Starting phenix.real_space_refine on Sat Mar 23 15:42:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uil_26548/03_2024/7uil_26548.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uil_26548/03_2024/7uil_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uil_26548/03_2024/7uil_26548.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uil_26548/03_2024/7uil_26548.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uil_26548/03_2024/7uil_26548.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uil_26548/03_2024/7uil_26548.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 Residue "c GLU 49": "OE1" <-> "OE2" Residue "e TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 768": "OE1" <-> "OE2" Residue "e PHE 1116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 1058": "OD1" <-> "OD2" Residue "o ASP 857": "OD1" <-> "OD2" Residue "o PHE 869": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 971": "OE1" <-> "OE2" Residue "2 GLU 49": "OE1" <-> "OE2" Residue "3 TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 768": "OE1" <-> "OE2" Residue "3 PHE 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 1116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 1058": "OD1" <-> "OD2" Residue "5 ASP 857": "OD1" <-> "OD2" Residue "5 PHE 869": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 971": "OE1" <-> "OE2" Residue "a TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 9": "OE1" <-> "OE2" Residue "a GLU 16": "OE1" <-> "OE2" Residue "a TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 29": "OE1" <-> "OE2" Residue "a GLU 41": "OE1" <-> "OE2" Residue "a GLU 45": "OE1" <-> "OE2" Residue "a GLU 46": "OE1" <-> "OE2" Residue "a GLU 50": "OE1" <-> "OE2" Residue "a TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 97": "OE1" <-> "OE2" Residue "a GLU 99": "OE1" <-> "OE2" Residue "a TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 170": "OE1" <-> "OE2" Residue "a TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 209": "OE1" <-> "OE2" Residue "a GLU 218": "OE1" <-> "OE2" Residue "a GLU 219": "OE1" <-> "OE2" Residue "a TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 230": "OE1" <-> "OE2" Residue "a TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 236": "OE1" <-> "OE2" Residue "a GLU 243": "OE1" <-> "OE2" Residue "a GLU 246": "OE1" <-> "OE2" Residue "a GLU 257": "OE1" <-> "OE2" Residue "a PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 275": "OE1" <-> "OE2" Residue "a PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 281": "OE1" <-> "OE2" Residue "a PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 340": "OE1" <-> "OE2" Residue "a GLU 534": "OE1" <-> "OE2" Residue "a GLU 544": "OE1" <-> "OE2" Residue "a GLU 559": "OE1" <-> "OE2" Residue "a PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: 18.64, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.44 Conformation dependent library (CDL) restraints added in 6.0 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: 4.78 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: 15.09 Time building geometry restraints manager: 16.60 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: 99.43 - 106.44: 902 106.44 - 113.46: 21227 113.46 - 120.47: 15131 120.47 - 127.48: 14307 127.48 - 134.50: 323 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: 0.67 - 1.51: 3 1.51 - 2.36: 97 2.36 - 3.21: 35061 3.21 - 4.05: 92024 4.05 - 4.90: 163605 Warning: very small nonbonded interaction distances. Nonbonded interactions: 290790 Sorted by model distance: nonbonded pdb=" NH2 ARG e 879 " pdb=" CG GLU 3 892 " model vdw 0.667 3.520 nonbonded pdb=" CZ ARG e 879 " pdb=" CG GLU 3 892 " model vdw 1.050 3.670 nonbonded pdb=" NH2 ARG e 879 " pdb=" CD GLU 3 892 " model vdw 1.266 3.350 nonbonded pdb=" NH1 ARG e 879 " pdb=" CG GLU 3 892 " model vdw 1.794 3.520 nonbonded pdb=" NH2 ARG e 879 " pdb=" OE2 GLU 3 892 " model vdw 1.937 2.520 ... (remaining 290785 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 2.