Starting phenix.real_space_refine on Mon Sep 30 01:25:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fm9_29289/09_2024/8fm9_29289.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fm9_29289/09_2024/8fm9_29289.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fm9_29289/09_2024/8fm9_29289.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fm9_29289/09_2024/8fm9_29289.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fm9_29289/09_2024/8fm9_29289.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fm9_29289/09_2024/8fm9_29289.cif" } resolution = 3.2 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= -0.008 sd= 0.814 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 108 5.16 5 C 27876 2.51 5 N 9276 2.21 5 O 9588 1.98 5 H 29916 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 76764 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 4986 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 18, 'TRANS': 289} Chain breaks: 1 Chain: "M" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 1411 Classifications: {'peptide': 333} Incomplete info: {'backbone_only': 301} Link IDs: {'PTRANS': 18, 'TRANS': 314} Chain breaks: 3 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1299 Unresolved non-hydrogen angles: 1884 Unresolved non-hydrogen dihedrals: 816 Unresolved non-hydrogen chiralities: 396 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 8, 'TYR:plan': 10, 'ASN:plan1': 13, 'TRP:plan': 2, 'ASP:plan': 24, 'PHE:plan': 12, 'GLU:plan': 20, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 620 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: 18.24, per 1000 atoms: 0.24 Number of scatterers: 76764 At special positions: 0 Unit cell: (237.491, 237.491, 126.662, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 108 16.00 O 9588 8.00 N 9276 7.00 C 27876 6.00 H 29916 1.00 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: 16.60 Conformation dependent library (CDL) restraints added in 6.3 seconds 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7416 Finding SS restraints... Secondary structure from input PDB file: 336 helices and 60 sheets defined 48.4% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.50 Creating SS restraints... Processing helix chain 'A' and resid 55 through 64 removed outlier: 4.345A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 115 Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 236 through 250 Proline residue: A 245 - end of helix removed outlier: 4.225A pdb=" N ILE A 249 " --> pdb=" O PRO A 245 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 347 removed outlier: 3.885A pdb=" N GLY A 347 " --> pdb=" O ASP A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 361 Processing helix chain 'A' and resid 365 through 378 removed outlier: 3.944A pdb=" N MET A 371 " --> pdb=" O GLN A 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 64 Processing helix chain 'B' and resid 95 through 115 Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 236 through 250 Proline residue: B 245 - end of helix removed outlier: 4.225A pdb=" N ILE B 249 " --> pdb=" O PRO B 245 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 347 removed outlier: 3.885A pdb=" N GLY B 347 " --> pdb=" O ASP B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 361 Processing helix chain 'B' and resid 365 through 378 removed outlier: 3.943A pdb=" N MET B 371 " --> pdb=" O GLN B 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 64 Processing helix chain 'C' and resid 95 through 115 Processing helix chain 'C' and resid 169 through 174 Processing helix chain 'C' and resid 236 through 250 Proline residue: C 245 - end of helix removed outlier: 4.224A pdb=" N ILE C 249 " --> pdb=" O PRO C 245 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 347 removed outlier: 3.885A pdb=" N GLY C 347 " --> pdb=" O ASP C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 361 Processing helix chain 'C' and resid 365 through 378 removed outlier: 3.943A pdb=" N MET C 371 " --> pdb=" O GLN C 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 64 Processing helix chain 'D' and resid 95 through 115 Processing helix chain 'D' and resid 169 through 174 Processing helix chain 'D' and resid 236 through 250 Proline residue: D 245 - end of helix removed outlier: 4.225A pdb=" N ILE D 249 " --> pdb=" O PRO D 245 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY D 250 " --> pdb=" O LEU D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 347 removed outlier: 3.885A pdb=" N GLY D 347 " --> pdb=" O ASP D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 361 Processing helix chain 'D' and resid 365 through 378 removed outlier: 3.944A pdb=" N MET D 371 " --> pdb=" O GLN D 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 64 Processing helix chain 'E' and resid 95 through 115 Processing helix chain 'E' and resid 169 through 174 Processing helix chain 'E' and resid 236 through 250 Proline residue: E 245 - end of helix removed outlier: 4.225A pdb=" N ILE E 249 " --> pdb=" O PRO E 245 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY E 250 " --> pdb=" O LEU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 347 removed outlier: 3.885A pdb=" N GLY E 347 " --> pdb=" O ASP E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 361 Processing helix chain 'E' and resid 365 through 378 removed outlier: 3.944A pdb=" N MET E 371 " --> pdb=" O GLN E 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 64 Processing helix chain 'F' and resid 95 through 115 Processing helix chain 'F' and resid 169 through 174 Processing helix chain 'F' and resid 236 through 250 Proline residue: F 245 - end of helix removed outlier: 4.224A pdb=" N ILE F 249 " --> pdb=" O PRO F 245 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY F 250 " --> pdb=" O LEU F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 347 removed outlier: 3.885A pdb=" N GLY F 347 " --> pdb=" O ASP F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 361 Processing helix chain 'F' and resid 365 through 378 removed outlier: 3.944A pdb=" N MET F 371 " --> pdb=" O GLN F 367 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 64 Processing helix chain 'G' and resid 95 through 115 Processing helix chain 'G' and resid 169 through 174 Processing helix chain 'G' and resid 236 through 250 Proline residue: G 245 - end of helix removed outlier: 4.225A pdb=" N ILE G 249 " --> pdb=" O PRO G 245 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY G 250 " --> pdb=" O LEU G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 347 removed outlier: 3.885A pdb=" N GLY G 347 " --> pdb=" O ASP G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 361 Processing helix chain 'G' and resid 365 through 378 removed outlier: 3.944A pdb=" N MET G 371 " --> pdb=" O GLN G 367 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 64 Processing helix chain 'H' and resid 95 through 115 Processing helix chain 'H' and resid 169 through 174 Processing helix chain 'H' and resid 236 through 250 Proline residue: H 245 - end of helix removed outlier: 4.225A pdb=" N ILE H 249 " --> pdb=" O PRO H 245 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY H 250 " --> pdb=" O LEU H 246 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 347 removed outlier: 3.886A pdb=" N GLY H 347 " --> pdb=" O ASP H 343 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 361 Processing helix chain 'H' and resid 365 through 378 removed outlier: 3.944A pdb=" N MET H 371 " --> pdb=" O GLN H 367 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 64 Processing helix chain 'I' and resid 95 through 115 Processing helix chain 'I' and resid 169 through 174 Processing helix chain 'I' and resid 236 through 250 Proline residue: I 245 - end of helix removed outlier: 4.224A pdb=" N ILE I 249 " --> pdb=" O PRO I 245 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY I 250 " --> pdb=" O LEU I 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 339 through 347 removed outlier: 3.885A pdb=" N GLY I 347 " --> pdb=" O ASP I 343 " (cutoff:3.500A) Processing helix chain 'I' and resid 350 through 361 Processing helix chain 'I' and resid 365 through 378 removed outlier: 3.944A pdb=" N MET I 371 " --> pdb=" O GLN I 367 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 64 Processing helix chain 'J' and resid 95 through 115 Processing helix chain 'J' and resid 169 through 174 Processing helix chain 'J' and resid 236 through 250 Proline residue: J 245 - end of helix removed outlier: 4.225A pdb=" N ILE J 249 " --> pdb=" O PRO J 245 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY J 250 " --> pdb=" O LEU J 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 339 through 347 removed outlier: 3.885A pdb=" N GLY J 347 " --> pdb=" O ASP J 343 " (cutoff:3.500A) Processing helix chain 'J' and resid 350 through 361 Processing helix chain 'J' and resid 365 through 378 removed outlier: 3.944A pdb=" N MET J 371 " --> pdb=" O GLN J 367 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 64 Processing helix chain 'K' and resid 95 through 115 Processing helix chain 'K' and resid 169 through 174 Processing helix chain 'K' and resid 236 through 250 Proline residue: K 245 - end of helix removed outlier: 4.225A pdb=" N ILE K 249 " --> pdb=" O PRO K 245 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY K 250 " --> pdb=" O LEU K 246 " (cutoff:3.500A) Processing helix chain 'K' and resid 339 through 347 removed outlier: 3.885A pdb=" N GLY K 347 " --> pdb=" O ASP K 343 " (cutoff:3.500A) Processing helix chain 'K' and resid 350 through 361 Processing helix chain 'K' and resid 365 through 378 removed outlier: 3.944A pdb=" N MET K 371 " --> pdb=" O GLN K 367 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 64 Processing helix chain 'L' and resid 95 through 115 Processing helix chain 'L' and resid 169 through 174 Processing helix chain 'L' and resid 236 through 250 Proline residue: L 245 - end of helix removed outlier: 4.225A pdb=" N ILE L 249 " --> pdb=" O PRO L 245 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY L 250 " --> pdb=" O LEU L 246 " (cutoff:3.500A) Processing helix chain 'L' and resid 339 through 347 removed outlier: 3.885A pdb=" N GLY L 347 " --> pdb=" O ASP L 343 " (cutoff:3.500A) Processing helix chain 'L' and resid 350 through 361 Processing helix chain 'L' and resid 365 through 378 removed outlier: 3.943A pdb=" N MET L 371 " --> pdb=" O GLN L 367 " (cutoff:3.500A) Processing helix chain 'M' and resid 453 through 469 removed outlier: 3.536A pdb=" N ALA M 457 " --> pdb=" O SER M 453 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS M 458 " --> pdb=" O ASP M 454 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE M 459 " --> pdb=" O ARG M 455 " (cutoff:3.500A) Processing helix chain 'M' and resid 478 through 485 Processing helix chain 'M' and resid 534 through 549 removed outlier: 4.115A pdb=" N VAL M 538 " --> pdb=" O PHE M 534 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TYR M 541 " --> pdb=" O LYS M 537 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA M 544 " --> pdb=" O ARG M 540 " (cutoff:3.500A) Processing helix chain 'M' and resid 552 through 556 removed outlier: 3.838A pdb=" N GLU M 556 " --> pdb=" O GLU M 553 " (cutoff:3.500A) Processing helix chain 'M' and resid 564 through 579 Processing helix chain 'M' and resid 596 through 603 Processing helix chain 'M' and resid 603 through 612 Processing helix chain 'M' and resid 613 through 615 No H-bonds generated for 'chain 'M' and resid 613 through 615' Processing helix chain 'M' and resid 616 through 629 Processing helix chain 'M' and resid 655 through 674 Processing helix chain 'M' and resid 678 through 684 Processing helix chain 'M' and resid 699 through 701 No H-bonds generated for 'chain 'M' and resid 699 through 701' Processing helix chain 'M' and resid 702 through 712 removed outlier: 4.094A pdb=" N ARG M 706 " --> pdb=" O LYS M 702 " (cutoff:3.500A) Processing helix chain 'M' and resid 745 through 751 removed outlier: 3.549A pdb=" N THR M 749 " --> pdb=" O ASP M 745 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG M 751 " --> pdb=" O LEU M 747 " (cutoff:3.500A) Processing helix chain 'M' and resid 763 through 780 removed outlier: 3.629A pdb=" N ALA M 780 " --> pdb=" O LEU M 776 " (cutoff:3.500A) Processing helix chain 'M' and resid 785 through 800 Proline residue: M 798 - end of helix Processing helix chain 'M' and resid 802 through 808 Processing helix chain 'M' and resid 809 through 814 removed outlier: 3.634A pdb=" N ASN M 813 " --> pdb=" O ARG M 810 " (cutoff:3.500A) Processing helix chain 'M' and resid 829 through 831 No H-bonds generated for 'chain 'M' and resid 829 through 831' Processing helix chain 'M' and resid 832 through 845 Processing helix chain 'M' and resid 847 through 861 Processing helix chain 'N' and resid 453 through 469 removed outlier: 3.537A pdb=" N ALA N 457 " --> pdb=" O SER N 453 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS N 458 " --> pdb=" O ASP N 454 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE N 459 " --> pdb=" O ARG N 455 " (cutoff:3.500A) Processing helix chain 'N' and resid 478 through 485 Processing helix chain 'N' and resid 534 through 549 removed outlier: 4.116A pdb=" N VAL N 538 " --> pdb=" O PHE N 534 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TYR N 541 " --> pdb=" O LYS N 537 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA N 544 " --> pdb=" O ARG N 540 " (cutoff:3.500A) Processing helix chain 'N' and resid 552 through 556 removed outlier: 3.838A pdb=" N GLU N 556 " --> pdb=" O GLU N 553 " (cutoff:3.500A) Processing helix chain 'N' and resid 564 through 579 Processing helix chain 'N' and resid 596 through 603 Processing helix chain 'N' and resid 603 through 612 Processing helix chain 'N' and resid 613 through 615 No H-bonds generated for 'chain 'N' and resid 613 through 615' Processing helix chain 'N' and resid 616 through 629 Processing helix chain 'N' and resid 655 through 674 Processing