Starting phenix.real_space_refine on Sat Mar 7 03:40:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uil_26548/03_2026/7uil_26548.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uil_26548/03_2026/7uil_26548.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uil_26548/03_2026/7uil_26548.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uil_26548/03_2026/7uil_26548.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uil_26548/03_2026/7uil_26548.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uil_26548/03_2026/7uil_26548.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 154 5.16 5 C 24158 2.51 5 N 6216 2.21 5 O 7086 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37614 Number of models: 1 Model: "" Number of chains: 13 Chain: "b" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 516 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain breaks: 1 Chain: "c" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 891 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "e" Number of atoms: 5916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5916 Classifications: {'peptide': 729} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 708} Chain breaks: 4 Chain: "n" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1780 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 9, 'TRANS': 210} Chain breaks: 1 Chain: "o" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 894 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain: "p" Number of atoms: 7306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 903, 7306 Classifications: {'peptide': 903} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 42, 'TRANS': 860} Chain breaks: 3 Chain: "1" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 516 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain breaks: 1 Chain: "2" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 891 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "3" Number of atoms: 5916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5916 Classifications: {'peptide': 729} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 708} Chain breaks: 4 Chain: "4" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1780 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 9, 'TRANS': 210} Chain breaks: 1 Chain: "5" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 894 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain: "6" Number of atoms: 7306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 903, 7306 Classifications: {'peptide': 903} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 42, 'TRANS': 860} Chain breaks: 3 Chain: "a" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 3008 Classifications: {'peptide': 365} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 356} Chain breaks: 3 Time building chain proxies: 8.01, per 1000 atoms: 0.21 Number of scatterers: 37614 At special positions: 0 Unit cell: (266.34, 224.94, 186.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 154 16.00 O 7086 8.00 N 6216 7.00 C 24158 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.02 Conformation dependent library (CDL) restraints added in 1.5 seconds 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9016 Finding SS restraints... Secondary structure from input PDB file: 189 helices and 36 sheets defined 54.3% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'b' and resid 28 through 51 removed outlier: 3.646A pdb=" N THR b 33 " --> pdb=" O LYS b 29 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE b 36 " --> pdb=" O LEU b 32 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU b 40 " --> pdb=" O PHE b 36 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU b 45 " --> pdb=" O LYS b 41 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET b 46 " --> pdb=" O VAL b 42 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN b 50 " --> pdb=" O MET b 46 " (cutoff:3.500A) Processing helix chain 'b' and resid 66 through 104 Processing helix chain 'c' and resid 10 through 19 Processing helix chain 'c' and resid 20 through 22 No H-bonds generated for 'chain 'c' and resid 20 through 22' Processing helix chain 'c' and resid 23 through 56 removed outlier: 4.113A pdb=" N LEU c 41 " --> pdb=" O ARG c 37 " (cutoff:3.500A) Proline residue: c 42 - end of helix Processing helix chain 'c' and resid 63 through 95 Processing helix chain 'c' and resid 95 through 100 Processing helix chain 'c' and resid 100 through 110 removed outlier: 4.078A pdb=" N GLU c 104 " --> pdb=" O SER c 100 " (cutoff:3.500A) Processing helix chain 'e' and resid 288 through 305 Processing helix chain 'e' and resid 312 through 325 removed outlier: 4.493A pdb=" N THR e 321 " --> pdb=" O TYR e 317 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER e 322 " --> pdb=" O SER e 318 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE e 325 " --> pdb=" O THR e 321 " (cutoff:3.500A) Processing helix chain 'e' and resid 334 through 356 Processing helix chain 'e' and resid 367 through 387 removed outlier: 4.555A pdb=" N LEU e 381 " --> pdb=" O ILE e 377 " (cutoff:3.500A) Proline residue: e 382 - end of helix Processing helix chain 'e' and resid 392 through 402 removed outlier: 3.847A pdb=" N VAL e 396 " --> pdb=" O SER e 392 " (cutoff:3.500A) Processing helix chain 'e' and resid 404 through 419 removed outlier: 4.448A pdb=" N VAL e 408 " --> pdb=" O ASP e 404 " (cutoff:3.500A) Processing helix chain 'e' and resid 438 through 450 removed outlier: 3.821A pdb=" N ASP e 442 " --> pdb=" O ASP e 438 " (cutoff:3.500A) Processing helix chain 'e' and resid 457 through 462 removed outlier: 3.847A pdb=" N TYR e 461 " --> pdb=" O VAL e 457 " (cutoff:3.500A) Processing helix chain 'e' and resid 493 through 505 removed outlier: 3.636A pdb=" N PHE e 497 " --> pdb=" O ASN e 493 " (cutoff:3.500A) Processing helix chain 'e' and resid 506 through 510 removed outlier: 3.680A pdb=" N ILE e 510 " --> pdb=" O LEU e 507 " (cutoff:3.500A) Processing helix chain 'e' and resid 520 through 528 removed outlier: 3.503A pdb=" N GLN e 524 " --> pdb=" O ASN e 520 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS e 527 " --> pdb=" O PHE e 523 " (cutoff:3.500A) Processing helix chain 'e' and resid 529 through 532 removed outlier: 3.712A pdb=" N VAL e 532 " --> pdb=" O PHE e 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 529 through 532' Processing helix chain 'e' and resid 533 through 555 removed outlier: 3.525A pdb=" N GLN e 537 " --> pdb=" O ALA e 533 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG e 538 " --> pdb=" O PRO e 534 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU e 539 " --> pdb=" O THR e 535 " (cutoff:3.500A) Processing helix chain 'e' and resid 556 through 570 removed outlier: 3.553A pdb=" N ILE e 560 " --> pdb=" O ASN e 556 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA e 561 " --> pdb=" O TYR e 557 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS e 562 " --> pdb=" O ASN e 558 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE e 569 " --> pdb=" O ALA e 565 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN e 570 " --> pdb=" O LEU e 566 " (cutoff:3.500A) Processing helix chain 'e' and resid 573 through 580 removed outlier: 3.764A pdb=" N THR e 577 " --> pdb=" O HIS e 573 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE e 578 " --> pdb=" O SER e 574 " (cutoff:3.500A) Processing helix chain 'e' and resid 583 through 598 Processing helix chain 'e' and resid 599 through 604 removed outlier: 3.592A pdb=" N ARG e 602 " --> pdb=" O ARG e 599 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN e 603 " --> pdb=" O ASN e 600 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY e 604 " --> pdb=" O GLY e 601 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 599 through 604' Processing helix chain 'e' and resid 611 through 637 removed outlier: 3.515A pdb=" N LEU e 628 " --> pdb=" O SER e 624 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE e 630 " --> pdb=" O ALA e 626 " (cutoff:3.500A) Processing helix chain 'e' and resid 640 through 648 removed outlier: 3.974A pdb=" N VAL e 644 " --> pdb=" O SER e 640 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA e 645 " --> pdb=" O VAL e 641 " (cutoff:3.500A) Processing helix chain 'e' and resid 656 through 664 removed outlier: 4.022A pdb=" N ASN e 660 " --> pdb=" O SER e 656 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER e 663 " --> pdb=" O ILE e 659 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN e 664 " --> pdb=" O ASN e 660 " (cutoff:3.500A) Processing helix chain 'e' and resid 682 through 701 removed outlier: 3.853A pdb=" N LYS e 687 " --> pdb=" O ASP e 683 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS e 689 " --> pdb=" O LEU e 685 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN e 690 " --> pdb=" O THR e 686 " (cutoff:3.500A) Processing helix chain 'e' and resid 706 through 713 removed outlier: 3.778A pdb=" N ILE e 710 " --> pdb=" O THR e 706 " (cutoff:3.500A) Processing helix chain 'e' and resid 714 through 736 removed outlier: 3.720A pdb=" N ASN e 720 " --> pdb=" O ARG e 716 " (cutoff:3.500A) Proline residue: e 723 - end of helix Processing helix chain 'e' and resid 741 through 750 removed outlier: 3.882A pdb=" N TYR e 750 " --> pdb=" O GLY e 746 " (cutoff:3.500A) Processing helix chain 'e' and resid 751 through 753 No H-bonds generated for 'chain 'e' and resid 751 through 753' Processing helix chain 'e' and resid 756 through 759 removed outlier: 3.534A pdb=" N GLY e 759 " --> pdb=" O LEU e 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 756 through 759' Processing helix chain 'e' and resid 760 through 777 removed outlier: 3.670A pdb=" N PHE e 764 " --> pdb=" O LEU e 760 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TYR e 765 " --> pdb=" O ILE e 761 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP e 766 " --> pdb=" O LYS e 762 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU e 767 " --> pdb=" O THR e 763 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU e 768 " --> pdb=" O PHE e 764 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLN e 769 " --> pdb=" O TYR e 765 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS e 773 " --> pdb=" O GLN e 769 " (cutoff:3.500A) Processing helix chain 'e' and resid 780 through 796 removed outlier: 3.956A pdb=" N LEU e 794 " --> pdb=" O LEU e 790 " (cutoff:3.500A) Processing helix chain 'e' and resid 804 through 815 removed outlier: 3.564A pdb=" N LEU e 814 " --> pdb=" O ALA e 810 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN e 815 " --> pdb=" O VAL e 811 " (cutoff:3.500A) Processing helix chain 'e' and resid 815 through 825 removed outlier: 4.019A pdb=" N LEU e 819 " --> pdb=" O ASN e 815 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS e 825 " --> pdb=" O LYS e 821 " (cutoff:3.500A) Processing helix chain 'e' and resid 847 through 859 removed outlier: 3.565A pdb=" N ILE e 851 " --> pdb=" O LEU e 847 " (cutoff:3.500A) Processing helix chain 'e' and resid 867 through 872 removed outlier: 3.877A pdb=" N ILE e 871 " --> pdb=" O ASP e 867 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN e 872 " --> pdb=" O PRO e 868 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 867 through 872' Processing helix chain 'e' and resid 894 through 909 removed outlier: 3.508A pdb=" N ILE e 898 " --> pdb=" O PRO e 894 " (cutoff:3.500A) Processing helix chain 'e' and resid 916 through 928 removed outlier: 3.859A pdb=" N GLU e 922 " --> pdb=" O ASP e 918 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU e 923 " --> pdb=" O TYR e 919 " (cutoff:3.500A) Processing helix chain 'e' and resid 928 through 947 removed outlier: 3.702A pdb=" N VAL e 936 " --> pdb=" O PHE e 932 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS e 938 " --> pdb=" O PHE e 934 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR e 939 " --> pdb=" O ASP e 935 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLU e 941 " --> pdb=" O LEU e 937 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR e 942 " --> pdb=" O LYS e 938 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS e 943 " --> pdb=" O THR e 939 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR e 946 " --> pdb=" O TYR e 942 " (cutoff:3.500A) Processing helix chain 'e' and resid 958 through 975 removed outlier: 3.787A pdb=" N VAL e 964 " --> pdb=" O ASP e 960 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE e 968 " --> pdb=" O VAL e 964 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU e 974 " --> pdb=" O TYR e 970 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR e 975 " --> pdb=" O PHE e 971 " (cutoff:3.500A) Processing helix chain 'e' and resid 980 through 992 removed outlier: 4.432A pdb=" N SER e 984 " --> pdb=" O ALA e 980 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN e 985 " --> pdb=" O GLU e 981 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLU e 988 " --> pdb=" O SER e 984 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN e 992 " --> pdb=" O GLU e 988 " (cutoff:3.500A) Processing helix chain 'e' and resid 1079 through 1083 removed outlier: 4.231A pdb=" N LEU e1083 " --> pdb=" O LYS e1079 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 1079 through 1083' Processing helix chain 'e' and resid 1087 through 1106 removed outlier: 3.669A pdb=" N LEU e1091 " --> pdb=" O SER e1087 " (cutoff:3.500A) Processing helix chain 'e' and resid 1109 through 1130 removed outlier: 3.735A pdb=" N TYR e1119 " --> pdb=" O LYS e1115 " (cutoff:3.500A) Processing helix chain 'n' and resid 835 through 850 Processing helix chain 'n' and resid 902 through 906 removed outlier: 4.125A pdb=" N ILE n 906 " --> pdb=" O PRO n 903 " (cutoff:3.500A) Processing helix chain 'n' and resid 907 through 914 Processing helix chain 'n' and resid 917 through 943 removed outlier: 5.146A pdb=" N SER n 930 " --> pdb=" O GLN n 926 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LEU n 931 " --> pdb=" O PHE n 927 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG n 942 " --> pdb=" O ILE n 938 " (cutoff:3.500A) Processing helix chain 'n' and resid 1015 through 1026 removed outlier: 4.042A pdb=" N MET n1019 " --> pdb=" O ALA n1015 " (cutoff:3.500A) Processing helix chain 'n' and resid 1058 through 1074 removed outlier: 4.578A pdb=" N GLU n1063 " --> pdb=" O PRO n1059 " (cutoff:3.500A) Proline residue: n1064 - end of helix removed outlier: 3.509A pdb=" N MET n1067 " --> pdb=" O GLU n1063 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE n1072 " --> pdb=" O GLU n1068 " (cutoff:3.500A) Processing helix chain 'o' and resid 849 through 876 removed outlier: 4.012A pdb=" N GLU o 874 " --> pdb=" O LYS o 870 " (cutoff:3.500A) Processing helix chain 'o' and resid 879 through 893 Processing helix chain 'o' and resid 906 through 915 removed outlier: 4.176A pdb=" N VAL o 910 " --> pdb=" O PRO o 906 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN o 914 " --> pdb=" O VAL o 910 " (cutoff:3.500A) Processing helix chain 'o' and resid 922 through 932 Processing helix chain 'p' and resid 272 through 277 removed outlier: 3.538A pdb=" N ASP p 277 " --> pdb=" O GLN p 273 " (cutoff:3.500A) Processing helix chain 'p' and resid 473 through 478 Processing helix chain 'p' and resid 490 through 494 Processing helix chain 'p' and resid 503 through 505 No H-bonds generated for 'chain 'p' and resid 503 through 505' Processing helix chain 'p' and resid 541 through 543 No H-bonds generated for 'chain 'p' and resid 541 through 543' Processing helix chain 'p' and resid 544 through 562 removed outlier: 3.528A pdb=" N THR p 550 " --> pdb=" O SER p 546 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR p 556 " --> pdb=" O LEU p 552 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL p 557 " --> pdb=" O ALA p 553 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER p 559 " --> pdb=" O GLY p 555 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS p 561 " --> pdb=" O VAL p 557 " (cutoff:3.500A) Processing helix chain 'p' and resid 566 through 584 removed outlier: 3.551A pdb=" N THR p 570 " --> pdb=" O ALA p 566 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE p 571 " --> pdb=" O GLU p 567 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS p 576 " --> pdb=" O ALA p 572 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU p 583 " --> pdb=" O ARG p 579 " (cutoff:3.500A) Processing helix chain 'p' and resid 584 through 603 removed outlier: 3.705A pdb=" N ALA p 588 " --> pdb=" O ASP p 584 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS p 589 " --> pdb=" O ARG p 585 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU p 590 " --> pdb=" O LYS p 586 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR p 593 " --> pdb=" O LYS p 589 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU p 599 " --> pdb=" O LEU p 595 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR p 600 " --> pdb=" O LEU p 596 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER p 601 " --> pdb=" O LYS p 597 " (cutoff:3.500A) Processing helix chain 'p' and resid 610 through 619 removed outlier: 3.840A pdb=" N MET p 614 " --> pdb=" O PRO p 610 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP p 615 " --> pdb=" O LYS p 611 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS p 616 " --> pdb=" O GLU p 612 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR p 619 " --> pdb=" O ASP p 615 " (cutoff:3.500A) Processing helix chain 'p' and resid 622 through 634 removed outlier: 4.340A pdb=" N LEU p 628 " --> pdb=" O GLN p 624 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN p 630 " --> pdb=" O ILE p 626 " (cutoff:3.500A) Processing helix chain 'p' and resid 640 through 676 removed outlier: 4.357A pdb=" N GLU p 644 " --> pdb=" O GLU p 640 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA p 646 " --> pdb=" O ILE p 642 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE p 659 " --> pdb=" O VAL p 655 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG p 664 " --> pdb=" O ASN p 660 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASN p 665 " --> pdb=" O GLY p 661 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA p 669 " --> pdb=" O ASN p 665 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE p 670 " --> pdb=" O PHE p 666 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU p 671 " --> pdb=" O HIS p 667 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE p 673 " --> pdb=" O ALA p 669 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER p 674 " --> pdb=" O ILE p 670 " (cutoff:3.500A) Processing helix chain 'p' and resid 682 through 723 removed outlier: 3.951A pdb=" N PHE p 686 " --> pdb=" O ASN p 682 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLN p 687 " --> pdb=" O PRO p 683 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN p 693 " --> pdb=" O ILE p 689 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE p 696 " --> pdb=" O LYS p 692 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N HIS p 697 " --> pdb=" O GLN p 693 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER p 698 " --> pdb=" O ASP p 694 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU p 699 " --> pdb=" O LEU p 695 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE p 700 " --> pdb=" O ILE p 696 " (cutoff:3.500A) Proline residue: p 701 - end of helix removed outlier: 3.714A pdb=" N TRP p 705 " --> pdb=" O PRO p 701 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE p 710 " --> pdb=" O PHE p 706 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR p 712 " --> pdb=" O LYS p 708 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU p 713 " --> pdb=" O PHE p 709 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU p 718 " --> pdb=" O THR p 714 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASN p 722 " --> pdb=" O LEU p 718 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP p 723 " --> pdb=" O ILE p 719 " (cutoff:3.500A) Processing helix chain 'p' and resid 726 through 729 removed outlier: 3.668A pdb=" N TYR p 729 " --> pdb=" O ASN p 726 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 726 through 729' Processing helix chain 'p' and resid 730 through 738 removed outlier: 3.992A pdb=" N GLY p 734 " --> pdb=" O THR p 730 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE p 736 " --> pdb=" O VAL p 732 " (cutoff:3.500A) Processing helix chain 'p' and resid 738 through 762 removed outlier: 3.702A pdb=" N ARG p 742 " --> pdb=" O ALA p 738 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR p 743 " --> pdb=" O LYS p 739 " (cutoff:3.500A) Processing helix chain 'p' and resid 767 through 769 No H-bonds generated for 'chain 'p' and resid 767 through 769' Processing helix chain 'p' and resid 770 through 783 removed outlier: 4.483A pdb=" N SER p 774 " --> pdb=" O LEU p 770 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU p 781 " --> pdb=" O LEU p 777 " (cutoff:3.500A) Processing helix chain 'p' and resid 787 through 809 removed outlier: 3.607A pdb=" N LEU p 795 " --> pdb=" O PHE p 791 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N CYS p 806 " --> pdb=" O PHE p 802 " (cutoff:3.500A) Processing helix chain 'p' and resid 812 through 820 removed outlier: 3.745A pdb=" N PHE p 816 " --> pdb=" O GLN p 812 " (cutoff:3.500A) Processing helix chain 'p' and resid 825 through 827 No H-bonds generated for 'chain 'p' and resid 825 through 827' Processing helix chain 'p' and resid 828 through 843 removed outlier: 3.595A pdb=" N GLY p 832 " --> pdb=" O TYR p 828 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP p 833 " --> pdb=" O ALA p 829 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE p 834 " --> pdb=" O LYS p 830 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU p 835 " --> pdb=" O VAL p 831 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU p 836 " --> pdb=" O GLY p 832 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN p 840 " --> pdb=" O LEU p 836 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASN p 841 " --> pdb=" O GLN p 837 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL p 843 " --> pdb=" O ALA p 839 " (cutoff:3.500A) Processing helix chain 'p' and resid 844 through 847 Processing helix chain 'p' and resid 848 through 855 removed outlier: 3.557A pdb=" N PHE p 854 " --> pdb=" O ALA p 850 " (cutoff:3.500A) Processing helix chain 'p' and resid 863 through 867 Processing helix chain 'p' and resid 878 through 882 Processing helix chain 'p' and resid 886 through 890 Processing helix chain 'p' and resid 891 through 895 removed outlier: 3.666A pdb=" N ARG p 895 " --> pdb=" O ILE p 892 " (cutoff:3.500A) Processing helix chain 'p' and resid 896 through 900 Processing helix chain 'p' and resid 914 through 920 Processing helix chain 'p' and resid 940 through 944 Processing helix chain 'p' and resid 954 through 960 removed outlier: 3.725A pdb=" N THR p 960 " --> pdb=" O THR p 957 " (cutoff:3.500A) Processing helix chain '1' and resid 29 through 51 removed outlier: 3.646A pdb=" N THR 1 33 " --> pdb=" O LYS 1 29 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE 1 36 " --> pdb=" O LEU 1 32 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU 1 40 " --> pdb=" O PHE 1 36 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU 1 45 " --> pdb=" O LYS 1 41 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET 1 46 " --> pdb=" O VAL 1 42 " (cutoff:3.500A) Processing helix chain '1' and resid 66 through 104 Processing helix chain '2' and resid 10 through 19 Processing helix chain '2' and resid 20 through 22 No H-bonds generated for 'chain '2' and resid 20 through 22' Processing helix chain '2' and resid 23 through 56 removed outlier: 4.112A pdb=" N LEU 2 41 " --> pdb=" O ARG 2 37 " (cutoff:3.500A) Proline residue: 2 42 - end of helix Processing helix chain '2' and resid 63 through 95 Processing helix chain '2' and resid 95 through 100 Processing helix chain '2' and resid 100 through 110 removed outlier: 4.078A pdb=" N GLU 2 104 " --> pdb=" O SER 2 100 " (cutoff:3.500A) Processing helix chain '3' and resid 288 through 305 Processing helix chain '3' and resid 312 through 325 removed outlier: 4.494A pdb=" N THR 3 321 " --> pdb=" O TYR 3 317 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER 3 322 " --> pdb=" O SER 3 318 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE 3 325 " --> pdb=" O THR 3 321 " (cutoff:3.500A) Processing helix chain '3' and resid 334 through 356 Processing helix chain '3' and resid 367 through 387 removed outlier: 4.555A pdb=" N LEU 3 381 " --> pdb=" O ILE 3 377 " (cutoff:3.500A) Proline residue: 3 382 - end of helix Processing helix chain '3' and resid 392 through 402 removed outlier: 3.847A pdb=" N VAL 3 396 " --> pdb=" O SER 3 392 " (cutoff:3.500A) Processing helix chain '3' and resid 404 through 419 removed outlier: 4.447A pdb=" N VAL 3 408 " --> pdb=" O ASP 3 404 " (cutoff:3.500A) Processing helix chain '3' and resid 438 through 450 removed outlier: 3.820A pdb=" N ASP 3 442 " --> pdb=" O ASP 3 438 " (cutoff:3.500A) Processing