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 12.020 Check model and map are aligned: 0.470 Set scattering table: 0.320 Process input model: 95.930 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.230 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.900 ------------------------------------------------------------------------------- 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 : 0.004 0.040 38367 Z= 0.262 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 : 0.667 Molprobity Statistics. All-atom Clashscore : 9.13 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.12), 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 TRP 0.088 0.004 TRP a 344 HIS 0.014 0.001 HIS a 536 PHE 0.055 0.002 PHE a 356 TYR 0.116 0.002 TYR a 216 ARG 0.008 0.000 ARG 3 869 *********************** 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 fitting. rotamer outliers: 3 poor density : 302 time to evaluate : 4.469 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: 0.7495 (ptp) REVERT: p 121 LEU cc_start: 0.7755 (tp) cc_final: 0.7389 (tp) REVERT: p 240 LEU cc_start: 0.7893 (tt) cc_final: 0.7647 (tp) REVERT: p 289 MET cc_start: 0.3048 (tpt) cc_final: 0.2728 (tpt) REVERT: p 645 MET cc_start: 0.7857 (tpt) cc_final: 0.7513 (tpp) REVERT: 2 40 ILE cc_start: 0.7392 (mm) cc_final: 0.6903 (mm) REVERT: 3 990 MET cc_start: -0.3044 (mmt) cc_final: -0.5336 (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: -0.7913 (mtt) REVERT: 6 289 MET cc_start: 0.0630 (tpt) cc_final: 0.0033 (tpt) outliers start: 3 outliers final: 0 residues processed: 305 average time/residue: 0.4824 time to fit residues: 243.5250 Evaluate side-chains 168 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 4.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 388 optimal weight: 2.9990 chunk 348 optimal weight: 7.9990 chunk 193 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 235 optimal weight: 20.0000 chunk 186 optimal weight: 5.9990 chunk 360 optimal weight: 20.0000 chunk 139 optimal weight: 8.9990 chunk 219 optimal weight: 4.9990 chunk 268 optimal weight: 5.9990 chunk 417 optimal weight: 0.8980 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 93 GLN ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 59 GLN ** c 80 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 488 GLN ** e 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 815 ASN ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1093 HIS ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n1024 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 40 ASN ** p 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 181 GLN p 187 ASN ** p 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 538 ASN ** 2 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 453 GLN 3 712 ASN 3 801 ASN 3 815 ASN ** 3 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 31093 HIS 31105 ASN ** 31113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 854 ASN ** 4 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 41025 GLN ** 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** ** 6 630 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** a 182 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4068 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 38367 Z= 0.228 Angle : 0.623 13.035 51890 Z= 0.325 Chirality : 0.043 0.186 5948 Planarity : 0.004 0.065 6566 Dihedral : 3.951 21.047 4927 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.12 % Favored : 97.86 % Rotamer: Outliers : 0.16 % Allowed : 4.35 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.12), residues: 4573 helix: 0.85 (0.11), residues: 2103 sheet: 0.06 (0.23), residues: 507 loop : -0.01 (0.14), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP p 280 HIS 0.008 0.001 HIS 4 962 PHE 0.039 0.002 PHE 1 80 TYR 0.016 0.001 TYR 4 972 ARG 0.014 0.001 ARG 6 814 *********************** 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 195 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 188 time to evaluate : 4.565 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: 0.8623 (ptp) cc_final: 0.8265 (ptp) REVERT: o 885 MET cc_start: 0.6695 (mmt) cc_final: 0.6035 (mtp) REVERT: p 645 MET cc_start: 0.8118 (tpt) cc_final: 0.7709 (tpp) REVERT: 3 990 MET cc_start: -0.2692 (mmt) cc_final: -0.4754 (ttt) REVERT: 5 945 MET cc_start: -0.5830 (tpt) cc_final: -0.7416 (mtt) REVERT: 6 289 MET cc_start: 0.0791 (tpt) cc_final: 0.0228 (tpt) REVERT: 6 644 GLU cc_start: 0.6647 (mp0) cc_final: 0.6306 (mp0) outliers start: 7 outliers final: 0 residues processed: 195 average time/residue: 0.4713 time to fit residues: 156.9507 Evaluate side-chains 142 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 4.