helix chain 'N' and resid 678 through 684 Processing helix chain 'N' and resid 699 through 701 No H-bonds generated for 'chain 'N' and resid 699 through 701' Processing helix chain 'N' and resid 702 through 712 removed outlier: 4.094A pdb=" N ARG N 706 " --> pdb=" O LYS N 702 " (cutoff:3.500A) Processing helix chain 'N' and resid 745 through 751 removed outlier: 3.549A pdb=" N THR N 749 " --> pdb=" O ASP N 745 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG N 751 " --> pdb=" O LEU N 747 " (cutoff:3.500A) Processing helix chain 'N' and resid 763 through 780 removed outlier: 3.629A pdb=" N ALA N 780 " --> pdb=" O LEU N 776 " (cutoff:3.500A) Processing helix chain 'N' and resid 785 through 800 Proline residue: N 798 - end of helix Processing helix chain 'N' and resid 802 through 808 Processing helix chain 'N' and resid 809 through 814 removed outlier: 3.635A pdb=" N ASN N 813 " --> pdb=" O ARG N 810 " (cutoff:3.500A) Processing helix chain 'N' and resid 829 through 831 No H-bonds generated for 'chain 'N' and resid 829 through 831' Processing helix chain 'N' and resid 832 through 845 Processing helix chain 'N' and resid 847 through 861 Processing helix chain 'O' and resid 453 through 469 removed outlier: 3.537A pdb=" N ALA O 457 " --> pdb=" O SER O 453 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS O 458 " --> pdb=" O ASP O 454 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE O 459 " --> pdb=" O ARG O 455 " (cutoff:3.500A) Processing helix chain 'O' and resid 478 through 485 Processing helix chain 'O' and resid 534 through 549 removed outlier: 4.116A pdb=" N VAL O 538 " --> pdb=" O PHE O 534 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TYR O 541 " --> pdb=" O LYS O 537 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA O 544 " --> pdb=" O ARG O 540 " (cutoff:3.500A) Processing helix chain 'O' and resid 552 through 556 removed outlier: 3.839A pdb=" N GLU O 556 " --> pdb=" O GLU O 553 " (cutoff:3.500A) Processing helix chain 'O' and resid 564 through 579 Processing helix chain 'O' and resid 596 through 603 Processing helix chain 'O' and resid 603 through 612 Processing helix chain 'O' and resid 613 through 615 No H-bonds generated for 'chain 'O' and resid 613 through 615' Processing helix chain 'O' and resid 616 through 629 Processing helix chain 'O' and resid 655 through 674 Processing helix chain 'O' and resid 678 through 684 Processing helix chain 'O' and resid 699 through 701 No H-bonds generated for 'chain 'O' and resid 699 through 701' Processing helix chain 'O' and resid 702 through 712 removed outlier: 4.094A pdb=" N ARG O 706 " --> pdb=" O LYS O 702 " (cutoff:3.500A) Processing helix chain 'O' and resid 745 through 751 removed outlier: 3.549A pdb=" N THR O 749 " --> pdb=" O ASP O 745 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG O 751 " --> pdb=" O LEU O 747 " (cutoff:3.500A) Processing helix chain 'O' and resid 763 through 780 removed outlier: 3.629A pdb=" N ALA O 780 " --> pdb=" O LEU O 776 " (cutoff:3.500A) Processing helix chain 'O' and resid 785 through 800 Proline residue: O 798 - end of helix Processing helix chain 'O' and resid 802 through 808 Processing helix chain 'O' and resid 809 through 814 removed outlier: 3.634A pdb=" N ASN O 813 " --> pdb=" O ARG O 810 " (cutoff:3.500A) Processing helix chain 'O' and resid 829 through 831 No H-bonds generated for 'chain 'O' and resid 829 through 831' Processing helix chain 'O' and resid 832 through 845 Processing helix chain 'O' and resid 847 through 861 Processing helix chain 'P' and resid 453 through 469 removed outlier: 3.537A pdb=" N ALA P 457 " --> pdb=" O SER P 453 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS P 458 " --> pdb=" O ASP P 454 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE P 459 " --> pdb=" O ARG P 455 " (cutoff:3.500A) Processing helix chain 'P' and resid 478 through 485 Processing helix chain 'P' and resid 534 through 549 removed outlier: 4.115A pdb=" N VAL P 538 " --> pdb=" O PHE P 534 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TYR P 541 " --> pdb=" O LYS P 537 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA P 544 " --> pdb=" O ARG P 540 " (cutoff:3.500A) Processing helix chain 'P' and resid 552 through 556 removed outlier: 3.838A pdb=" N GLU P 556 " --> pdb=" O GLU P 553 " (cutoff:3.500A) Processing helix chain 'P' and resid 564 through 579 Processing helix chain 'P' and resid 596 through 603 Processing helix chain 'P' and resid 603 through 612 Processing helix chain 'P' and resid 613 through 615 No H-bonds generated for 'chain 'P' and resid 613 through 615' Processing helix chain 'P' and resid 616 through 629 Processing helix chain 'P' and resid 655 through 674 Processing helix chain 'P' and resid 678 through 684 Processing helix chain 'P' and resid 699 through 701 No H-bonds generated for 'chain 'P' and resid 699 through 701' Processing helix chain 'P' and resid 702 through 712 removed outlier: 4.094A pdb=" N ARG P 706 " --> pdb=" O LYS P 702 " (cutoff:3.500A) Processing helix chain 'P' and resid 745 through 751 removed outlier: 3.550A pdb=" N THR P 749 " --> pdb=" O ASP P 745 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG P 751 " --> pdb=" O LEU P 747 " (cutoff:3.500A) Processing helix chain 'P' and resid 763 through 780 removed outlier: 3.630A pdb=" N ALA P 780 " --> pdb=" O LEU P 776 " (cutoff:3.500A) Processing helix chain 'P' and resid 785 through 800 Proline residue: P 798 - end of helix Processing helix chain 'P' and resid 802 through 808 Processing helix chain 'P' and resid 809 through 814 removed outlier: 3.635A pdb=" N ASN P 813 " --> pdb=" O ARG P 810 " (cutoff:3.500A) Processing helix chain 'P' and resid 829 through 831 No H-bonds generated for 'chain 'P' and resid 829 through 831' Processing helix chain 'P' and resid 832 through 845 Processing helix chain 'P' and resid 847 through 861 Processing helix chain 'Q' and resid 453 through 469 removed outlier: 3.536A pdb=" N ALA Q 457 " --> pdb=" O SER Q 453 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS Q 458 " --> pdb=" O ASP Q 454 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE Q 459 " --> pdb=" O ARG Q 455 " (cutoff:3.500A) Processing helix chain 'Q' and resid 478 through 485 Processing helix chain 'Q' and resid 534 through 549 removed outlier: 4.116A pdb=" N VAL Q 538 " --> pdb=" O PHE Q 534 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TYR Q 541 " --> pdb=" O LYS Q 537 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA Q 544 " --> pdb=" O ARG Q 540 " (cutoff:3.500A) Processing helix chain 'Q' and resid 552 through 556 removed outlier: 3.838A pdb=" N GLU Q 556 " --> pdb=" O GLU Q 553 " (cutoff:3.500A) Processing helix chain 'Q' and resid 564 through 579 Processing helix chain 'Q' and resid 596 through 603 Processing helix chain 'Q' and resid 603 through 612 Processing helix chain 'Q' and resid 613 through 615 No H-bonds generated for 'chain 'Q' and resid 613 through 615' Processing helix chain 'Q' and resid 616 through 629 Processing helix chain 'Q' and resid 655 through 674 Processing helix chain 'Q' and resid 678 through 684 Processing helix chain 'Q' and resid 699 through 701 No H-bonds generated for 'chain 'Q' and resid 699 through 701' Processing helix chain 'Q' and resid 702 through 712 removed outlier: 4.093A pdb=" N ARG Q 706 " --> pdb=" O LYS Q 702 " (cutoff:3.500A) Processing helix chain 'Q' and resid 745 through 751 removed outlier: 3.549A pdb=" N THR Q 749 " --> pdb=" O ASP Q 745 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG Q 751 " --> pdb=" O LEU Q 747 " (cutoff:3.500A) Processing helix chain 'Q' and resid 763 through 780 removed outlier: 3.630A pdb=" N ALA Q 780 " --> pdb=" O LEU Q 776 " (cutoff:3.500A) Processing helix chain 'Q' and resid 785 through 800 Proline residue: Q 798 - end of helix Processing helix chain 'Q' and resid 802 through 808 Processing helix chain 'Q' and resid 809 through 814 removed outlier: 3.634A pdb=" N ASN Q 813 " --> pdb=" O ARG Q 810 " (cutoff:3.500A) Processing helix chain 'Q' and resid 829 through 831 No H-bonds generated for 'chain 'Q' and resid 829 through 831' Processing helix chain 'Q' and resid 832 through 845 Processing helix chain 'Q' and resid 847 through 861 Processing helix chain 'R' and resid 453 through 469 removed outlier: 3.537A pdb=" N ALA R 457 " --> pdb=" O SER R 453 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS R 458 " --> pdb=" O ASP R 454 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE R 459 " --> pdb=" O ARG R 455 " (cutoff:3.500A) Processing helix chain 'R' and resid 478 through 485 Processing helix chain 'R' and resid 534 through 549 removed outlier: 4.115A pdb=" N VAL R 538 " --> pdb=" O PHE R 534 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TYR R 541 " --> pdb=" O LYS R 537 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA R 544 " --> pdb=" O ARG R 540 " (cutoff:3.500A) Processing helix chain 'R' and resid 552 through 556 removed outlier: 3.839A pdb=" N GLU R 556 " --> pdb=" O GLU R 553 " (cutoff:3.500A) Processing helix chain 'R' and resid 564 through 579 Processing helix chain 'R' and resid 596 through 603 Processing helix chain 'R' and resid 603 through 612 Processing helix chain 'R' and resid 613 through 615 No H-bonds generated for 'chain 'R' and resid 613 through 615' Processing helix chain 'R' and resid 616 through 629 Processing helix chain 'R' and resid 655 through 674 Processing helix chain 'R' and resid 678 through 684 Processing helix chain 'R' and resid 699 through 701 No H-bonds generated for 'chain 'R' and resid 699 through 701' Processing helix chain 'R' and resid 702 through 712 removed outlier: 4.094A pdb=" N ARG R 706 " --> pdb=" O LYS R 702 " (cutoff:3.500A) Processing helix chain 'R' and resid 745 through 751 removed outlier: 3.549A pdb=" N THR R 749 " --> pdb=" O ASP R 745 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG R 751 " --> pdb=" O LEU R 747 " (cutoff:3.500A) Processing helix chain 'R' and resid 763 through 780 removed outlier: 3.629A pdb=" N ALA R 780 " --> pdb=" O LEU R 776 " (cutoff:3.500A) Processing helix chain 'R' and resid 785 through 800 Proline residue: R 798 - end of helix Processing helix chain 'R' and resid 802 through 808 Processing helix chain 'R' and resid 809 through 814 removed outlier: 3.635A pdb=" N ASN R 813 " --> pdb=" O ARG R 810 " (cutoff:3.500A) Processing helix chain 'R' and resid 829 through 831 No H-bonds generated for 'chain 'R' and resid 829 through 831' Processing helix chain 'R' and resid 832 through 845 Processing helix chain 'R' and resid 847 through 861 Processing helix chain 'S' and resid 453 through 469 removed outlier: 3.536A pdb=" N ALA S 457 " --> pdb=" O SER S 453 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS S 458 " --> pdb=" O ASP S 454 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE S 459 " --> pdb=" O ARG S 455 " (cutoff:3.500A) Processing helix chain 'S' and resid 478 through 485 Processing helix chain 'S' and resid 534 through 549 removed outlier: 4.115A pdb=" N VAL S 538 " --> pdb=" O PHE S 534 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TYR S 541 " --> pdb=" O LYS S 537 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA S 544 " --> pdb=" O ARG S 540 " (cutoff:3.500A) Processing helix chain 'S' and resid 552 through 556 removed outlier: 3.838A pdb=" N GLU S 556 " --> pdb=" O GLU S 553 " (cutoff:3.500A) Processing helix chain 'S' and resid 564 through 579 Processing helix chain 'S' and resid 596 through 603 Processing helix chain 'S' and resid 603 through 612 Processing helix chain 'S' and resid 613 through 615 No H-bonds generated for 'chain 'S' and resid 613 through 615' Processing helix chain 'S' and resid 616 through 629 Processing helix chain 'S' and resid 655 through 674 Processing helix chain 'S' and resid 678 through 684 Processing helix chain 'S' and resid 699 through 701 No H-bonds generated for 'chain 'S' and resid 699 through 701' Processing helix chain 'S' and resid 702 through 712 removed outlier: 4.094A pdb=" N ARG S 706 " --> pdb=" O LYS S 702 " (cutoff:3.500A) Processing helix chain 'S' and resid 745 through 751 removed outlier: 3.549A pdb=" N THR S 749 " --> pdb=" O ASP S 745 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ARG S 751 " --> pdb=" O LEU S 747 " (cutoff:3.500A) Processing helix chain 'S' and resid 763 through 780 removed outlier: 3.629A pdb=" N ALA S 780 " --> pdb=" O LEU S 776 " (cutoff:3.500A) Processing helix chain 'S' and resid 785 through 800 Proline residue: S 798 - end of helix Processing helix chain 'S' and resid 802 through 808 Processing helix chain 'S' and resid 809 through 814 removed outlier: 3.634A pdb=" N ASN S 813 " --> pdb=" O ARG S 810 " (cutoff:3.500A) Processing helix chain 'S' and resid 829 through 831 No H-bonds generated for 'chain 'S' and resid 829 through 831' Processing helix chain 'S' and resid 832 through 845 Processing helix chain 'S' and resid 847 through 861 Processing helix chain 'T' and resid 453 through 469 removed outlier: 3.537A pdb=" N ALA T 457 " --> pdb=" O SER T 453 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS T 458 " --> pdb=" O ASP T 454 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE T 459 " --> pdb=" O ARG T 455 " (cutoff:3.500A) Processing helix chain 'T' and resid 478 through 485 Processing helix chain 'T' and resid 534 through 549 removed outlier: 4.115A pdb=" N VAL T 538 " --> pdb=" O PHE T 534 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TYR T 541 " --> pdb=" O LYS T 537 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA T 544 " --> pdb=" O ARG T 540 " (cutoff:3.500A) Processing helix chain 'T' and resid 552 through 556 removed outlier: 3.839A pdb=" N GLU T 556 " --> pdb=" O GLU T 553 " (cutoff:3.500A) Processing helix chain 'T' and resid 564 through 579 Processing helix chain 'T' and resid 596 through 603 Processing helix chain 'T' and resid 603 through 612 Processing helix chain 'T' and resid 613 through 615 No