helix chain '3' and resid 457 through 462 removed outlier: 3.846A pdb=" N TYR 3 461 " --> pdb=" O VAL 3 457 " (cutoff:3.500A) Processing helix chain '3' and resid 493 through 505 removed outlier: 3.637A pdb=" N PHE 3 497 " --> pdb=" O ASN 3 493 " (cutoff:3.500A) Processing helix chain '3' and resid 506 through 510 removed outlier: 3.679A pdb=" N ILE 3 510 " --> pdb=" O LEU 3 507 " (cutoff:3.500A) Processing helix chain '3' and resid 520 through 528 removed outlier: 3.503A pdb=" N GLN 3 524 " --> pdb=" O ASN 3 520 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS 3 527 " --> pdb=" O PHE 3 523 " (cutoff:3.500A) Processing helix chain '3' and resid 529 through 532 removed outlier: 3.711A pdb=" N VAL 3 532 " --> pdb=" O PHE 3 529 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 529 through 532' Processing helix chain '3' and resid 533 through 555 removed outlier: 3.525A pdb=" N GLN 3 537 " --> pdb=" O ALA 3 533 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG 3 538 " --> pdb=" O PRO 3 534 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU 3 539 " --> pdb=" O THR 3 535 " (cutoff:3.500A) Processing helix chain '3' and resid 556 through 570 removed outlier: 3.553A pdb=" N ILE 3 560 " --> pdb=" O ASN 3 556 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA 3 561 " --> pdb=" O TYR 3 557 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS 3 562 " --> pdb=" O ASN 3 558 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE 3 569 " --> pdb=" O ALA 3 565 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN 3 570 " --> pdb=" O LEU 3 566 " (cutoff:3.500A) Processing helix chain '3' and resid 573 through 580 removed outlier: 3.764A pdb=" N THR 3 577 " --> pdb=" O HIS 3 573 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE 3 578 " --> pdb=" O SER 3 574 " (cutoff:3.500A) Processing helix chain '3' and resid 583 through 598 Processing helix chain '3' and resid 599 through 604 removed outlier: 3.592A pdb=" N ARG 3 602 " --> pdb=" O ARG 3 599 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN 3 603 " --> pdb=" O ASN 3 600 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY 3 604 " --> pdb=" O GLY 3 601 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 599 through 604' Processing helix chain '3' and resid 611 through 637 removed outlier: 3.515A pdb=" N LEU 3 628 " --> pdb=" O SER 3 624 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE 3 630 " --> pdb=" O ALA 3 626 " (cutoff:3.500A) Processing helix chain '3' and resid 640 through 648 removed outlier: 3.973A pdb=" N VAL 3 644 " --> pdb=" O SER 3 640 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA 3 645 " --> pdb=" O VAL 3 641 " (cutoff:3.500A) Processing helix chain '3' and resid 656 through 664 removed outlier: 4.023A pdb=" N ASN 3 660 " --> pdb=" O SER 3 656 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER 3 663 " --> pdb=" O ILE 3 659 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN 3 664 " --> pdb=" O ASN 3 660 " (cutoff:3.500A) Processing helix chain '3' and resid 682 through 701 removed outlier: 3.853A pdb=" N LYS 3 687 " --> pdb=" O ASP 3 683 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS 3 689 " --> pdb=" O LEU 3 685 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN 3 690 " --> pdb=" O THR 3 686 " (cutoff:3.500A) Processing helix chain '3' and resid 706 through 713 removed outlier: 3.777A pdb=" N ILE 3 710 " --> pdb=" O THR 3 706 " (cutoff:3.500A) Processing helix chain '3' and resid 714 through 736 removed outlier: 3.719A pdb=" N ASN 3 720 " --> pdb=" O ARG 3 716 " (cutoff:3.500A) Proline residue: 3 723 - end of helix Processing helix chain '3' and resid 741 through 750 removed outlier: 3.882A pdb=" N TYR 3 750 " --> pdb=" O GLY 3 746 " (cutoff:3.500A) Processing helix chain '3' and resid 751 through 753 No H-bonds generated for 'chain '3' and resid 751 through 753' Processing helix chain '3' and resid 756 through 759 removed outlier: 3.534A pdb=" N GLY 3 759 " --> pdb=" O LEU 3 756 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 756 through 759' Processing helix chain '3' and resid 760 through 777 removed outlier: 3.670A pdb=" N PHE 3 764 " --> pdb=" O LEU 3 760 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TYR 3 765 " --> pdb=" O ILE 3 761 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP 3 766 " --> pdb=" O LYS 3 762 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU 3 767 " --> pdb=" O THR 3 763 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU 3 768 " --> pdb=" O PHE 3 764 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN 3 769 " --> pdb=" O TYR 3 765 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS 3 773 " --> pdb=" O GLN 3 769 " (cutoff:3.500A) Processing helix chain '3' and resid 780 through 796 removed outlier: 3.958A pdb=" N LEU 3 794 " --> pdb=" O LEU 3 790 " (cutoff:3.500A) Processing helix chain '3' and resid 804 through 815 removed outlier: 3.563A pdb=" N LEU 3 814 " --> pdb=" O ALA 3 810 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN 3 815 " --> pdb=" O VAL 3 811 " (cutoff:3.500A) Processing helix chain '3' and resid 815 through 825 removed outlier: 4.020A pdb=" N LEU 3 819 " --> pdb=" O ASN 3 815 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS 3 825 " --> pdb=" O LYS 3 821 " (cutoff:3.500A) Processing helix chain '3' and resid 847 through 859 removed outlier: 3.565A pdb=" N ILE 3 851 " --> pdb=" O LEU 3 847 " (cutoff:3.500A) Processing helix chain '3' and resid 867 through 872 removed outlier: 3.877A pdb=" N ILE 3 871 " --> pdb=" O ASP 3 867 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN 3 872 " --> pdb=" O PRO 3 868 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 867 through 872' Processing helix chain '3' and resid 894 through 909 removed outlier: 3.509A pdb=" N ILE 3 898 " --> pdb=" O PRO 3 894 " (cutoff:3.500A) Processing helix chain '3' and resid 916 through 928 removed outlier: 3.859A pdb=" N GLU 3 922 " --> pdb=" O ASP 3 918 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU 3 923 " --> pdb=" O TYR 3 919 " (cutoff:3.500A) Processing helix chain '3' and resid 928 through 947 removed outlier: 3.702A pdb=" N VAL 3 936 " --> pdb=" O PHE 3 932 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS 3 938 " --> pdb=" O PHE 3 934 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N THR 3 939 " --> pdb=" O ASP 3 935 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLU 3 941 " --> pdb=" O LEU 3 937 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR 3 942 " --> pdb=" O LYS 3 938 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS 3 943 " --> pdb=" O THR 3 939 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR 3 946 " --> pdb=" O TYR 3 942 " (cutoff:3.500A) Processing helix chain '3' and resid 958 through 975 removed outlier: 3.787A pdb=" N VAL 3 964 " --> pdb=" O ASP 3 960 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE 3 968 " --> pdb=" O VAL 3 964 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU 3 974 " --> pdb=" O TYR 3 970 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR 3 975 " --> pdb=" O PHE 3 971 " (cutoff:3.500A) Processing helix chain '3' and resid 980 through 992 removed outlier: 4.432A pdb=" N SER 3 984 " --> pdb=" O ALA 3 980 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN 3 985 " --> pdb=" O GLU 3 981 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLU 3 988 " --> pdb=" O SER 3 984 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN 3 992 " --> pdb=" O GLU 3 988 " (cutoff:3.500A) Processing helix chain '3' and resid 1079 through 1083 removed outlier: 4.231A pdb=" N LEU 31083 " --> pdb=" O LYS 31079 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 1079 through 1083' Processing helix chain '3' and resid 1087 through 1106 removed outlier: 3.669A pdb=" N LEU 31091 " --> pdb=" O SER 31087 " (cutoff:3.500A) Processing helix chain '3' and resid 1109 through 1130 removed outlier: 3.734A pdb=" N TYR 31119 " --> pdb=" O LYS 31115 " (cutoff:3.500A) Processing helix chain '4' and resid 835 through 850 Processing helix chain '4' and resid 902 through 906 removed outlier: 4.124A pdb=" N ILE 4 906 " --> pdb=" O PRO 4 903 " (cutoff:3.500A) Processing helix chain '4' and resid 907 through 914 Processing helix chain '4' and resid 917 through 943 removed outlier: 5.146A pdb=" N SER 4 930 " --> pdb=" O GLN 4 926 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LEU 4 931 " --> pdb=" O PHE 4 927 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG 4 942 " --> pdb=" O ILE 4 938 " (cutoff:3.500A) Processing helix chain '4' and resid 1015 through 1026 removed outlier: 4.042A pdb=" N MET 41019 " --> pdb=" O ALA 41015 " (cutoff:3.500A) Processing helix chain '4' and resid 1058 through 1074 removed outlier: 4.578A pdb=" N GLU 41063 " --> pdb=" O PRO 41059 " (cutoff:3.500A) Proline residue: 41064 - end of helix removed outlier: 3.509A pdb=" N MET 41067 " --> pdb=" O GLU 41063 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE 41072 " --> pdb=" O GLU 41068 " (cutoff:3.500A) Processing helix chain '5' and resid 849 through 876 removed outlier: 4.012A pdb=" N GLU 5 874 " --> pdb=" O LYS 5 870 " (cutoff:3.500A) Processing helix chain '5' and resid 879 through 893 Processing helix chain '5' and resid 906 through 915 removed outlier: 4.177A pdb=" N VAL 5 910 " --> pdb=" O PRO 5 906 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN 5 914 " --> pdb=" O VAL 5 910 " (cutoff:3.500A) Processing helix chain '5' and resid 922 through 932 Processing helix chain '6' and resid 272 through 277 removed outlier: 3.538A pdb=" N ASP 6 277 " --> pdb=" O GLN 6 273 " (cutoff:3.500A) Processing helix chain '6' and resid 473 through 478 Processing helix chain '6' and resid 490 through 494 Processing helix chain '6' and resid 503 through 505 No H-bonds generated for 'chain '6' and resid 503 through 505' Processing helix chain '6' and resid 541 through 543 No H-bonds generated for 'chain '6' and resid 541 through 543' Processing helix chain '6' and resid 544 through 562 removed outlier: 3.528A pdb=" N THR 6 550 " --> pdb=" O SER 6 546 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR 6 556 " --> pdb=" O LEU 6 552 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL 6 557 " --> pdb=" O ALA 6 553 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER 6 559 " --> pdb=" O GLY 6 555 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS 6 561 " --> pdb=" O VAL 6 557 " (cutoff:3.500A) Processing helix chain '6' and resid 566 through 584 removed outlier: 3.551A pdb=" N THR 6 570 " --> pdb=" O ALA 6 566 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE 6 571 " --> pdb=" O GLU 6 567 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N HIS 6 576 " --> pdb=" O ALA 6 572 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU 6 583 " --> pdb=" O ARG 6 579 " (cutoff:3.500A) Processing helix chain '6' and resid 584 through 603 removed outlier: 3.706A pdb=" N ALA 6 588 " --> pdb=" O ASP 6 584 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS 6 589 " --> pdb=" O ARG 6 585 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU 6 590 " --> pdb=" O LYS 6 586 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR 6 593 " --> pdb=" O LYS 6 589 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU 6 599 " --> pdb=" O LEU 6 595 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR 6 600 " --> pdb=" O LEU 6 596 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER 6 601 " --> pdb=" O LYS 6 597 " (cutoff:3.500A) Processing helix chain '6' and resid 610 through 619 removed outlier: 3.841A pdb=" N MET 6 614 " --> pdb=" O PRO 6 610 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP 6 615 " --> pdb=" O LYS 6 611 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS 6 616 " --> pdb=" O GLU 6 612 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR 6 619 " --> pdb=" O ASP 6 615 " (cutoff:3.500A) Processing helix chain '6' and resid 622 through 634 removed outlier: 4.341A pdb=" N LEU 6 628 " --> pdb=" O GLN 6 624 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN 6 630 " --> pdb=" O ILE 6 626 " (cutoff:3.500A) Processing helix chain '6' and resid 640 through 676 removed outlier: 4.357A pdb=" N GLU 6 644 " --> pdb=" O GLU 6 640 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA 6 646 " --> pdb=" O ILE 6 642 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE 6 659 " --> pdb=" O VAL 6 655 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG 6 664 " --> pdb=" O ASN 6 660 