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 232 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 347 optimal weight: 30.0000 chunk 284 optimal weight: 30.0000 chunk 115 optimal weight: 30.0000 chunk 418 optimal weight: 0.5980 chunk 452 optimal weight: 20.0000 chunk 372 optimal weight: 1.9990 chunk 414 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 chunk 335 optimal weight: 9.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 527 HIS e 712 ASN ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n1021 GLN n1025 GLN p 430 HIS ** p 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 527 HIS ** 3 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 31093 HIS 31105 ASN ** 31113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 41025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 941 ASN 6 40 ASN ** 6 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 349 HIS 6 430 HIS ** 6 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4107 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 38367 Z= 0.184 Angle : 0.533 8.633 51890 Z= 0.278 Chirality : 0.041 0.236 5948 Planarity : 0.004 0.068 6566 Dihedral : 3.874 21.282 4927 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.01 % Favored : 97.97 % Rotamer: Outliers : 0.02 % Allowed : 3.01 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.12), residues: 4573 helix: 1.04 (0.11), residues: 2123 sheet: 0.10 (0.23), residues: 525 loop : 0.01 (0.14), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP p 280 HIS 0.015 0.001 HIS 4 962 PHE 0.039 0.001 PHE 1 80 TYR 0.022 0.001 TYR a 90 ARG 0.007 0.001 ARG a 189 *********************** 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 172 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 4.204 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: b 47 MET cc_start: 0.8701 (ptp) cc_final: 0.8446 (ptp) REVERT: p 8 MET cc_start: 0.7686 (tmm) cc_final: 0.7312 (tmm) REVERT: p 645 MET cc_start: 0.7981 (tpt) cc_final: 0.7600 (tpp) REVERT: 3 493 ASN cc_start: 0.5657 (m-40) cc_final: 0.5323 (m110) REVERT: 3 990 MET cc_start: -0.3048 (mmt) cc_final: -0.4757 (ttt) REVERT: 5 881 MET cc_start: -0.5267 (tpt) cc_final: -0.5514 (tpt) REVERT: 5 945 MET cc_start: -0.5814 (tpt) cc_final: -0.7009 (mtt) REVERT: 6 289 MET cc_start: 0.0320 (tpt) cc_final: -0.0329 (tpt) REVERT: 6 644 GLU cc_start: 0.7083 (mp0) cc_final: 0.6666 (mp0) outliers start: 1 outliers final: 0 residues processed: 172 average time/residue: 0.4706 time to fit residues: 139.9571 Evaluate side-chains 141 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 4.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 413 optimal weight: 8.9990 chunk 314 optimal weight: 4.9990 chunk 217 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 199 optimal weight: 9.9990 chunk 281 optimal weight: 30.0000 chunk 419 optimal weight: 20.0000 chunk 444 optimal weight: 4.9990 chunk 219 optimal weight: 50.0000 chunk 398 optimal weight: 1.9990 chunk 119 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 91 HIS ** e 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 527 HIS e 528 ASN ** e 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 720 ASN ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 854 ASN ** n1020 HIS ** 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 426 ASN p 465 GLN p 687 GLN p 697 HIS ** p 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 32 GLN 2 80 GLN ** 3 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 527 HIS 3 720 ASN ** 3 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 31105 ASN 41002 HIS ** 41025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 523 GLN 6 530 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: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4329 