H-bonds generated for 'chain 'T' and resid 613 through 615' Processing helix chain 'T' and resid 616 through 629 Processing helix chain 'T' and resid 655 through 674 Processing helix chain 'T' and resid 678 through 684 Processing helix chain 'T' and resid 699 through 701 No H-bonds generated for 'chain 'T' and resid 699 through 701' Processing helix chain 'T' and resid 702 through 712 removed outlier: 4.094A pdb=" N ARG T 706 " --> pdb=" O LYS T 702 " (cutoff:3.500A) Processing helix chain 'T' and resid 745 through 751 removed outlier: 3.549A pdb=" N THR T 749 " --> pdb=" O ASP T 745 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG T 751 " --> pdb=" O LEU T 747 " (cutoff:3.500A) Processing helix chain 'T' and resid 763 through 780 removed outlier: 3.630A pdb=" N ALA T 780 " --> pdb=" O LEU T 776 " (cutoff:3.500A) Processing helix chain 'T' and resid 785 through 800 Proline residue: T 798 - end of helix Processing helix chain 'T' and resid 802 through 808 Processing helix chain 'T' and resid 809 through 814 removed outlier: 3.634A pdb=" N ASN T 813 " --> pdb=" O ARG T 810 " (cutoff:3.500A) Processing helix chain 'T' and resid 829 through 831 No H-bonds generated for 'chain 'T' and resid 829 through 831' Processing helix chain 'T' and resid 832 through 845 Processing helix chain 'T' and resid 847 through 861 Processing helix chain 'U' and resid 453 through 469 removed outlier: 3.536A pdb=" N ALA U 457 " --> pdb=" O SER U 453 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS U 458 " --> pdb=" O ASP U 454 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE U 459 " --> pdb=" O ARG U 455 " (cutoff:3.500A) Processing helix chain 'U' and resid 478 through 485 Processing helix chain 'U' and resid 534 through 549 removed outlier: 4.116A pdb=" N VAL U 538 " --> pdb=" O PHE U 534 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TYR U 541 " --> pdb=" O LYS U 537 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA U 544 " --> pdb=" O ARG U 540 " (cutoff:3.500A) Processing helix chain 'U' and resid 552 through 556 removed outlier: 3.838A pdb=" N GLU U 556 " --> pdb=" O GLU U 553 " (cutoff:3.500A) Processing helix chain 'U' and resid 564 through 579 Processing helix chain 'U' and resid 596 through 603 Processing helix chain 'U' and resid 603 through 612 Processing helix chain 'U' and resid 613 through 615 No H-bonds generated for 'chain 'U' and resid 613 through 615' Processing helix chain 'U' and resid 616 through 629 Processing helix chain 'U' and resid 655 through 674 Processing helix chain 'U' and resid 678 through 684 Processing helix chain 'U' and resid 699 through 701 No H-bonds generated for 'chain 'U' and resid 699 through 701' Processing helix chain 'U' and resid 702 through 712 removed outlier: 4.094A pdb=" N ARG U 706 " --> pdb=" O LYS U 702 " (cutoff:3.500A) Processing helix chain 'U' and resid 745 through 751 removed outlier: 3.550A pdb=" N THR U 749 " --> pdb=" O ASP U 745 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG U 751 " --> pdb=" O LEU U 747 " (cutoff:3.500A) Processing helix chain 'U' and resid 763 through 780 removed outlier: 3.629A pdb=" N ALA U 780 " --> pdb=" O LEU U 776 " (cutoff:3.500A) Processing helix chain 'U' and resid 785 through 800 Proline residue: U 798 - end of helix Processing helix chain 'U' and resid 802 through 808 Processing helix chain 'U' and resid 809 through 814 removed outlier: 3.634A pdb=" N ASN U 813 " --> pdb=" O ARG U 810 " (cutoff:3.500A) Processing helix chain 'U' and resid 829 through 831 No H-bonds generated for 'chain 'U' and resid 829 through 831' Processing helix chain 'U' and resid 832 through 845 Processing helix chain 'U' and resid 847 through 861 Processing helix chain 'V' and resid 453 through 469 removed outlier: 3.536A pdb=" N ALA V 457 " --> pdb=" O SER V 453 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS V 458 " --> pdb=" O ASP V 454 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE V 459 " --> pdb=" O ARG V 455 " (cutoff:3.500A) Processing helix chain 'V' and resid 478 through 485 Processing helix chain 'V' and resid 534 through 549 removed outlier: 4.116A pdb=" N VAL V 538 " --> pdb=" O PHE V 534 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TYR V 541 " --> pdb=" O LYS V 537 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA V 544 " --> pdb=" O ARG V 540 " (cutoff:3.500A) Processing helix chain 'V' and resid 552 through 556 removed outlier: 3.838A pdb=" N GLU V 556 " --> pdb=" O GLU V 553 " (cutoff:3.500A) Processing helix chain 'V' and resid 564 through 579 Processing helix chain 'V' and resid 596 through 603 Processing helix chain 'V' and resid 603 through 612 Processing helix chain 'V' and resid 613 through 615 No H-bonds generated for 'chain 'V' and resid 613 through 615' Processing helix chain 'V' and resid 616 through 629 Processing helix chain 'V' and resid 655 through 674 Processing helix chain 'V' and resid 678 through 684 Processing helix chain 'V' and resid 699 through 701 No H-bonds generated for 'chain 'V' and resid 699 through 701' Processing helix chain 'V' and resid 702 through 712 removed outlier: 4.095A pdb=" N ARG V 706 " --> pdb=" O LYS V 702 " (cutoff:3.500A) Processing helix chain 'V' and resid 745 through 751 removed outlier: 3.550A pdb=" N THR V 749 " --> pdb=" O ASP V 745 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG V 751 " --> pdb=" O LEU V 747 " (cutoff:3.500A) Processing helix chain 'V' and resid 763 through 780 removed outlier: 3.630A pdb=" N ALA V 780 " --> pdb=" O LEU V 776 " (cutoff:3.500A) Processing helix chain 'V' and resid 785 through 800 Proline residue: V 798 - end of helix Processing helix chain 'V' and resid 802 through 808 Processing helix chain 'V' and resid 809 through 814 removed outlier: 3.634A pdb=" N ASN V 813 " --> pdb=" O ARG V 810 " (cutoff:3.500A) Processing helix chain 'V' and resid 829 through 831 No H-bonds generated for 'chain 'V' and resid 829 through 831' Processing helix chain 'V' and resid 832 through 845 Processing helix chain 'V' and resid 847 through 861 Processing helix chain 'W' and resid 453 through 469 removed outlier: 3.537A pdb=" N ALA W 457 " --> pdb=" O SER W 453 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS W 458 " --> pdb=" O ASP W 454 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE W 459 " --> pdb=" O ARG W 455 " (cutoff:3.500A) Processing helix chain 'W' and resid 478 through 485 Processing helix chain 'W' and resid 534 through 549 removed outlier: 4.115A pdb=" N VAL W 538 " --> pdb=" O PHE W 534 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TYR W 541 " --> pdb=" O LYS W 537 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA W 544 " --> pdb=" O ARG W 540 " (cutoff:3.500A) Processing helix chain 'W' and resid 552 through 556 removed outlier: 3.838A pdb=" N GLU W 556 " --> pdb=" O GLU W 553 " (cutoff:3.500A) Processing helix chain 'W' and resid 564 through 579 Processing helix chain 'W' and resid 596 through 603 Processing helix chain 'W' and resid 603 through 612 Processing helix chain 'W' and resid 613 through 615 No H-bonds generated for 'chain 'W' and resid 613 through 615' Processing helix chain 'W' and resid 616 through 629 Processing helix chain 'W' and resid 655 through 674 Processing helix chain 'W' and resid 678 through 684 Processing helix chain 'W' and resid 699 through 701 No H-bonds generated for 'chain 'W' and resid 699 through 701' Processing helix chain 'W' and resid 702 through 712 removed outlier: 4.094A pdb=" N ARG W 706 " --> pdb=" O LYS W 702 " (cutoff:3.500A) Processing helix chain 'W' and resid 745 through 751 removed outlier: 3.549A pdb=" N THR W 749 " --> pdb=" O ASP W 745 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG W 751 " --> pdb=" O LEU W 747 " (cutoff:3.500A) Processing helix chain 'W' and resid 763 through 780 removed outlier: 3.629A pdb=" N ALA W 780 " --> pdb=" O LEU W 776 " (cutoff:3.500A) Processing helix chain 'W' and resid 785 through 800 Proline residue: W 798 - end of helix Processing helix chain 'W' and resid 802 through 808 Processing helix chain 'W' and resid 809 through 814 removed outlier: 3.634A pdb=" N ASN W 813 " --> pdb=" O ARG W 810 " (cutoff:3.500A) Processing helix chain 'W' and resid 829 through 831 No H-bonds generated for 'chain 'W' and resid 829 through 831' Processing helix chain 'W' and resid 832 through 845 Processing helix chain 'W' and resid 847 through 861 Processing helix chain 'X' and resid 453 through 469 removed outlier: 3.536A pdb=" N ALA X 457 " --> pdb=" O SER X 453 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS X 458 " --> pdb=" O ASP X 454 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE X 459 " --> pdb=" O ARG X 455 " (cutoff:3.500A) Processing helix chain 'X' and resid 478 through 485 Processing helix chain 'X' and resid 534 through 549 removed outlier: 4.115A pdb=" N VAL X 538 " --> pdb=" O PHE X 534 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N TYR X 541 " --> pdb=" O LYS X 537 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA X 544 " --> pdb=" O ARG X 540 " (cutoff:3.500A) Processing helix chain 'X' and resid 552 through 556 removed outlier: 3.839A pdb=" N GLU X 556 " --> pdb=" O GLU X 553 " (cutoff:3.500A) Processing helix chain 'X' and resid 564 through 579 Processing helix chain 'X' and resid 596 through 603 Processing helix chain 'X' and resid 603 through 612 Processing helix chain 'X' and resid 613 through 615 No H-bonds generated for 'chain 'X' and resid 613 through 615' Processing helix chain 'X' and resid 616 through 629 Processing helix chain 'X' and resid 655 through 674 Processing helix chain 'X' and resid 678 through 684 Processing helix chain 'X' and resid 699 through 701 No H-bonds generated for 'chain 'X' and resid 699 through 701' Processing helix chain 'X' and resid 702 through 712 removed outlier: 4.094A pdb=" N ARG X 706 " --> pdb=" O LYS X 702 " (cutoff:3.500A) Processing helix chain 'X' and resid 745 through 751 removed outlier: 3.550A pdb=" N THR X 749 " --> pdb=" O ASP X 745 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG X 751 " --> pdb=" O LEU X 747 " (cutoff:3.500A) Processing helix chain 'X' and resid 763 through 780 removed outlier: 3.630A pdb=" N ALA X 780 " --> pdb=" O LEU X 776 " (cutoff:3.500A) Processing helix chain 'X' and resid 785 through 800 Proline residue: X 798 - end of helix Processing helix chain 'X' and resid 802 through 808 Processing helix chain 'X' and resid 809 through 814 removed outlier: 3.634A pdb=" N ASN X 813 " --> pdb=" O ARG X 810 " (cutoff:3.500A) Processing helix chain 'X' and resid 829 through 831 No H-bonds generated for 'chain 'X' and resid 829 through 831' Processing helix chain 'X' and resid 832 through 845 Processing helix chain 'X' and resid 847 through 861 Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 120 removed outlier: 6.220A pdb=" N PHE A 119 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N VAL A 160 " --> pdb=" O PHE A 119 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL A 179 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TYR A 256 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL A 281 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A 254 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TRP A 283 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLU A 252 " --> pdb=" O TRP A 283 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS A 257 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 229 " --> pdb=" O HIS A 257 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 193 removed outlier: 3.687A pdb=" N THR A 199 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 335 through 338 removed outlier: 8.904A pdb=" N VAL L 389 " --> pdb=" O ARG A 312 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLU A 314 " --> pdb=" O VAL L 389 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AA5, first strand: chain 'B' and resid 119 through 120 removed outlier: 6.221A pdb=" N PHE B 119 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N VAL B 160 " --> pdb=" O PHE B 119 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL B 179 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TYR B 256 " --> pdb=" O GLN B 279 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL B 281 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B 254 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TRP B 283 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLU B 252 " --> pdb=" O TRP B 283 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS B 257 " --> pdb=" O ILE B 229 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 229 " --> pdb=" O HIS B 257 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 193 removed outlier: 3.687A pdb=" N THR B 199 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 388 through 389 Processing sheet with id=AA8, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.220A pdb=" N PHE C 119 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N VAL C 160 " --> pdb=" O PHE C 119 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL C 179 " --> pdb=" O THR C 276 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TYR C 256 " --> pdb=" O GLN C 279 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL C 281 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL C 254 " --> pdb=" O VAL C 281 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TRP C 283 " --> pdb=" O GLU C 252 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLU C 252 " --> pdb=" O TRP C 283 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS C 257 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE C 229 " --> pdb=" O HIS C 257 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 191 through 193 removed outlier: 3.687A pdb=" N THR C 199 " --> pdb=" O GLU C 206 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 388 through 389 Processing sheet with id=AB2, first strand: chain 'D' and resid 119 through 120 removed outlier: 6.220A pdb=" N PHE D 