Starting phenix.real_space_refine on Mon Aug 25 15:34:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gtd_34250/08_2025/8gtd_34250.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gtd_34250/08_2025/8gtd_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_34250/08_2025/8gtd_34250.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gtd_34250/08_2025/8gtd_34250.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gtd_34250/08_2025/8gtd_34250.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gtd_34250/08_2025/8gtd_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-2.0-5787/lib/python3.9/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: 2.90, per 1000 atoms: 0.10 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: 3.26 Conformation dependent library (CDL) restraints added in 1.9 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.00 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: 6.84 Time building geometry restraints manager: 4.06 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: 0.19 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 26.020 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4289 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 aren 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 covalent geometry : bond 0.01423 (29532) covalent geometry : angle 2.15645 (36840) hydrogen bonds : bond 0.22966 ( 2604) hydrogen bonds : angle 6.84787 ( 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 : 0.066 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0100 time to fit residues: 0.2957 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 : 0.065 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 : 0.026 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0045 time to fit residues: 0.0457 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 : 0.026 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- 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 = 60)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.089054 restraints weight = 8428.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.087686 restraints weight = 18308.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.088374 restraints weight = 17004.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.088021 restraints weight = 13981.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.088157 restraints weight = 12990.073| |-----------------------------------------------------------------------------| r_work (final): 0.3095 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.101449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.085745 restraints weight = 3162.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.085749 restraints weight = 3101.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.085749 restraints weight = 3081.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.085749 restraints weight = 3081.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.085749 restraints weight = 3081.770| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4850 moved from start: 0.7033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29532 Z= 0.248 Angle : 0.714 6.404 36840 Z= 0.440 Chirality : 0.000 0.000 0 Planarity : 0.004 0.020 7356 Dihedral : 6.143 29.212 7356 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 0.32 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 aren not related in a simple way. whole: -0.35 (0.10), residues: 7296 helix: 2.38 (0.09), residues: 2880 sheet: -0.69 (0.17), residues: 948 loop : -2.56 (0.10), residues: 3468 Details of bonding type rmsd covalent geometry : bond 0.00323 (29532) covalent geometry : angle 0.71377 (36840) hydrogen bonds : bond 0.06266 ( 2604) hydrogen bonds : angle 5.40304 ( 7488) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 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 : 0.056 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0084 time to fit residues: 0.2770 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 : 0.038 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 : 0.016 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0030 time to fit residues: 0.0293 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 : 0.024 ------------------------------------------------------------------------------- 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: 30.0000 chunk 618 optimal weight: 50.0000 chunk 325 optimal weight: 50.0000 chunk 569 optimal weight: 50.0000 chunk 201 optimal weight: 30.0000 chunk 0 optimal weight: 40.0000 chunk 44 optimal weight: 50.0000 chunk 63 optimal weight: 40.0000 chunk 137 optimal weight: 40.0000 overall best weight: 36.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.086339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.078008 restraints weight = 8673.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.077439 restraints weight = 14349.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.077502 restraints weight = 16699.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.077178 restraints weight = 14628.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.077383 restraints weight = 13583.103| |-----------------------------------------------------------------------------| r_work (final): 0.2901 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.085377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.072061 restraints weight = 3378.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.072070 restraints weight = 3321.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.072070 restraints weight = 3294.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.072070 restraints weight = 3294.