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 38367 Z= 0.247 Angle : 0.640 11.872 51890 Z= 0.334 Chirality : 0.043 0.205 5948 Planarity : 0.004 0.065 6566 Dihedral : 4.232 21.546 4927 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.67 % Favored : 97.29 % Rotamer: Outliers : 0.05 % Allowed : 4.33 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.12), residues: 4573 helix: 0.65 (0.11), residues: 2166 sheet: -0.20 (0.22), residues: 573 loop : -0.03 (0.14), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP p 280 HIS 0.013 0.002 HIS n 962 PHE 0.029 0.002 PHE a 91 TYR 0.018 0.002 TYR a 21 ARG 0.010 0.001 ARG 2 67 *********************** 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 168 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 166 time to evaluate : 5.021 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: b 47 MET cc_start: 0.8336 (ptp) cc_final: 0.8101 (ptp) REVERT: b 80 PHE cc_start: 0.6733 (m-80) cc_final: 0.6426 (m-80) REVERT: p 33 LEU cc_start: 0.7801 (tp) cc_final: 0.7553 (tp) REVERT: p 645 MET cc_start: 0.8155 (tpt) cc_final: 0.7676 (tpp) REVERT: 2 1 MET cc_start: 0.7239 (pmm) cc_final: 0.5884 (tpt) REVERT: 3 493 ASN cc_start: 0.5842 (m-40) cc_final: 0.5415 (m110) REVERT: 3 990 MET cc_start: -0.3374 (mmt) cc_final: -0.4928 (ttt) REVERT: 4 834 MET cc_start: 0.4143 (tmm) cc_final: 0.2745 (mpp) REVERT: 5 945 MET cc_start: -0.5167 (tpt) cc_final: -0.6363 (mtt) REVERT: 6 8 MET cc_start: 0.3748 (tmm) cc_final: 0.3220 (tmm) REVERT: 6 644 GLU cc_start: 0.7082 (mp0) cc_final: 0.6519 (mp0) outliers start: 2 outliers final: 0 residues processed: 167 average time/residue: 0.4551 time to fit residues: 133.1858 Evaluate side-chains 128 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 4.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 370 optimal weight: 0.6980 chunk 252 optimal weight: 0.5980 chunk 6 optimal weight: 0.0010 chunk 331 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 379 optimal weight: 6.9990 chunk 307 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 227 optimal weight: 0.7980 chunk 399 optimal weight: 0.0270 chunk 112 optimal weight: 7.9990 overall best weight: 0.4244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 712 ASN ** 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** n 849 ASN n 919 HIS ** n1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 223 GLN p 812 GLN 1 50 GLN ** 3 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 360 HIS ** 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** 4 991 HIS ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 220 ASN a 529 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4158 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 38367 Z= 0.136 Angle : 0.523 11.786 51890 Z= 0.264 Chirality : 0.041 0.220 5948 Planarity : 0.004 0.065 6566 Dihedral : 3.933 22.197 4927 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.73 % Favored : 98.23 % Rotamer: Outliers : 0.05 % Allowed : 1.50 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.12), residues: 4573 helix: 1.07 (0.11), residues: 2146 sheet: -0.07 (0.22), residues: 575 loop : 0.10 (0.15), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP p 280 HIS 0.011 0.001 HIS n1008 PHE 0.034 0.001 PHE e 795 TYR 0.012 0.001 TYR 4 972 ARG 0.018 0.000 ARG 6 814 *********************** 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 171 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 169 time to evaluate : 5.651 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: b 47 MET cc_start: 0.8605 (ptp) cc_final: 0.8351 (ptp) REVERT: n 834 MET cc_start: 0.4946 (tmm) cc_final: 0.4711 (tmm) REVERT: p 120 MET cc_start: 0.6726 (mmp) cc_final: 0.6510 (mmm) REVERT: p 645 MET cc_start: 0.8059 (tpt) cc_final: 0.7573 (tpp) REVERT: 2 1 MET cc_start: 0.7275 (pmm) cc_final: 0.6025 (tpt) REVERT: 3 492 HIS cc_start: 0.5196 (p-80) cc_final: 0.4926 (p90) REVERT: 3 493 ASN cc_start: 0.5636 (m-40) cc_final: 0.5346 (m-40) REVERT: 3 990 MET cc_start: -0.3451 (mmt) cc_final: -0.5064 (ttt) REVERT: 4 834 MET cc_start: 0.4073 (tmm) cc_final: 0.2719 (mpp) REVERT: 4 956 MET cc_start: 0.3913 (ppp) cc_final: 0.3363 (ptp) REVERT: 5 899 MET cc_start: 0.0657 (mtt) cc_final: 0.0303 (mtt) REVERT: 5 945 MET cc_start: -0.5902 (tpt) cc_final: -0.7019 (mtt) REVERT: 6 8 MET cc_start: 0.3653 (tmm) cc_final: 0.3308 (tmm) REVERT: 6 289 MET cc_start: 0.0371 (tpt) cc_final: 0.0073 (tpt) REVERT: 6 644 GLU cc_start: 0.7267 (mp0) cc_final: 0.6761 (mp0) REVERT: 6 968 MET cc_start: 0.1056 (tmm) cc_final: 0.0758 (tpt) outliers start: 2 outliers final: 1 residues processed: 171 average time/residue: 0.4752 time to fit residues: 142.5132 Evaluate side-chains 142 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 5.