119 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N VAL D 160 " --> pdb=" O PHE D 119 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL D 179 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TYR D 256 " --> pdb=" O GLN D 279 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL D 281 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL D 254 " --> pdb=" O VAL D 281 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TRP D 283 " --> pdb=" O GLU D 252 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLU D 252 " --> pdb=" O TRP D 283 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS D 257 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE D 229 " --> pdb=" O HIS D 257 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 191 through 193 removed outlier: 3.687A pdb=" N THR D 199 " --> pdb=" O GLU D 206 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 388 through 389 Processing sheet with id=AB5, first strand: chain 'E' and resid 119 through 120 removed outlier: 6.221A pdb=" N PHE E 119 " --> pdb=" O VAL E 158 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N VAL E 160 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL E 179 " --> pdb=" O THR E 276 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TYR E 256 " --> pdb=" O GLN E 279 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL E 281 " --> pdb=" O VAL E 254 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL E 254 " --> pdb=" O VAL E 281 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TRP E 283 " --> pdb=" O GLU E 252 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLU E 252 " --> pdb=" O TRP E 283 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS E 257 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE E 229 " --> pdb=" O HIS E 257 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 191 through 193 removed outlier: 3.687A pdb=" N THR E 199 " --> pdb=" O GLU E 206 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 388 through 389 Processing sheet with id=AB8, first strand: chain 'F' and resid 119 through 120 removed outlier: 6.220A pdb=" N PHE F 119 " --> pdb=" O VAL F 158 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N VAL F 160 " --> pdb=" O PHE F 119 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL F 179 " --> pdb=" O THR F 276 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TYR F 256 " --> pdb=" O GLN F 279 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL F 281 " --> pdb=" O VAL F 254 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL F 254 " --> pdb=" O VAL F 281 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TRP F 283 " --> pdb=" O GLU F 252 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLU F 252 " --> pdb=" O TRP F 283 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS F 257 " --> pdb=" O ILE F 229 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE F 229 " --> pdb=" O HIS F 257 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 191 through 193 removed outlier: 3.688A pdb=" N THR F 199 " --> pdb=" O GLU F 206 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 388 through 389 Processing sheet with id=AC2, first strand: chain 'G' and resid 119 through 120 removed outlier: 6.220A pdb=" N PHE G 119 " --> pdb=" O VAL G 158 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N VAL G 160 " --> pdb=" O PHE G 119 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL G 179 " --> pdb=" O THR G 276 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TYR G 256 " --> pdb=" O GLN G 279 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL G 281 " --> pdb=" O VAL G 254 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL G 254 " --> pdb=" O VAL G 281 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TRP G 283 " --> pdb=" O GLU G 252 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLU G 252 " --> pdb=" O TRP G 283 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS G 257 " --> pdb=" O ILE G 229 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE G 229 " --> pdb=" O HIS G 257 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 191 through 193 removed outlier: 3.687A pdb=" N THR G 199 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 388 through 389 Processing sheet with id=AC5, first strand: chain 'H' and resid 119 through 120 removed outlier: 6.221A pdb=" N PHE H 119 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N VAL H 160 " --> pdb=" O PHE H 119 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL H 179 " --> pdb=" O THR H 276 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N TYR H 256 " --> pdb=" O GLN H 279 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL H 281 " --> pdb=" O VAL H 254 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL H 254 " --> pdb=" O VAL H 281 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TRP H 283 " --> pdb=" O GLU H 252 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLU H 252 " --> pdb=" O TRP H 283 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS H 257 " --> pdb=" O ILE H 229 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE H 229 " --> pdb=" O HIS H 257 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 191 through 193 removed outlier: 3.687A pdb=" N THR H 199 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 388 through 389 Processing sheet with id=AC8, first strand: chain 'I' and resid 119 through 120 removed outlier: 6.220A pdb=" N PHE I 119 " --> pdb=" O VAL I 158 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N VAL I 160 " --> pdb=" O PHE I 119 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL I 179 " --> pdb=" O THR I 276 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TYR I 256 " --> pdb=" O GLN I 279 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL I 281 " --> pdb=" O VAL I 254 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL I 254 " --> pdb=" O VAL I 281 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TRP I 283 " --> pdb=" O GLU I 252 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLU I 252 " --> pdb=" O TRP I 283 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS I 257 " --> pdb=" O ILE I 229 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE I 229 " --> pdb=" O HIS I 257 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 191 through 193 removed outlier: 3.688A pdb=" N THR I 199 " --> pdb=" O GLU I 206 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 388 through 389 Processing sheet with id=AD2, first strand: chain 'J' and resid 119 through 120 removed outlier: 6.221A pdb=" N PHE J 119 " --> pdb=" O VAL J 158 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N VAL J 160 " --> pdb=" O PHE J 119 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL J 179 " --> pdb=" O THR J 276 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TYR J 256 " --> pdb=" O GLN J 279 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL J 281 " --> pdb=" O VAL J 254 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL J 254 " --> pdb=" O VAL J 281 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TRP J 283 " --> pdb=" O GLU J 252 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLU J 252 " --> pdb=" O TRP J 283 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS J 257 " --> pdb=" O ILE J 229 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE J 229 " --> pdb=" O HIS J 257 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 191 through 193 removed outlier: 3.687A pdb=" N THR J 199 " --> pdb=" O GLU J 206 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 388 through 389 Processing sheet with id=AD5, first strand: chain 'K' and resid 119 through 120 removed outlier: 6.220A pdb=" N PHE K 119 " --> pdb=" O VAL K 158 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N VAL K 160 " --> pdb=" O PHE K 119 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL K 179 " --> pdb=" O THR K 276 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TYR K 256 " --> pdb=" O GLN K 279 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL K 281 " --> pdb=" O VAL K 254 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL K 254 " --> pdb=" O VAL K 281 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TRP K 283 " --> pdb=" O GLU K 252 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLU K 252 " --> pdb=" O TRP K 283 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS K 257 " --> pdb=" O ILE K 229 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE K 229 " --> pdb=" O HIS K 257 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 191 through 193 removed outlier: 3.688A pdb=" N THR K 199 " --> pdb=" O GLU K 206 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 388 through 389 Processing sheet with id=AD8, first strand: chain 'L' and resid 119 through 120 removed outlier: 6.220A pdb=" N PHE L 119 " --> pdb=" O VAL L 158 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N VAL L 160 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL L 179 " --> pdb=" O THR L 276 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TYR L 256 " --> pdb=" O GLN L 279 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL L 281 " --> pdb=" O VAL L 254 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL L 254 " --> pdb=" O VAL L 281 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TRP L 283 " --> pdb=" O GLU L 252 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLU L 252 " --> pdb=" O TRP L 283 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS L 257 " --> pdb=" O ILE L 229 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE L 229 " --> pdb=" O HIS L 257 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 191 through 193 removed outlier: 3.687A pdb=" N THR L 199 " --> pdb=" O GLU L 206 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 689 through 690 removed outlier: 4.070A pdb=" N GLY M 694 " --> pdb=" O THR M 586 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR M 586 " --> pdb=" O GLY M 694 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU M 585 " --> pdb=" O GLU M 718 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU M 718 " --> pdb=" O GLU M 585 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 726 through 728 removed outlier: 3.750A pdb=" N LEU M 726 " --> pdb=" O PHE M 733 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 689 through 690 removed outlier: 4.070A pdb=" N GLY N 694 " --> pdb=" O THR N 586 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR N 586 " --> pdb=" O GLY N 694 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU N 585 " --> pdb=" O GLU N 718 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU N 718 " --> pdb=" O GLU N 585 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 726 through 728 removed outlier: 3.749A pdb=" N LEU N 726 " --> pdb=" O PHE N 733 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'O' and resid 689 through 690 removed outlier: 4.069A pdb=" N GLY O 694 " --> pdb=" O THR O 586 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR O 586 " --> pdb=" O GLY O 694 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU O 585 " --> pdb=" O GLU O 718 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU O 718 " --> pdb=" O GLU O 585 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'O' and resid 726 through 728 removed outlier: 3.750A pdb=" N LEU O 726 " --> pdb=" O PHE O 733 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'P' and resid 689 through 690 removed outlier: 4.070A pdb=" N GLY P 694 " --> pdb=" O THR P 586 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR P 586 " --> pdb=" O GLY P 694 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU P 585 " --> pdb=" O GLU P 718 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU P 718 " --> pdb=" O GLU P 585 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'P' and resid 726 through 728 removed outlier: 3.749A pdb=" N LEU P 726 " --> pdb=" O PHE P 733 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 689 through 690 removed outlier: 4.070A pdb=" N GLY Q 694 " --> pdb=" O THR Q 586 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR Q 586 " --> pdb=" O GLY Q 694 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU Q 585 " --> pdb=" O GLU Q 718 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU Q 718 " --> pdb=" O GLU Q 585 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Q' and resid 726 through 728 removed outlier: 3.750A pdb=" N LEU Q 726 " --> pdb=" O PHE Q 733 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'R' and resid 689 through 690 removed outlier: 4.070A pdb=" N GLY R 694 " --> pdb=" O THR R 586 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR R 586 " --> pdb=" O GLY R 694 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU R 585 " --> pdb=" O GLU R 718 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU R 718 " --> pdb=" O GLU R 585 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'R' and resid 726 through 728 removed outlier: 3.750A pdb=" N LEU R 726 " --> pdb=" O PHE R 733 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'S' and resid 689 through 690 removed outlier: 4.069A pdb=" N GLY S 694 " --> pdb=" O THR S 586 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR S 586 " --> pdb=" O GLY S 694 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU S 585 " --> pdb=" O GLU S 718 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU S 718 " --> pdb=" O GLU S 585 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'S' and resid 726 through 728 removed outlier: 3.750A pdb=" N LEU S 726 " --> pdb=" O PHE S 733 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'T' and resid 689 through 690 removed outlier: 4.069A pdb=" N GLY T 694 " --> pdb=" O THR T 586 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR T 586 " --> pdb=" O GLY T 694 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU T 585 " --> pdb=" O GLU T 718 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU T 718 " --> pdb=" O GLU T 585 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'T' and