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.072070 restraints weight = 3294.462| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4969 moved from start: 0.8751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 29532 Z= 0.346 Angle : 0.789 7.216 36840 Z= 0.505 Chirality : 0.000 0.000 0 Planarity : 0.004 0.015 7356 Dihedral : 6.304 24.205 7356 Min Nonbonded Distance : 2.518 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 aren not related in a simple way. whole: -1.02 (0.10), residues: 7296 helix: 1.77 (0.09), residues: 2904 sheet: -1.21 (0.17), residues: 960 loop : -2.87 (0.10), residues: 3432 Details of bonding type rmsd covalent geometry : bond 0.00458 (29532) covalent geometry : angle 0.78927 (36840) hydrogen bonds : bond 0.07501 ( 2604) hydrogen bonds : angle 5.83925 ( 7488) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 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 : 0.042 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0060 time to fit residues: 0.1854 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 : 0.065 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 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0043 time to fit residues: 0.0488 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 : 0.016 ------------------------------------------------------------------------------- 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: 0.6980 chunk 635 optimal weight: 40.0000 chunk 640 optimal weight: 40.0000 chunk 163 optimal weight: 0.0010 overall best weight: 24.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.088163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.080270 restraints weight = 8418.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.078830 restraints weight = 18265.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.079283 restraints weight = 18248.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.078974 restraints weight = 16910.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.079085 restraints weight = 14697.599| |-----------------------------------------------------------------------------| r_work (final): 0.2926 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.087119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.075432 restraints weight = 3496.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 15)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.075471 restraints weight = 3330.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.075471 restraints weight = 3260.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.075471 restraints weight = 3260.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.075471 restraints weight = 3260.507| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4960 moved from start: 0.9744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 29532 Z= 0.215 Angle : 0.577 5.533 36840 Z= 0.358 Chirality : 0.000 0.000 0 Planarity : 0.003 0.017 7356 Dihedral : 5.466 23.370 7356 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 0.61 Ramachandran Plot: Outliers : 0.66 % Allowed : 9.54 % Favored : 89.80 % 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 aren not related in a simple way. whole: -1.05 (0.10), residues: 7296 helix: 1.89 (0.09), residues: 2892 sheet: -1.46 (0.17), residues: 960 loop : -2.93 (0.10), residues: 3444 Details of bonding type rmsd covalent geometry : bond 0.00281 (29532) covalent geometry : angle 0.57729 (36840) hydrogen bonds : bond 0.05342 ( 2604) hydrogen bonds : angle 5.09575 ( 7488) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11812 Ramachandran restraints generated. 5906 Oldfield, 0 Emsley, 5906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11812 Ramachandran restraints generated. 5906 Oldfield, 0 Emsley, 5906 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 : 0.076 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0075 time to fit residues: 0.2369 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 : 0.038 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 : 0.026 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0043 time to fit residues: 0.0480 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 : 0.026 ------------------------------------------------------------------------------- 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: 20.0000 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: 30.0000 chunk 326 optimal weight: 0.9980 overall best weight: 26.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.085453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.077002 restraints weight = 8244.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.076025 restraints weight = 17158.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.076434 restraints weight = 17094.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.076590 restraints weight = 12358.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.076635 restraints weight = 12441.770| |-----------------------------------------------------------------------------| r_work (final): 0.2875 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.082800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.070832 restraints weight = 3607.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.070854 restraints weight = 3487.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.070854 restraints weight = 3417.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.070854 restraints weight = 3417.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.070854 restraints weight = 3417.740| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4989 moved from start: 1.0138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 29532 Z= 0.237 Angle : 0.624 5.757 36840 Z= 0.392 Chirality : 0.000 0.000 0 Planarity : 0.003 0.015 7356 Dihedral : 5.869 22.302 7356 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 1.27 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 aren not related in a simple way. whole: -1.41 (0.10), residues: 7296 helix: 1.61 (0.09), residues: 2832 sheet: -1.42 (0.18), residues: 900 loop : -3.12 (0.10), residues: 3564 Details of bonding type rmsd covalent geometry : bond 0.00311 (29532) covalent geometry : angle 0.62411 (36840) hydrogen bonds : bond 0.06446 ( 2604) hydrogen bonds : angle 5.47607 ( 7488) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11460 Ramachandran restraints generated. 