Starting phenix.real_space_refine on Wed Jun 25 02:50:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gtd_34250/06_2025/8gtd_34250.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gtd_34250/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8gtd_34250/06_2025/8gtd_34250.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gtd_34250/06_2025/8gtd_34250.map" model { file = "/net/cci-nas-00/data/ceres_data/8gtd_34250/06_2025/8gtd_34250.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gtd_34250/06_2025/8gtd_34250.cif" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 15, 'ASP:plan': 27, 'TYR:plan': 8, 'ASN:plan1': 12, 'TRP:plan': 9, 'HIS:plan': 8, 'PHE:plan': 19, 'GLU:plan': 29, 'ARG:plan': 40} 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: {'GLN:plan1': 3, 'ARG:plan': 18, 'TYR:plan': 4, 'PHE%COO:plan': 1, 'TRP:plan': 5, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 11, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 316 Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, L, O, N, Q, P, S, R, U, T, W, V, X Time building chain proxies: 7.89, per 1000 atoms: 0.27 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: 10.52 Conformation dependent library (CDL) restraints added in 6.5 seconds 14592 Ramachandran restraints generated. 7296 Oldfield, 0 Emsley, 7296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 0 Finding SS restraints... Secondary structure from input PDB file: 228 helices and 84 sheets defined 46.1% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.28 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: 13.72 Time building geometry restraints manager: 11.68 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: 0.49 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' selection = chain 'W' selection = chain 'V' selection = chain 'X' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'L' } pdb_interpretation.ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' selection = chain 'W' selection = chain 'V' 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.230 Check model and map are aligned: 0.240 Set scattering table: 0.280 Process input model: 69.300 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.130 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: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.140 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 hydrogen bonds : bond 0.22966 ( 2604) hydrogen bonds : angle 6.84787 ( 7488) covalent geometry : bond 0.01423 (29532) covalent geometry : angle 2.15645 (36840) *********************** 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 : 0.200 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0283 time to fit residues: 0.8803 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 : 0.199 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 : 0.082 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0095 time to fit residues: 0.1504 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 : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 607 optimal weight: 30.0000 chunk 545 optimal weight: 50.0000 chunk 302 optimal weight: 30.0000 chunk 186 optimal weight: 0.0970 chunk 368 optimal weight: 50.0000 chunk 291 optimal weight: 0.1980 chunk 564 optimal weight: 50.0000 chunk 218 optimal weight: 20.0000 chunk 343 optimal weight: 6.9990 chunk 420 optimal weight: 40.0000 chunk 653 optimal weight: 50.0000 overall best weight: 11.4588 ------------------------------------------------------------------------------- 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 = 0.3348 r_free = 0.3348 target = 0.103414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.095715 restraints weight = 8096.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.094237 restraints weight = 17311.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.094352 restraints weight = 21487.842| |-----------------------------------------------------------------------------| r_work (final): 0.3192 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.106004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.092300 restraints weight = 3161.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.090866 restraints weight = 3628.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.091308 restraints weight = 3099.192| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4700 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29532 Z= 0.224 Angle : 0.616 5.937 36840 Z= 0.378 Chirality : 0.000 0.000 0 Planarity : 0.003 0.016 7356 Dihedral : 5.485 32.573 7356 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 0.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.09 % Favored : 93.75 % 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 : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.10), residues: 7296 helix: 2.73 (0.09), residues: 2904 sheet: -0.54 (0.16), residues: 972 loop : -2.62 (0.10), residues: 3420 Details of bonding type rmsd hydrogen bonds : bond 0.05888 ( 2604) hydrogen bonds : angle 4.93740 ( 7488) covalent geometry : bond 0.00288 (29532) covalent geometry : angle 0.61585 (36840) *********************** 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 : 0.178 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0174 time to fit residues: 0.6460 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 : 0.218 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 : 0.082 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0105 time to fit residues: 0.1552 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 : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 619 optimal weight: 50.0000 chunk 492 optimal weight: 9.9990 chunk 424 optimal weight: 30.0000 chunk 335 optimal weight: 40.0000 chunk 187 optimal weight: 40.0000 chunk 421 optimal weight: 40.0000 chunk 505 optimal weight: 20.0000 chunk 570 optimal weight: 40.0000 chunk 116 optimal weight: 50.0000 chunk 450 optimal weight: 50.0000 chunk 488 optimal weight: 50.0000 overall best weight: 27.9998 ------------------------------------------------------------------------------- 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 = 0.3116 r_free = 0.3116 target = 0.089049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.079889 restraints weight = 8238.