resid 726 through 728 removed outlier: 3.750A pdb=" N LEU T 726 " --> pdb=" O PHE T 733 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'U' and resid 689 through 690 removed outlier: 4.070A pdb=" N GLY U 694 " --> pdb=" O THR U 586 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR U 586 " --> pdb=" O GLY U 694 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU U 585 " --> pdb=" O GLU U 718 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU U 718 " --> pdb=" O GLU U 585 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'U' and resid 726 through 728 removed outlier: 3.750A pdb=" N LEU U 726 " --> pdb=" O PHE U 733 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'V' and resid 689 through 690 removed outlier: 4.071A pdb=" N GLY V 694 " --> pdb=" O THR V 586 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR V 586 " --> pdb=" O GLY V 694 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU V 585 " --> pdb=" O GLU V 718 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU V 718 " --> pdb=" O GLU V 585 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'V' and resid 726 through 728 removed outlier: 3.750A pdb=" N LEU V 726 " --> pdb=" O PHE V 733 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 689 through 690 removed outlier: 4.070A pdb=" N GLY W 694 " --> pdb=" O THR W 586 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR W 586 " --> pdb=" O GLY W 694 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU W 585 " --> pdb=" O GLU W 718 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU W 718 " --> pdb=" O GLU W 585 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'W' and resid 726 through 728 removed outlier: 3.750A pdb=" N LEU W 726 " --> pdb=" O PHE W 733 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 689 through 690 removed outlier: 4.070A pdb=" N GLY X 694 " --> pdb=" O THR X 586 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR X 586 " --> pdb=" O GLY X 694 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU X 585 " --> pdb=" O GLU X 718 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU X 718 " --> pdb=" O GLU X 585 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'X' and resid 726 through 728 removed outlier: 3.750A pdb=" N LEU X 726 " --> pdb=" O PHE X 733 " (cutoff:3.500A) 2758 hydrogen bonds defined for protein. 7914 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: 34.57 Time building geometry restraints manager: 20.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 29880 1.03 - 1.23: 36 1.23 - 1.42: 21168 1.42 - 1.61: 26268 1.61 - 1.81: 180 Bond restraints: 77532 Sorted by residual: bond pdb=" N THR I 55 " pdb=" CA THR I 55 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N THR L 55 " pdb=" CA THR L 55 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N THR F 55 " pdb=" CA THR F 55 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N THR G 55 " pdb=" CA THR G 55 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N THR A 55 " pdb=" CA THR A 55 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 ... (remaining 77527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 125914 1.12 - 2.25: 4639 2.25 - 3.37: 271 3.37 - 4.50: 96 4.50 - 5.62: 24 Bond angle restraints: 130944 Sorted by residual: angle pdb=" CA LYS U 458 " pdb=" CB LYS U 458 " pdb=" CG LYS U 458 " ideal model delta sigma weight residual 114.10 118.22 -4.12 2.00e+00 2.50e-01 4.24e+00 angle pdb=" CA LYS R 458 " pdb=" CB LYS R 458 " pdb=" CG LYS R 458 " ideal model delta sigma weight residual 114.10 118.22 -4.12 2.00e+00 2.50e-01 4.24e+00 angle pdb=" CA LYS N 458 " pdb=" CB LYS N 458 " pdb=" CG LYS N 458 " ideal model delta sigma weight residual 114.10 118.20 -4.10 2.00e+00 2.50e-01 4.20e+00 angle pdb=" CA LYS T 458 " pdb=" CB LYS T 458 " pdb=" CG LYS T 458 " ideal model delta sigma weight residual 114.10 118.20 -4.10 2.00e+00 2.50e-01 4.20e+00 angle pdb=" CA LYS M 458 " pdb=" CB LYS M 458 " pdb=" CG LYS M 458 " ideal model delta sigma weight residual 114.10 118.20 -4.10 2.00e+00 2.50e-01 4.20e+00 ... (remaining 130939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.50: 29974 15.50 - 31.00: 2507 31.00 - 46.50: 639 46.50 - 62.01: 180 62.01 - 77.51: 60 Dihedral angle restraints: 33360 sinusoidal: 15996 harmonic: 17364 Sorted by residual: dihedral pdb=" CA LYS B 391 " pdb=" C LYS B 391 " pdb=" N PRO B 392 " pdb=" CA PRO B 392 " ideal model delta harmonic sigma weight residual 180.00 163.15 16.85 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA LYS J 391 " pdb=" C LYS J 391 " pdb=" N PRO J 392 " pdb=" CA PRO J 392 " ideal model delta harmonic sigma weight residual 180.00 163.17 16.83 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA LYS G 391 " pdb=" C LYS G 391 " pdb=" N PRO G 392 " pdb=" CA PRO G 392 " ideal model delta harmonic sigma weight residual 180.00 163.18 16.82 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 33357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2826 0.028 - 0.055: 1291 0.055 - 0.083: 324 0.083 - 0.111: 319 0.111 - 0.138: 100 Chirality restraints: 4860 Sorted by residual: chirality pdb=" CA ILE X 743 " pdb=" N ILE X 743 " pdb=" C ILE X 743 " pdb=" CB ILE X 743 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA ILE O 743 " pdb=" N ILE O 743 " pdb=" C ILE O 743 " pdb=" CB ILE O 743 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA ILE R 743 " pdb=" N ILE R 743 " pdb=" C ILE R 743 " pdb=" CB ILE R 743 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 4857 not shown) Planarity restraints: 12780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS E 391 " -0.017 5.00e-02 4.00e+02 2.64e-02 1.11e+00 pdb=" N PRO E 392 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO E 392 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO E 392 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 391 " -0.017 5.00e-02 4.00e+02 2.64e-02 1.11e+00 pdb=" N PRO A 392 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 392 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 392 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS I 391 " -0.017 5.00e-02 4.00e+02 2.63e-02 1.11e+00 pdb=" N PRO I 392 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO I 392 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO I 392 " -0.015 5.00e-02 4.00e+02 ... (remaining 12777 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 2628 2.16 - 2.77: 120492 2.77 - 3.38: 179749 3.38 - 3.99: 226669 3.99 - 4.60: 348449 Nonbonded interactions: 877987 Sorted by model distance: nonbonded pdb=" O ILE F 200 " pdb=" H GLY F 330 " model vdw 1.552 2.450 nonbonded pdb=" O ILE G 200 " pdb=" H GLY G 330 " model vdw 1.553 2.450 nonbonded pdb=" O ILE J 200 " pdb=" H GLY J 330 " model vdw 1.553 2.450 nonbonded pdb=" O ILE D 200 " pdb=" H GLY D 330 " model vdw 1.553 2.450 nonbonded pdb=" O ILE K 200 " pdb=" H GLY K 330 " model vdw 1.553 2.450 ... (remaining 877982 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 18.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.460 Extract box with map and model: 2.790 Check model and map are aligned: 0.500 Set scattering table: 0.580 Process input model: 134.260 Find NCS groups from input model: 2.070 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 163.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 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 : 0.002 0.033 47616 Z= 0.150 Angle : 0.448 5.622 62940 Z= 0.249 Chirality : 0.042 0.138 4860 Planarity : 0.002 0.026 9324 Dihedral : 11.342 68.714 15816 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: 0.35 (0.10), residues: 7548 helix: 1.59 (0.10), residues: 3324 sheet: -1.20 (0.16), residues: 1068 loop : -0.66 (0.11), residues: 3156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 220 HIS 0.005 0.001 HIS H 261 PHE 0.007 0.001 PHE E 285 TYR 0.010 0.001 TYR G 368 ARG 0.002 0.000 ARG K 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 840 time to evaluate : 5.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASN cc_start: 0.7097 (m-40) cc_final: 0.6550 (m110) REVERT: A 243 GLN cc_start: 0.8237 (pt0) cc_final: 0.7949 (tt0) REVERT: A 296 LYS cc_start: 0.8530 (mtmm) cc_final: 0.8103 (mtpp) REVERT: B 122 ASN cc_start: 0.7041 (m-40) cc_final: 0.6372 (m-40) REVERT: B 296 LYS cc_start: 0.8375 (mtmm) cc_final: 0.7965 (mtpp) REVERT: C 122 ASN cc_start: 0.7028 (m-40) cc_final: 0.6460 (m110) REVERT: C 243 GLN cc_start: 0.8124 (pt0) cc_final: 0.7861 (tt0) REVERT: C 296 LYS cc_start: 0.8569 (mtmm) cc_final: 0.8097 (mtpp) REVERT: D 122 ASN cc_start: 0.7121 (m-40) cc_final: 0.6525 (m110) REVERT: D 243 GLN cc_start: 0.8243 (pt0) cc_final: 0.7945 (tt0) REVERT: D 296 LYS cc_start: 0.8485 (mtmm) cc_final: 0.8061 (mtpp) REVERT: E 122 ASN cc_start: 0.7041 (m-40) cc_final: 0.6369 (m-40) REVERT: E 296 LYS cc_start: 0.8375 (mtmm) cc_final: 0.7965 (mtpp) REVERT: F 122 ASN cc_start: 0.7040 (m-40) cc_final: 0.6460 (m110) REVERT: F 243 GLN cc_start: 0.8125 (pt0) cc_final: 0.7831 (tt0) REVERT: F 296 LYS cc_start: 0.8563 (mtmm) cc_final: 0.8107 (mtpp) REVERT: G 122 ASN cc_start: 0.7106 (m-40) cc_final: 0.6568 (m110) REVERT: G 227 GLU cc_start: 0.7172 (mp0) cc_final: 0.6868 (mp0) REVERT: G 243 GLN cc_start: 0.8233 (pt0) cc_final: 0.7950 (tt0) REVERT: G 296 LYS cc_start: 0.8511 (mtmm) cc_final: 0.8095 (mtpp) REVERT: H 122 ASN cc_start: 0.7010 (m-40) cc_final: 0.6357 (m110) REVERT: H 296 LYS cc_start: 0.8378 (mtmm) cc_final: 0.7955 (mtpp) REVERT: I 122 ASN cc_start: 0.7044 (m-40) cc_final: 0.6452 (m110) REVERT: I 243 GLN cc_start: 0.8124 (pt0) cc_final: 0.7831 (tt0) REVERT: I 296 LYS cc_start: 0.8579 (mtmm) cc_final: 0.8116 (mtpp) REVERT: J 122 ASN cc_start: 0.7145 (m-40) cc_final: 0.6592 (m110) REVERT: J 227 GLU cc_start: 0.7175 (mp0) cc_final: 0.6884 (mp0) REVERT: J 243 GLN cc_start: 0.8238 (pt0) cc_final: 0.7946 (tt0) REVERT: J 296 LYS cc_start: 0.8531 (mtmm) cc_final: 0.8101 (mtpp) REVERT: K 122 ASN cc_start: 0.7015 (m-40) cc_final: 0.6359 (m110) REVERT: K 296 LYS cc_start: 0.8405 (mtmm) cc_final: 0.7986 (mtpp) REVERT: L 122 ASN cc_start: 0.7040 (m-40) cc_final: 0.6462 (m110) REVERT: L 243 GLN cc_start: 0.8123 (pt0) cc_final: 0.7860 (tt0) REVERT: L 296 LYS cc_start: 0.8575 (mtmm) cc_final: 0.8107 (mtpp) outliers start: 0 outliers final: 0 residues processed: 840 average time/residue: 0.8907 time to fit residues: 1211.2778 Evaluate side-chains 656 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 656 time to evaluate : 5.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 638 optimal weight: 10.0000 chunk 573 optimal weight: 3.9990 chunk 317 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 386 optimal weight: 9.9990 chunk 306 optimal weight: 6.9990 chunk 592 optimal weight: 20.0000 chunk 229 optimal weight: 4.9990 chunk 360 optimal weight: 30.0000 chunk 441 optimal weight: 3.9990 chunk 686 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS B 293 HIS D 293 HIS E 293 HIS G 293 HIS H 293 HIS J 293 HIS K 293 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 47616 Z= 0.453 Angle : 0.604 5.616 62940 Z= 0.332 Chirality : 0.049 0.143 4860 Planarity : 0.004 0.038 9324 Dihedral : 4.476 23.102 8016 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.55 % Allowed : 6.95 % Favored : 92.50 % 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: 0.44 (0.10), residues: 7548 helix: 1.90 (0.09), residues: 3360 sheet: -1.16 (0.16), residues: 1020 loop : -0.95 (0.10), residues: 3168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 265 HIS 0.006 0.001 HIS L 257 PHE 0.012 0.002 PHE W 672 TYR 0.017 0.002 TYR G 368 ARG 0.005 0.001 ARG E 271 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 651 time to evaluate : 5.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.8462 (mmm) cc_final: 0.8119 (mmm) REVERT: A 206 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8159 (mt-10) REVERT: A 243 GLN cc_start: 0.8310 (pt0) cc_final: 0.8006 (tt0) REVERT: A 256 TYR cc_start: 0.8581 (m-10) cc_final: 0.8294 (m-10) REVERT: A 296 LYS cc_start: 0.8505 (mtmm) cc_final: 0.8098 (mtpp) REVERT: A 311 ASN cc_start: 0.8985 (m-40) cc_final: 0.8706 (m-40) REVERT: B 296 LYS cc_start: 0.8452 (mtmm) cc_final: 0.8063 (mtpp) REVERT: B 311 ASN cc_start: 0.8997 (m-40) cc_final: 0.8721 (m-40) REVERT: B 331 GLU cc_start: 0.7728 (tt0) cc_final: 0.7504 (mt-10) REVERT: C 206 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8255 (mt-10) REVERT: C 243 GLN cc_start: 0.8356 (pt0) cc_final: 0.8021 (tt0) REVERT: C 296 LYS cc_start: 0.8594 (mtmm) cc_final: 0.8146 (mtpp) REVERT: D 176 MET cc_start: 0.8494 (mmm) cc_final: 0.8201 (mmm) REVERT: D 206 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8159 (mt-10) REVERT: D 243 GLN cc_start: 0.8349 (pt0) cc_final: 0.8044 (tt0) REVERT: D 256 TYR cc_start: 0.8587 (m-10) cc_final: 0.8291 (m-10) REVERT: D 296 LYS cc_start: 0.8504 (mtmm) cc_final: 0.8093 (mtpp) REVERT: D 311 ASN cc_start: 0.8983 (m-40) cc_final: 0.8697 (m-40) REVERT: E 296 LYS cc_start: 0.8456 (mtmm) cc_final: 0.8065 (mtpp) REVERT: E 311 ASN cc_start: 0.8997 (m-40) cc_final: 0.8722 (m-40) REVERT: E 331 GLU cc_start: 0.7733 (tt0) cc_final: 0.7499 (mt-10) REVERT: F 206 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8262 (mt-10) REVERT: F 243 GLN cc_start: 0.8370 (pt0) cc_final: 0.8040 (tt0) REVERT: F 296 LYS cc_start: 0.8584 (mtmm) cc_final: 0.8151 (mtpp) REVERT: G 176 MET cc_start: 0.8473 (mmm) cc_final: 0.8127 (mmm) REVERT: G 206 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8156 (mt-10) REVERT: G 243 GLN cc_start: 0.8314 (pt0) cc_final: 0.8018 (tt0) REVERT: G 256 TYR cc_start: 0.8576 (m-10) cc_final: 0.8285 (m-10) REVERT: G 296 LYS cc_start: 0.8503 (mtmm) cc_final: 0.8096 (mtpp) REVERT: G 311 ASN cc_start: 0.8987 (m-40) cc_final: 0.8699 (m-40) REVERT: H 296 LYS cc_start: 0.8447 (mtmm) cc_final: 0.8055 (mtpp) REVERT: H 311 ASN cc_start: 0.8996 (m-40) cc_final: 0.8721 (m-40) REVERT: H 331 GLU cc_start: 0.7732 (tt0) cc_final: 0.7497 (mt-10) REVERT: I 206 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8255 (mt-10) REVERT: I 243 GLN cc_start: 0.8368 (pt0) cc_final: 0.8044 (tt0) REVERT: I 296 LYS cc_start: 0.8585 (mtmm) cc_final: 0.8151 (mtpp) REVERT: J 176 MET cc_start: 0.8490 (mmm) cc_final: 0.8202 (mmm) REVERT: J 206 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8157 (mt-10) REVERT: J 227 GLU cc_start: 0.7355 (mp0) cc_final: 0.7142 (mp0) REVERT: J 243 GLN cc_start: 0.8344 (pt0) cc_final: 0.8044 (tt0) REVERT: J 256 TYR cc_start: 0.8588 (m-10) cc_final: 0.8289 (m-10) REVERT: J 296 LYS cc_start: 0.8503 (mtmm) cc_final: 0.8091 (mtpp) REVERT: J 311 ASN cc_start: 0.8982 (m-40) cc_final: 0.8700 (m-40) REVERT: K 206 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8163 (mt-10) REVERT: K 296 LYS cc_start: 0.8458 (mtmm) cc_final: 0.8072 (mtpp) REVERT: K 311 ASN cc_start: 0.8994 (m-40) cc_final: 0.8717 (m-40) REVERT: K 331 GLU cc_start: 0.7727 (tt0) cc_final: 0.7502 (mt-10) REVERT: L 206 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8257 (mt-10) REVERT: L 243 GLN cc_start: 0.8377 (pt0) cc_final: 0.8067 (tt0) REVERT: L 296 LYS cc_start: 0.8595 (mtmm) cc_final: 0.8145 (mtpp) outliers start: 19 outliers final: 8 residues processed: 661 average time/residue: 0.8434 time to fit residues: 941.5079 Evaluate side-chains 590 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 582 time to evaluate : 5.