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASN 6 665 " --> pdb=" O GLY 6 661 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA 6 669 " --> pdb=" O ASN 6 665 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE 6 670 " --> pdb=" O PHE 6 666 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU 6 671 " --> pdb=" O HIS 6 667 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE 6 673 " --> pdb=" O ALA 6 669 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER 6 674 " --> pdb=" O ILE 6 670 " (cutoff:3.500A) Processing helix chain '6' and resid 682 through 723 removed outlier: 3.951A pdb=" N PHE 6 686 " --> pdb=" O ASN 6 682 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLN 6 687 " --> pdb=" O PRO 6 683 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN 6 693 " --> pdb=" O ILE 6 689 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE 6 696 " --> pdb=" O LYS 6 692 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N HIS 6 697 " --> pdb=" O GLN 6 693 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER 6 698 " --> pdb=" O ASP 6 694 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU 6 699 " --> pdb=" O LEU 6 695 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE 6 700 " --> pdb=" O ILE 6 696 " (cutoff:3.500A) Proline residue: 6 701 - end of helix removed outlier: 3.715A pdb=" N TRP 6 705 " --> pdb=" O PRO 6 701 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE 6 710 " --> pdb=" O PHE 6 706 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR 6 712 " --> pdb=" O LYS 6 708 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU 6 713 " --> pdb=" O PHE 6 709 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU 6 718 " --> pdb=" O THR 6 714 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASN 6 722 " --> pdb=" O LEU 6 718 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP 6 723 " --> pdb=" O ILE 6 719 " (cutoff:3.500A) Processing helix chain '6' and resid 726 through 729 removed outlier: 3.669A pdb=" N TYR 6 729 " --> pdb=" O ASN 6 726 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 726 through 729' Processing helix chain '6' and resid 730 through 738 removed outlier: 3.992A pdb=" N GLY 6 734 " --> pdb=" O THR 6 730 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE 6 736 " --> pdb=" O VAL 6 732 " (cutoff:3.500A) Processing helix chain '6' and resid 738 through 762 removed outlier: 3.702A pdb=" N ARG 6 742 " --> pdb=" O ALA 6 738 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR 6 743 " --> pdb=" O LYS 6 739 " (cutoff:3.500A) Processing helix chain '6' and resid 767 through 769 No H-bonds generated for 'chain '6' and resid 767 through 769' Processing helix chain '6' and resid 770 through 783 removed outlier: 4.483A pdb=" N SER 6 774 " --> pdb=" O LEU 6 770 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU 6 781 " --> pdb=" O LEU 6 777 " (cutoff:3.500A) Processing helix chain '6' and resid 787 through 809 removed outlier: 3.606A pdb=" N LEU 6 795 " --> pdb=" O PHE 6 791 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N CYS 6 806 " --> pdb=" O PHE 6 802 " (cutoff:3.500A) Processing helix chain '6' and resid 812 through 820 removed outlier: 3.746A pdb=" N PHE 6 816 " --> pdb=" O GLN 6 812 " (cutoff:3.500A) Processing helix chain '6' and resid 825 through 827 No H-bonds generated for 'chain '6' and resid 825 through 827' Processing helix chain '6' and resid 828 through 843 removed outlier: 3.596A pdb=" N GLY 6 832 " --> pdb=" O TYR 6 828 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP 6 833 " --> pdb=" O ALA 6 829 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE 6 834 " --> pdb=" O LYS 6 830 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU 6 835 " --> pdb=" O VAL 6 831 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU 6 836 " --> pdb=" O GLY 6 832 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN 6 840 " --> pdb=" O LEU 6 836 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASN 6 841 " --> pdb=" O GLN 6 837 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL 6 843 " --> pdb=" O ALA 6 839 " (cutoff:3.500A) Processing helix chain '6' and resid 844 through 847 Processing helix chain '6' and resid 848 through 855 removed outlier: 3.558A pdb=" N PHE 6 854 " --> pdb=" O ALA 6 850 " (cutoff:3.500A) Processing helix chain '6' and resid 863 through 867 Processing helix chain '6' and resid 878 through 882 Processing helix chain '6' and resid 886 through 890 Processing helix chain '6' and resid 891 through 895 removed outlier: 3.666A pdb=" N ARG 6 895 " --> pdb=" O ILE 6 892 " (cutoff:3.500A) Processing helix chain '6' and resid 896 through 900 Processing helix chain '6' and resid 914 through 920 Processing helix chain '6' and resid 940 through 944 Processing helix chain '6' and resid 954 through 960 removed outlier: 3.725A pdb=" N THR 6 960 " --> pdb=" O THR 6 957 " (cutoff:3.500A) Processing helix chain 'a' and resid 7 through 22 Processing helix chain 'a' and resid 27 through 38 Processing helix chain 'a' and resid 102 through 110 Processing helix chain 'a' and resid 114 through 131 Processing helix chain 'a' and resid 163 through 182 removed outlier: 3.800A pdb=" N SER a 172 " --> pdb=" O PHE a 168 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N HIS a 173 " --> pdb=" O THR a 169 " (cutoff:3.500A) Processing helix chain 'a' and resid 279 through 281 No H-bonds generated for 'chain 'a' and resid 279 through 281' Processing helix chain 'a' and resid 297 through 305 Processing helix chain 'a' and resid 331 through 335 Processing helix chain 'a' and resid 336 through 351 removed outlier: 4.256A pdb=" N GLU a 340 " --> pdb=" O ASP a 336 " (cutoff:3.500A) Processing helix chain 'a' and resid 351 through 361 Processing helix chain 'a' and resid 550 through 566 Processing sheet with id=AA1, first strand: chain 'e' and resid 479 through 482 removed outlier: 4.472A pdb=" N LEU e 479 " --> pdb=" O VAL e 491 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'n' and resid 856 through 860 removed outlier: 7.168A pdb=" N SER n 866 " --> pdb=" O ILE n 858 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU n 860 " --> pdb=" O GLU n 864 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N GLU n 864 " --> pdb=" O LEU n 860 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE n 867 " --> pdb=" O CYS n 880 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR n 895 " --> pdb=" O LYS n 883 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER n 885 " --> pdb=" O ASN n 893 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN n 893 " --> pdb=" O SER n 885 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'n' and resid 956 through 963 removed outlier: 3.544A pdb=" N ASN n 958 " --> pdb=" O VAL n 970 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N HIS n 962 " --> pdb=" O GLU n 966 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU n 966 " --> pdb=" O HIS n 962 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU n 985 " --> pdb=" O HIS n1000 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS n 987 " --> pdb=" O GLN n 998 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE n 999 " --> pdb=" O CYS n1057 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'o' and resid 938 through 939 Processing sheet with id=AA5, first strand: chain 'p' and resid 8 through 10 Processing sheet with id=AA6, first strand: chain 'p' and resid 33 through 35 Processing sheet with id=AA7, first strand: chain 'p' and resid 101 through 102 removed outlier: 3.538A pdb=" N PHE p 102 " --> pdb=" O GLU p 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'p' and resid 105 through 110 removed outlier: 7.145A pdb=" N CYS p 124 " --> pdb=" O SER p 106 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ILE p 108 " --> pdb=" O ALA p 122 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ALA p 122 " --> pdb=" O ILE p 108 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N TRP p 110 " --> pdb=" O MET p 120 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N MET p 120 " --> pdb=" O TRP p 110 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N MET p 130 " --> pdb=" O GLN p 153 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLN p 153 " --> pdb=" O MET p 130 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N MET p 132 " --> pdb=" O VAL p 151 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN p 153 " --> pdb=" O TYR p 160 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR p 160 " --> pdb=" O GLN p 153 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'p' and resid 190 through 195 removed outlier: 6.906A pdb=" N ILE p 242 " --> pdb=" O LEU p 191 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N PHE p 193 " --> pdb=" O LEU p 240 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU p 240 " --> pdb=" O PHE p 193 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N TRP p 195 " --> pdb=" O ALA p 238 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ALA p 238 " --> pdb=" O TRP p 195 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLN p 253 " --> pdb=" O LYS p 236 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA p 238 " --> pdb=" O TRP p 251 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N TRP p 251 " --> pdb=" O ALA p 238 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU p 240 " --> pdb=" O ASP p 249 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASP p 249 " --> pdb=" O LEU p 240 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ILE p 242 " --> pdb=" O GLN p 247 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLN p 247 " --> pdb=" O ILE p 242 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'p' and resid 216 through 224 removed outlier: 3.765A pdb=" N ARG p 220 " --> pdb=" O PHE p 207 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N PHE p 207 " --> pdb=" O ARG p 220 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLN p 222 " --> pdb=" O SER p 205 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N SER p 205 " --> pdb=" O GLN p 222 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL p 224 " --> pdb=" O ILE p 203 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ILE p 203 " --> pdb=" O VAL p 224 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N CYS p 208 " --> pdb=" O ILE p 487 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE p 487 " --> pdb=" O CYS p 208 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS p 485 " --> pdb=" O PHE p 210 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'p' and resid 281 through 288 removed outlier: 3.967A pdb=" N PHE p 283 " --> pdb=" O TYR p 300 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER p 301 " --> pdb=" O ASN p 306 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN p 306 " --> pdb=" O SER p 301 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR p 339 " --> pdb=" O ILE p 307 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU p 337 " --> pdb=" O PHE p 309 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LYS p 311 " --> pdb=" O PHE p 335 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N PHE p 335 " --> pdb=" O LYS p 311 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N HIS p 313 " --> pdb=" O ILE p 333 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ILE p 333 " --> pdb=" O HIS p 313 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ASN p 315 " --> pdb=" O LEU p 331 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU p 331 " --> pdb=" O ASN p 315 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'p' and resid 353 through 358 removed outlier: 6.660A pdb=" N LEU p 353 " --> pdb=" O ASN p 377 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ASN p 377 " --> pdb=" O LEU p 353 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASN p 355 " --> pdb=" O LEU p 375 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE p 433 " --> pdb=" O VAL p 386 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG p 388 " --> pdb=" O SER p 431 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N SER p 431 " --> pdb=" O ARG p 388 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ARG p 390 " --> pdb=" O ARG p 429 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ARG p 429 " --> pdb=" O ARG p 390 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA p 392 " --> pdb=" O LEU p 427 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N LEU p 427 " --> pdb=" O ALA p 392 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'p' and resid 439 through 444 removed outlier: 6.907A pdb=" N TYR p 454 " --> pdb=" O