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.079535 restraints weight = 18186.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.079089 restraints weight = 22675.139| |-----------------------------------------------------------------------------| r_work (final): 0.2931 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.088963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.075649 restraints weight = 3304.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.075662 restraints weight = 3185.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.075662 restraints weight = 3162.009| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4948 moved from start: 0.8420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 29532 Z= 0.274 Angle : 0.708 6.801 36840 Z= 0.448 Chirality : 0.000 0.000 0 Planarity : 0.003 0.015 7356 Dihedral : 5.806 20.228 7356 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.33 % Allowed : 10.69 % Favored : 88.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.10), residues: 7296 helix: 2.46 (0.09), residues: 2916 sheet: -0.62 (0.17), residues: 948 loop : -2.60 (0.10), residues: 3432 Details of bonding type rmsd hydrogen bonds : bond 0.07759 ( 2604) hydrogen bonds : angle 5.38567 ( 7488) covalent geometry : bond 0.00364 (29532) covalent geometry : angle 0.70810 (36840) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13028 Ramachandran restraints generated. 6514 Oldfield, 0 Emsley, 6514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13028 Ramachandran restraints generated. 6514 Oldfield, 0 Emsley, 6514 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 : 0.206 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0187 time to fit residues: 0.7164 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 : 0.235 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 : 0.074 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0085 time to fit residues: 0.1319 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 : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 314 optimal weight: 50.0000 chunk 245 optimal weight: 50.0000 chunk 471 optimal weight: 50.0000 chunk 327 optimal weight: 30.0000 chunk 80 optimal weight: 50.0000 chunk 488 optimal weight: 50.0000 chunk 700 optimal weight: 50.0000 chunk 296 optimal weight: 50.0000 chunk 23 optimal weight: 30.0000 chunk 390 optimal weight: 40.0000 chunk 459 optimal weight: 50.0000 overall best weight: 40.0000 ------------------------------------------------------------------------------- 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 = 0.3033 r_free = 0.3033 target = 0.084363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.076640 restraints weight = 8206.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.075753 restraints weight = 18384.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.075933 restraints weight = 19661.230| |-----------------------------------------------------------------------------| r_work (final): 0.2871 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.083574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.071888 restraints weight = 3604.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.071888 restraints weight = 3453.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.071888 restraints weight = 3453.015| |-----------------------------------------------------------------------------| r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4992 moved from start: 0.9915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 29532 Z= 0.357 Angle : 0.815 7.223 36840 Z= 0.523 Chirality : 0.000 0.000 0 Planarity : 0.005 0.018 7356 Dihedral : 7.024 28.734 7356 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.82 % Allowed : 13.16 % Favored : 86.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.10), residues: 7296 helix: 1.04 (0.09), residues: 2964 sheet: -1.05 (0.19), residues: 864 loop : -3.45 (0.09), residues: 3468 Details of bonding type rmsd hydrogen bonds : bond 0.07490 ( 2604) hydrogen bonds : angle 6.23385 ( 7488) covalent geometry : bond 0.00471 (29532) covalent geometry : angle 0.81480 (36840) *********************** 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 : 0.207 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0177 time to fit residues: 0.6950 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 : 0.205 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 : 0.086 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0100 time to fit residues: 0.1520 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 : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 496 optimal weight: 50.0000 chunk 332 optimal weight: 40.0000 chunk 282 optimal weight: 50.0000 chunk 626 optimal weight: 50.0000 chunk 154 optimal weight: 40.0000 chunk 421 optimal weight: 40.0000 chunk 135 optimal weight: 50.0000 chunk 671 optimal weight: 50.0000 chunk 72 optimal weight: 0.0020 chunk 674 optimal weight: 50.0000 chunk 645 optimal weight: 40.0000 overall best weight: 32.0004 ------------------------------------------------------------------------------- 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 = 0.084457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.076838 restraints weight = 8554.