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain G residue 231 SER Chi-restraints excluded: chain I residue 317 THR Chi-restraints excluded: chain J residue 231 SER Chi-restraints excluded: chain L residue 317 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 381 optimal weight: 40.0000 chunk 213 optimal weight: 0.1980 chunk 571 optimal weight: 5.9990 chunk 467 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 chunk 687 optimal weight: 6.9990 chunk 742 optimal weight: 0.0970 chunk 612 optimal weight: 30.0000 chunk 682 optimal weight: 10.0000 chunk 234 optimal weight: 0.7980 chunk 551 optimal weight: 20.0000 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 47616 Z= 0.194 Angle : 0.444 5.005 62940 Z= 0.235 Chirality : 0.044 0.137 4860 Planarity : 0.003 0.025 9324 Dihedral : 3.744 18.201 8016 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.49 % Allowed : 8.88 % Favored : 90.63 % 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: 1.16 (0.10), residues: 7548 helix: 2.49 (0.10), residues: 3408 sheet: -0.94 (0.16), residues: 996 loop : -0.58 (0.11), residues: 3144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 265 HIS 0.004 0.001 HIS L 257 PHE 0.004 0.001 PHE L 241 TYR 0.020 0.001 TYR B 275 ARG 0.002 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 572 time to evaluate : 5.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.8457 (mmm) cc_final: 0.8099 (mmm) REVERT: A 243 GLN cc_start: 0.8301 (pt0) cc_final: 0.7962 (tt0) REVERT: A 256 TYR cc_start: 0.8571 (m-10) cc_final: 0.8290 (m-10) REVERT: A 296 LYS cc_start: 0.8492 (mtmm) cc_final: 0.8064 (mtpp) REVERT: B 206 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8013 (mt-10) REVERT: B 296 LYS cc_start: 0.8425 (mtmm) cc_final: 0.8015 (mtpp) REVERT: C 206 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8234 (mt-10) REVERT: C 243 GLN cc_start: 0.8381 (pt0) cc_final: 0.8043 (tt0) REVERT: C 293 HIS cc_start: 0.6052 (OUTLIER) cc_final: 0.5836 (m-70) REVERT: C 296 LYS cc_start: 0.8614 (mtmm) cc_final: 0.8146 (mtpp) REVERT: D 176 MET cc_start: 0.8455 (mmm) cc_final: 0.8182 (mmm) REVERT: D 243 GLN cc_start: 0.8360 (pt0) cc_final: 0.8031 (tt0) REVERT: D 256 TYR cc_start: 0.8585 (m-10) cc_final: 0.8287 (m-10) REVERT: D 296 LYS cc_start: 0.8492 (mtmm) cc_final: 0.8058 (mtpp) REVERT: E 206 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8013 (mt-10) REVERT: E 296 LYS cc_start: 0.8425 (mtmm) cc_final: 0.8015 (mtpp) REVERT: F 206 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8239 (mt-10) REVERT: F 243 GLN cc_start: 0.8386 (pt0) cc_final: 0.8031 (tt0) REVERT: F 293 HIS cc_start: 0.5980 (OUTLIER) cc_final: 0.5758 (m-70) REVERT: F 296 LYS cc_start: 0.8596 (mtmm) cc_final: 0.8128 (mtpp) REVERT: G 176 MET cc_start: 0.8457 (mmm) cc_final: 0.8097 (mmm) REVERT: G 243 GLN cc_start: 0.8314 (pt0) cc_final: 0.7971 (tt0) REVERT: G 296 LYS cc_start: 0.8488 (mtmm) cc_final: 0.8057 (mtpp) REVERT: H 206 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8161 (mt-10) REVERT: H 240 TRP cc_start: 0.6484 (t60) cc_final: 0.5904 (t-100) REVERT: H 296 LYS cc_start: 0.8421 (mtmm) cc_final: 0.8009 (mtpp) REVERT: I 206 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8238 (mt-10) REVERT: I 243 GLN cc_start: 0.8388 (pt0) cc_final: 0.8032 (tt0) REVERT: I 293 HIS cc_start: 0.5984 (OUTLIER) cc_final: 0.5752 (m-70) REVERT: I 296 LYS cc_start: 0.8594 (mtmm) cc_final: 0.8125 (mtpp) REVERT: J 176 MET cc_start: 0.8456 (mmm) cc_final: 0.8169 (mmm) REVERT: J 243 GLN cc_start: 0.8362 (pt0) cc_final: 0.8036 (tt0) REVERT: J 256 TYR cc_start: 0.8581 (m-10) cc_final: 0.8284 (m-10) REVERT: J 296 LYS cc_start: 0.8488 (mtmm) cc_final: 0.8054 (mtpp) REVERT: K 206 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8006 (mt-10) REVERT: K 296 LYS cc_start: 0.8427 (mtmm) cc_final: 0.8021 (mtpp) REVERT: L 206 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8235 (mt-10) REVERT: L 243 GLN cc_start: 0.8384 (pt0) cc_final: 0.8049 (tt0) REVERT: L 293 HIS cc_start: 0.6043 (OUTLIER) cc_final: 0.5838 (m-70) REVERT: L 296 LYS cc_start: 0.8616 (mtmm) cc_final: 0.8140 (mtpp) outliers start: 17 outliers final: 9 residues processed: 585 average time/residue: 0.8061 time to fit residues: 803.8726 Evaluate side-chains 561 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 548 time to evaluate : 5.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 293 HIS Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 293 HIS Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 293 HIS Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain J residue 340 GLU Chi-restraints excluded: chain L residue 189 VAL Chi-restraints excluded: chain L residue 293 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 679 optimal weight: 20.0000 chunk 517 optimal weight: 10.0000 chunk 356 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 328 optimal weight: 1.9990 chunk 461 optimal weight: 30.0000 chunk 690 optimal weight: 40.0000 chunk 730 optimal weight: 0.3980 chunk 360 optimal weight: 40.0000 chunk 654 optimal weight: 0.9980 chunk 196 optimal weight: 0.0980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 47616 Z= 0.180 Angle : 0.422 5.151 62940 Z= 0.221 Chirality : 0.043 0.136 4860 Planarity : 0.002 0.025 9324 Dihedral : 3.525 17.470 8016 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.03 % Allowed : 9.54 % Favored : 89.43 % 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: 1.60 (0.10), residues: 7548 helix: 2.90 (0.10), residues: 3348 sheet: -0.80 (0.17), residues: 996 loop : -0.31 (0.11), residues: 3204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 265 HIS 0.004 0.001 HIS C 257 PHE 0.004 0.001 PHE W 672 TYR 0.018 0.001 TYR H 275 ARG 0.002 0.000 ARG H 271 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 541 time to evaluate : 5.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8242 (mt-10) REVERT: A 296 LYS cc_start: 0.8481 (mtmm) cc_final: 0.8045 (mtpp) REVERT: B 206 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8004 (mt-10) REVERT: B 240 TRP cc_start: 0.6442 (t60) cc_final: 0.5882 (t-100) REVERT: B 296 LYS cc_start: 0.8428 (mtmm) cc_final: 0.8008 (mtpp) REVERT: C 293 HIS cc_start: 0.6047 (OUTLIER) cc_final: 0.5799 (m-70) REVERT: C 296 LYS cc_start: 0.8636 (mtmm) cc_final: 0.8131 (mtpp) REVERT: C 348 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8394 (mp) REVERT: D 176 MET cc_start: 0.8438 (mmm) cc_final: 0.8143 (mmm) REVERT: D 206 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8243 (mt-10) REVERT: D 296 LYS cc_start: 0.8485 (mtmm) cc_final: 0.8056 (mtpp) REVERT: D 314 GLU cc_start: 0.7966 (pt0) cc_final: 0.7678 (mt-10) REVERT: E 206 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8006 (mt-10) REVERT: E 240 TRP cc_start: 0.6444 (t60) cc_final: 0.5884 (t-100) REVERT: E 296 LYS cc_start: 0.8429 (mtmm) cc_final: 0.8011 (mtpp) REVERT: F 293 HIS cc_start: 0.6037 (OUTLIER) cc_final: 0.5786 (m-70) REVERT: F 296 LYS cc_start: 0.8570 (mtmm) cc_final: 0.8091 (mtpp) REVERT: F 348 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8386 (mp) REVERT: G 176 MET cc_start: 0.8477 (mmm) cc_final: 0.8143 (mmm) REVERT: G 206 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8243 (mt-10) REVERT: G 296 LYS cc_start: 0.8485 (mtmm) cc_final: 0.8041 (mtpp) REVERT: G 314 GLU cc_start: 0.7963 (pt0) cc_final: 0.7677 (mt-10) REVERT: H 206 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8023 (mt-10) REVERT: H 240 TRP cc_start: 0.6436 (t60) cc_final: 0.5880 (t-100) REVERT: H 296 LYS cc_start: 0.8430 (mtmm) cc_final: 0.8007 (mtpp) REVERT: I 293 HIS cc_start: 0.6038 (OUTLIER) cc_final: 0.5789 (m-70) REVERT: I 296 LYS cc_start: 0.8570 (mtmm) cc_final: 0.8087 (mtpp) REVERT: I 348 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8388 (mp) REVERT: J 176 MET cc_start: 0.8439 (mmm) cc_final: 0.8144 (mmm) REVERT: J 206 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8240 (mt-10) REVERT: J 256 TYR cc_start: 0.8591 (m-10) cc_final: 0.8186 (m-10) REVERT: J 296 LYS cc_start: 0.8475 (mtmm) cc_final: 0.8046 (mtpp) REVERT: J 314 GLU cc_start: 0.7963 (pt0) cc_final: 0.7678 (mt-10) REVERT: K 206 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8040 (mt-10) REVERT: K 240 TRP cc_start: 0.6443 (t60) cc_final: 0.5883 (t-100) REVERT: K 296 LYS cc_start: 0.8427 (mtmm) cc_final: 0.8014 (mtpp) REVERT: L 293 HIS cc_start: 0.6036 (OUTLIER) cc_final: 0.5792 (m-70) REVERT: L 296 LYS cc_start: 0.8615 (mtmm) cc_final: 0.8117 (mtpp) REVERT: L 348 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8393 (mp) outliers start: 36 outliers final: 21 residues processed: 558 average time/residue: 0.8035 time to fit residues: 755.7869 Evaluate side-chains 561 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 532 time to evaluate : 5.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 293 HIS Chi-restraints excluded: chain C residue 331 GLU Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 331 GLU Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 293 HIS Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 231 SER Chi-restraints excluded: chain G residue 331 GLU Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 293 HIS Chi-restraints excluded: chain I residue 331 GLU Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain J residue 231 SER Chi-restraints excluded: chain J residue 331 GLU Chi-restraints excluded: chain J residue 340 GLU Chi-restraints excluded: chain L residue 189 VAL Chi-restraints excluded: chain L residue 293 HIS Chi-restraints excluded: chain L residue 331 GLU Chi-restraints excluded: chain L residue 348 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 608 optimal weight: 30.0000 chunk 414 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 544 optimal weight: 0.6980 chunk 301 optimal weight: 9.9990 chunk 623 optimal weight: 40.0000 chunk 505 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 373 optimal weight: 7.9990 chunk 655 optimal weight: 50.0000 chunk 184 optimal weight: 4.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 47616 Z= 0.556 Angle : 0.639 7.259 62940 Z= 0.353 Chirality : 0.051 0.156 4860 Planarity : 0.004 0.035 9324 Dihedral : 4.759 25.683 8016 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.39 % Allowed : 11.03 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.58 (0.10), residues: 7548 helix: 2.19 (0.09), residues: 3300 sheet: -1.00 (0.18), residues: 876 loop : -1.10 (0.10), residues: 3372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 265 HIS 0.009 0.002 HIS G 257 PHE 0.011 0.002 PHE N 672 TYR 0.014 0.002 TYR K 275 ARG 0.005 0.001 ARG K 328 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 552 time to evaluate : 5.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.8587 (mmm) cc_final: 0.8345 (mmm) REVERT: A 296 LYS cc_start: 0.8550 (mtmm) cc_final: 0.8116 (mtpp) REVERT: B 206 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8227 (mt-10) REVERT: B 361 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.7502 (mpp) REVERT: C 293 HIS cc_start: 0.6581 (OUTLIER) cc_final: 0.6273 (m-70) REVERT: C 296 LYS cc_start: 0.8591 (mtmm) cc_final: 0.8097 (mtpp) REVERT: C 361 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.7358 (mpp) REVERT: D 176 MET cc_start: 0.8465 (mmm) cc_final: 0.8254 (mmm) REVERT: D 296 LYS cc_start: 0.8562 (mtmm) cc_final: 0.8124 (mtpp) REVERT: E 206 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8232 (mt-10) REVERT: E 361 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.7501 (mpp) REVERT: F 293 HIS cc_start: 0.6622 (OUTLIER) cc_final: 0.6314 (m-70) REVERT: F 296 LYS cc_start: 0.8598 (mtmm) cc_final: 0.8107 (mtpp) REVERT: F 361 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7365 (mpp) REVERT: G 176 MET cc_start: 0.8536 (mmm) cc_final: 0.8199 (mmm) REVERT: G 296 LYS cc_start: 0.8562 (mtmm) cc_final: 0.8130 (mtpp) REVERT: H 206 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8228 (mt-10) REVERT: H 296 LYS cc_start: 0.8527 (mtmm) cc_final: 0.8133 (mtpp) REVERT: H 361 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.7503 (mpp) REVERT: I 293 HIS cc_start: 0.6622 (OUTLIER) cc_final: 0.6317 (m-70) REVERT: I 296 LYS cc_start: 0.8593 (mtmm) cc_final: 0.8105 (mtpp) REVERT: I 361 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7363 (mpp) REVERT: J 176 MET cc_start: 0.8466 (mmm) cc_final: 0.8256 (mmm) REVERT: J 296 LYS cc_start: 0.8557 (mtmm) cc_final: 0.8130 (mtpp) REVERT: K 206 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8235 (mt-10) REVERT: K 361 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7500 (mpp) REVERT: L 293 HIS cc_start: 0.6587 (OUTLIER) cc_final: 0.6281 (m-70) REVERT: L 296 LYS cc_start: 0.8593 (mtmm) cc_final: 0.8102 (mtpp) REVERT: L 361 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7365 (mpp) outliers start: 83 outliers final: 51 residues processed: 592 average time/residue: 0.8583 time to fit residues: 857.3423 Evaluate side-chains 605 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 542 time to evaluate : 5.