THR p 440 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE p 442 " --> pdb=" O SER p 452 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N SER p 452 " --> pdb=" O ILE p 442 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER p 444 " --> pdb=" O PHE p 450 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N PHE p 450 " --> pdb=" O SER p 444 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE p 453 " --> pdb=" O GLU p 461 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU p 461 " --> pdb=" O PHE p 453 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'p' and resid 497 through 498 removed outlier: 4.020A pdb=" N TRP p 509 " --> pdb=" O LYS p 522 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'p' and resid 932 through 933 Processing sheet with id=AB7, first strand: chain '3' and resid 479 through 482 removed outlier: 4.471A pdb=" N LEU 3 479 " --> pdb=" O VAL 3 491 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '4' and resid 856 through 860 removed outlier: 7.168A pdb=" N SER 4 866 " --> pdb=" O ILE 4 858 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU 4 860 " --> pdb=" O GLU 4 864 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N GLU 4 864 " --> pdb=" O LEU 4 860 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE 4 867 " --> pdb=" O CYS 4 880 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR 4 895 " --> pdb=" O LYS 4 883 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER 4 885 " --> pdb=" O ASN 4 893 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN 4 893 " --> pdb=" O SER 4 885 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '4' and resid 956 through 963 removed outlier: 3.545A pdb=" N ASN 4 958 " --> pdb=" O VAL 4 970 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N HIS 4 962 " --> pdb=" O GLU 4 966 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N GLU 4 966 " --> pdb=" O HIS 4 962 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU 4 985 " --> pdb=" O HIS 41000 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS 4 987 " --> pdb=" O GLN 4 998 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE 4 999 " --> pdb=" O CYS 41057 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '5' and resid 938 through 939 Processing sheet with id=AC2, first strand: chain '6' and resid 8 through 10 Processing sheet with id=AC3, first strand: chain '6' and resid 33 through 35 Processing sheet with id=AC4, first strand: chain '6' and resid 101 through 102 removed outlier: 3.539A pdb=" N PHE 6 102 " --> pdb=" O GLU 6 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain '6' and resid 105 through 110 removed outlier: 7.144A pdb=" N CYS 6 124 " --> pdb=" O SER 6 106 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ILE 6 108 " --> pdb=" O ALA 6 122 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ALA 6 122 " --> pdb=" O ILE 6 108 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N TRP 6 110 " --> pdb=" O MET 6 120 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N MET 6 120 " --> pdb=" O TRP 6 110 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N MET 6 130 " --> pdb=" O GLN 6 153 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLN 6 153 " --> pdb=" O MET 6 130 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N MET 6 132 " --> pdb=" O VAL 6 151 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN 6 153 " --> pdb=" O TYR 6 160 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR 6 160 " --> pdb=" O GLN 6 153 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '6' and resid 190 through 195 removed outlier: 6.906A pdb=" N ILE 6 242 " --> pdb=" O LEU 6 191 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N PHE 6 193 " --> pdb=" O LEU 6 240 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU 6 240 " --> pdb=" O PHE 6 193 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N TRP 6 195 " --> pdb=" O ALA 6 238 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ALA 6 238 " --> pdb=" O TRP 6 195 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLN 6 253 " --> pdb=" O LYS 6 236 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ALA 6 238 " --> pdb=" O TRP 6 251 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N TRP 6 251 " --> pdb=" O ALA 6 238 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU 6 240 " --> pdb=" O ASP 6 249 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASP 6 249 " --> pdb=" O LEU 6 240 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ILE 6 242 " --> pdb=" O GLN 6 247 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLN 6 247 " --> pdb=" O ILE 6 242 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '6' and resid 216 through 224 removed outlier: 3.765A pdb=" N ARG 6 220 " --> pdb=" O PHE 6 207 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N PHE 6 207 " --> pdb=" O ARG 6 220 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLN 6 222 " --> pdb=" O SER 6 205 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N SER 6 205 " --> pdb=" O GLN 6 222 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL 6 224 " --> pdb=" O ILE 6 203 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ILE 6 203 " --> pdb=" O VAL 6 224 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N CYS 6 208 " --> pdb=" O ILE 6 487 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE 6 487 " --> pdb=" O CYS 6 208 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS 6 485 " --> pdb=" O PHE 6 210 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '6' and resid 281 through 288 removed outlier: 3.966A pdb=" N PHE 6 283 " --> pdb=" O TYR 6 300 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER 6 301 " --> pdb=" O ASN 6 306 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN 6 306 " --> pdb=" O SER 6 301 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR 6 339 " --> pdb=" O ILE 6 307 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU 6 337 " --> pdb=" O PHE 6 309 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LYS 6 311 " --> pdb=" O PHE 6 335 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N PHE 6 335 " --> pdb=" O LYS 6 311 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N HIS 6 313 " --> pdb=" O ILE 6 333 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ILE 6 333 " --> pdb=" O HIS 6 313 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ASN 6 315 " --> pdb=" O LEU 6 331 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU 6 331 " --> pdb=" O ASN 6 315 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '6' and resid 353 through 358 removed outlier: 6.660A pdb=" N LEU 6 353 " --> pdb=" O ASN 6 377 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ASN 6 377 " --> pdb=" O LEU 6 353 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASN 6 355 " --> pdb=" O LEU 6 375 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE 6 433 " --> pdb=" O VAL 6 386 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG 6 388 " --> pdb=" O SER 6 431 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N SER 6 431 " --> pdb=" O ARG 6 388 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ARG 6 390 " --> pdb=" O ARG 6 429 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ARG 6 429 " --> pdb=" O ARG 6 390 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA 6 392 " --> pdb=" O LEU 6 427 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N LEU 6 427 " --> pdb=" O ALA 6 392 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '6' and resid 439 through 444 removed outlier: 6.909A pdb=" N TYR 6 454 " --> pdb=" O THR 6 440 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE 6 442 " --> pdb=" O SER 6 452 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N SER 6 452 " --> pdb=" O ILE 6 442 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER 6 444 " --> pdb=" O PHE 6 450 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N PHE 6 450 " --> pdb=" O SER 6 444 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE 6 453 " --> pdb=" O GLU 6 461 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU 6 461 " --> pdb=" O PHE 6 453 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '6' and resid 497 through 498 removed outlier: 4.021A pdb=" N TRP 6 509 " --> pdb=" O LYS 6 522 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '6' and resid 932 through 933 Processing sheet with id=AD4, first strand: chain 'a' and resid 41 through 46 removed outlier: 6.790A pdb=" N VAL a 62 " --> pdb=" O LEU a 79 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU a 79 " --> pdb=" O VAL a 62 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASP a 64 " --> pdb=" O VAL a 77 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL a 77 " --> pdb=" O ASP a 64 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASP a 66 " --> pdb=" O GLN a 75 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'a' and resid 187 through 190 removed outlier: 6.381A pdb=" N ILE a 198 " --> pdb=" O LYS a 214 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS a 214 " --> pdb=" O ILE a 198 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE a 200 " --> pdb=" O LEU a 212 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS a 326 " --> pdb=" O ILE a 258 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'a' and resid 187 through 190 removed outlier: 6.381A pdb=" N ILE a 198 " --> pdb=" O LYS a 214 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS a 214 " --> pdb=" O ILE a 198 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE a 200 " --> pdb=" O LEU a 212 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS a 326 " --> pdb=" O ILE a 258 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASP a 285 " --> pdb=" O LYS a 326 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N PHE a 328 " --> pdb=" O ILE a 283 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE a 283 " --> pdb=" O PHE a 328 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'a' and resid 227 through 229 Processing sheet with id=AD8, first strand: chain 'a' and resid 232 through 234 removed outlier: 3.652A pdb=" N SER a 239 " --> pdb=" O SER a 234 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'a' and resid 312 through 316 1732 hydrogen bonds defined for protein. 4974 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: 8.77 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9133 1.33 - 1.45: 7453 1.45 - 1.58: 21534 1.58 - 1.70: 0 1.70 - 1.82: 247 Bond restraints: 38367 Sorted by residual: bond pdb=" CZ ARG a 189 " pdb=" NH2 ARG a 189 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 9.21e+00 bond pdb=" CZ ARG a 349 " pdb=" NH2 ARG a 349 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.79e+00 bond pdb=" CZ ARG a 33 " pdb=" NH2 ARG a 33 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.72e+00 bond pdb=" ND1 HIS a 536 " pdb=" CE1 HIS a 536 " ideal model delta sigma weight residual 1.321 1.346 -0.025 1.00e-02 1.00e+04 6.44e+00 bond pdb=" CE1 HIS a 536 " pdb=" NE2 HIS a 536 " ideal model delta sigma weight residual 1.321 1.346 -0.025 1.00e-02 1.00e+04 6.07e+00 ... (remaining 38362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 50384 1.85 - 3.71: 1254 3.71 - 5.56: 212 5.56 - 7.42: 33 7.42 - 9.27: 7 Bond angle restraints: 51890 Sorted by residual: angle pdb=" C PRO a 298 " pdb=" N ILE a 299 " pdb=" CA ILE a 299 " ideal model delta sigma weight residual 120.56 127.46 -6.90 1.26e+00 6.30e-01 3.00e+01 angle pdb=" OE1 GLN a 529 " pdb=" CD GLN a 529 " pdb=" NE2 GLN a 529 " ideal model delta sigma weight residual 122.60 117.20 5.40 1.00e+00 1.00e+00 2.92e+01 angle pdb=" OD1 ASN a 324 " pdb=" CG ASN a 324 " pdb=" ND2 ASN a 324 " ideal model delta sigma weight residual 122.60 117.48 5.12 1.00e+00 1.00e+00 2.62e+01 angle pdb=" C LYS a 22 " pdb=" N PRO a 23 " pdb=" CA PRO a 23 " ideal model delta sigma weight residual 119.56 124.69 -5.13 1.02e+00 9.61e-01 2.53e+01 angle pdb=" OE1 GLN a 225 " pdb=" CD GLN a 225 " pdb=" NE2 GLN a 225 " ideal model delta sigma weight residual 122.60 117.63 4.97 1.00e+00 1.00e+00 2.47e+01 ... (remaining 51885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 21042 17.23 - 34.46: 1885 34.46 - 51.69: 328 51.69 - 68.92: 50 68.92 - 86.15: 26 Dihedral angle restraints: 23331 sinusoidal: 9542 harmonic: 13789 Sorted by residual: dihedral pdb=" CA SER a 295 " pdb=" C SER a 295 " pdb=" N SER a 296 " pdb=" CA SER a 296 " ideal model delta harmonic sigma weight residual 180.00 154.71 25.29 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA TYR a 308 " pdb=" C TYR a 308 " pdb=" N ASN a 309 " pdb=" CA ASN a 309 " ideal model delta harmonic sigma weight residual 180.00 158.42 21.58 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA SER a 290 " pdb=" C SER a 290 " pdb=" N SER a 291 " pdb=" CA SER a 291 " ideal model delta harmonic sigma weight residual -180.00 -159.78 -20.22 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 23328 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 4275 0.042 - 0.084: 1233 0.084 - 0.126: 367 0.126 - 0.168: 61 0.168 - 0.210: 12 Chirality restraints: 5948 Sorted by residual: chirality pdb=" CG LEU a 352 " pdb=" CB LEU a 352 " pdb=" CD1 LEU a 352 " pdb=" CD2 LEU a 352 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ASP a 194 " pdb=" N ASP a 194 " pdb=" C ASP a 194 " pdb=" CB ASP a 194 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CB THR a 319 " pdb=" CA THR a 319 " pdb=" OG1 THR a 319 " pdb=" CG2 THR a 319 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 5945 not shown) Planarity restraints: 6566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR a 216 " 0.109 2.00e-02 2.50e+03 6.74e-02 9.09e+01 pdb=" CG TYR a 216 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR a 216 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR a 216 " -0.063 2.00e-02 2.50e+03 pdb=" CE1 TYR a 216 " -0.063 2.00e-02 2.50e+03 pdb=" CE2 TYR a 216 " -0.041 2.00e-02 2.50e+03 pdb=" CZ TYR a 216 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR a 216 " 0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP a 344 " -0.088 2.00e-02 2.50e+03 4.64e-02 5.39e+01 pdb=" CG TRP a 344 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP a 344 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP a 344 " 0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP a 344 " 0.042 2.00e-02 2.50e+03 pdb=" CE2 TRP a 344 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP a 344 " 0.040 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 344 " -0.080 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 344 " 0.033 2.00e-02 2.50e+03 pdb=" CH2 TRP a 344 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR a 67 " 0.055 2.00e-02 2.50e+03 4.39e-02 3.86e+01 pdb=" CG TYR a 67 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR a 67 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR a 67 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR a 67 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 TYR a 67 " -0.040 2.00e-02 2.50e+03 pdb=" CZ TYR a 67 " -0.023 2.00e-02 2.50e+03 pdb=" OH TYR a 67 " 0.085 2.00e-02 2.50e+03 ... (remaining 6563 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 133 2.41 - 3.04: 22019 3.04 - 3.66: 56418 3.66 - 4.28: 80818 4.28 - 4.90: 131398 Nonbonded interactions: 290786 Sorted by model distance: nonbonded pdb=" NH1 ARG e 879 " pdb=" CG GLU 3 892 " model vdw 1.794 2.816 nonbonded pdb=" NH2 ARG e 879 " pdb=" OE2 GLU 3 892 " model vdw 1.937 2.496 nonbonded pdb=" CZ ARG e 879 " pdb=" CD GLU 3 892 " model vdw 1.943 2.800 nonbonded pdb=" NE ARG e 879 " pdb=" CG GLU 3 892 " model vdw 2.205 2.816 nonbonded pdb=" OE1 GLN 3 902 " pdb=" OG1 THR 3 913 " model vdw 2.212 3.040 ... (remaining 290781 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 '1' selection = chain 'b' } ncs_group { reference = chain '2' selection = chain 'c' } ncs_group { reference = chain '3' selection = chain 'e' } ncs_group { reference = chain '4' selection = chain 'n' } ncs_group { reference = chain '5' selection = chain 'o' } ncs_group { reference = chain '6' selection = chain 'p' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.580 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 33.140 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.150 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: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3783 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 : 0.006 0.763 38368 Z= 0.446 Angle : 0.666 9.273 51890 Z= 0.385 Chirality : 0.044 0.210 5948 Planarity : 0.005 0.074 6566 Dihedral : 13.363 86.148 14315 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.20 % Favored : 98.73 % Rotamer: Outliers : 0.07 % Allowed : 0.37 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.12), residues: 4573 helix: 0.75 (0.11), residues: 2044 sheet: -0.33 (0.23), residues: 511 loop : 0.01 (0.14), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 3 869 TYR 0.116 0.002 TYR a 216 PHE 0.055 0.002 PHE a 356 TRP 0.088 0.004 TRP a 344 HIS 0.014 0.001 HIS a 536 Details of bonding type rmsd covalent geometry : bond 0.00404 (38367) covalent geometry : angle 0.66612 (51890) hydrogen bonds : bond 0.25247 ( 1716) hydrogen bonds : angle 7.46862 ( 4974) Misc. bond : bond 0.76315 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 302 time to evaluate : 1.302 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: b 47 MET cc_start: 0.8145 (ptp) cc_final: 0.7496 (ptp) REVERT: p 121 LEU cc_start: 0.7755 (tp) cc_final: 0.7415 (tp) REVERT: p 240 LEU cc_start: 0.7893 (tt) cc_final: 0.7650 (tp) REVERT: p 289 MET cc_start: 0.3048 (tpt) cc_final: 0.2726 (tpt) REVERT: p 645 MET cc_start: 0.7857 (tpt) cc_final: 0.7512 (tpp) REVERT: 2 40 ILE cc_start: 0.7392 (mm) cc_final: 0.6901 (mm) REVERT: 3 990 MET cc_start: -0.3044 (mmt) cc_final: -0.5335 (mtt) REVERT: 4 967 TYR cc_start: 0.3360 (m-80) cc_final: 0.2816 (m-10) REVERT: 5 945 MET cc_start: -0.6335 (tpt) cc_final: -0.7914 (mtt) REVERT: 6 289 MET cc_start: 0.0630 (tpt) cc_final: 0.0026 (tpt) outliers start: 3 outliers final: 0 residues processed: 305 average time/residue: 0.2134 time to fit residues: 108.6250 Evaluate side-chains 169 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 4.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 32 GLN c 59 GLN ** c 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 453 GLN e 488 GLN e 815 ASN ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1093 HIS ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n1020 HIS n1024 ASN p 40 ASN ** p 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 187 ASN ** p 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 319 ASN p 327 ASN p 349 HIS ** p 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 32 GLN 3 301 ASN ** 3 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 453 GLN 3 815 ASN ** 3 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 31093 HIS ** 31113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 319 ASN 6 327 ASN 6 349 HIS 6 480 GLN ** 6 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 118 HIS ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.061982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.060701 restraints weight = 828362.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.057092 restraints weight = 1568179.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.055947 restraints weight = 2154409.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.055987 restraints weight = 2689386.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.055898 restraints weight = 2972069.531| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5368 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 38368 Z= 0.141 Angle : 0.574 9.258 51890 Z= 0.300 Chirality : 0.042 0.192 5948 Planarity : 0.004 0.069 6566 Dihedral : 3.817 19.776 4927 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.64 % Favored : 98.34 % Rotamer: Outliers : 0.12 % Allowed : 3.38 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.12), residues: 4573 helix: 0.93 (0.11), residues: 2113 sheet: 0.10 (0.23), residues: 509 loop : -0.05 (0.14), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG 2 84 TYR 0.015 0.001 TYR 4 972 PHE 0.035 0.001 PHE 1 80 TRP 0.020 0.001 TRP p 280 HIS 0.007 0.001 HIS 2 91 Details of bonding type rmsd covalent geometry : bond 0.00283 (38367) covalent geometry : angle 0.57353 (51890) hydrogen bonds : bond 0.05470 ( 1716) hydrogen bonds : angle 5.40925 ( 4974) Misc. bond : bond 0.02678 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 198 time to evaluate : 1.308 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: p 33 LEU cc_start: 0.9100 (tp) cc_final: 0.8878 (tp) REVERT: p 120 MET cc_start: 0.8470 (tpp) cc_final: 0.8244 (tpp) REVERT: p 132 MET cc_start: 0.8048 (tpt) cc_final: 0.7832 (tpp) REVERT: p 567 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8571 (mt-10) REVERT: p 645 MET cc_start: 0.8116 (tpt) cc_final: 0.7721 (tpp) REVERT: p 704 LYS cc_start: 0.5577 (mttt) cc_final: 0.5217 (mmmt) REVERT: p 972 MET cc_start: 0.7050 (mmm) cc_final: 0.6408 (tpp) REVERT: 3 990 MET cc_start: -0.3554 (mmt) cc_final: -0.4860 (ttt) REVERT: 5 899 MET cc_start: -0.2582 (mtt) cc_final: -0.2862 (mtt) REVERT: 5 945 MET cc_start: -0.5335 (tpt) cc_final: -0.7401 (mtt) outliers start: 5 outliers final: 1 residues processed: 203 average time/residue: 0.2000 time to fit residues: 69.4346 Evaluate side-chains 143 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 181 optimal weight: 6.9990 chunk 385 optimal weight: 3.9990 chunk 211 optimal weight: 9.9990 chunk 122 optimal weight: 0.5980 chunk 299 optimal weight: 4.9990 chunk 173 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 260 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 324 optimal weight: 30.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 93 GLN ** e 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 527 HIS ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n1024 ASN ** p 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 430 HIS ** p 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 81 HIS ** 3 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 453 GLN 3 488 GLN ** 3 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 31093 HIS 31105 ASN ** 31113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 941 ASN ** 6 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 430 HIS 6 530 GLN ** 6 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.060819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.051987 restraints weight = 8386412.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.051747 restraints weight = 7759500.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.051687 restraints weight = 7570555.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.051707 restraints weight = 7346782.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.051710 restraints weight = 7262644.968| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5971 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 38368 Z= 0.137 Angle : 0.543 12.818 51890 Z= 0.282 Chirality : 0.041 0.210 5948 Planarity : 0.004 0.068 6566 Dihedral : 3.830 20.857 4927 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.66 % Favored : 98.32 % Rotamer: Outliers : 0.09 % Allowed : 3.63 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.12), residues: 4573 helix: 1.06 (0.11), residues: 2126 sheet: 0.05 (0.23), residues: 503 loop : -0.01 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG p 390 TYR 0.013 0.001 TYR a 21 PHE 0.041 0.002 PHE 1 80 TRP 0.018 0.001 TRP p 280 HIS 0.011 0.001 HIS 4 962 Details of bonding type rmsd covalent geometry : bond 0.00278 (38367) covalent geometry : angle 0.54300 (51890) hydrogen bonds : bond 0.04402 ( 1716) hydrogen bonds : angle 5.07771 ( 4974) Misc. bond : bond 0.00159 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 177 time to evaluate : 1.291 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: e 760 LEU cc_start: 0.9537 (mp) cc_final: 0.9119 (mp) REVERT: n 1019 MET cc_start: 0.8893 (mpp) cc_final: 0.8573 (mpp) REVERT: n 1067 MET cc_start: 0.8491 (mmp) cc_final: 0.8189 (mmm) REVERT: p 8 MET cc_start: 0.9191 (tmm) cc_final: 0.8955 (tmm) REVERT: p 120 MET cc_start: 0.8718 (tpp) cc_final: 0.8410 (tpp) REVERT: p 645 MET cc_start: 0.8390 (tpt) cc_final: 0.7718 (tpp) REVERT: 3 990 MET cc_start: -0.2883 (mmt) cc_final: -0.4052 (ttt) REVERT: 4 834 MET cc_start: 0.4531 (tmm) cc_final: 0.2917 (mpp) REVERT: 5 881 MET cc_start: -0.3356 (tpt) cc_final: -0.3557 (tpt) REVERT: 5 941 ASN cc_start: -0.5744 (OUTLIER) cc_final: -0.6246 (m110) REVERT: 5 945 MET cc_start: -0.3065 (tpt) cc_final: -0.5773 (mtt) REVERT: 6 510 MET cc_start: 0.7015 (mmm) cc_final: 0.6736 (mmm) outliers start: 4 outliers final: 0 residues processed: 181 average time/residue: 0.1936 time to fit residues: 61.0122 Evaluate side-chains 138 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 27 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 217 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 459 optimal weight: 10.0000 chunk 334 optimal weight: 2.9990 chunk 268 optimal weight: 5.9990 chunk 365 optimal weight: 8.9990 chunk 356 optimal weight: 6.9990 chunk 316 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 527 HIS e 720 ASN e 801 ASN ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 527 HIS ** 3 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 901 ASN ** 3 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 31105 ASN ** 31113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 40 ASN ** 6 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 480 GLN 6 523 GLN ** a 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.059833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.050394 restraints weight = 8205693.