 635 optimal weight: 40.0000 chunk 640 optimal weight: 30.0000 chunk 163 optimal weight: 0.9990 overall best weight: 32.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.085649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.078129 restraints weight = 8822.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.078120 restraints weight = 16392.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.077413 restraints weight = 15387.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.077522 restraints weight = 16283.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.077137 restraints weight = 15399.251| |-----------------------------------------------------------------------------| r_work (final): 0.2896 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.082630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.070613 restraints weight = 3462.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.070613 restraints weight = 3437.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.070613 restraints weight = 3436.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.070613 restraints weight = 3436.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.070613 restraints weight = 3436.493| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5010 moved from start: 0.9898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 29532 Z= 0.289 Angle : 0.694 6.520 36840 Z= 0.438 Chirality : 0.000 0.000 0 Planarity : 0.004 0.017 7356 Dihedral : 6.325 25.638 7356 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.66 % Allowed : 11.68 % Favored : 87.66 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -1.36 (0.10), residues: 7296 helix: 1.62 (0.09), residues: 2892 sheet: -1.59 (0.18), residues: 900 loop : -3.09 (0.10), residues: 3504 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.29 (29532) covalent geometry : angle 0.69351 / 0.44 (36840) hydrogen bonds : bond 0.06401 / 5.08 ( 2604) hydrogen bonds : angle 5.74241 / 4.71 ( 7488) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14592 Ramachandran restraints generated. 7296 Oldfield, 0 Emsley, 7296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14592 Ramachandran restraints generated. 7296 Oldfield, 0 Emsley, 7296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.068 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0086 time to fit residues: 0.2904 Evaluate side-chains 12 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.072 Evaluate side-chains 1 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.028 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0043 time to fit residues: 0.0504 Evaluate side-chains 1 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 551 optimal weight: 40.0000 chunk 222 optimal weight: 50.0000 chunk 701 optimal weight: 40.0000 chunk 117 optimal weight: 0.2980 chunk 517 optimal weight: 50.0000 chunk 414 optimal weight: 50.0000 chunk 120 optimal weight: 50.0000 chunk 562 optimal weight: 50.0000 chunk 54 optimal weight: 50.0000 chunk 268 optimal weight: 50.0000 chunk 326 optimal weight: 0.0070 overall best weight: 26.0610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.085446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.078112 restraints weight = 8307.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.076705 restraints weight = 18013.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.076585 restraints weight = 20571.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.076065 restraints weight = 21767.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.076098 restraints weight = 21567.571| |-----------------------------------------------------------------------------| r_work (final): 0.2868 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.080877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.069333 restraints weight = 3609.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.069333 restraints weight = 3470.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.069333 restraints weight = 3470.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.069333 restraints weight = 3470.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.069335 restraints weight = 3470.877| |-----------------------------------------------------------------------------| r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5018 moved from start: 1.0316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 29532 Z= 0.238 Angle : 0.620 5.596 36840 Z= 0.391 Chirality : 0.000 0.000 0 Planarity : 0.003 0.016 7356 Dihedral : 5.907 21.973 7356 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.33 % Allowed : 12.17 % Favored : 87.50 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -1.28 (0.10), residues: 7296 helix: 1.70 (0.09), residues: 2904 sheet: -1.24 (0.19), residues: 876 loop : -3.17 (0.10), residues: 3516 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.24 (29532) covalent geometry : angle 0.62043 / 0.39 (36840) hydrogen bonds : bond 0.06262 / 4.98 ( 2604) hydrogen bonds : angle 5.50701 / 4.51 ( 7488) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14592 Ramachandran restraints generated. 7296 Oldfield, 0 Emsley, 7296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14592 Ramachandran restraints generated. 7296 Oldfield, 0 Emsley, 7296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.072 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0082 time to fit residues: 0.2735 Evaluate side-chains 12 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.064 Evaluate side-chains 1 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.028 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0043 time to fit residues: 0.0491 Evaluate side-chains 1 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 594 optimal weight: 50.0000 chunk 533 optimal weight: 50.0000 chunk 621 optimal weight: 40.0000 chunk 455 optimal weight: 50.0000 chunk 539 optimal weight: 40.0000 chunk 111 optimal weight: 30.0000 chunk 407 optimal weight: 0.6980 chunk 384 optimal weight: 50.0000 chunk 299 optimal weight: 40.0000 chunk 340 optimal weight: 50.0000 chunk 452 optimal weight: 40.0000 overall best weight: 30.