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 293 HIS Chi-restraints excluded: chain C residue 331 GLU Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 361 MET Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 331 GLU Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 361 MET Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 361 MET Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 293 HIS Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 340 GLU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 231 SER Chi-restraints excluded: chain G residue 331 GLU Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain G residue 348 LEU Chi-restraints excluded: chain G residue 361 MET Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 361 MET Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 231 SER Chi-restraints excluded: chain I residue 293 HIS Chi-restraints excluded: chain I residue 331 GLU Chi-restraints excluded: chain I residue 340 GLU Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain I residue 361 MET Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 231 SER Chi-restraints excluded: chain J residue 331 GLU Chi-restraints excluded: chain J residue 340 GLU Chi-restraints excluded: chain J residue 348 LEU Chi-restraints excluded: chain J residue 361 MET Chi-restraints excluded: chain K residue 300 ILE Chi-restraints excluded: chain K residue 361 MET Chi-restraints excluded: chain L residue 189 VAL Chi-restraints excluded: chain L residue 231 SER Chi-restraints excluded: chain L residue 293 HIS Chi-restraints excluded: chain L residue 331 GLU Chi-restraints excluded: chain L residue 340 GLU Chi-restraints excluded: chain L residue 361 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 245 optimal weight: 5.9990 chunk 658 optimal weight: 8.9990 chunk 144 optimal weight: 0.6980 chunk 429 optimal weight: 20.0000 chunk 180 optimal weight: 9.9990 chunk 731 optimal weight: 9.9990 chunk 607 optimal weight: 20.0000 chunk 338 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 241 optimal weight: 2.9990 chunk 384 optimal weight: 0.0000 overall best weight: 2.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 367 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 47616 Z= 0.293 Angle : 0.485 5.904 62940 Z= 0.260 Chirality : 0.045 0.142 4860 Planarity : 0.003 0.032 9324 Dihedral : 4.127 20.054 8016 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.01 % Allowed : 12.44 % Favored : 85.55 % 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: 1.16 (0.10), residues: 7548 helix: 2.86 (0.10), residues: 3216 sheet: -1.00 (0.18), residues: 876 loop : -0.82 (0.10), residues: 3456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 265 HIS 0.005 0.001 HIS G 257 PHE 0.006 0.001 PHE J 285 TYR 0.017 0.001 TYR H 275 ARG 0.002 0.000 ARG E 271 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 570 time to evaluate : 5.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LYS cc_start: 0.8537 (mtmm) cc_final: 0.8080 (mtpp) REVERT: B 206 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8193 (mt-10) REVERT: B 240 TRP cc_start: 0.6348 (t60) cc_final: 0.5743 (t-100) REVERT: B 296 LYS cc_start: 0.8544 (mtmm) cc_final: 0.8134 (mtpp) REVERT: B 361 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.7361 (mpp) REVERT: C 293 HIS cc_start: 0.6632 (OUTLIER) cc_final: 0.6279 (m-70) REVERT: C 296 LYS cc_start: 0.8574 (mtmm) cc_final: 0.8072 (mtpp) REVERT: D 296 LYS cc_start: 0.8539 (mtmm) cc_final: 0.8080 (mtpp) REVERT: E 206 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8179 (mt-10) REVERT: E 240 TRP cc_start: 0.6348 (t60) cc_final: 0.5744 (t-100) REVERT: E 296 LYS cc_start: 0.8545 (mtmm) cc_final: 0.8135 (mtpp) REVERT: E 361 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7363 (mpp) REVERT: F 293 HIS cc_start: 0.6626 (OUTLIER) cc_final: 0.6271 (m-70) REVERT: F 296 LYS cc_start: 0.8595 (mtmm) cc_final: 0.8094 (mtpp) REVERT: G 176 MET cc_start: 0.8515 (mmm) cc_final: 0.8279 (mmm) REVERT: G 296 LYS cc_start: 0.8527 (mtmm) cc_final: 0.8076 (mtpp) REVERT: G 314 GLU cc_start: 0.8142 (pt0) cc_final: 0.7914 (pt0) REVERT: H 206 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8170 (mt-10) REVERT: H 240 TRP cc_start: 0.6427 (t60) cc_final: 0.5796 (t-100) REVERT: H 296 LYS cc_start: 0.8542 (mtmm) cc_final: 0.8127 (mtpp) REVERT: H 361 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7363 (mpp) REVERT: I 293 HIS cc_start: 0.6620 (OUTLIER) cc_final: 0.6271 (m-70) REVERT: I 296 LYS cc_start: 0.8592 (mtmm) cc_final: 0.8093 (mtpp) REVERT: J 296 LYS cc_start: 0.8526 (mtmm) cc_final: 0.8074 (mtpp) REVERT: K 206 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8191 (mt-10) REVERT: K 296 LYS cc_start: 0.8541 (mtmm) cc_final: 0.8139 (mtpp) REVERT: K 361 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7366 (mpp) REVERT: L 293 HIS cc_start: 0.6588 (OUTLIER) cc_final: 0.6229 (m-70) REVERT: L 296 LYS cc_start: 0.8583 (mtmm) cc_final: 0.8079 (mtpp) outliers start: 70 outliers final: 42 residues processed: 601 average time/residue: 0.8129 time to fit residues: 824.0076 Evaluate side-chains 597 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 547 time to evaluate : 5.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 293 HIS Chi-restraints excluded: chain C residue 331 GLU Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 361 MET Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 293 HIS Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 340 GLU Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 231 SER Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain G residue 348 LEU Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 361 MET Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 293 HIS Chi-restraints excluded: chain I residue 331 GLU Chi-restraints excluded: chain I residue 340 GLU Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 231 SER Chi-restraints excluded: chain J residue 340 GLU Chi-restraints excluded: chain J residue 348 LEU Chi-restraints excluded: chain J residue 367 GLN Chi-restraints excluded: chain K residue 189 VAL Chi-restraints excluded: chain K residue 300 ILE Chi-restraints excluded: chain K residue 361 MET Chi-restraints excluded: chain L residue 189 VAL Chi-restraints excluded: chain L residue 293 HIS Chi-restraints excluded: chain L residue 331 GLU Chi-restraints excluded: chain L residue 340 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 705 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 416 optimal weight: 0.0050 chunk 534 optimal weight: 30.0000 chunk 413 optimal weight: 2.9990 chunk 615 optimal weight: 4.9990 chunk 408 optimal weight: 5.9990 chunk 728 optimal weight: 20.0000 chunk 456 optimal weight: 8.9990 chunk 444 optimal weight: 9.9990 chunk 336 optimal weight: 7.9990 overall best weight: 3.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 367 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.5562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 47616 Z= 0.379 Angle : 0.525 9.446 62940 Z= 0.283 Chirality : 0.047 0.142 4860 Planarity : 0.003 0.040 9324 Dihedral : 4.233 21.939 8016 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.50 % Favored : 94.48 % Rotamer: Outliers : 1.93 % Allowed : 13.65 % Favored : 84.43 % 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: 1.07 (0.10), residues: 7548 helix: 2.72 (0.10), residues: 3252 sheet: -1.00 (0.18), residues: 876 loop : -0.84 (0.10), residues: 3420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 265 HIS 0.005 0.001 HIS J 257 PHE 0.006 0.001 PHE P 672 TYR 0.018 0.002 TYR H 275 ARG 0.002 0.000 ARG G 177 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 572 time to evaluate : 5.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LYS cc_start: 0.8570 (mtmm) cc_final: 0.8108 (mtpp) REVERT: B 206 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8227 (mt-10) REVERT: B 240 TRP cc_start: 0.6356 (t60) cc_final: 0.5738 (t-100) REVERT: B 296 LYS cc_start: 0.8526 (mtmm) cc_final: 0.8108 (mtpp) REVERT: C 293 HIS cc_start: 0.6702 (OUTLIER) cc_final: 0.6338 (m-70) REVERT: C 296 LYS cc_start: 0.8601 (mtmm) cc_final: 0.8089 (mtpp) REVERT: D 296 LYS cc_start: 0.8541 (mtmm) cc_final: 0.8087 (mtpp) REVERT: E 206 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8242 (mt-10) REVERT: E 240 TRP cc_start: 0.6398 (t60) cc_final: 0.5772 (t-100) REVERT: E 296 LYS cc_start: 0.8526 (mtmm) cc_final: 0.8109 (mtpp) REVERT: F 293 HIS cc_start: 0.6629 (OUTLIER) cc_final: 0.6270 (m-70) REVERT: F 296 LYS cc_start: 0.8571 (mtmm) cc_final: 0.8075 (mtpp) REVERT: G 176 MET cc_start: 0.8518 (mmm) cc_final: 0.8313 (mmm) REVERT: G 296 LYS cc_start: 0.8543 (mtmm) cc_final: 0.8077 (mtpp) REVERT: H 206 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8238 (mt-10) REVERT: H 240 TRP cc_start: 0.6342 (t60) cc_final: 0.5721 (t-100) REVERT: H 296 LYS cc_start: 0.8532 (mtmm) cc_final: 0.8108 (mtpp) REVERT: I 195 ASP cc_start: 0.8989 (p0) cc_final: 0.8772 (p0) REVERT: I 293 HIS cc_start: 0.6699 (OUTLIER) cc_final: 0.6346 (m-70) REVERT: I 296 LYS cc_start: 0.8565 (mtmm) cc_final: 0.8061 (mtpp) REVERT: J 296 LYS cc_start: 0.8541 (mtmm) cc_final: 0.8074 (mtpp) REVERT: K 206 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8238 (mt-10) REVERT: K 240 TRP cc_start: 0.6340 (t60) cc_final: 0.5738 (t-100) REVERT: K 275 TYR cc_start: 0.8068 (t80) cc_final: 0.7806 (t80) REVERT: K 296 LYS cc_start: 0.8528 (mtmm) cc_final: 0.8125 (mtpp) REVERT: K 361 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7381 (mpp) REVERT: L 293 HIS cc_start: 0.6670 (OUTLIER) cc_final: 0.6314 (m-70) REVERT: L 296 LYS cc_start: 0.8601 (mtmm) cc_final: 0.8089 (mtpp) outliers start: 67 outliers final: 50 residues processed: 612 average time/residue: 0.8123 time to fit residues: 838.1118 Evaluate side-chains 604 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 549 time to evaluate : 5.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 293 HIS Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 331 GLU Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 331 GLU Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 293 HIS Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 340 GLU Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 231 SER Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 331 GLU Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 293 HIS Chi-restraints excluded: chain I residue 331 GLU Chi-restraints excluded: chain I residue 340 GLU Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 231 SER Chi-restraints excluded: chain J residue 300 ILE Chi-restraints excluded: chain J residue 331 GLU Chi-restraints excluded: chain J residue 340 GLU Chi-restraints excluded: chain J residue 367 GLN Chi-restraints excluded: chain K residue 189 VAL Chi-restraints excluded: chain K residue 300 ILE Chi-restraints excluded: chain K residue 361 MET Chi-restraints excluded: chain L residue 189 VAL Chi-restraints excluded: chain L residue 293 HIS Chi-restraints excluded: chain L residue 331 GLU Chi-restraints excluded: chain L residue 340 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 450 optimal weight: 5.9990 chunk 290 optimal weight: 0.7980 chunk 435 optimal weight: 8.9990 chunk 219 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 141 optimal weight: 0.5980 chunk 463 optimal weight: 9.9990 chunk 496 optimal weight: 40.0000 chunk 360 optimal weight: 30.0000 chunk 67 optimal weight: 3.9990 chunk 572 optimal weight: 30.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 367 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.5644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 47616 Z= 0.217 Angle : 0.462 7.876 62940 Z= 0.242 Chirality : 0.045 0.147 4860 Planarity : 0.003 0.026 9324 Dihedral : 3.927 20.097 8016 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.13 % Favored : 96.81 % Rotamer: Outliers : 1.26 % Allowed : 15.14 % Favored : 83.59 % 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: 1.38 (0.10), residues: 7548 helix: 3.06 (0.10), residues: 3228 sheet: -1.00 (0.18), residues: 876 loop : -0.70 (0.10), residues: 3444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 265 HIS 0.003 0.001 HIS J 257 PHE 0.004 0.001 PHE G 285 TYR 0.023 0.001 TYR B 275 ARG 0.002 0.000 ARG I 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 583 time to evaluate : 5.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LYS cc_start: 0.8514 (mtmm) cc_final: 0.8044 (mtpp) REVERT: B 206 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8200 (mt-10) REVERT: B 240 TRP cc_start: 0.6359 (t60) cc_final: 0.5732 (t-100) REVERT: B 296 LYS cc_start: 0.8525 (mtmm) cc_final: 0.8099 (mtpp) REVERT: C 293 HIS cc_start: 0.6651 (OUTLIER) cc_final: 0.6293 (m-70) REVERT: C 296 LYS cc_start: 0.8588 (mtmm) cc_final: 0.8066 (mtpp) REVERT: D 296 LYS cc_start: 0.8513 (mtmm) cc_final: 0.8038 (mtpp) REVERT: E 206 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8203 (mt-10) REVERT: E 240 TRP cc_start: 0.6360 (t60) cc_final: 0.5734 (t-100) REVERT: E 296 LYS cc_start: 0.8527 (mtmm) cc_final: 0.8101 (mtpp) REVERT: F 293 HIS cc_start: 0.6607 (OUTLIER) cc_final: 0.6248 (m-70) REVERT: F 296 LYS cc_start: 0.8581 (mtmm) cc_final: 0.8057 (mtpp) REVERT: G 176 MET cc_start: 0.8505 (mmm) cc_final: 0.8280 (mmm) REVERT: G 296 LYS cc_start: 0.8543 (mtmm) cc_final: 0.8064 (mtpp) REVERT: H 206 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8211 (mt-10) REVERT: H 240 TRP cc_start: 0.6382 (t60) cc_final: 0.5753 (t-100) REVERT: H 296 LYS cc_start: 0.8526 (mtmm) cc_final: 0.8098 (mtpp) REVERT: I 293 HIS cc_start: 0.6625 (OUTLIER) cc_final: 0.6273 (m-70) REVERT: I 296 LYS cc_start: 0.8571 (mtmm) cc_final: 0.8056 (mtpp) REVERT: J 296 LYS cc_start: 0.8514 (mtmm) cc_final: 0.8041 (mtpp) REVERT: K 206 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8211 (mt-10) REVERT: K 240 TRP cc_start: 0.6360 (t60) cc_final: 0.5748 (t-100) REVERT: K 296 LYS cc_start: 0.8527 (mtmm) cc_final: 0.8113 (mtpp) REVERT: K 361 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7325 (mpp) REVERT: L 293 HIS cc_start: 0.6616 (OUTLIER) cc_final: 0.6255 (m-70) REVERT: L 296 LYS cc_start: 0.8555 (mtmm) cc_final: 0.8044 (mtpp) outliers start: 44 outliers final: 36 residues processed: 605 average time/residue: 0.7832 time to fit residues: 804.6327 Evaluate side-chains 611 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 570 time to evaluate : 5.