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.050068 restraints weight = 7727674.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.050018 restraints weight = 7441635.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.050024 restraints weight = 7218011.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.049999 restraints weight = 7131192.173| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6200 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 38368 Z= 0.145 Angle : 0.543 10.389 51890 Z= 0.282 Chirality : 0.041 0.270 5948 Planarity : 0.004 0.066 6566 Dihedral : 3.887 21.173 4927 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.97 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.12), residues: 4573 helix: 1.06 (0.11), residues: 2125 sheet: 0.12 (0.23), residues: 518 loop : 0.01 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 2 75 TYR 0.014 0.001 TYR n 967 PHE 0.040 0.002 PHE e 544 TRP 0.019 0.001 TRP p 280 HIS 0.007 0.001 HIS n 962 Details of bonding type rmsd covalent geometry : bond 0.00284 (38367) covalent geometry : angle 0.54327 (51890) hydrogen bonds : bond 0.03880 ( 1716) hydrogen bonds : angle 4.98099 ( 4974) Misc. bond : bond 0.00063 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 1.432 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: e 760 LEU cc_start: 0.9547 (mp) cc_final: 0.9301 (mp) REVERT: n 1019 MET cc_start: 0.8965 (mpp) cc_final: 0.8679 (mpp) REVERT: o 885 MET cc_start: 0.5073 (mmt) cc_final: 0.4659 (mtp) REVERT: p 120 MET cc_start: 0.9121 (tpp) cc_final: 0.8879 (tpp) REVERT: p 645 MET cc_start: 0.8507 (tpt) cc_final: 0.7779 (tpp) REVERT: 3 990 MET cc_start: -0.4989 (mmt) cc_final: -0.5866 (ttt) REVERT: 4 834 MET cc_start: 0.5005 (tmm) cc_final: 0.3650 (mpp) REVERT: 5 945 MET cc_start: 0.1072 (tpt) cc_final: -0.2098 (mtt) REVERT: 6 8 MET cc_start: 0.6809 (tmm) cc_final: 0.6294 (tmm) REVERT: 6 510 MET cc_start: 0.7312 (mmm) cc_final: 0.7084 (mmm) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.2014 time to fit residues: 60.3852 Evaluate side-chains 136 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 294 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 255 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 396 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 86 optimal weight: 9.9990 chunk 426 optimal weight: 3.9990 chunk 280 optimal weight: 20.0000 chunk 337 optimal weight: 9.9990 chunk 441 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 91 HIS ** e 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 901 ASN ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1086 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e1105 ASN ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1120 HIS n 847 HIS n 919 HIS p 47 GLN ** p 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 181 GLN p 223 GLN ** p 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 538 ASN ** p 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 687 GLN p 697 HIS ** p 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 80 GLN 3 527 HIS ** 3 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 720 ASN ** 3 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 31086 HIS 31105 ASN ** 31113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 919 HIS 41002 HIS ** 6 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 153 GLN ** 6 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 874 HIS a 106 ASN ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.055400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.044259 restraints weight = 7215274.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.043578 restraints weight = 7556879.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.043476 restraints weight = 7370428.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.043345 restraints weight = 7163593.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.043266 restraints weight = 6986351.736| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 38368 Z= 0.277 Angle : 0.818 14.330 51890 Z= 0.428 Chirality : 0.050 0.317 5948 Planarity : 0.006 0.072 6566 Dihedral : 5.022 35.393 4927 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 23.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.54 % Favored : 96.41 % Rotamer: Outliers : 0.12 % Allowed : 3.75 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.12), residues: 4573 helix: 0.05 (0.10), residues: 2164 sheet: -0.53 (0.22), residues: 537 loop : -0.39 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG 6 925 TYR 0.027 0.003 TYR 3 765 PHE 0.091 0.003 PHE 6 152 TRP 0.030 0.003 TRP p 280 HIS 0.021 0.003 HIS n1070 Details of bonding type rmsd covalent geometry : bond 0.00567 (38367) covalent geometry : angle 0.81814 (51890) hydrogen bonds : bond 0.05153 ( 1716) hydrogen bonds : angle 5.85383 ( 4974) Misc. bond : bond 0.00053 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 158 time to evaluate : 1.273 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: e 760 LEU cc_start: 0.9365 (mp) cc_final: 0.9105 (pp) REVERT: n 834 MET cc_start: 0.6981 (tmm) cc_final: 0.6556 (tmm) REVERT: o 899 MET cc_start: 0.5533 (mmp) cc_final: 0.5208 (mmm) REVERT: p 120 MET cc_start: 0.9298 (tpp) cc_final: 0.9081 (mmm) REVERT: p 645 MET cc_start: 0.8990 (tpt) cc_final: 0.8222 (tpt) REVERT: 2 49 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8279 (pt0) REVERT: 2 54 MET cc_start: 0.1256 (mtt) cc_final: 0.0981 (mtm) REVERT: 3 492 HIS cc_start: 0.9128 (p-80) cc_final: 0.8882 (p-80) REVERT: 3 990 MET cc_start: -0.4225 (mmt) cc_final: -0.5306 (ttt) REVERT: 4 834 MET cc_start: 0.5048 (tmm) cc_final: 0.3473 (mpp) REVERT: 5 945 MET cc_start: 0.6929 (tpt) cc_final: 0.5532 (mtm) REVERT: 6 130 MET cc_start: 0.7797 (ppp) cc_final: 0.7362 (ppp) REVERT: 6 446 MET cc_start: 0.4177 (mmp) cc_final: 0.3473 (tmm) REVERT: 6 645 MET cc_start: 0.5330 (tmm) cc_final: 0.4972 (tmm) REVERT: 6 968 MET cc_start: 0.3073 (ttt) cc_final: 0.2872 (tpt) outliers start: 5 outliers final: 1 residues processed: 163 average time/residue: 0.1954 time to fit residues: 55.5849 Evaluate side-chains 130 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 59 optimal weight: 4.9990 chunk 189 optimal weight: 8.9990 chunk 101 optimal weight: 0.2980 chunk 176 optimal weight: 7.9990 chunk 249 optimal weight: 8.9990 chunk 254 optimal weight: 30.0000 chunk 417 optimal weight: 30.0000 chunk 307 optimal weight: 10.0000 chunk 379 optimal weight: 0.9990 chunk 289 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 776 ASN ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1086 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n1008 HIS ** p 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 223 GLN ** p 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 812 GLN 2 46 GLN ** 3 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 728 GLN ** 3 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 31105 ASN ** 31113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 153 GLN ** 6 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.055849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.045392 restraints weight = 7589478.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.044848 restraints weight = 7513061.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.044768 restraints weight = 7248838.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.044659 restraints weight = 7082411.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.044583 restraints weight = 6907809.445| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 38368 Z= 0.170 Angle : 0.611 9.303 51890 Z= 0.319 Chirality : 0.043 0.186 5948 Planarity : 0.004 0.068 6566 Dihedral : 4.695 24.028 4927 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.78 % Favored : 97.18 % Rotamer: Outliers : 0.05 % Allowed : 2.38 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.12), residues: 4573 helix: 0.36 (0.11), residues: 2164 sheet: -0.71 (0.22), residues: 552 loop : -0.29 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG p 928 TYR 0.022 0.002 TYR n 967 PHE 0.035 0.002 PHE n 927 TRP 0.026 0.002 TRP p 280 HIS 0.008 0.001 HIS p 430 Details of bonding type rmsd covalent geometry : bond 0.00346 (38367) covalent geometry : angle 0.61098 (51890) hydrogen bonds : bond 0.04047 ( 1716) hydrogen bonds : angle 5.43690 ( 4974) Misc. bond : bond 0.00056 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 151 time to evaluate : 1.395 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: e 684 MET cc_start: 0.7809 (ptm) cc_final: 0.7026 (pmm) REVERT: n 834 MET cc_start: 0.7167 (tmm) cc_final: 0.6714 (tmm) REVERT: n 1019 MET cc_start: 0.9350 (mpp) cc_final: 0.9073 (mpp) REVERT: o 899 MET cc_start: 0.5981 (mmp) cc_final: 0.5384 (mmm) REVERT: p 132 MET cc_start: 0.8535 (tpt) cc_final: 0.7106 (tpp) REVERT: p 645 MET cc_start: 0.8707 (tpt) cc_final: 0.8087 (tpt) REVERT: 3 990 MET cc_start: -0.4117 (mmt) cc_final: -0.5311 (ttt) REVERT: 4 834 MET cc_start: 0.4315 (tmm) cc_final: 0.3145 (mpp) REVERT: 5 945 MET cc_start: 0.6125 (tpt) cc_final: 0.4185 (mtm) REVERT: 6 8 MET cc_start: 0.6704 (tmm) cc_final: 0.6269 (tmm) REVERT: 6 130 MET cc_start: 0.8464 (ppp) cc_final: 0.8196 (ppp) REVERT: 6 446 MET cc_start: 0.4077 (mmp) cc_final: 0.2993 (ppp) REVERT: 6 645 MET cc_start: 0.5405 (tmm) cc_final: 0.5131 (tmm) REVERT: 6 972 MET cc_start: 0.6140 (mmp) cc_final: 0.5726 (mmm) outliers start: 2 outliers final: 0 residues processed: 153 average time/residue: 0.1970 time to fit residues: 52.4009 Evaluate side-chains 123 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 271 optimal weight: 30.0000 chunk 28 optimal weight: 5.9990 chunk 156 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 362 optimal weight: 10.0000 chunk 94 optimal weight: 20.0000 chunk 6 optimal weight: 30.0000 chunk 2 optimal weight: 0.0000 chunk 304 optimal weight: 10.0000 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 901 ASN ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1105 ASN ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 849 ASN ** n1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 388 ASN ** 3 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 31105 ASN ** 31113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 847 HIS 6 22 GLN ** 6 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 354 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.053923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.043109 restraints weight = 7181692.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.042397 restraints weight = 7579136.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.042257 restraints weight = 7449044.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.042133 restraints weight = 7230097.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.042061 restraints weight = 7045573.183| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.6350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 38368 Z= 0.255 Angle : 0.769 13.185 51890 Z= 0.404 Chirality : 0.048 0.251 5948 Planarity : 0.006 0.086 6566 Dihedral : 5.265 26.746 4927 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 23.