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.076003 restraints weight = 18500.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.076245 restraints weight = 18873.923| |-----------------------------------------------------------------------------| r_work (final): 0.2874 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.081460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.070008 restraints weight = 3521.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.070027 restraints weight = 3395.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.070110 restraints weight = 3345.472| |-----------------------------------------------------------------------------| r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4986 moved from start: 1.0420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 29532 Z= 0.280 Angle : 0.666 5.948 36840 Z= 0.425 Chirality : 0.000 0.000 0 Planarity : 0.004 0.018 7356 Dihedral : 6.146 23.432 7356 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.49 % Allowed : 13.32 % Favored : 86.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.10), residues: 7296 helix: 0.97 (0.09), residues: 2904 sheet: -1.64 (0.19), residues: 828 loop : -3.52 (0.09), residues: 3564 Details of bonding type rmsd hydrogen bonds : bond 0.06449 ( 2604) hydrogen bonds : angle 5.78064 ( 7488) covalent geometry : bond 0.00368 (29532) covalent geometry : angle 0.66609 (36840) *********************** 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 : 0.216 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0195 time to fit residues: 0.7526 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 : 0.208 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 : 0.087 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0102 time to fit residues: 0.1546 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 : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 551 optimal weight: 40.0000 chunk 28 optimal weight: 30.0000 chunk 285 optimal weight: 50.0000 chunk 415 optimal weight: 50.0000 chunk 659 optimal weight: 30.0000 chunk 363 optimal weight: 30.0000 chunk 672 optimal weight: 50.0000 chunk 412 optimal weight: 50.0000 chunk 333 optimal weight: 30.0000 chunk 228 optimal weight: 50.0000 chunk 543 optimal weight: 30.0000 overall best weight: 30.0000 ------------------------------------------------------------------------------- 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 = 0.3024 r_free = 0.3024 target = 0.084075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.076397 restraints weight = 8431.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.075170 restraints weight = 18349.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.075677 restraints weight = 17103.384| |-----------------------------------------------------------------------------| r_work (final): 0.2861 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.079770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.068362 restraints weight = 3734.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.068384 restraints weight = 3529.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.068384 restraints weight = 3484.595| |-----------------------------------------------------------------------------| r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5001 moved from start: 1.0763 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= 0.274 Angle : 0.658 5.491 36840 Z= 0.416 Chirality : 0.000 0.000 0 Planarity : 0.003 0.016 7356 Dihedral : 6.264 23.605 7356 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 1.16 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.10), residues: 7296 helix: 0.77 (0.09), residues: 2904 sheet: -1.80 (0.19), residues: 852 loop : -3.68 (0.09), residues: 3540 Details of bonding type rmsd hydrogen bonds : bond 0.06570 ( 2604) hydrogen bonds : angle 5.90946 ( 7488) covalent geometry : bond 0.00358 (29532) covalent geometry : angle 0.65790 (36840) *********************** 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 : 0.273 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0244 time to fit residues: 0.9173 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 : 0.175 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 : 0.071 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0096 time to fit residues: 0.1416 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 : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 407 optimal weight: 0.0020 chunk 655 optimal weight: 40.0000 chunk 462 optimal weight: 50.0000 chunk 667 optimal weight: 50.0000 chunk 504 optimal weight: 4.9990 chunk 545 optimal weight: 50.0000 chunk 330 optimal weight: 50.0000 chunk 608 optimal weight: 50.0000 chunk 575 optimal weight: 50.0000 chunk 633 optimal weight: 50.0000 chunk 490 optimal weight: 50.0000 overall best weight: 29.0002 ------------------------------------------------------------------------------- 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 = 0.3023 r_free = 0.3023 target = 0.083924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.075737 restraints weight = 8355.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.074722 restraints weight = 18783.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.075128 restraints weight = 18201.396| |-----------------------------------------------------------------------------| r_work (final): 0.2853 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.079622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.068742 restraints weight = 3852.