Starting phenix.real_space_refine on Mon Mar 11 17:02:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pe7_13347/03_2024/7pe7_13347_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pe7_13347/03_2024/7pe7_13347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pe7_13347/03_2024/7pe7_13347.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pe7_13347/03_2024/7pe7_13347.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pe7_13347/03_2024/7pe7_13347_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pe7_13347/03_2024/7pe7_13347_updated.pdb" } resolution = 3.41 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= -0.002 sd= 0.045 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 12 5.49 5 S 350 5.16 5 C 37076 2.51 5 N 10408 2.21 5 O 10734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 729": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1030": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2074": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 729": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1030": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2074": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 58582 Number of models: 1 Model: "" Number of chains: 16 Chain: "B" Number of atoms: 16419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2194, 16419 Classifications: {'peptide': 2194} Incomplete info: {'truncation_to_alanine': 359} Link IDs: {'PTRANS': 88, 'TRANS': 2105} Chain breaks: 20 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1315 Unresolved non-hydrogen angles: 1672 Unresolved non-hydrogen dihedrals: 1079 Unresolved non-hydrogen chiralities: 129 Planarities with less than four sites: {'GLN:plan1': 23, 'ASP:plan': 18, 'TYR:plan': 8, 'ASN:plan1': 10, 'TRP:plan': 4, 'HIS:plan': 9, 'PHE:plan': 19, 'GLU:plan': 33, 'ARG:plan': 31} Unresolved non-hydrogen planarities: 714 Chain: "D" Number of atoms: 2465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2465 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 305} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 8917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1115, 8917 Classifications: {'peptide': 1115} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 37, 'TRANS': 1077} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "H" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 655 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "A" Number of atoms: 16419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2194, 16419 Classifications: {'peptide': 2194} Incomplete info: {'truncation_to_alanine': 359} Link IDs: {'PTRANS': 88, 'TRANS': 2105} Chain breaks: 20 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1315 Unresolved non-hydrogen angles: 1672 Unresolved non-hydrogen dihedrals: 1079 Unresolved non-hydrogen chiralities: 129 Planarities with less than four sites: {'GLN:plan1': 23, 'ASP:plan': 18, 'TYR:plan': 8, 'ASN:plan1': 10, 'TRP:plan': 4, 'HIS:plan': 9, 'PHE:plan': 19, 'GLU:plan': 33, 'ARG:plan': 31} Unresolved non-hydrogen planarities: 714 Chain: "C" Number of atoms: 2465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2465 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 305} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 8917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1115, 8917 Classifications: {'peptide': 1115} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 37, 'TRANS': 1077} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "G" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 655 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "I" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 795 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 97} Chain: "J" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 795 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 97} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 26955 SG CYS F1520 26.590 81.817 44.238 1.00145.74 S ATOM 26981 SG CYS F1523 22.851 82.062 43.729 1.00158.81 S ATOM 27441 SG CYS F1651 24.338 78.700 44.831 1.00127.63 S ATOM 55411 SG CYS E1520 25.630 124.627 204.184 1.00178.71 S ATOM 55437 SG CYS E1523 21.873 124.563 204.610 1.00196.92 S ATOM 55897 SG CYS E1651 23.546 127.849 203.544 1.00161.06 S Time building chain proxies: 23.64, per 1000 atoms: 0.40 Number of scatterers: 58582 At special positions: 0 Unit cell: (153.41, 207.368, 249.688, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 350 16.00 P 12 15.00 O 10734 8.00 N 10408 7.00 C 37076 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 16.88 Conformation dependent library (CDL) restraints added in 8.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E4801 " pdb="ZN ZN E4801 " - pdb=" NE2 HIS E1515 " pdb="ZN ZN E4801 " - pdb=" SG CYS E1523 " pdb="ZN ZN E4801 " - pdb=" SG CYS E1520 " pdb="ZN ZN E4801 " - pdb=" SG CYS E1651 " pdb=" ZN F4801 " pdb="ZN ZN F4801 " - pdb=" NE2 HIS F1515 " pdb="ZN ZN F4801 " - pdb=" SG CYS F1523 " pdb="ZN ZN F4801 " - pdb=" SG CYS F1520 " pdb="ZN ZN F4801 " - pdb=" SG CYS F1651 " Number of angles added : 6 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14620 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 400 helices and 28 sheets defined 59.2% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 15.28 Creating SS restraints... Processing helix chain 'B' and resid 18 through 29 Processing helix chain 'B' and resid 38 through 52 Processing helix chain 'B' and resid 61 through 73 Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'B' and resid 102 through 115 removed outlier: 3.544A pdb=" N ARG B 106 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 114 " --> pdb=" O TYR B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 136 Processing helix chain 'B' and resid 141 through 155 Processing helix chain 'B' and resid 165 through 178 Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'B' and resid 188 through 197 Processing helix chain 'B' and resid 204 through 222 removed outlier: 3.550A pdb=" N GLY B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 245 Processing helix chain 'B' and resid 262 through 275 Processing helix chain 'B' and resid 278 through 288 removed outlier: 3.872A pdb=" N LEU B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 360 No H-bonds generated for 'chain 'B' and resid 357 through 360' Processing helix chain 'B' and resid 363 through 375 Processing helix chain 'B' and resid 387 through 402 Proline residue: B 397 - end of helix Processing helix chain 'B' and resid 411 through 424 Processing helix chain 'B' and resid 430 through 443 Processing helix chain 'B' and resid 452 through 465 removed outlier: 3.944A pdb=" N ALA B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Proline residue: B 464 - end of helix Processing helix chain 'B' and resid 480 through 490 Processing helix chain 'B' and resid 500 through 511 removed outlier: 5.161A pdb=" N GLU B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) Proline residue: B 507 - end of helix Processing helix chain 'B' and resid 515 through 527 Processing helix chain 'B' and resid 532 through 548 Processing helix chain 'B' and resid 581 through 589 removed outlier: 3.599A pdb=" N ALA B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 612 removed outlier: 3.658A pdb=" N ARG B 604 " --> pdb=" O THR B 600 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASP B 608 " --> pdb=" O ARG B 604 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N HIS B 609 " --> pdb=" O HIS B 605 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N PHE B 610 " --> pdb=" O CYS B 606 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU B 611 " --> pdb=" O ALA B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 628 removed outlier: 3.549A pdb=" N GLU B 621 " --> pdb=" O GLU B 617 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG B 624 " --> pdb=" O MET B 620 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER B 627 " --> pdb=" O ALA B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 664 removed outlier: 3.587A pdb=" N SER B 657 " --> pdb=" O ALA B 653 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS B 658 " --> pdb=" O ASP B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 678 removed outlier: 3.510A pdb=" N CYS B 674 " --> pdb=" O ASP B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 685 removed outlier: 4.638A pdb=" N ALA B 685 " --> pdb=" O ARG B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 700 removed outlier: 3.517A pdb=" N GLN B 694 " --> pdb=" O ALA B 690 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA B 695 " --> pdb=" O GLU B 691 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA B 699 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 700 " --> pdb=" O LEU B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 720 removed outlier: 3.542A pdb=" N LEU B 710 " --> pdb=" O GLU B 706 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N CYS B 713 " --> pdb=" O GLU B 709 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER B 720 " --> pdb=" O GLY B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 742 Proline residue: B 728 - end of helix removed outlier: 4.024A pdb=" N LYS B 732 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 741 " --> pdb=" O ILE B 737 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU B 742 " --> pdb=" O LEU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 763 removed outlier: 3.518A pdb=" N MET B 756 " --> pdb=" O GLN B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 783 Proline residue: B 770 - end of helix removed outlier: 5.988A pdb=" N GLU B 773 " --> pdb=" O ARG B 769 " (cutoff:3.500A) Proline residue: B 774 - end of helix removed outlier: 3.649A pdb=" N ALA B 778 " --> pdb=" O PRO B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 808 removed outlier: 3.648A pdb=" N ASN B 797 " --> pdb=" O GLY B 793 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA B 800 " --> pdb=" O ASN B 796 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU B 804 " --> pdb=" O ALA B 800 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN B 807 " --> pdb=" O GLY B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 828 removed outlier: 4.301A pdb=" N ILE B 822 " --> pdb=" O ASP B 818 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ILE B 823 " --> pdb=" O GLU B 819 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET B 827 " --> pdb=" O ILE B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 846 Processing helix chain 'B' and resid 848 through 851 No H-bonds generated for 'chain 'B' and resid 848 through 851' Processing helix chain 'B' and resid 856 through 860 removed outlier: 3.642A pdb=" N LYS B 860 " --> pdb=" O PRO B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 874 removed outlier: 3.691A pdb=" N LEU B 872 " --> pdb=" O LEU B 868 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS B 873 " --> pdb=" O LEU B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 891 removed outlier: 3.759A pdb=" N ARG B 886 " --> pdb=" O ARG B 882 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 901 Processing helix chain 'B' and resid 930 through 936 removed outlier: 3.674A pdb=" N VAL B 936 " --> pdb=" O SER B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 957 removed outlier: 3.951A pdb=" N TYR B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) Proline residue: B 948 - end of helix Processing helix chain 'B' and resid 962 through 964 No H-bonds generated for 'chain 'B' and resid 962 through 964' Processing helix chain 'B' and resid 966 through 982 removed outlier: 3.884A pdb=" N THR B 969 " --> pdb=" O HIS B 966 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL B 971 " --> pdb=" O HIS B 968 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL B 972 " --> pdb=" O THR B 969 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N THR B 976 " --> pdb=" O GLN B 973 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE B 979 " --> pdb=" O THR B 976 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B 982 " --> pdb=" O PHE B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 1003 Proline residue: B 991 - end of helix removed outlier: 4.949A pdb=" N MET B 994 " --> pdb=" O PRO B 991 " (cutoff:3.500A) Proline residue: B 995 - end of helix removed outlier: 4.031A pdb=" N LEU B 998 " --> pdb=" O PRO B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1019 removed outlier: 3.861A pdb=" N GLN B1014 " --> pdb=" O GLU B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1031 through 1041 removed outlier: 3.971A pdb=" N GLU B1040 " --> pdb=" O THR B1036 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE B1041 " --> pdb=" O LEU B1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1063 removed outlier: 3.680A pdb=" N VAL B1061 " --> pdb=" O GLU B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1081 removed outlier: 3.770A pdb=" N LEU B1071 " --> pdb=" O LYS B1068 " (cutoff:3.500A) Proline residue: B1072 - end of helix Proline residue: B1076 - end of helix removed outlier: 3.530A pdb=" N ARG B1080 " --> pdb=" O HIS B1077 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B1081 " --> pdb=" O MET B1078 " (cutoff:3.500A) Processing helix chain 'B' and resid 1088 through 1100 removed outlier: 3.848A pdb=" N ILE B1091 " --> pdb=" O PRO B1088 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL B1092 " --> pdb=" O GLY B1089 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA B1098 " --> pdb=" O LYS B1095 " (cutoff:3.500A) Processing helix chain 'B' and resid 1104 through 1106 No H-bonds generated for 'chain 'B' and resid 1104 through 1106' Processing helix chain 'B' and resid 1111 through 1119 Proline residue: B1116 - end of helix Processing helix chain 'B' and resid 1129 through 1145 removed outlier: 3.722A pdb=" N VAL B1139 " --> pdb=" O ALA B1135 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP B1140 " --> pdb=" O LEU B1136 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU B1144 " --> pdb=" O ASP B1140 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N SER B1145 " --> pdb=" O ARG B1141 " (cutoff:3.500A) Processing helix chain 'B' and resid 1153 through 1163 removed outlier: 4.039A pdb=" N HIS B1157 " --> pdb=" O SER B1153 " (cutoff:3.500A) Proline residue: B1158 - end of helix Processing helix chain 'B' and resid 1170 through 1181 removed outlier: 3.623A pdb=" N ASP B1175 " --> pdb=" O SER B1171 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR B1176 " --> pdb=" O THR B1172 " (cutoff:3.500A) Processing helix chain 'B' and resid 1186 through 1202 removed outlier: 3.918A pdb=" N ILE B1190 " --> pdb=" O LYS B1187 " (cutoff:3.500A) Proline residue: B1193 - end of helix removed outlier: 3.853A pdb=" N ASN B1196 " --> pdb=" O PRO B1193 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS B1197 " --> pdb=" O MET B1194 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B1199 " --> pdb=" O ASN B1196 