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.22 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.12), residues: 4573 helix: -0.06 (0.11), residues: 2130 sheet: -0.93 (0.22), residues: 542 loop : -0.55 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG c 75 TYR 0.023 0.003 TYR e1119 PHE 0.037 0.003 PHE n 927 TRP 0.033 0.003 TRP p 280 HIS 0.013 0.002 HIS n1070 Details of bonding type rmsd covalent geometry : bond 0.00521 (38367) covalent geometry : angle 0.76889 (51890) hydrogen bonds : bond 0.04835 ( 1716) hydrogen bonds : angle 5.95299 ( 4974) Misc. bond : bond 0.00039 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.407 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: b 80 PHE cc_start: 0.7977 (m-80) cc_final: 0.7478 (m-80) REVERT: e 760 LEU cc_start: 0.9298 (mp) cc_final: 0.8933 (pp) REVERT: n 1019 MET cc_start: 0.9422 (mpp) cc_final: 0.9180 (mpp) REVERT: n 1067 MET cc_start: 0.8181 (mmp) cc_final: 0.7949 (mmm) REVERT: o 899 MET cc_start: 0.6740 (mmp) cc_final: 0.5744 (mmm) REVERT: p 120 MET cc_start: 0.9318 (tpp) cc_final: 0.9098 (mmm) REVERT: p 645 MET cc_start: 0.8970 (tpt) cc_final: 0.8194 (tpt) REVERT: 3 750 TYR cc_start: 0.8843 (m-80) cc_final: 0.8639 (m-10) REVERT: 3 990 MET cc_start: -0.3786 (mmt) cc_final: -0.5000 (ttt) REVERT: 4 834 MET cc_start: 0.5048 (tmm) cc_final: 0.4253 (mpp) REVERT: 5 945 MET cc_start: 0.7370 (tpt) cc_final: 0.5266 (mtm) REVERT: 6 8 MET cc_start: 0.7297 (tmm) cc_final: 0.6929 (tmm) REVERT: 6 645 MET cc_start: 0.6227 (tmm) cc_final: 0.5905 (tmm) REVERT: 6 972 MET cc_start: 0.6323 (mmp) cc_final: 0.5965 (mmm) REVERT: a 14 MET cc_start: 0.8848 (tmm) cc_final: 0.8611 (tmm) REVERT: a 315 MET cc_start: 0.6816 (ptm) cc_final: 0.6262 (ppp) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1931 time to fit residues: 47.0224 Evaluate side-chains 125 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 417 optimal weight: 20.0000 chunk 33 optimal weight: 0.6980 chunk 112 optimal weight: 6.9990 chunk 267 optimal weight: 0.8980 chunk 178 optimal weight: 7.9990 chunk 311 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 271 optimal weight: 5.9990 chunk 260 optimal weight: 2.9990 chunk 384 optimal weight: 20.0000 chunk 181 optimal weight: 5.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 51 GLN ** c 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 388 ASN ** e 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 901 ASN ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n1025 GLN ** p 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 91 HIS ** 3 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 776 ASN ** 3 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 31105 ASN ** 31113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 41025 GLN 5 871 HIS 5 912 HIS ** 6 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 177 GLN ** a 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.055195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.044752 restraints weight = 7542010.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.044236 restraints weight = 7532234.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.044157 restraints weight = 7255359.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.044052 restraints weight = 7040903.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.044011 restraints weight = 6902529.629| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.6264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 38368 Z= 0.138 Angle : 0.602 9.699 51890 Z= 0.310 Chirality : 0.043 0.245 5948 Planarity : 0.004 0.068 6566 Dihedral : 4.868 26.475 4927 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.08 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.12), residues: 4573 helix: 0.32 (0.11), residues: 2176 sheet: -0.73 (0.22), residues: 561 loop : -0.31 (0.15), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG 6 220 TYR 0.014 0.001 TYR 3 648 PHE 0.034 0.002 PHE e 544 TRP 0.022 0.002 TRP p 10 HIS 0.010 0.001 HIS 2 91 Details of bonding type rmsd covalent geometry : bond 0.00294 (38367) covalent geometry : angle 0.60188 (51890) hydrogen bonds : bond 0.03811 ( 1716) hydrogen bonds : angle 5.47642 ( 4974) Misc. bond : bond 0.00055 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 80 PHE cc_start: 0.7833 (m-80) cc_final: 0.7248 (m-80) REVERT: e 760 LEU cc_start: 0.9357 (mp) cc_final: 0.9021 (pp) REVERT: n 1019 MET cc_start: 0.9402 (mpp) cc_final: 0.9178 (mpp) REVERT: o 899 MET cc_start: 0.6171 (mmp) cc_final: 0.5257 (mmm) REVERT: p 645 MET cc_start: 0.8507 (tpt) cc_final: 0.7879 (tpt) REVERT: 3 990 MET cc_start: -0.4074 (mmt) cc_final: -0.5126 (ttt) REVERT: 4 834 MET cc_start: 0.4827 (tmm) cc_final: 0.4265 (mpp) REVERT: 5 945 MET cc_start: 0.6220 (tpt) cc_final: 0.3544 (mtt) REVERT: 6 8 MET cc_start: 0.7489 (tmm) cc_final: 0.7119 (tmm) REVERT: 6 972 MET cc_start: 0.6382 (mmp) cc_final: 0.6022 (mmm) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.1947 time to fit residues: 50.9057 Evaluate side-chains 129 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 278 optimal weight: 1.9990 chunk 324 optimal weight: 8.9990 chunk 355 optimal weight: 5.9990 chunk 276 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 260 optimal weight: 2.9990 chunk 332 optimal weight: 0.0000 chunk 372 optimal weight: 8.9990 chunk 113 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 50 GLN ** c 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1120 HIS ** p 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 327 ASN ** p 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 894 ASN ** 3 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 31105 ASN ** 31113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.055903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.045425 restraints weight = 7479883.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.044848 restraints weight = 7277832.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.044796 restraints weight = 7160785.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.044652 restraints weight = 6972006.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.044611 restraints weight = 6885375.997| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.6184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 38368 Z= 0.113 Angle : 0.577 13.333 51890 Z= 0.293 Chirality : 0.043 0.198 5948 Planarity : 0.004 0.065 6566 Dihedral : 4.543 25.959 4927 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.76 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.12), residues: 4573 helix: 0.61 (0.11), residues: 2170 sheet: -0.56 (0.22), residues: 563 loop : -0.19 (0.15), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG o 872 TYR 0.012 0.001 TYR 3 648 PHE 0.040 0.001 PHE e 795 TRP 0.028 0.001 TRP p 10 HIS 0.007 0.001 HIS 1 81 Details of bonding type rmsd covalent geometry : bond 0.00245 (38367) covalent geometry : angle 0.57749 (51890) hydrogen bonds : bond 0.03508 ( 1716) hydrogen bonds : angle 5.13927 ( 4974) Misc. bond : bond 0.00058 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 48 MET cc_start: 0.9518 (mmm) cc_final: 0.9226 (mmm) REVERT: b 80 PHE cc_start: 0.7819 (m-80) cc_final: 0.7253 (m-80) REVERT: n 1019 MET cc_start: 0.9376 (mpp) cc_final: 0.9176 (mpp) REVERT: o 899 MET cc_start: 0.5944 (mmp) cc_final: 0.5054 (mmm) REVERT: p 295 MET cc_start: 0.8896 (mmp) cc_final: 0.8619 (tpp) REVERT: p 645 MET cc_start: 0.8540 (tpt) cc_final: 0.7819 (tpt) REVERT: p 740 MET cc_start: 0.8919 (pmm) cc_final: 0.8234 (tpt) REVERT: 3 990 MET cc_start: -0.4203 (mmt) cc_final: -0.5187 (ttt) REVERT: 4 834 MET cc_start: 0.4833 (tmm) cc_final: 0.4515 (mpp) REVERT: 5 945 MET cc_start: 0.6186 (tpt) cc_final: 0.3674 (mtt) REVERT: 6 8 MET cc_start: 0.7327 (tmm) cc_final: 0.7008 (tmm) REVERT: 6 510 MET cc_start: 0.6876 (mmp) cc_final: 0.5841 (mmm) REVERT: 6 972 MET cc_start: 0.6051 (mmp) cc_final: 0.5720 (mmm) REVERT: a 14 MET cc_start: 0.8150 (tmm) cc_final: 0.7828 (tmm) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1913 time to fit residues: 51.1500 Evaluate side-chains 129 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 443 optimal weight: 7.9990 chunk 277 optimal weight: 4.9990 chunk 377 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 174 optimal weight: 6.9990 chunk 266 optimal weight: 9.9990 chunk 30 optimal weight: 0.0970 chunk 198 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 382 optimal weight: 7.9990 chunk 292 optimal weight: 7.9990 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 801 ASN ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 313 HIS p 465 GLN p 894 ASN ** 3 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 31105 ASN ** 31113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 480 GLN ** a 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.055785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.045252 restraints weight = 7507987.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.044719 restraints weight = 7387272.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.044643 restraints weight = 7175731.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.044543 restraints weight = 7033271.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.044499 restraints weight = 6820816.075| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.6267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 38368 Z= 0.111 Angle : 0.558 10.349 51890 Z= 0.283 Chirality : 0.042 0.202 5948 Planarity : 0.004 0.106 6566 Dihedral : 4.384 24.168 4927 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.36 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.12), residues: 4573 helix: 0.75 (0.11), residues: 2170 sheet: -0.48 (0.22), residues: 565 loop : -0.13 (0.15), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG o 872 TYR 0.013 0.001 TYR 3 750 PHE 0.021 0.001 PHE 5 869 TRP 0.019 0.001 TRP p 10 HIS 0.009 0.001 HIS n1070 Details of bonding type rmsd covalent geometry : bond 0.00240 (38367) covalent geometry : angle 0.55844 (51890) hydrogen bonds : bond 0.03407 ( 1716) hydrogen bonds : angle 5.02247 ( 4974) Misc. bond : bond 0.00039 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 48 MET cc_start: 0.9404 (mmm) cc_final: 0.9125 (mmm) REVERT: b 80 PHE cc_start: 0.7869 (m-80) cc_final: 0.7330 (m-80) REVERT: n 1019 MET cc_start: 0.9355 (mpp) cc_final: 0.9079 (mpp) REVERT: o 899 MET cc_start: 0.5328 (mmp) cc_final: 0.4388 (mmm) REVERT: p 295 MET cc_start: 0.8940 (mmp) cc_final: 0.8695 (tpp) REVERT: p 645 MET cc_start: 0.8486 (tpt) cc_final: 0.7842 (tpt) REVERT: 3 750 TYR cc_start: 0.8611 (m-80) cc_final: 0.8390 (m-10) REVERT: 3 990 MET cc_start: -0.4435 (mmt) cc_final: -0.5416 (ttt) REVERT: 4 834 MET cc_start: 0.4846 (tmm) cc_final: 0.4581 (mpp) REVERT: 5 945 MET cc_start: 0.6448 (tpt) cc_final: 0.4057 (mtt) REVERT: 6 8 MET cc_start: 0.7150 (tmm) cc_final: 0.6874 (tmm) REVERT: 6 510 MET cc_start: 0.6789 (mmp) cc_final: 0.5849 (mmm) REVERT: 6 972 MET cc_start: 0.6830 (mmp) cc_final: 0.6478 (mmm) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.2005 time to fit residues: 53.1227 Evaluate side-chains 132 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 346 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 112 optimal weight: 20.0000 chunk 28 optimal weight: 0.9980 chunk 309 optimal weight: 0.3980 chunk 88 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 380 optimal weight: 0.1980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 894 ASN ** 3 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 808 HIS ** 3 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 31086 HIS 31105 ASN ** 31113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.056452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.045756 restraints weight = 7431893.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.045256 restraints weight = 7307245.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.045240 restraints weight = 7076803.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.045118 restraints weight = 6863187.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.045065 restraints weight = 6714749.979| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.6222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 38368 Z= 0.101 Angle : 0.553 11.204 51890 Z= 0.278 Chirality : 0.042 0.190 5948 Planarity : 0.004 0.065 6566 Dihedral : 4.206 22.085 4927 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.06 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.13), residues: 4573 helix: 0.82 (0.11), residues: 2198 sheet: -0.34 (0.22), residues: 553 loop : -0.06 (0.15), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG o 872 TYR 0.010 0.001 TYR 3 648 PHE 0.022 0.001 PHE 5 869 TRP 0.020 0.001 TRP p 10 HIS 0.007 0.001 HIS 1 81 Details of bonding type rmsd covalent geometry : bond 0.00213 (38367) covalent geometry : angle 0.55268 (51890) hydrogen bonds : bond 0.03243 ( 1716) hydrogen bonds : angle 4.81917 ( 4974) Misc. bond : bond 0.00039 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5505.18 seconds wall clock time: 96 minutes 58.26 seconds (5818.26 seconds total)