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 149 optimal weight: 0.2980 chunk 400 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 261 optimal weight: 20.0000 chunk 109 optimal weight: 0.9980 chunk 445 optimal weight: 8.9990 chunk 369 optimal weight: 0.0470 chunk 206 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 147 optimal weight: 0.9990 chunk 233 optimal weight: 0.9990 overall best weight: 0.6682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 776 ASN e 801 ASN ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 919 HIS ** n1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 223 GLN ** p 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 50 GLN ** 3 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 728 GLN 3 776 ASN ** 3 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 31105 ASN ** 31113 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** a 177 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4146 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 38367 Z= 0.121 Angle : 0.500 10.802 51890 Z= 0.251 Chirality : 0.041 0.195 5948 Planarity : 0.003 0.065 6566 Dihedral : 3.755 18.419 4927 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.90 % Favored : 98.05 % Rotamer: Outliers : 0.05 % Allowed : 1.37 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.12), residues: 4573 helix: 1.23 (0.11), residues: 2135 sheet: -0.04 (0.22), residues: 579 loop : 0.16 (0.15), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP p 280 HIS 0.007 0.001 HIS n1008 PHE 0.019 0.001 PHE 2 50 TYR 0.011 0.001 TYR p 556 ARG 0.009 0.000 ARG 6 814 *********************** 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 166 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 164 time to evaluate : 5.149 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: b 47 MET cc_start: 0.8556 (ptp) cc_final: 0.8338 (ptt) REVERT: n 834 MET cc_start: 0.4982 (tmm) cc_final: 0.4721 (tmm) REVERT: p 645 MET cc_start: 0.8016 (tpt) cc_final: 0.7543 (tpt) REVERT: p 972 MET cc_start: 0.6207 (tpt) cc_final: 0.6002 (tpt) REVERT: 1 88 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8395 (mp0) REVERT: 2 1 MET cc_start: 0.7272 (pmm) cc_final: 0.6153 (tpt) REVERT: 3 493 ASN cc_start: 0.5812 (m-40) cc_final: 0.5497 (m110) REVERT: 3 990 MET cc_start: -0.3456 (mmt) cc_final: -0.5039 (ttt) REVERT: 4 834 MET cc_start: 0.3651 (tmm) cc_final: 0.1989 (mpp) REVERT: 4 956 MET cc_start: 0.4200 (ppp) cc_final: 0.3508 (ptp) REVERT: 5 899 MET cc_start: 0.0728 (mtt) cc_final: 0.0403 (mtt) REVERT: 5 945 MET cc_start: -0.5756 (tpt) cc_final: -0.7003 (mtt) REVERT: 6 8 MET cc_start: 0.3879 (tmm) cc_final: 0.3632 (tmm) REVERT: 6 289 MET cc_start: 0.0088 (tpt) cc_final: -0.0141 (tpt) REVERT: 6 644 GLU cc_start: 0.7256 (mp0) cc_final: 0.6737 (mp0) REVERT: 6 968 MET cc_start: 0.1138 (tmm) cc_final: 0.0784 (tpt) outliers start: 2 outliers final: 0 residues processed: 166 average time/residue: 0.4615 time to fit residues: 133.6513 Evaluate side-chains 145 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 144 time to evaluate : 4.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 429 optimal weight: 0.0270 chunk 50 optimal weight: 0.7980 chunk 253 optimal weight: 5.9990 chunk 325 optimal weight: 0.9980 chunk 251 optimal weight: 30.0000 chunk 374 optimal weight: 8.9990 chunk 248 optimal weight: 0.9980 chunk 443 optimal weight: 40.0000 chunk 277 optimal weight: 8.9990 chunk 270 optimal weight: 10.0000 chunk 204 optimal weight: 5.9990 overall best weight: 1.