5730 Oldfield, 0 Emsley, 5730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11460 Ramachandran restraints generated. 5730 Oldfield, 0 Emsley, 5730 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 : 0.065 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0085 time to fit residues: 0.2853 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 : 0.040 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 : 0.017 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0033 time to fit residues: 0.0309 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 : 0.026 ------------------------------------------------------------------------------- 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: 40.0000 chunk 621 optimal weight: 40.0000 chunk 455 optimal weight: 50.0000 chunk 539 optimal weight: 50.0000 chunk 111 optimal weight: 30.0000 chunk 407 optimal weight: 40.0000 chunk 384 optimal weight: 50.0000 chunk 299 optimal weight: 30.0000 chunk 340 optimal weight: 50.0000 chunk 452 optimal weight: 40.0000 overall best weight: 36.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.082985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.074799 restraints weight = 8277.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.073660 restraints weight = 17635.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.074229 restraints weight = 17538.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.074023 restraints weight = 14066.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.074213 restraints weight = 12350.829| |-----------------------------------------------------------------------------| r_work (final): 0.2833 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.079646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.068629 restraints weight = 3725.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.068630 restraints weight = 3675.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.068630 restraints weight = 3673.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.068630 restraints weight = 3673.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.068630 restraints weight = 3673.728| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5026 moved from start: 1.0788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 29532 Z= 0.320 Angle : 0.740 6.432 36840 Z= 0.475 Chirality : 0.000 0.000 0 Planarity : 0.004 0.016 7356 Dihedral : 6.724 25.479 7356 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.66 % Allowed : 15.95 % 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 aren not related in a simple way. whole: -2.34 (0.10), residues: 7296 helix: 0.76 (0.09), residues: 2832 sheet: -1.82 (0.20), residues: 816 loop : -3.60 (0.09), residues: 3648 Details of bonding type rmsd covalent geometry : bond 0.00421 (29532) covalent geometry : angle 0.73968 (36840) hydrogen bonds : bond 0.07269 ( 2604) hydrogen bonds : angle 6.28243 ( 7488) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11460 Ramachandran restraints generated. 5730 Oldfield, 0 Emsley, 5730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11460 Ramachandran restraints generated. 5730 Oldfield, 0 Emsley, 5730 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 : 0.039 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0057 time to fit residues: 0.1789 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 : 0.048 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 : 0.021 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0031 time to fit residues: 0.0306 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 129 optimal weight: 20.0000 chunk 34 optimal weight: 40.0000 chunk 625 optimal weight: 20.0000 chunk 107 optimal weight: 50.0000 chunk 403 optimal weight: 50.0000 chunk 255 optimal weight: 30.0000 chunk 2 optimal weight: 50.0000 chunk 303 optimal weight: 40.0000 chunk 236 optimal weight: 0.9980 chunk 319 optimal weight: 0.0570 chunk 102 optimal weight: 50.0000 overall best weight: 14.2110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.087189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.079824 restraints weight = 8285.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.078568 restraints weight = 15847.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.078666 restraints weight = 17377.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.078413 restraints weight = 15376.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.078455 restraints weight = 14918.647| |-----------------------------------------------------------------------------| r_work (final): 0.2904 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.082626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.071309 restraints weight = 3494.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.071309 restraints weight = 3325.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.071309 restraints weight = 3325.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.071309 restraints weight = 3325.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.071309 restraints weight = 3325.161| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4984 moved from start: 1.0781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 29532 Z= 0.144 Angle : 0.489 6.140 36840 Z= 0.297 Chirality : 0.000 0.000 0 Planarity : 0.002 0.015 7356 Dihedral : 5.127 29.773 7356 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.49 % Allowed : 11.35 % Favored : 88.16 % 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 aren not related in a simple way. whole: -1.41 (0.10), residues: 7296 helix: 1.94 (0.10), residues: 2916 sheet: -1.92 (0.20), residues: 816 loop : -3.41 (0.09), residues: 3564 Details of bonding type rmsd covalent geometry : bond 0.00187 (29532) covalent geometry : angle 0.48860 (36840) hydrogen bonds : bond 0.05008 ( 2604) hydrogen bonds : angle 4.89377 ( 7488) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11460 Ramachandran restraints generated. 5730 Oldfield, 0 Emsley, 5730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11460 Ramachandran restraints generated. 