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.084163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.075924 restraints weight = 8235.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.075109 restraints weight = 16517.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.075343 restraints weight = 16698.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.075094 restraints weight = 14742.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.075301 restraints weight = 13897.469| |-----------------------------------------------------------------------------| r_work (final): 0.2851 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.080634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.069651 restraints weight = 3719.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.069650 restraints weight = 3710.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.069650 restraints weight = 3709.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.069650 restraints weight = 3709.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.069650 restraints weight = 3709.288| |-----------------------------------------------------------------------------| r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5052 moved from start: 1.0699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 29532 Z= 0.273 Angle : 0.666 5.788 36840 Z= 0.422 Chirality : 0.000 0.000 0 Planarity : 0.004 0.017 7356 Dihedral : 6.287 23.541 7356 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.49 % Allowed : 13.65 % Favored : 85.86 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -1.70 (0.10), residues: 7296 helix: 1.38 (0.09), residues: 2904 sheet: -1.63 (0.20), residues: 816 loop : -3.36 (0.09), residues: 3576 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.27 (29532) covalent geometry : angle 0.66590 / 0.42 (36840) hydrogen bonds : bond 0.06643 / 5.28 ( 2604) hydrogen bonds : angle 5.86872 / 4.81 ( 7488) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14592 Ramachandran restraints generated. 7296 Oldfield, 0 Emsley, 7296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14592 Ramachandran restraints generated. 7296 Oldfield, 0 Emsley, 7296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.091 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0092 time to fit residues: 0.3198 Evaluate side-chains 12 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.086 Evaluate side-chains 1 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.029 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0045 time to fit residues: 0.0512 Evaluate side-chains 1 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 129 optimal weight: 50.0000 chunk 34 optimal weight: 40.0000 chunk 625 optimal weight: 30.0000 chunk 107 optimal weight: 30.0000 chunk 403 optimal weight: 40.0000 chunk 255 optimal weight: 40.0000 chunk 2 optimal weight: 50.0000 chunk 303 optimal weight: 30.0000 chunk 236 optimal weight: 40.0000 chunk 319 optimal weight: 40.0000 chunk 102 optimal weight: 50.0000 overall best weight: 34.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.083176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.074947 restraints weight = 8301.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.074235 restraints weight = 15811.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.074487 restraints weight = 16324.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.074272 restraints weight = 13868.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.074422 restraints weight = 13507.993| |-----------------------------------------------------------------------------| r_work (final): 0.2842 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.079499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.068745 restraints weight = 3595.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.068740 restraints weight = 3684.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.068740 restraints weight = 3632.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.068740 restraints weight = 3632.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.068740 restraints weight = 3632.843| |-----------------------------------------------------------------------------| r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5043 moved from start: 1.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 29532 Z= 0.303 Angle : 0.706 5.858 36840 Z= 0.450 Chirality : 0.000 0.000 0 Planarity : 0.004 0.017 7356 Dihedral : 6.435 24.169 7356 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.33 % Allowed : 15.13 % Favored : 84.54 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -1.84 (0.10), residues: 7296 helix: 1.34 (0.09), residues: 2832 sheet: -1.48 (0.20), residues: 888 loop : -3.52 (0.09), residues: 3576 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.30 (29532) covalent geometry : angle 0.70592 / 0.45 (36840) hydrogen bonds : bond 0.06835 / 5.44 ( 2604) hydrogen bonds : angle 6.02673 / 4.93 ( 7488) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14592 Ramachandran restraints generated. 7296 Oldfield, 0 Emsley, 7296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14592 Ramachandran restraints generated. 