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B1200 " --> pdb=" O LYS B1197 " (cutoff:3.500A) Processing helix chain 'B' and resid 1207 through 1217 Processing helix chain 'B' and resid 1229 through 1237 Processing helix chain 'B' and resid 1265 through 1269 Processing helix chain 'B' and resid 1277 through 1293 Processing helix chain 'B' and resid 1298 through 1309 removed outlier: 4.077A pdb=" N CYS B1303 " --> pdb=" O SER B1299 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TRP B1304 " --> pdb=" O LEU B1300 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ALA B1305 " --> pdb=" O ARG B1301 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LEU B1306 " --> pdb=" O SER B1302 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA B1309 " --> pdb=" O ALA B1305 " (cutoff:3.500A) Processing helix chain 'B' and resid 1312 through 1315 No H-bonds generated for 'chain 'B' and resid 1312 through 1315' Processing helix chain 'B' and resid 1318 through 1328 removed outlier: 3.872A pdb=" N GLU B1328 " --> pdb=" O SER B1324 " (cutoff:3.500A) Processing helix chain 'B' and resid 1331 through 1345 removed outlier: 3.645A pdb=" N GLU B1336 " --> pdb=" O ASP B1332 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B1337 " --> pdb=" O GLN B1333 " (cutoff:3.500A) Processing helix chain 'B' and resid 1351 through 1366 Processing helix chain 'B' and resid 1377 through 1388 removed outlier: 3.505A pdb=" N ILE B1380 " --> pdb=" O ASP B1377 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N VAL B1381 " --> pdb=" O ASN B1378 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B1383 " --> pdb=" O ILE B1380 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU B1385 " --> pdb=" O LEU B1382 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA B1387 " --> pdb=" O GLY B1384 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA B1388 " --> pdb=" O GLU B1385 " (cutoff:3.500A) Processing helix chain 'B' and resid 1393 through 1406 removed outlier: 3.504A pdb=" N HIS B1398 " --> pdb=" O ALA B1394 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS B1406 " --> pdb=" O LEU B1402 " (cutoff:3.500A) Processing helix chain 'B' and resid 1410 through 1423 Processing helix chain 'B' and resid 1426 through 1438 removed outlier: 3.695A pdb=" N VAL B1432 " --> pdb=" O ALA B1428 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B1433 " --> pdb=" O ALA B1429 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS B1438 " --> pdb=" O GLU B1434 " (cutoff:3.500A) Processing helix chain 'B' and resid 1447 through 1453 removed outlier: 3.887A pdb=" N GLU B1451 " --> pdb=" O ALA B1447 " (cutoff:3.500A) Processing helix chain 'B' and resid 1457 through 1468 removed outlier: 3.863A pdb=" N VAL B1461 " --> pdb=" O GLU B1457 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS B1466 " --> pdb=" O ALA B1462 " (cutoff:3.500A) Processing helix chain 'B' and resid 1476 through 1487 removed outlier: 3.755A pdb=" N ALA B1486 " --> pdb=" O ARG B1482 " (cutoff:3.500A) Processing helix chain 'B' and resid 1490 through 1501 removed outlier: 3.613A pdb=" N GLN B1495 " --> pdb=" O GLY B1491 " (cutoff:3.500A) Processing helix chain 'B' and resid 1506 through 1523 removed outlier: 3.897A pdb=" N LYS B1511 " --> pdb=" O GLU B1507 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET B1512 " --> pdb=" O THR B1508 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG B1514 " --> pdb=" O ALA B1510 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N MET B1515 " --> pdb=" O LYS B1511 " (cutoff:3.500A) Processing helix chain 'B' and resid 1526 through 1535 removed outlier: 3.811A pdb=" N GLU B1530 " --> pdb=" O TRP B1526 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLU B1531 " --> pdb=" O ASP B1527 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N MET B1535 " --> pdb=" O GLU B1531 " (cutoff:3.500A) Processing helix chain 'B' and resid 1541 through 1553 removed outlier: 4.215A pdb=" N ARG B1547 " --> pdb=" O GLY B1543 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU B1550 " --> pdb=" O TYR B1546 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B1552 " --> pdb=" O ALA B1548 " (cutoff:3.500A) Processing helix chain 'B' and resid 1557 through 1580 removed outlier: 3.771A pdb=" N GLN B1562 " --> pdb=" O SER B1558 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP B1569 " --> pdb=" O ASP B1565 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B1570 " --> pdb=" O LYS B1566 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA B1573 " --> pdb=" O ASP B1569 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU B1574 " --> pdb=" O LEU B1570 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B1577 " --> pdb=" O ALA B1573 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N MET B1578 " --> pdb=" O GLU B1574 " (cutoff:3.500A) Processing helix chain 'B' and resid 1585 through 1587 No H-bonds generated for 'chain 'B' and resid 1585 through 1587' Processing helix chain 'B' and resid 1590 through 1607 removed outlier: 3.651A pdb=" N GLU B1600 " --> pdb=" O LEU B1596 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B1601 " --> pdb=" O SER B1597 " (cutoff:3.500A) Processing helix chain 'B' and resid 1609 through 1611 No H-bonds generated for 'chain 'B' and resid 1609 through 1611' Processing helix chain 'B' and resid 1615 through 1623 removed outlier: 5.436A pdb=" N TRP B1620 " --> pdb=" O ARG B1616 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU B1621 " --> pdb=" O GLN B1617 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B1623 " --> pdb=" O TRP B1619 " (cutoff:3.500A) Processing helix chain 'B' and resid 1630 through 1641 removed outlier: 3.862A pdb=" N SER B1641 " --> pdb=" O LEU B1637 " (cutoff:3.500A) Processing helix chain 'B' and resid 1646 through 1648 No H-bonds generated for 'chain 'B' and resid 1646 through 1648' Processing helix chain 'B' and resid 1650 through 1663 removed outlier: 4.085A pdb=" N LYS B1655 " --> pdb=" O ARG B1651 " (cutoff:3.500A) Processing helix chain 'B' and resid 1666 through 1677 removed outlier: 3.842A pdb=" N LEU B1673 " --> pdb=" O ALA B1669 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU B1676 " --> pdb=" O THR B1672 " (cutoff:3.500A) Processing helix chain 'B' and resid 1694 through 1707 removed outlier: 3.517A pdb=" N LYS B1702 " --> pdb=" O TYR B1698 " (cutoff:3.500A) Processing helix chain 'B' and resid 1712 through 1728 removed outlier: 3.717A pdb=" N GLN B1725 " --> pdb=" O VAL B1721 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN B1726 " --> pdb=" O GLN B1722 " (cutoff:3.500A) Processing helix chain 'B' and resid 1739 through 1761 Processing helix chain 'B' and resid 1768 through 1782 removed outlier: 3.526A pdb=" N GLU B1781 " --> pdb=" O SER B1777 " (cutoff:3.500A) Processing helix chain 'B' and resid 1787 through 1808 removed outlier: 3.537A pdb=" N ALA B1792 " --> pdb=" O LYS B1788 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B1802 " --> pdb=" O PHE B1798 " (cutoff:3.500A) Processing helix chain 'B' and resid 1878 through 1895 Proline residue: B1883 - end of helix Processing helix chain 'B' and resid 1900 through 1913 removed outlier: 3.544A pdb=" N VAL B1906 " --> pdb=" O ASP B1902 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU B1907 " --> pdb=" O THR B1903 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR B1908 " --> pdb=" O LEU B1904 " (cutoff:3.500A) Processing helix chain 'B' and resid 1917 through 1929 removed outlier: 3.801A pdb=" N