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 388 ASN ** e 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 50 GLN ** 3 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 360 HIS ** 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** ** 6 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 536 GLN ** a 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4186 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 38367 Z= 0.133 Angle : 0.501 8.655 51890 Z= 0.254 Chirality : 0.040 0.220 5948 Planarity : 0.004 0.065 6566 Dihedral : 3.728 18.040 4927 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.99 % Favored : 97.97 % Rotamer: Outliers : 0.02 % Allowed : 1.23 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.12), residues: 4573 helix: 1.24 (0.11), residues: 2165 sheet: -0.01 (0.22), residues: 570 loop : 0.12 (0.15), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP p 280 HIS 0.005 0.001 HIS n1008 PHE 0.040 0.001 PHE b 80 TYR 0.010 0.001 TYR n 967 ARG 0.007 0.000 ARG o 872 *********************** 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 166 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 4.515 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: b 80 PHE cc_start: 0.6964 (m-80) cc_final: 0.6758 (m-80) REVERT: p 120 MET cc_start: 0.6898 (mmp) cc_final: 0.6680 (mmm) REVERT: p 645 MET cc_start: 0.8047 (tpt) cc_final: 0.7527 (tpp) REVERT: p 972 MET cc_start: 0.6089 (tpt) cc_final: 0.5752 (tpt) REVERT: 2 1 MET cc_start: 0.7260 (pmm) cc_final: 0.6204 (tpt) REVERT: 3 493 ASN cc_start: 0.5600 (m-40) cc_final: 0.5259 (m-40) REVERT: 3 990 MET cc_start: -0.3476 (mmt) cc_final: -0.5064 (ttt) REVERT: 4 834 MET cc_start: 0.3211 (tmm) cc_final: 0.1898 (mpp) REVERT: 4 956 MET cc_start: 0.4858 (ppp) cc_final: 0.3573 (ptp) REVERT: 5 945 MET cc_start: -0.5600 (tpt) cc_final: -0.6679 (mtt) REVERT: 6 8 MET cc_start: 0.3912 (tmm) cc_final: 0.3691 (tmm) REVERT: 6 644 GLU cc_start: 0.7271 (mp0) cc_final: 0.6757 (mp0) REVERT: 6 968 MET cc_start: 0.1206 (tmm) cc_final: 0.0839 (tpt) outliers start: 1 outliers final: 0 residues processed: 166 average time/residue: 0.4543 time to fit residues: 132.3395 Evaluate side-chains 141 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 4.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 274 optimal weight: 6.9990 chunk 177 optimal weight: 0.9980 chunk 264 optimal weight: 0.6980 chunk 133 optimal weight: 0.6980 chunk 87 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 281 optimal weight: 30.0000 chunk 302 optimal weight: 10.0000 chunk 219 optimal weight: 40.0000 chunk 41 optimal weight: 4.9990 chunk 348 optimal weight: 9.9990 overall best weight: 2.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 301 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 6 22 GLN ** 6 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 536 GLN ** a 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 529 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4278 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 38367 Z= 0.165 Angle : 0.536 8.876 51890 Z= 0.275 Chirality : 0.041 0.220 5948 Planarity : 0.004 0.065 6566 Dihedral : 3.879 19.862 4927 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.41 % Favored : 97.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.12), residues: 4573 helix: 1.22 (0.11), residues: 2145 sheet: -0.07 (0.22), residues: 568 loop : 0.09 (0.15), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP p 280 HIS 0.008 0.001 HIS n1070 PHE 0.044 0.002 PHE p 447 TYR 0.017 0.001 TYR n 967 ARG 0.008 0.000 ARG 3 292 *********************** 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 162 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 4.434 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: b 80 PHE cc_start: 0.7084 (m-80) cc_final: 0.6738 (m-80) REVERT: e 449 MET cc_start: 0.6759 (mpp) cc_final: 0.6366 (mpp) REVERT: p 645 MET cc_start: 0.7899 (tpt) cc_final: 0.7418 (tpt) REVERT: p 972 MET cc_start: 0.6079 (tpt) cc_final: 0.5744 (tpt) REVERT: 2 1 MET cc_start: 0.7248 (pmm) cc_final: 0.6160 (tpt) REVERT: 3 492 HIS cc_start: 0.4949 (p-80) cc_final: 0.4682 (p90) REVERT: 3 493 ASN cc_start: 0.5555 (m-40) cc_final: 0.5274 (m-40) REVERT: 3 990 MET cc_start: -0.3351 (mmt) cc_final: -0.4982 (ttt) REVERT: 4 834 MET cc_start: 0.3248 (tmm) cc_final: 0.2054 (mpp) REVERT: 4 956 MET cc_start: 0.4421 (ppp) cc_final: 0.4086 (ptp) REVERT: 5 945 MET cc_start: -0.5303 (tpt) cc_final: -0.6627 (mtt) REVERT: 6 644 GLU cc_start: 0.7410 (mp0) cc_final: 0.6859 (mp0) REVERT: 6 972 MET cc_start: -0.0365 (mmt) cc_final: -0.0793 (mmt) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.4497 time to fit residues: 127.3330 Evaluate side-chains 137 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 4.