5730 Oldfield, 0 Emsley, 5730 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 : 0.064 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0084 time to fit residues: 0.2745 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 : 0.048 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: 0.0053 time to fit residues: 0.0511 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 : 0.026 ------------------------------------------------------------------------------- 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: 50.0000 chunk 226 optimal weight: 40.0000 chunk 485 optimal weight: 40.0000 chunk 597 optimal weight: 20.0000 chunk 330 optimal weight: 50.0000 chunk 289 optimal weight: 6.9990 chunk 158 optimal weight: 30.0000 chunk 73 optimal weight: 0.2980 chunk 399 optimal weight: 50.0000 chunk 11 optimal weight: 50.0000 chunk 541 optimal weight: 50.0000 overall best weight: 19.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.085946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.077943 restraints weight = 8250.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.076674 restraints weight = 19819.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.077027 restraints weight = 19254.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.076898 restraints weight = 15649.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.076992 restraints weight = 14943.086| |-----------------------------------------------------------------------------| r_work (final): 0.2877 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.080705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.071641 restraints weight = 3776.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.071641 restraints weight = 3773.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.071641 restraints weight = 3773.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.071641 restraints weight = 3773.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.071641 restraints weight = 3773.225| |-----------------------------------------------------------------------------| r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5004 moved from start: 1.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 29532 Z= 0.182 Angle : 0.514 5.840 36840 Z= 0.319 Chirality : 0.000 0.000 0 Planarity : 0.002 0.016 7356 Dihedral : 5.199 25.529 7356 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.49 % Allowed : 14.97 % 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 aren not related in a simple way. whole: -1.48 (0.10), residues: 7296 helix: 1.88 (0.10), residues: 2916 sheet: -1.82 (0.20), residues: 816 loop : -3.50 (0.09), residues: 3564 Details of bonding type rmsd covalent geometry : bond 0.00238 (29532) covalent geometry : angle 0.51364 (36840) hydrogen bonds : bond 0.05590 ( 2604) hydrogen bonds : angle 5.06544 ( 7488) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11460 Ramachandran restraints generated. 5730 Oldfield, 0 Emsley, 5730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11460 Ramachandran restraints generated. 5730 Oldfield, 0 Emsley, 5730 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 : 0.044 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0082 time to fit residues: 0.2472 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 : 0.045 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 : 0.016 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0031 time to fit residues: 0.0291 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 204 optimal weight: 20.0000 chunk 333 optimal weight: 30.0000 chunk 590 optimal weight: 0.0050 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: 40.0000 chunk 476 optimal weight: 50.0000 chunk 11 optimal weight: 50.0000 chunk 576 optimal weight: 50.0000 overall best weight: 26.0010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.084328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.076569 restraints weight = 8305.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.075633 restraints weight = 15523.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.075993 restraints weight = 15814.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.075772 restraints weight = 13558.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.075850 restraints weight = 12934.178| |-----------------------------------------------------------------------------| r_work (final): 0.2862 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.079756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.068757 restraints weight = 3610.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.068757 restraints weight = 3545.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.068757 restraints weight = 3545.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.068757 restraints weight = 3545.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.068757 restraints weight = 3545.168| |-----------------------------------------------------------------------------| r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5016 moved from start: 1.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 29532 Z= 0.235 Angle : 0.588 5.494 36840 Z= 0.371 Chirality : 0.000 0.000 0 Planarity : 0.003 0.016 7356 Dihedral : 5.663 22.929 7356 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.49 % Allowed : 16.61 % Favored : 82.89 % 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 aren not related in a simple way. whole: -1.93 (0.10), residues: 7296 helix: 1.46 (0.10), residues: 2916 sheet: -2.04 (0.19), residues: 900 loop : -3.73 (0.09), residues: 3480 Details of bonding type rmsd covalent geometry : bond 0.00308 (29532) covalent geometry : angle 0.58826 (36840) hydrogen bonds : bond 0.06161 ( 2604) hydrogen bonds : angle 5.48012 ( 7488) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11460 Ramachandran restraints generated. 5730 Oldfield, 0 Emsley, 5730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11460 Ramachandran restraints generated. 