7296 Oldfield, 0 Emsley, 7296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.071 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0089 time to fit residues: 0.2931 Evaluate side-chains 12 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.071 Evaluate side-chains 1 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.029 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0052 time to fit residues: 0.0565 Evaluate side-chains 1 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 318 optimal weight: 40.0000 chunk 226 optimal weight: 50.0000 chunk 485 optimal weight: 50.0000 chunk 597 optimal weight: 0.0170 chunk 330 optimal weight: 50.0000 chunk 289 optimal weight: 0.9980 chunk 158 optimal weight: 8.9990 chunk 73 optimal weight: 0.7980 chunk 399 optimal weight: 60.0000 chunk 11 optimal weight: 50.0000 chunk 541 optimal weight: 50.0000 overall best weight: 10.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.087893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.080190 restraints weight = 8184.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.078838 restraints weight = 17101.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.079195 restraints weight = 17913.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.079053 restraints weight = 15483.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.079067 restraints weight = 13997.072| |-----------------------------------------------------------------------------| r_work (final): 0.2922 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.083212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.072075 restraints weight = 3729.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.072075 restraints weight = 3500.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.072075 restraints weight = 3500.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.072075 restraints weight = 3500.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.072075 restraints weight = 3500.940| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4996 moved from start: 1.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 29532 Z= 0.124 Angle : 0.472 6.234 36840 Z= 0.283 Chirality : 0.000 0.000 0 Planarity : 0.002 0.014 7356 Dihedral : 4.989 29.689 7356 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 0.64 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.38 % Favored : 90.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -0.67 (0.11), residues: 7296 helix: 2.64 (0.10), residues: 2916 sheet: -1.58 (0.19), residues: 876 loop : -3.08 (0.10), residues: 3504 Details of bonding type rmsd/Z covalent geometry : bond 0.00162 / 0.12 (29532) covalent geometry : angle 0.47166 / 0.28 (36840) hydrogen bonds : bond 0.04847 / 3.84 ( 2604) hydrogen bonds : angle 4.80514 / 3.94 ( 7488) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14592 Ramachandran restraints generated. 7296 Oldfield, 0 Emsley, 7296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14592 Ramachandran restraints generated. 7296 Oldfield, 0 Emsley, 7296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.071 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0087 time to fit residues: 0.2899 Evaluate side-chains 12 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.070 Evaluate side-chains 1 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.030 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0047 time to fit residues: 0.0531 Evaluate side-chains 1 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 204 optimal weight: 50.0000 chunk 333 optimal weight: 30.0000 chunk 590 optimal weight: 30.0000 chunk 519 optimal weight: 50.0000 chunk 250 optimal weight: 50.0000 chunk 259 optimal weight: 50.0000 chunk 281 optimal weight: 40.0000 chunk 320 optimal weight: 50.0000 chunk 476 optimal weight: 50.0000 chunk 11 optimal weight: 50.0000 chunk 576 optimal weight: 50.0000 overall best weight: 40.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.082223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.074570 restraints weight = 8475.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.073794 restraints weight = 17989.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.074015 restraints weight = 17581.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.073562 restraints weight = 18422.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.073783 restraints weight = 15932.766| |-----------------------------------------------------------------------------| r_work (final): 0.2829 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.078210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.067484 restraints weight = 3652.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.067484 restraints weight = 3521.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.067484 restraints weight = 3521.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.067484 restraints weight = 3521.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.067484 restraints weight = 3521.549| |-----------------------------------------------------------------------------| r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5045 moved from start: 1.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 29532 Z= 0.344 Angle : 0.745 6.592 36840 Z= 0.480 Chirality : 0.000 0.000 0 Planarity : 0.004 0.018 7356 Dihedral : 6.538 25.955 7356 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.33 % Allowed : 16.28 % Favored : 83.39 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -1.84 (0.10), residues: 7296 helix: 1.37 (0.09), residues: 2832 sheet: -1.62 (0.19), residues: 900 loop : -3.51 (0.09), residues: 3564 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.34 (29532) covalent geometry : angle 0.74475 / 0.48 (36840) hydrogen bonds : bond 0.07349 / 5.85 ( 2604) hydrogen bonds : angle 6.22772 / 5.09 ( 7488) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14592 Ramachandran restraints generated. 7296 Oldfield, 0 Emsley, 7296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14592 Ramachandran restraints generated. 