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 293 HIS Chi-restraints excluded: chain C residue 331 GLU Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 331 GLU Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 293 HIS Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 340 GLU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 231 SER Chi-restraints excluded: chain G residue 331 GLU Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain G residue 348 LEU Chi-restraints excluded: chain G residue 367 GLN Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 293 HIS Chi-restraints excluded: chain I residue 331 GLU Chi-restraints excluded: chain I residue 340 GLU Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 231 SER Chi-restraints excluded: chain J residue 331 GLU Chi-restraints excluded: chain J residue 340 GLU Chi-restraints excluded: chain J residue 348 LEU Chi-restraints excluded: chain K residue 361 MET Chi-restraints excluded: chain L residue 189 VAL Chi-restraints excluded: chain L residue 293 HIS Chi-restraints excluded: chain L residue 331 GLU Chi-restraints excluded: chain L residue 340 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 662 optimal weight: 40.0000 chunk 698 optimal weight: 9.9990 chunk 636 optimal weight: 40.0000 chunk 679 optimal weight: 20.0000 chunk 697 optimal weight: 8.9990 chunk 408 optimal weight: 6.9990 chunk 295 optimal weight: 1.9990 chunk 533 optimal weight: 10.0000 chunk 208 optimal weight: 1.9990 chunk 613 optimal weight: 30.0000 chunk 642 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 GLN K 367 GLN L 367 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.6226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.091 47616 Z= 0.671 Angle : 0.674 7.666 62940 Z= 0.373 Chirality : 0.054 0.164 4860 Planarity : 0.004 0.033 9324 Dihedral : 4.893 25.539 8016 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.17 % Favored : 92.67 % Rotamer: Outliers : 2.30 % Allowed : 15.03 % Favored : 82.67 % 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: 7548 helix: 2.17 (0.09), residues: 3228 sheet: -1.18 (0.18), residues: 876 loop : -1.22 (0.10), residues: 3444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP J 265 HIS 0.008 0.002 HIS G 257 PHE 0.011 0.002 PHE Q 672 TYR 0.020 0.002 TYR G 368 ARG 0.006 0.001 ARG G 177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 595 time to evaluate : 5.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8580 (mm) REVERT: A 296 LYS cc_start: 0.8554 (mtmm) cc_final: 0.8117 (mtpp) REVERT: B 206 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8293 (mt-10) REVERT: B 240 TRP cc_start: 0.6415 (t60) cc_final: 0.5769 (t-100) REVERT: B 296 LYS cc_start: 0.8482 (mtmm) cc_final: 0.8076 (mtpp) REVERT: C 240 TRP cc_start: 0.6383 (t60) cc_final: 0.5721 (t-100) REVERT: C 293 HIS cc_start: 0.6623 (OUTLIER) cc_final: 0.6286 (m-70) REVERT: C 296 LYS cc_start: 0.8540 (mtmm) cc_final: 0.8054 (mtpp) REVERT: D 181 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8587 (mm) REVERT: D 296 LYS cc_start: 0.8555 (mtmm) cc_final: 0.8115 (mtpp) REVERT: E 206 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8294 (mt-10) REVERT: E 240 TRP cc_start: 0.6416 (t60) cc_final: 0.5771 (t-100) REVERT: E 296 LYS cc_start: 0.8485 (mtmm) cc_final: 0.8079 (mtpp) REVERT: F 293 HIS cc_start: 0.6588 (OUTLIER) cc_final: 0.6207 (m-70) REVERT: F 296 LYS cc_start: 0.8553 (mtmm) cc_final: 0.8070 (mtpp) REVERT: G 181 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8586 (mm) REVERT: G 296 LYS cc_start: 0.8555 (mtmm) cc_final: 0.8117 (mtpp) REVERT: H 206 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8287 (mt-10) REVERT: H 240 TRP cc_start: 0.6392 (t60) cc_final: 0.5733 (t-100) REVERT: H 296 LYS cc_start: 0.8478 (mtmm) cc_final: 0.8075 (mtpp) REVERT: I 293 HIS cc_start: 0.6595 (OUTLIER) cc_final: 0.6262 (m-70) REVERT: I 296 LYS cc_start: 0.8568 (mtmm) cc_final: 0.8081 (mtpp) REVERT: J 181 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8587 (mm) REVERT: J 296 LYS cc_start: 0.8557 (mtmm) cc_final: 0.8117 (mtpp) REVERT: K 206 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8289 (mt-10) REVERT: K 240 TRP cc_start: 0.6415 (t60) cc_final: 0.5775 (t-100) REVERT: K 296 LYS cc_start: 0.8482 (mtmm) cc_final: 0.8085 (mtpp) REVERT: K 361 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.7641 (mpp) REVERT: L 293 HIS cc_start: 0.6551 (OUTLIER) cc_final: 0.6213 (m-70) REVERT: L 296 LYS cc_start: 0.8545 (mtmm) cc_final: 0.8059 (mtpp) outliers start: 80 outliers final: 65 residues processed: 650 average time/residue: 0.8185 time to fit residues: 889.7579 Evaluate side-chains 652 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 578 time to evaluate : 5.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 367 GLN Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 293 HIS Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 331 GLU Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 331 GLU Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 293 HIS Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 340 GLU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 231 SER Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 331 GLU Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain G residue 348 LEU Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 231 SER Chi-restraints excluded: chain I residue 293 HIS Chi-restraints excluded: chain I residue 300 ILE Chi-restraints excluded: chain I residue 331 GLU Chi-restraints excluded: chain I residue 340 GLU Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 181 LEU Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 231 SER Chi-restraints excluded: chain J residue 300 ILE Chi-restraints excluded: chain J residue 331 GLU Chi-restraints excluded: chain J residue 340 GLU Chi-restraints excluded: chain J residue 348 LEU Chi-restraints excluded: chain K residue 189 VAL Chi-restraints excluded: chain K residue 231 SER Chi-restraints excluded: chain K residue 300 ILE Chi-restraints excluded: chain K residue 361 MET Chi-restraints excluded: chain K residue 367 GLN Chi-restraints excluded: chain L residue 189 VAL Chi-restraints excluded: chain L residue 231 SER Chi-restraints excluded: chain L residue 293 HIS Chi-restraints excluded: chain L residue 300 ILE Chi-restraints excluded: chain L residue 331 GLU Chi-restraints excluded: chain L residue 340 GLU Chi-restraints excluded: chain L residue 367 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 676 optimal weight: 20.0000 chunk 445 optimal weight: 20.0000 chunk 718 optimal weight: 30.0000 chunk 438 optimal weight: 5.9990 chunk 340 optimal weight: 0.6980 chunk 499 optimal weight: 9.9990 chunk 753 optimal weight: 50.0000 chunk 693 optimal weight: 8.9990 chunk 599 optimal weight: 8.9990 chunk 62 optimal weight: 0.4980 chunk 463 optimal weight: 20.0000 overall best weight: 5.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 367 GLN H 367 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.6306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 47616 Z= 0.548 Angle : 0.617 8.742 62940 Z= 0.337 Chirality : 0.051 0.157 4860 Planarity : 0.004 0.033 9324 Dihedral : 4.772 24.549 8016 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.90 % Favored : 92.94 % Rotamer: Outliers : 2.16 % Allowed : 16.01 % Favored : 81.84 % 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: 7548 helix: 2.20 (0.09), residues: 3168 sheet: -1.16 (0.18), residues: 876 loop : -1.21 (0.10), residues: 3504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 222 HIS 0.008 0.002 HIS A 257 PHE 0.008 0.002 PHE Q 672 TYR 0.018 0.002 TYR A 368 ARG 0.003 0.001 ARG D 177 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 562 time to evaluate : 5.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8576 (mm) REVERT: A 296 LYS cc_start: 0.8552 (mtmm) cc_final: 0.8109 (mtpp) REVERT: B 206 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8287 (mt-10) REVERT: B 240 TRP cc_start: 0.6407 (t60) cc_final: 0.5762 (t-100) REVERT: B 296 LYS cc_start: 0.8461 (mtmm) cc_final: 0.8063 (mtpp) REVERT: C 293 HIS cc_start: 0.6618 (OUTLIER) cc_final: 0.6217 (m-70) REVERT: C 296 LYS cc_start: 0.8555 (mtmm) cc_final: 0.8063 (mtpp) REVERT: D 181 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8585 (mm) REVERT: D 296 LYS cc_start: 0.8551 (mtmm) cc_final: 0.8108 (mtpp) REVERT: E 206 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8289 (mt-10) REVERT: E 240 TRP cc_start: 0.6443 (t60) cc_final: 0.5787 (t-100) REVERT: E 296 LYS cc_start: 0.8472 (mtmm) cc_final: 0.8077 (mtpp) REVERT: F 293 HIS cc_start: 0.6582 (OUTLIER) cc_final: 0.6185 (m-70) REVERT: F 296 LYS cc_start: 0.8564 (mtmm) cc_final: 0.8064 (mtpp) REVERT: G 181 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8584 (mm) REVERT: G 296 LYS cc_start: 0.8551 (mtmm) cc_final: 0.8111 (mtpp) REVERT: H 206 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8286 (mt-10) REVERT: H 240 TRP cc_start: 0.6382 (t60) cc_final: 0.5747 (t-100) REVERT: H 296 LYS cc_start: 0.8455 (mtmm) cc_final: 0.8060 (mtpp) REVERT: I 293 HIS cc_start: 0.6621 (OUTLIER) cc_final: 0.6226 (m-70) REVERT: I 296 LYS cc_start: 0.8557 (mtmm) cc_final: 0.8061 (mtpp) REVERT: J 296 LYS cc_start: 0.8552 (mtmm) cc_final: 0.8108 (mtpp) REVERT: K 206 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8288 (mt-10) REVERT: K 240 TRP cc_start: 0.6383 (t60) cc_final: 0.5753 (t-100) REVERT: K 296 LYS cc_start: 0.8475 (mtmm) cc_final: 0.8107 (mtpp) REVERT: K 361 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.7553 (mpp) REVERT: L 293 HIS cc_start: 0.6614 (OUTLIER) cc_final: 0.6214 (m-70) REVERT: L 296 LYS cc_start: 0.8542 (mtmm) cc_final: 0.8049 (mtpp) outliers start: 75 outliers final: 59 residues processed: 612 average time/residue: 0.8193 time to fit residues: 846.2168 Evaluate side-chains 628 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 561 time to evaluate : 5.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 293 HIS Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 331 GLU Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 314 GLU Chi-restraints excluded: chain D residue 331 GLU Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 367 GLN Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 293 HIS Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 340 GLU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 231 SER Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain G residue 348 LEU Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 343 ASP Chi-restraints excluded: chain H residue 367 GLN Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 231 SER Chi-restraints excluded: chain I residue 293 HIS Chi-restraints excluded: chain I residue 300 ILE Chi-restraints excluded: chain I residue 331 GLU Chi-restraints excluded: chain I residue 340 GLU Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 231 SER Chi-restraints excluded: chain J residue 300 ILE Chi-restraints excluded: chain J residue 331 GLU Chi-restraints excluded: chain J residue 340 GLU Chi-restraints excluded: chain J residue 348 LEU Chi-restraints excluded: chain K residue 189 VAL Chi-restraints excluded: chain K residue 231 SER Chi-restraints excluded: chain K residue 300 ILE Chi-restraints excluded: chain K residue 361 MET Chi-restraints excluded: chain L residue 189 VAL Chi-restraints excluded: chain L residue 231 SER Chi-restraints excluded: chain L residue 293 HIS Chi-restraints excluded: chain L residue 300 ILE Chi-restraints excluded: chain L residue 331 GLU Chi-restraints excluded: chain L residue 340 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 367 optimal weight: 8.9990 chunk 476 optimal weight: 40.0000 chunk 638 optimal weight: 30.0000 chunk 183 optimal weight: 3.9990 chunk 553 optimal weight: 20.0000 chunk 88 optimal weight: 0.5980 chunk 166 optimal weight: 5.9990 chunk 600 optimal weight: 40.0000 chunk 251 optimal weight: 0.5980 chunk 616 optimal weight: 30.0000 chunk 76 optimal weight: 4.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 367 GLN H 367 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.198475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.131327 restraints weight = 145209.665| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 3.38 r_work: 0.3358 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.6326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.340 47616 Z= 0.550 Angle : 0.760 59.114 62940 Z= 0.447 Chirality : 0.050 0.674 4860 Planarity : 0.004 0.033 9324 Dihedral : 4.762 24.605 8016 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.88 % Favored : 92.97 % Rotamer: Outliers : 2.21 % Allowed : 16.15 % Favored : 81.64 % Cbeta Deviations : 0.03 % 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: 0.40 (0.10), residues: 7548 helix: 2.20 (0.09), residues: 3168 sheet: -1.16 (0.18), residues: 876 loop : -1.21 (0.10), residues: 3504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 265 HIS 0.007 0.001 HIS G 257 PHE 0.008 0.001 PHE Q 672 TYR 0.016 0.002 TYR A 368 ARG 0.003 0.000 ARG D 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17672.43 seconds wall clock time: 301 minutes 19.55 seconds (18079.55 seconds total)