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 403 optimal weight: 0.0870 chunk 424 optimal weight: 8.9990 chunk 387 optimal weight: 7.9990 chunk 413 optimal weight: 5.9990 chunk 248 optimal weight: 3.9990 chunk 179 optimal weight: 5.9990 chunk 324 optimal weight: 7.9990 chunk 126 optimal weight: 20.0000 chunk 373 optimal weight: 7.9990 chunk 390 optimal weight: 6.9990 chunk 411 optimal weight: 3.9990 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n1020 HIS ** 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 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 50 GLN 1 69 GLN ** 3 301 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** 4 854 ASN ** 41025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 215 ASN ** 6 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 106 ASN ** a 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4387 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 38367 Z= 0.205 Angle : 0.584 10.500 51890 Z= 0.302 Chirality : 0.042 0.210 5948 Planarity : 0.004 0.065 6566 Dihedral : 4.176 20.281 4927 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.71 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.12), residues: 4573 helix: 0.94 (0.11), residues: 2174 sheet: -0.33 (0.22), residues: 553 loop : 0.02 (0.15), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP 6 509 HIS 0.016 0.001 HIS 41008 PHE 0.030 0.002 PHE 6 900 TYR 0.023 0.001 TYR n 967 ARG 0.008 0.001 ARG o 872 *********************** 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 157 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 4.597 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: b 80 PHE cc_start: 0.7247 (m-80) cc_final: 0.6861 (m-80) REVERT: o 899 MET cc_start: 0.7388 (mmp) cc_final: 0.6914 (mmm) REVERT: p 33 LEU cc_start: 0.7837 (tp) cc_final: 0.7612 (tp) REVERT: p 120 MET cc_start: 0.7083 (mmp) cc_final: 0.6743 (mmm) REVERT: p 645 MET cc_start: 0.8018 (tpt) cc_final: 0.7575 (tpt) REVERT: p 972 MET cc_start: 0.6286 (tpt) cc_final: 0.6000 (tpt) REVERT: 2 1 MET cc_start: 0.7399 (pmm) cc_final: 0.6352 (tpt) REVERT: 3 492 HIS cc_start: 0.5365 (p-80) cc_final: 0.4995 (p90) REVERT: 3 493 ASN cc_start: 0.5570 (m-40) cc_final: 0.5343 (m-40) REVERT: 3 990 MET cc_start: -0.3070 (mmt) cc_final: -0.4625 (ttt) REVERT: 4 834 MET cc_start: 0.3405 (tmm) cc_final: 0.2283 (mpp) REVERT: 5 945 MET cc_start: -0.4380 (tpt) cc_final: -0.5732 (mtm) REVERT: 6 644 GLU cc_start: 0.7225 (mp0) cc_final: 0.6668 (mp0) REVERT: 6 968 MET cc_start: 0.3047 (tmm) cc_final: 0.2842 (tmm) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.4614 time to fit residues: 126.7395 Evaluate side-chains 131 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 4.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 271 optimal weight: 8.9990 chunk 436 optimal weight: 40.0000 chunk 266 optimal weight: 8.9990 chunk 207 optimal weight: 20.0000 chunk 303 optimal weight: 1.9990 chunk 458 optimal weight: 10.0000 chunk 421 optimal weight: 9.9990 chunk 364 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 281 optimal weight: 20.0000 chunk 223 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 50 GLN ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 901 ASN ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 992 ASN ** n1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 47 GLN ** p 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 426 ASN ** p 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 69 GLN ** 3 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 453 GLN ** 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** ** 41025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 912 HIS ** 6 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 223 GLN ** 6 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 346 GLN ** a 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4595 moved from start: 0.6427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 38367 Z= 0.320 Angle : 0.759 15.393 51890 Z= 0.396 Chirality : 0.046 0.245 5948 Planarity : 0.005 0.080 6566 Dihedral : 4.986 23.248 4927 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 27.