GLU B1921 " --> pdb=" O PRO B1917 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA B1922 " --> pdb=" O ASP B1918 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU B1925 " --> pdb=" O GLU B1921 " (cutoff:3.500A) Processing helix chain 'B' and resid 1936 through 1944 Proline residue: B1940 - end of helix removed outlier: 3.542A pdb=" N ILE B1943 " --> pdb=" O PRO B1940 " (cutoff:3.500A) Processing helix chain 'B' and resid 1951 through 1967 removed outlier: 4.391A pdb=" N LEU B1956 " --> pdb=" O LEU B1952 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE B1957 " --> pdb=" O VAL B1953 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS B1958 " --> pdb=" O GLY B1954 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU B1960 " --> pdb=" O LEU B1956 " (cutoff:3.500A) Processing helix chain 'B' and resid 1973 through 1980 Processing helix chain 'B' and resid 1985 through 2001 removed outlier: 3.575A pdb=" N ASN B1997 " --> pdb=" O LYS B1993 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU B2000 " --> pdb=" O LYS B1996 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N HIS B2001 " --> pdb=" O ASN B1997 " (cutoff:3.500A) Processing helix chain 'B' and resid 2003 through 2020 Processing helix chain 'B' and resid 2023 through 2040 Processing helix chain 'B' and resid 2045 through 2060 removed outlier: 3.550A pdb=" N GLU B2049 " --> pdb=" O LYS B2045 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL B2050 " --> pdb=" O GLY B2046 " (cutoff:3.500A) Proline residue: B2053 - end of helix removed outlier: 4.019A pdb=" N MET B2058 " --> pdb=" O LEU B2054 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU B2059 " --> pdb=" O HIS B2055 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG B2060 " --> pdb=" O ALA B2056 " (cutoff:3.500A) Processing helix chain 'B' and resid 2065 through 2073 Processing helix chain 'B' and resid 2075 through 2090 removed outlier: 3.784A pdb=" N LYS B2090 " --> pdb=" O ARG B2086 " (cutoff:3.500A) Processing helix chain 'B' and resid 2094 through 2113 removed outlier: 3.967A pdb=" N LEU B2103 " --> pdb=" O GLN B2099 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS B2106 " --> pdb=" O ASP B2102 " (cutoff:3.500A) Processing helix chain 'B' and resid 2123 through 2126 No H-bonds generated for 'chain 'B' and resid 2123 through 2126' Processing helix chain 'B' and resid 2193 through 2210 Processing helix chain 'B' and resid 2213 through 2216 No H-bonds generated for 'chain 'B' and resid 2213 through 2216' Processing helix chain 'B' and resid 2246 through 2256 Processing helix chain 'B' and resid 2263 through 2271 Processing helix chain 'B' and resid 2275 through 2277 No H-bonds generated for 'chain 'B' and resid 2275 through 2277' Processing helix chain 'B' and resid 2280 through 2293 removed outlier: 3.526A pdb=" N VAL B2284 " --> pdb=" O LEU B2280 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU B2285 " --> pdb=" O MET B2281 " (cutoff:3.500A) Processing helix chain 'B' and resid 2298 through 2305 removed outlier: 3.816A pdb=" N TRP B2304 " --> pdb=" O ALA B2300 " (cutoff:3.500A) Processing helix chain 'B' and resid 2310 through 2334 removed outlier: 3.860A pdb=" N VAL B2326 " --> pdb=" O ARG B2322 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET B2327 " --> pdb=" O SER B2323 " (cutoff:3.500A) Processing helix chain 'B' and resid 2341 through 2343 No H-bonds generated for 'chain 'B' and resid 2341 through 2343' Processing helix chain 'B' and resid 2364 through 2367 No H-bonds generated for 'chain 'B' and resid 2364 through 2367' Processing helix chain 'B' and resid 2381 through 2384 No H-bonds generated for 'chain 'B' and resid 2381 through 2384' Processing helix chain 'B' and resid 2395 through 2409 Processing helix chain 'B' and resid 2411 through 2422 removed outlier: 3.873A pdb=" N VAL B2417 " --> pdb=" O SER B2413 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B2418 " --> pdb=" O VAL B2414 " (cutoff:3.500A) Processing helix chain 'B' and resid 2495 through 2507 removed outlier: 3.538A pdb=" N GLN B2499 " --> pdb=" O LYS B2495 " (cutoff:3.500A) Processing helix chain 'B' and resid 2521 through 2533 Processing helix chain 'B' and resid 2535 through 2539 Processing helix chain 'B' and resid 2543 through 2545 No H-bonds generated for 'chain 'B' and resid 2543 through 2545' Processing helix chain 'F' and resid 33 through 43 removed outlier: 4.103A pdb=" N ARG F 39 " --> pdb=" O SER F 35 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU F 40 " --> pdb=" O ASP F 36 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE F 41 " --> pdb=" O ASN F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 48 No H-bonds generated for 'chain 'F' and resid 46 through 48' Processing helix chain 'F' and resid 53 through 69 removed outlier: 3.549A pdb=" N ASN F 61 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP F 69 " --> pdb=" O LYS F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 91 removed outlier: 3.521A pdb=" N LEU F 90 " --> pdb=" O ILE F 86 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ALA F 91 " --> pdb=" O CYS F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 110 Processing helix chain 'F' and resid 114 through 122 Processing helix chain 'F' and resid 125 through 133 removed outlier: 4.429A pdb=" N ALA F 130 " --> pdb=" O TYR F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 156 removed outlier: 3.510A pdb=" N GLN F 145 " --> pdb=" O VAL F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 160 No H-bonds generated for 'chain 'F' and resid 158 through 160' Processing helix chain 'F' and resid 163 through 174 Processing helix chain 'F' and resid 185 through 197 removed outlier: 3.925A pdb=" N ILE F 190 " --> pdb=" O ALA F 186 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU F 193 " --> pdb=" O ALA F 189 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN F 197 " --> pdb=" O GLU F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 204 Processing helix chain 'F' and resid 207 through 217 removed outlier: 3.658A pdb=" N ILE F 211 " --> pdb=" O GLY F 207 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE F 216 " --> pdb=" O LEU F 212 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP F 217 " --> pdb=" O LYS F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 234 removed outlier: 3.670A pdb=" N ILE F 231 " --> pdb=" O LEU F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 243 No H-bonds generated for 'chain 'F' and resid 241 through 243' Processing helix chain 'F' and resid 250 through 258 removed outlier: 3.616A pdb=" N ILE F 253 " --> pdb=" O LEU F 250 " (cutoff:3.500A) Proline residue: F 256 - end of helix Processing helix chain 'F' and resid 273 through 292 removed outlier: 3.602A pdb=" N GLU F 278 " --> pdb=" O LYS F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 298 No H-bonds generated for 'chain 'F' and resid 295 through 298' Processing helix chain 'F' and resid 300 through 302 No H-bonds generated for 'chain 'F' and resid 300 through 302' Processing helix chain 'F' and resid 308 through 317 removed outlier: 3.741A pdb=" N LEU F 316 " --> pdb=" O LEU F 312 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N CYS F 317 " --> pdb=" O ILE F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 335 removed outlier: 3.676A pdb=" N GLU F 329 " --> pdb=" O ARG F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 350 Processing helix chain 'F' and resid 360 through 362 No