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 16)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.068742 restraints weight = 3630.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.068742 restraints weight = 3628.935| |-----------------------------------------------------------------------------| r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5022 moved from start: 1.0953 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= 0.260 Angle : 0.631 5.789 36840 Z= 0.400 Chirality : 0.000 0.000 0 Planarity : 0.003 0.017 7356 Dihedral : 6.027 24.869 7356 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.49 % Allowed : 15.79 % Favored : 83.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.10), residues: 7296 helix: 0.83 (0.09), residues: 2916 sheet: -1.62 (0.20), residues: 888 loop : -3.95 (0.09), residues: 3492 Details of bonding type rmsd hydrogen bonds : bond 0.06317 ( 2604) hydrogen bonds : angle 5.80161 ( 7488) covalent geometry : bond 0.00342 (29532) covalent geometry : angle 0.63129 (36840) *********************** 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 : 0.228 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0288 time to fit residues: 1.1368 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 : 0.177 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 : 0.079 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0112 time to fit residues: 0.1536 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 : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 587 optimal weight: 50.0000 chunk 224 optimal weight: 40.0000 chunk 199 optimal weight: 0.9980 chunk 170 optimal weight: 40.0000 chunk 695 optimal weight: 50.0000 chunk 50 optimal weight: 0.9980 chunk 369 optimal weight: 50.0000 chunk 88 optimal weight: 30.0000 chunk 343 optimal weight: 50.0000 chunk 154 optimal weight: 40.0000 chunk 197 optimal weight: 50.0000 overall best weight: 22.3992 ------------------------------------------------------------------------------- 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 = 0.3048 r_free = 0.3048 target = 0.085276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.077126 restraints weight = 8339.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.076415 restraints weight = 15167.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.076534 restraints weight = 14771.550| |-----------------------------------------------------------------------------| r_work (final): 0.2878 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.080307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.071275 restraints weight = 3653.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.071274 restraints weight = 3714.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.071274 restraints weight = 3713.903| |-----------------------------------------------------------------------------| r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5006 moved from start: 1.1040 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= 0.206 Angle : 0.549 5.610 36840 Z= 0.344 Chirality : 0.000 0.000 0 Planarity : 0.003 0.016 7356 Dihedral : 5.535 24.341 7356 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.66 % Allowed : 14.64 % Favored : 84.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.10), residues: 7296 helix: 1.24 (0.09), residues: 2928 sheet: -1.68 (0.20), residues: 864 loop : -3.84 (0.09), residues: 3504 Details of bonding type rmsd hydrogen bonds : bond 0.05705 ( 2604) hydrogen bonds : angle 5.38430 ( 7488) covalent geometry : bond 0.00271 (29532) covalent geometry : angle 0.54903 (36840) *********************** 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 : 0.195 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0171 time to fit residues: 0.6455 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 : 0.183 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 : 0.074 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0099 time to fit residues: 0.1333 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 : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 414 optimal weight: 50.0000 chunk 300 optimal weight: 50.0000 chunk 647 optimal weight: 30.0000 chunk 468 optimal weight: 40.0000 chunk 163 optimal weight: 0.0050 chunk 274 optimal weight: 40.0000 chunk 496 optimal weight: 50.0000 chunk 516 optimal weight: 50.0000 chunk 185 optimal weight: 50.0000 chunk 32 optimal weight: 40.0000 chunk 155 optimal weight: 50.0000 overall best weight: 30.0010 ------------------------------------------------------------------------------- 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 = 0.3023 r_free = 0.3023 target = 0.083856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.076154 restraints weight = 8357.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.075100 restraints weight = 19201.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.075335 restraints weight = 19596.564| |-----------------------------------------------------------------------------| r_work (final): 0.2860 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.079398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.067836 restraints weight = 3749.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.067876 restraints weight = 3522.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.067951 restraints weight = 3427.862| |-----------------------------------------------------------------------------| r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5017 moved from start: 1.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 29532 Z= 0.260 Angle : 0.629 5.634 36840 Z= 0.399 Chirality : 0.000 0.000 0 Planarity : 0.003 0.016 7356 Dihedral : 5.996 25.066 7356 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.66 % Allowed : 16.94 % Favored : 82.