7296 Oldfield, 0 Emsley, 7296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.070 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0089 time to fit residues: 0.2974 Evaluate side-chains 12 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.071 Evaluate side-chains 1 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.031 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0048 time to fit residues: 0.0580 Evaluate side-chains 1 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 47 optimal weight: 50.0000 chunk 460 optimal weight: 50.0000 chunk 593 optimal weight: 50.0000 chunk 145 optimal weight: 40.0000 chunk 645 optimal weight: 40.0000 chunk 351 optimal weight: 50.0000 chunk 587 optimal weight: 40.0000 chunk 48 optimal weight: 8.9990 chunk 552 optimal weight: 0.0060 chunk 523 optimal weight: 0.0170 chunk 152 optimal weight: 40.0000 overall best weight: 17.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.085726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.077916 restraints weight = 8462.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.077507 restraints weight = 16907.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.077357 restraints weight = 16940.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.077200 restraints weight = 16566.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.077381 restraints weight = 14613.811| |-----------------------------------------------------------------------------| r_work (final): 0.2893 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.081019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.069881 restraints weight = 3654.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.069951 restraints weight = 3415.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.069951 restraints weight = 3290.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.069951 restraints weight = 3290.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.069951 restraints weight = 3290.499| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5026 moved from start: 1.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 29532 Z= 0.173 Angle : 0.530 6.102 36840 Z= 0.325 Chirality : 0.000 0.000 0 Planarity : 0.003 0.016 7356 Dihedral : 5.408 26.247 7356 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.49 % Allowed : 11.02 % Favored : 88.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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 (0.10), residues: 7296 helix: 2.14 (0.10), residues: 2916 sheet: -1.64 (0.20), residues: 828 loop : -3.22 (0.10), residues: 3552 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.17 (29532) covalent geometry : angle 0.53041 / 0.32 (36840) hydrogen bonds : bond 0.05461 / 4.33 ( 2604) hydrogen bonds : angle 5.16011 / 4.23 ( 7488) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14592 Ramachandran restraints generated. 7296 Oldfield, 0 Emsley, 7296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14592 Ramachandran restraints generated. 7296 Oldfield, 0 Emsley, 7296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.086 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0089 time to fit residues: 0.3166 Evaluate side-chains 12 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.074 Evaluate side-chains 1 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.030 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0048 time to fit residues: 0.0530 Evaluate side-chains 1 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 543 optimal weight: 30.0000 chunk 5 optimal weight: 50.0000 chunk 397 optimal weight: 50.0000 chunk 184 optimal weight: 40.0000 chunk 654 optimal weight: 50.0000 chunk 13 optimal weight: 0.4980 chunk 529 optimal weight: 50.0000 chunk 139 optimal weight: 0.7980 chunk 460 optimal weight: 0.0670 chunk 296 optimal weight: 50.0000 chunk 534 optimal weight: 50.0000 overall best weight: 14.2726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.090504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.085866 restraints weight = 8416.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.084013 restraints weight = 11982.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.083849 restraints weight = 16808.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.083777 restraints weight = 17542.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.083747 restraints weight = 15868.428| |-----------------------------------------------------------------------------| r_work (final): 0.2979 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.082882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.071076 restraints weight = 3820.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.071129 restraints weight = 3718.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.071130 restraints weight = 3624.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.071130 restraints weight = 3622.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.071130 restraints weight = 3622.036| |-----------------------------------------------------------------------------| r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5001 moved from start: 1.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 29532 Z= 0.144 Angle : 0.459 5.980 36840 Z= 0.280 Chirality : 0.000 0.000 0 Planarity : 0.002 0.016 7356 Dihedral : 4.779 23.984 7356 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 0.61 Ramachandran Plot: Outliers : 0.49 % Allowed : 12.99 % Favored : 86.51 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -0.59 (0.11), residues: 7296 helix: 2.54 (0.10), residues: 3000 sheet: -1.61 (0.21), residues: 828 loop : -2.97 (0.10), residues: 3468 Details of bonding type rmsd/Z covalent geometry : bond 0.00188 / 0.14 (29532) covalent geometry : angle 0.45890 / 0.28 (36840) hydrogen bonds : bond 0.04897 / 3.89 ( 2604) hydrogen bonds : angle 4.76111 / 3.90 ( 7488) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2056.23 seconds wall clock time: 36 minutes 16.50 seconds (2176.50 seconds total)