H-bonds generated for 'chain 'F' and resid 360 through 362' Processing helix chain 'F' and resid 370 through 376 removed outlier: 4.236A pdb=" N THR F 375 " --> pdb=" O ALA F 371 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE F 376 " --> pdb=" O GLU F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 402 Processing helix chain 'F' and resid 404 through 413 Processing helix chain 'F' and resid 417 through 437 removed outlier: 3.662A pdb=" N VAL F 421 " --> pdb=" O ASP F 417 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ARG F 422 " --> pdb=" O HIS F 418 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR F 436 " --> pdb=" O HIS F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 443 No H-bonds generated for 'chain 'F' and resid 440 through 443' Processing helix chain 'F' and resid 450 through 454 Processing helix chain 'F' and resid 463 through 485 removed outlier: 3.534A pdb=" N HIS F 480 " --> pdb=" O LEU F 476 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU F 481 " --> pdb=" O LYS F 477 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET F 482 " --> pdb=" O ARG F 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 506 removed outlier: 3.643A pdb=" N ILE F 497 " --> pdb=" O HIS F 493 " (cutoff:3.500A) Processing helix chain 'F' and resid 525 through 535 Processing helix chain 'F' and resid 548 through 555 removed outlier: 3.840A pdb=" N THR F 553 " --> pdb=" O ASN F 549 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE F 554 " --> pdb=" O LEU F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 568 through 580 removed outlier: 3.903A pdb=" N PHE F 580 " --> pdb=" O ARG F 576 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 614 removed outlier: 3.775A pdb=" N PHE F 611 " --> pdb=" O GLN F 607 " (cutoff:3.500A) Processing helix chain 'F' and resid 620 through 637 removed outlier: 3.767A pdb=" N ASP F 625 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU F 626 " --> pdb=" O TYR F 622 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP F 629 " --> pdb=" O ASP F 625 " (cutoff:3.500A) Processing helix chain 'F' and resid 648 through 653 Processing helix chain 'F' and resid 655 through 657 No H-bonds generated for 'chain 'F' and resid 655 through 657' Processing helix chain 'F' and resid 660 through 667 removed outlier: 3.804A pdb=" N LEU F 666 " --> pdb=" O PHE F 662 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER F 667 " --> pdb=" O ILE F 663 " (cutoff:3.500A) Processing helix chain 'F' and resid 670 through 679 removed outlier: 3.948A pdb=" N LYS F 674 " --> pdb=" O PRO F 670 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET F 675 " --> pdb=" O HIS F 671 " (cutoff:3.500A) Processing helix chain 'F' and resid 682 through 689 removed outlier: 3.630A pdb=" N CYS F 689 " --> pdb=" O LEU F 685 " (cutoff:3.500A) Processing helix chain 'F' and resid 696 through 702 removed outlier: 3.511A pdb=" N THR F 701 " --> pdb=" O LEU F 697 " (cutoff:3.500A) Processing helix chain 'F' and resid 712 through 722 removed outlier: 3.640A pdb=" N LEU F 717 " --> pdb=" O ALA F 713 " (cutoff:3.500A) Processing helix chain 'F' and resid 726 through 736 Processing helix chain 'F' and resid 738 through 741 No H-bonds generated for 'chain 'F' and resid 738 through 741' Processing helix chain 'F' and resid 747 through 760 removed outlier: 4.772A pdb=" N ILE F 752 " --> pdb=" O ASN F 748 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU F 753 " --> pdb=" O ASN F 749 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU F 754 " --> pdb=" O TRP F 750 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR F 757 " --> pdb=" O GLU F 753 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HIS F 760 " --> pdb=" O VAL F 756 " (cutoff:3.500A) Processing helix chain 'F' and resid 764 through 779 removed outlier: 3.617A pdb=" N GLU F 776 " --> pdb=" O ASP F 772 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU F 779 " --> pdb=" O ASP F 775 " (cutoff:3.500A) Processing helix chain 'F' and resid 781 through 790 Processing helix chain 'F' and resid 799 through 810 removed outlier: 3.737A pdb=" N ARG F 807 " --> pdb=" O LEU F 803 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N PHE F 808 " --> pdb=" O LEU F 804 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LEU F 809 " --> pdb=" O LEU F 805 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N SER F 810 " --> pdb=" O LEU F 806 " (cutoff:3.500A) Processing helix chain 'F' and resid 812 through 820 removed outlier: 3.536A pdb=" N TYR F 817 " --> pdb=" O LYS F 813 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU F 820 " --> pdb=" O SER F 816 " (cutoff:3.500A) Processing helix chain 'F' and resid 824 through 833 Processing helix chain 'F' and resid 838 through 850 Processing helix chain 'F' and resid 882 through 885 No H-bonds generated for 'chain 'F' and resid 882 through 885' Processing helix chain 'F' and resid 890 through 898 removed outlier: 3.724A pdb=" N LEU F 895 " --> pdb=" O THR F 891 " (cutoff:3.500A) Processing helix chain 'F' and resid 902 through 910 removed outlier: 3.618A pdb=" N ASN F 908 " --> pdb=" O GLU F 904 " (cutoff:3.500A) Processing helix chain 'F' and resid 917 through 935 removed outlier: 3.835A pdb=" N LYS F 921 " --> pdb=" O TRP F 917 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS F 922 " --> pdb=" O GLU F 918 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA F 929 " --> pdb=" O ALA F 925 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN F 932 " --> pdb=" O TRP F 928 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE F 933 " --> pdb=" O ALA F 929 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER F 935 " --> pdb=" O GLY F 931 " (cutoff:3.500A) Processing helix chain 'F' and resid 937 through 940 No H-bonds generated for 'chain 'F' and resid 937 through 940' Processing helix chain 'F' and resid 949 through 957 removed outlier: 3.536A pdb=" N LYS F 957 " --> pdb=" O LEU F 953 " (cutoff:3.500A) Processing helix chain 'F' and resid 962 through 977 removed outlier: 3.900A pdb=" N VAL F 969 " --> pdb=" O ARG F 965 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR F 970 " --> pdb=" O GLY F 966 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU F 974 " --> pdb=" O TYR F 970 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE F 975 " --> pdb=" O VAL F 971 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA F 976 " --> pdb=" O LEU F 972 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS F 977 " --> pdb=" O GLY F 973 " (cutoff:3.500A) Processing helix chain 'F' and resid 979 through 988 removed outlier: 3.563A pdb=" N ILE F 984 " --> pdb=" O GLN F 980 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS F 988 " --> pdb=" O ILE F 984 " (cutoff:3.500A) Processing helix chain 'F' and resid 1433 through 1435 No H-bonds generated for 'chain 'F' and resid 1433 through 1435' Processing helix chain 'F' and resid 1480 through 1486 removed outlier: 4.097A pdb=" N GLN F1485 " --> pdb=" O HIS F1481 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLN F1486 " --> pdb=" O LEU F1482 " (cutoff:3.500A) Processing helix chain 'F' and resid 1489 through 1493 removed outlier: 3.770A pdb=" N MET F1493 " --> pdb=" O LEU F1489 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1489 through 1493' Processing helix chain 'F' and resid 1523 through 1525 No H-bonds generated for 'chain 'F' and resid 1523 through 1525' Processing helix chain 'F' and resid 1610 