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.10), residues: 7296 helix: 1.09 (0.09), residues: 2844 sheet: -1.72 (0.21), residues: 780 loop : -3.85 (0.09), residues: 3672 Details of bonding type rmsd hydrogen bonds : bond 0.06532 ( 2604) hydrogen bonds : angle 5.80603 ( 7488) covalent geometry : bond 0.00341 (29532) covalent geometry : angle 0.62917 (36840) *********************** 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 : 0.200 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0189 time to fit residues: 0.7139 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 : 0.189 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 : 0.083 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0103 time to fit residues: 0.1457 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 : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 144 optimal weight: 50.0000 chunk 186 optimal weight: 0.0020 chunk 503 optimal weight: 30.0000 chunk 470 optimal weight: 20.0000 chunk 116 optimal weight: 30.0000 chunk 641 optimal weight: 40.0000 chunk 685 optimal weight: 30.0000 chunk 234 optimal weight: 50.0000 chunk 46 optimal weight: 50.0000 chunk 243 optimal weight: 30.0000 chunk 125 optimal weight: 50.0000 overall best weight: 22.0004 ------------------------------------------------------------------------------- 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 = 0.3043 r_free = 0.3043 target = 0.085020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.077305 restraints weight = 8245.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.076380 restraints weight = 17419.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.076567 restraints weight = 18203.192| |-----------------------------------------------------------------------------| r_work (final): 0.2882 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.080410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.068799 restraints weight = 3539.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.068799 restraints weight = 3457.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.068799 restraints weight = 3456.878| |-----------------------------------------------------------------------------| r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4994 moved from start: 1.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 29532 Z= 0.201 Angle : 0.545 5.681 36840 Z= 0.340 Chirality : 0.000 0.000 0 Planarity : 0.003 0.016 7356 Dihedral : 5.483 23.820 7356 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.66 % Allowed : 15.30 % Favored : 84.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.10), residues: 7296 helix: 1.36 (0.10), residues: 2916 sheet: -1.72 (0.22), residues: 708 loop : -3.79 (0.09), residues: 3672 Details of bonding type rmsd hydrogen bonds : bond 0.05707 ( 2604) hydrogen bonds : angle 5.37113 ( 7488) covalent geometry : bond 0.00264 (29532) covalent geometry : angle 0.54474 (36840) ********************** 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 : 0.205 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0182 time to fit residues: 0.6849 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 : 0.177 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 : 0.082 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0096 time to fit residues: 0.1315 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 : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 107 optimal weight: 40.0000 chunk 371 optimal weight: 40.0000 chunk 128 optimal weight: 50.0000 chunk 217 optimal weight: 50.0000 chunk 307 optimal weight: 50.0000 chunk 586 optimal weight: 0.0050 chunk 50 optimal weight: 3.9990 chunk 613 optimal weight: 50.0000 chunk 135 optimal weight: 40.0000 chunk 59 optimal weight: 40.0000 chunk 328 optimal weight: 20.0000 overall best weight: 20.8008 ------------------------------------------------------------------------------- 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 = 0.3050 r_free = 0.3050 target = 0.085271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.078035 restraints weight = 8285.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.076953 restraints weight = 16310.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.077031 restraints weight = 16102.773| |-----------------------------------------------------------------------------| r_work (final): 0.2880 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.080077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.068525 restraints weight = 3539.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.068525 restraints weight = 3378.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.068525 restraints weight = 3378.576| |-----------------------------------------------------------------------------| r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5010 moved from start: 1.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 29532 Z= 0.195 Angle : 0.527 5.678 36840 Z= 0.328 Chirality : 0.000 0.000 0 Planarity : 0.003 0.016 7356 Dihedral : 5.256 21.814 7356 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 0.98 Ramachandran Plot: Outliers : 0.49 % Allowed : 16.78 % Favored : 82.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.10), residues: 7296 helix: 1.69 (0.10), residues: 2856 sheet: -1.92 (0.20), residues: 780 loop : -3.76 (0.09), residues: 3660 Details of bonding type rmsd hydrogen bonds : bond 0.05538 ( 2604) hydrogen bonds : angle 5.25592 ( 7488) covalent geometry : bond 0.00255 (29532) covalent geometry : angle 0.52681 (36840) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4281.50 seconds wall clock time: 75 minutes 1.43 seconds (4501.43 seconds total)