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.94 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.12), residues: 4573 helix: 0.18 (0.11), residues: 2162 sheet: -0.82 (0.21), residues: 547 loop : -0.27 (0.14), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP e 306 HIS 0.019 0.002 HIS n1070 PHE 0.038 0.003 PHE 5 869 TYR 0.029 0.002 TYR e1119 ARG 0.011 0.001 ARG 3 602 ********************** 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 151 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 3.772 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: 0.6925 (m-80) cc_final: 0.6646 (m-80) REVERT: o 899 MET cc_start: 0.7763 (mmp) cc_final: 0.7217 (mmm) REVERT: p 33 LEU cc_start: 0.7954 (tp) cc_final: 0.7715 (tp) REVERT: p 120 MET cc_start: 0.7399 (mmp) cc_final: 0.7198 (mmm) REVERT: p 645 MET cc_start: 0.8379 (tpt) cc_final: 0.7789 (tpt) REVERT: 2 1 MET cc_start: 0.7366 (pmm) cc_final: 0.6334 (tpt) REVERT: 3 492 HIS cc_start: 0.5824 (p-80) cc_final: 0.4982 (p-80) REVERT: 3 990 MET cc_start: -0.2458 (mmt) cc_final: -0.4004 (ttt) REVERT: 4 834 MET cc_start: 0.3483 (tmm) cc_final: 0.2300 (mpp) REVERT: 6 968 MET cc_start: 0.3770 (tmm) cc_final: 0.3568 (tmm) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.4679 time to fit residues: 124.0482 Evaluate side-chains 123 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 4.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 289 optimal weight: 5.9990 chunk 388 optimal weight: 6.9990 chunk 111 optimal weight: 0.3980 chunk 336 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 365 optimal weight: 20.0000 chunk 152 optimal weight: 0.9990 chunk 375 optimal weight: 30.0000 chunk 46 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 51 GLN ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 891 ASN ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1105 ASN ** e1113 ASN ** 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 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 894 ASN ** 3 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 493 ASN ** 3 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 31105 ASN ** 31113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 109 HIS ** 6 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 346 GLN ** a 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 354 ASN ** 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 = 0.4197 r_free = 0.4197 target = 0.062622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.045154 restraints weight = 539570.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.045126 restraints weight = 561121.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.045059 restraints weight = 526715.184| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.6294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 38367 Z= 0.163 Angle : 0.576 10.343 51890 Z= 0.295 Chirality : 0.042 0.250 5948 Planarity : 0.004 0.065 6566 Dihedral : 4.530 22.948 4927 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.78 % Favored : 97.18 % Rotamer: Outliers : 0.02 % Allowed : 0.37 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.12), residues: 4573 helix: 0.62 (0.11), residues: 2170 sheet: -0.57 (0.21), residues: 555 loop : -0.10 (0.15), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP 6 509 HIS 0.008 0.001 HIS n1070 PHE 0.029 0.002 PHE b 80 TYR 0.018 0.001 TYR e 293 ARG 0.008 0.001 ARG o 872 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5909.30 seconds wall clock time: 112 minutes 50.79 seconds (6770.79 seconds total)