through 1624 removed outlier: 3.934A pdb=" N LYS F1614 " --> pdb=" O ILE F1610 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU F1615 " --> pdb=" O LEU F1611 " (cutoff:3.500A) Processing helix chain 'F' and resid 1629 through 1642 removed outlier: 3.598A pdb=" N ILE F1639 " --> pdb=" O GLY F1635 " (cutoff:3.500A) Processing helix chain 'F' and resid 1650 through 1662 removed outlier: 3.606A pdb=" N SER F1661 " --> pdb=" O SER F1657 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS F1662 " --> pdb=" O HIS F1658 " (cutoff:3.500A) Processing helix chain 'F' and resid 1667 through 1672 Processing helix chain 'F' and resid 1683 through 1693 Processing helix chain 'H' and resid 7 through 20 removed outlier: 3.553A pdb=" N ALA H 12 " --> pdb=" O THR H 8 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL H 19 " --> pdb=" O ARG H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 30 No H-bonds generated for 'chain 'H' and resid 27 through 30' Processing helix chain 'H' and resid 33 through 35 No H-bonds generated for 'chain 'H' and resid 33 through 35' Processing helix chain 'H' and resid 85 through 99 removed outlier: 3.901A pdb=" N GLU H 96 " --> pdb=" O ARG H 92 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASN H 99 " --> pdb=" O LYS H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 123 removed outlier: 3.811A pdb=" N LEU H 123 " --> pdb=" O LEU H 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 29 Processing helix chain 'A' and resid 38 through 52 Processing helix chain 'A' and resid 61 through 73 Processing helix chain 'A' and resid 83 through 93 Processing helix chain 'A' and resid 102 through 115 removed outlier: 3.545A pdb=" N ARG A 106 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 114 " --> pdb=" O TYR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 136 Processing helix chain 'A' and resid 141 through 155 Processing helix chain 'A' and resid 165 through 178 Processing helix chain 'A' and resid 182 through 184 No H-bonds generated for 'chain 'A' and resid 182 through 184' Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'A' and resid 204 through 222 removed outlier: 3.550A pdb=" N GLY A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 245 Processing helix chain 'A' and resid 262 through 275 Processing helix chain 'A' and resid 278 through 288 removed outlier: 3.873A pdb=" N LEU A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 360 No H-bonds generated for 'chain 'A' and resid 357 through 360' Processing helix chain 'A' and resid 363 through 375 Processing helix chain 'A' and resid 387 through 402 Proline residue: A 397 - end of helix Processing helix chain 'A' and resid 411 through 424 Processing helix chain 'A' and resid 430 through 443 Processing helix chain 'A' and resid 452 through 465 removed outlier: 3.943A pdb=" N ALA A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Proline residue: A 464 - end of helix Processing helix chain 'A' and resid 480 through 490 Processing helix chain 'A' and resid 500 through 511 removed outlier: 5.162A pdb=" N GLU A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Proline residue: A 507 - end of helix Processing helix chain 'A' and resid 515 through 527 Processing helix chain 'A' and resid 532 through 548 Processing helix chain 'A' and resid 581 through 589 removed outlier: 3.599A pdb=" N ALA A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 612 removed outlier: 3.658A pdb=" N ARG A 604 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASP A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N HIS A 609 " --> pdb=" O HIS A 605 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N PHE A 610 " --> pdb=" O CYS A 606 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LEU A 611 " --> pdb=" O ALA A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 628 removed outlier: 3.551A pdb=" N GLU A 621 " --> pdb=" O GLU A 617 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 624 " --> pdb=" O MET A 620 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A 627 " --> pdb=" O ALA A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 664 removed outlier: 3.587A pdb=" N SER A 657 " --> pdb=" O ALA A 653 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS A 658 " --> pdb=" O ASP A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 678 removed outlier: 3.510A pdb=" N CYS A 674 " --> pdb=" O ASP A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 685 removed outlier: 4.638A pdb=" N ALA A 685 " --> pdb=" O ARG A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 700 removed outlier: 3.518A pdb=" N GLN A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA A 699 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 700 " --> pdb=" O LEU A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 720 removed outlier: 3.541A pdb=" N LEU A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N CYS A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER A 720 " --> pdb=" O GLY A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 742 Proline residue: A 728 - end of helix removed outlier: 4.023A pdb=" N LYS A 732 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 741 " --> pdb=" O ILE A 737 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU A 742 " --> pdb=" O LEU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 763 removed outlier: 3.518A pdb=" N MET A 756 " --> pdb=" O GLN A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 783 Proline residue: A 770 - end of helix removed outlier: 5.988A pdb=" N GLU A 773 " --> pdb=" O ARG A 769 " (cutoff:3.500A) Proline residue: A 774 - end of helix removed outlier: 3.649A pdb=" N ALA A 778 " --> pdb=" O PRO A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 808 removed outlier: 3.648A pdb=" N ASN A 797 " --> pdb=" O GLY A 793 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA A 800 " --> pdb=" O ASN A 796 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A 804 " --> pdb=" O ALA A 800 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN A 807 " --> pdb=" O GLY A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 828 removed outlier: 4.300A pdb=" N ILE A 822 " --> pdb=" O ASP A 818 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ILE A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET A 827 " --> pdb=" O ILE A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 846 Processing helix chain 'A' and resid 848 through 851 No H-bonds generated for 'chain 'A' and resid 848 through 851' Processing helix chain 'A' and resid 856 through 860 removed outlier: 3.641A pdb=" N LYS A 860 " --> pdb=" O PRO A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 874 removed outlier: 3.690A pdb=" N LEU A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS A 873 " --> pdb=" O LEU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 891 removed outlier: 3.759A pdb=" N ARG A 886 " --> pdb=" O ARG A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 901 Processing helix chain 'A' and resid 930 through 936 removed outlier: 3.674A pdb=" N VAL A 936 " --> pdb=" O SER A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 957 removed outlier: 3.952A pdb=" N TYR A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Proline residue: A 948 - end of helix Processing helix chain 'A' and resid 962 through 964 No H-bonds generated for 'chain 'A' and resid 962 through 964' Processing helix chain 'A' and resid 966 through 982 removed outlier: 3.884A pdb=" N