5730 Oldfield, 0 Emsley, 5730 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 : 0.039 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0056 time to fit residues: 0.1754 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 : 0.037 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 : 0.016 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0031 time to fit residues: 0.0289 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 : 0.016 ------------------------------------------------------------------------------- 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: 40.0000 chunk 593 optimal weight: 50.0000 chunk 145 optimal weight: 40.0000 chunk 645 optimal weight: 50.0000 chunk 351 optimal weight: 50.0000 chunk 587 optimal weight: 40.0000 chunk 48 optimal weight: 40.0000 chunk 552 optimal weight: 0.0170 chunk 523 optimal weight: 50.0000 chunk 152 optimal weight: 40.0000 overall best weight: 32.0034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.082909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.075028 restraints weight = 8495.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.074262 restraints weight = 18237.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.074473 restraints weight = 17336.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.074308 restraints weight = 15326.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.074465 restraints weight = 13766.180| |-----------------------------------------------------------------------------| r_work (final): 0.2838 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.079194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.067354 restraints weight = 3784.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.067354 restraints weight = 3654.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.067354 restraints weight = 3654.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.067354 restraints weight = 3654.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.067354 restraints weight = 3654.380| |-----------------------------------------------------------------------------| r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5021 moved from start: 1.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 29532 Z= 0.281 Angle : 0.651 5.617 36840 Z= 0.415 Chirality : 0.000 0.000 0 Planarity : 0.003 0.017 7356 Dihedral : 6.033 24.945 7356 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.66 % Allowed : 16.28 % Favored : 83.06 % 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 aren not related in a simple way. whole: -2.26 (0.10), residues: 7296 helix: 1.15 (0.09), residues: 2844 sheet: -1.99 (0.20), residues: 780 loop : -3.80 (0.09), residues: 3672 Details of bonding type rmsd covalent geometry : bond 0.00369 (29532) covalent geometry : angle 0.65053 (36840) hydrogen bonds : bond 0.06643 ( 2604) hydrogen bonds : angle 5.91141 ( 7488) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11460 Ramachandran restraints generated. 5730 Oldfield, 0 Emsley, 5730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11460 Ramachandran restraints generated. 5730 Oldfield, 0 Emsley, 5730 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 : 0.064 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0088 time to fit residues: 0.2926 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 : 0.037 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 : 0.020 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0031 time to fit residues: 0.0283 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 : 0.015 ------------------------------------------------------------------------------- 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: 40.0000 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: 0.0060 chunk 529 optimal weight: 9.9990 chunk 139 optimal weight: 50.0000 chunk 460 optimal weight: 50.0000 chunk 296 optimal weight: 50.0000 chunk 534 optimal weight: 50.0000 overall best weight: 28.0010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.083500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.075612 restraints weight = 8286.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.074641 restraints weight = 18983.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.074917 restraints weight = 17968.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.074825 restraints weight = 14417.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.074965 restraints weight = 13688.382| |-----------------------------------------------------------------------------| r_work (final): 0.2849 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.079463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.067588 restraints weight = 3793.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.067588 restraints weight = 3661.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.067588 restraints weight = 3661.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.067588 restraints weight = 3661.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.067588 restraints weight = 3661.888| |-----------------------------------------------------------------------------| r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5017 moved from start: 1.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 29532 Z= 0.251 Angle : 0.608 5.568 36840 Z= 0.384 Chirality : 0.000 0.000 0 Planarity : 0.003 0.017 7356 Dihedral : 5.821 22.735 7356 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.66 % Allowed : 17.11 % Favored : 82.24 % 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 aren not related in a simple way. whole: -2.34 (0.10), residues: 7296 helix: 1.23 (0.10), residues: 2832 sheet: -2.48 (0.19), residues: 900 loop : -3.87 (0.09), residues: 3564 Details of bonding type rmsd covalent geometry : bond 0.00330 (29532) covalent geometry : angle 0.60764 (36840) hydrogen bonds : bond 0.06207 ( 2604) hydrogen bonds : angle 5.71333 ( 7488) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1507.02 seconds wall clock time: 26 minutes 54.48 seconds (1614.48 seconds total)