THR A 969 " --> pdb=" O HIS A 966 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL A 971 " --> pdb=" O HIS A 968 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL A 972 " --> pdb=" O THR A 969 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N THR A 976 " --> pdb=" O GLN A 973 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE A 979 " --> pdb=" O THR A 976 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 982 " --> pdb=" O PHE A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 1003 Proline residue: A 991 - end of helix removed outlier: 4.949A pdb=" N MET A 994 " --> pdb=" O PRO A 991 " (cutoff:3.500A) Proline residue: A 995 - end of helix removed outlier: 4.030A pdb=" N LEU A 998 " --> pdb=" O PRO A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1019 removed outlier: 3.862A pdb=" N GLN A1014 " --> pdb=" O GLU A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1041 removed outlier: 3.971A pdb=" N GLU A1040 " --> pdb=" O THR A1036 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE A1041 " --> pdb=" O LEU A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1063 removed outlier: 3.679A pdb=" N VAL A1061 " --> pdb=" O GLU A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1081 removed outlier: 3.771A pdb=" N LEU A1071 " --> pdb=" O LYS A1068 " (cutoff:3.500A) Proline residue: A1072 - end of helix Proline residue: A1076 - end of helix removed outlier: 3.531A pdb=" N ARG A1080 " --> pdb=" O HIS A1077 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A1081 " --> pdb=" O MET A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1100 removed outlier: 3.848A pdb=" N ILE A1091 " --> pdb=" O PRO A1088 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL A1092 " --> pdb=" O GLY A1089 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA A1098 " --> pdb=" O LYS A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1106 No H-bonds generated for 'chain 'A' and resid 1104 through 1106' Processing helix chain 'A' and resid 1111 through 1119 Proline residue: A1116 - end of helix Processing helix chain 'A' and resid 1129 through 1145 removed outlier: 3.723A pdb=" N VAL A1139 " --> pdb=" O ALA A1135 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP A1140 " --> pdb=" O LEU A1136 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU A1144 " --> pdb=" O ASP A1140 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N SER A1145 " --> pdb=" O ARG A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1163 removed outlier: 4.039A pdb=" N HIS A1157 " --> pdb=" O SER A1153 " (cutoff:3.500A) Proline residue: A1158 - end of helix Processing helix chain 'A' and resid 1170 through 1181 removed outlier: 3.623A pdb=" N ASP A1175 " --> pdb=" O SER A1171 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A1176 " --> pdb=" O THR A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1202 removed outlier: 3.918A pdb=" N ILE A1190 " --> pdb=" O LYS A1187 " (cutoff:3.500A) Proline residue: A1193 - end of helix removed outlier: 3.853A pdb=" N ASN A1196 " --> pdb=" O PRO A1193 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS A1197 " --> pdb=" O MET A1194 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A1199 " --> pdb=" O ASN A1196 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL A1200 " --> pdb=" O LYS A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1217 Processing helix chain 'A' and resid 1229 through 1237 Processing helix chain 'A' and resid 1265 through 1269 Processing helix chain 'A' and resid 1277 through 1293 Processing helix chain 'A' and resid 1298 through 1309 removed outlier: 4.078A pdb=" N CYS A1303 " --> pdb=" O SER A1299 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TRP A1304 " --> pdb=" O LEU A1300 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ALA A1305 " --> pdb=" O ARG A1301 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LEU A1306 " --> pdb=" O SER A1302 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A1309 " --> pdb=" O ALA A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1315 No H-bonds generated for 'chain 'A' and resid 1312 through 1315' Processing helix chain 'A' and resid 1318 through 1328 removed outlier: 3.872A pdb=" N GLU A1328 " --> pdb=" O SER A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1345 removed outlier: 3.646A pdb=" N GLU A1336 " --> pdb=" O ASP A1332 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A1337 " --> pdb=" O GLN A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1351 through 1366 Processing helix chain 'A' and resid 1377 through 1388 removed outlier: 3.505A pdb=" N ILE A1380 " --> pdb=" O ASP A1377 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N VAL A1381 " --> pdb=" O ASN A1378 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A1383 " --> pdb=" O ILE A1380 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A1385 " --> pdb=" O LEU A1382 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA A1387 " --> pdb=" O GLY A1384 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A1388 " --> pdb=" O GLU A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1393 through 1406 removed outlier: 3.503A pdb=" N HIS A1398 " --> pdb=" O ALA A1394 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS A1406 " --> pdb=" O LEU A1402 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1423 Processing helix chain 'A' and resid 1426 through 1438 removed outlier: 3.696A pdb=" N VAL A1432 " --> pdb=" O ALA A1428 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A1433 " --> pdb=" O ALA A1429 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS A1438 " --> pdb=" O GLU A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1453 removed outlier: 3.887A pdb=" N GLU A1451 " --> pdb=" O ALA A1447 " (cutoff:3.500A) Processing helix chain 'A' and resid 1457 through 1468 removed outlier: 3.862A pdb=" N VAL A1461 " --> pdb=" O GLU A1457 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A1466 " --> pdb=" O ALA A1462 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1487 removed outlier: 3.757A pdb=" N ALA A1486 " --> pdb=" O ARG A1482 " (cutoff:3.500A) Processing helix chain 'A' and resid 1490 through 1501 removed outlier: 3.613A pdb=" N GLN A1495 " --> pdb=" O GLY A1491 " (cutoff:3.500A) Processing helix chain 'A' and resid 1506 through 1523 removed outlier: 3.898A pdb=" N LYS A1511 " --> pdb=" O GLU A1507 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET A1512 " --> pdb=" O THR A1508 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG A1514 " --> pdb=" O ALA A1510 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N MET A1515 " --> pdb=" O LYS A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1526 through 1535 removed outlier: 3.811A pdb=" N GLU A1530 " --> pdb=" O TRP A1526 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLU A1531 " --> pdb=" O ASP A1527 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N MET A1535 " --> pdb=" O GLU A1531 " (cutoff:3.500A) Processing helix chain 'A' and resid 1541 through 1553 removed outlier: 4.215A pdb=" N ARG A1547 " --> pdb=" O GLY A1543 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU A1550 " --> pdb=" O TYR A1546 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A1552 " --> pdb=" O ALA A1548 " (cutoff:3.500A) Processing helix chain 'A' and resid 1557 through 1580 removed outlier: 3.771A pdb=" N GLN A1562 " --> pdb=" O SER A1558 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP A1569 " --> pdb=" O ASP A1565 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A1570 " --> pdb=" O LYS A1566 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA A1573 " --> pdb=" O ASP A1569 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU A1574 " --> pdb=" O LEU A1570 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A1577 " --> pdb=" O ALA A1573 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET A1578 " --> pdb=" O GLU A1574 " (cutoff:3.500A) Processing helix chain 'A' and resid 1585 through 1587 No H-bonds generated for 'chain 'A' and resid 1585 through 1587' Processing helix chain 'A' and resid 1590 through 1607 removed outlier: 3.651A pdb=" N GLU A1600 " --> pdb=" O LEU A1596 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A1601 " --> pdb=" O SER A1597 " (cutoff:3.500A) Processing helix chain 'A' and resid 1609 through 1611 No H-bonds generated for 'chain 'A' and resid 1609 through 1611' Processing helix chain 'A' and resid 1615 through 1623 removed outlier: 5.437A pdb=" N TRP A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU A1621 " --> pdb=" O GLN A1617 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A1623 " --> pdb=" O TRP A1619 " (cutoff:3.500A) Processing helix chain 'A' and resid 1630 through 1641 removed outlier: 3.863A pdb=" N SER A1641 " --> pdb=" O LEU A1637 " (cutoff:3.500A) Processing helix chain 'A' and resid 1646 through 1648 No H-bonds generated for 'chain 'A' and resid 1646 through 1648' Processing helix chain 'A' and resid 1650 through 1663 removed outlier: 4.086A pdb=" N LYS A1655 " --> pdb=" O ARG A1651 " (cutoff:3.500A) Processing helix chain 'A' and resid 1666 through 1677 removed outlier: 3.843A pdb=" N LEU A1673 " --> pdb=" O ALA A1669 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A1676 " --> pdb=" O THR A1672 " (cutoff:3.500A) Processing helix chain 'A' and resid 1694 through 1707 removed outlier: 3.517A pdb=" N LYS A1702 " --> pdb=" O TYR A1698 " (cutoff:3.500A) Processing helix chain 'A' and resid 1712 through 1728 removed outlier: 3.715A pdb=" N GLN A1725 " --> pdb=" O VAL A1721 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN A1726 " --> pdb=" O GLN A1722 " (cutoff:3.500A) Processing helix chain 'A' and resid 1739 through 1761 Processing helix chain 'A' and resid 1768 through 1782 removed outlier: 3.526A pdb=" N GLU A1781 " --> pdb=" O SER A1777 " (cutoff:3.500A) Processing helix chain 'A' and resid 1787 through 1808 removed outlier: 3.536A pdb=" N ALA A1792 " --> pdb=" O LYS A1788 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A1802 " --> pdb=" O PHE A1798 " (cutoff:3.500A) Processing helix chain 'A' and resid 1878 through 1895 Proline residue: A1883 - end of helix Processing helix chain 'A' and resid 1900 through 1913 removed outlier: 3.544A pdb=" N VAL A1906 " --> pdb=" O ASP A1902 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU A1907 " --> pdb=" O THR A1903 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A1908 " --> pdb=" O LEU A1904 " (cutoff:3.500A) Processing helix chain 'A' and resid 1917 through 1929 removed outlier: 3.801A pdb=" N GLU A1921 " --> pdb=" O PRO A1917 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA A1922 " --> pdb=" O ASP A1918 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU A1925 " --> pdb=" O GLU A1921 " (cutoff:3.500A) Processing helix chain 'A' and resid 1936 through 1944 Proline residue: A1940 - end of helix removed outlier: 3.542A pdb=" N ILE A1943 " --> pdb=" O PRO A1940 " (cutoff:3.500A) Processing helix chain 'A' and resid 1951 through 1967 removed outlier: 4.391A pdb=" N LEU A1956 " --> pdb=" O LEU A1952 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE A1957 " --> pdb=" O VAL A1953 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS A1958 " --> pdb=" O GLY A1954 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A1960 " --> pdb=" O LEU A1956 " (cutoff:3.500A) Processing helix chain 'A' and resid 1973 through 1980 Processing helix chain 'A' and resid 1985 through 2001 removed outlier: 3.576A pdb=" N ASN A1997 " --> pdb=" O LYS A1993 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU A2000 " --> pdb=" O LYS A1996 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N HIS A2001 " --> pdb=" O ASN A1997 " (cutoff:3.500A) Processing helix chain 'A' and resid 2003 through 2020 Processing helix chain 'A' and resid 2023 through 2040 Processing helix chain 'A' and resid 2045 through 2060 removed outlier: 3.549A pdb=" N GLU A2049 " --> pdb=" O LYS A2045 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A2050 " --> pdb=" O GLY A2046 " (cutoff:3.500A) Proline residue: A2053 - end of helix removed outlier: 4.020A pdb=" N MET A2058 " --> pdb=" O LEU A2054 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A2059 " --> pdb=" O HIS A2055 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG A2060 " --> pdb=" O ALA A2056 " (cutoff:3.500A) Processing helix chain 'A' and resid 2065 through 2073 Processing helix chain 'A' and resid 2075 through 2090 removed outlier: 3.785A pdb=" N LYS A2090 " --> pdb=" O ARG A2086 " (cutoff:3.500A) Processing helix chain 'A' and resid 2094 through 2113 removed outlier: 3.968A pdb=" N LEU A2103 " --> pdb=" O GLN A2099 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS A2106 " --> pdb=" O ASP A2102 " (cutoff:3.500A) Processing helix chain 'A' and resid 2123 through 2126 No H-bonds generated for 'chain 'A' and resid 2123 through 2126' Processing helix chain 'A' and resid 2193 through 2210 Processing helix chain 'A' and resid 2213 through 2216 No H-bonds generated for 'chain 'A' and resid 2213 through 2216' Processing helix chain 'A' and resid 2246 through 2256 Processing helix chain 'A' and resid 2263 through 2271 Processing helix chain 'A' and resid 2275 through 2277 No H-bonds generated for 'chain 'A' and resid 2275 through 2277' Processing helix chain 'A' and resid 2280 through 2293 removed outlier: 3.526A pdb=" N VAL A2284 " --> pdb=" O LEU A2280 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU A2285 " --> pdb=" O MET A2281 " (cutoff:3.500A) Processing helix chain 'A' and resid 2298 through 2305 removed outlier: 3.816A pdb=" N TRP A2304 " --> pdb=" O ALA A2300 " (cutoff:3.500A) Processing helix chain 'A' and resid 2310 through 2334 removed outlier: 3.859A pdb=" N VAL A2326 " --> pdb=" O ARG A2322 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET A2327 " --> pdb=" O SER A2323 " (cutoff:3.500A) Processing helix chain 'A' and resid 2341 through 2343 No H-bonds generated for 'chain 'A' and resid 2341 through 2343' Processing helix chain 'A' and resid 2364 through 2367 No H-bonds generated for 'chain 'A' and resid 2364 through 2367' Processing helix chain 'A' and resid 2381 through 2384 No H-bonds generated for 'chain 'A' and resid 2381 through 2384' Processing helix chain 'A' and resid 2395 through 2409 Processing helix chain 'A' and resid 2411 through 2422 removed outlier: 3.873A pdb=" N VAL A2417 " --> pdb=" O SER A2413 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A2418 " --> pdb=" O VAL A2414 " (cutoff:3.500A) Processing helix chain 'A' and resid 2495 through 2507 removed outlier: 3.538A pdb=" N GLN A2499 " --> pdb=" O LYS A2495 " (cutoff:3.500A) Processing helix chain 'A' and resid 2521 through 2533 Processing helix chain 'A' and resid 2535 through 2539 Processing helix chain 'A' and resid 2543 through 2545 No H-bonds generated for 'chain 'A' and resid 2543 through 2545' Processing helix chain 'E' and resid 33 through 43 removed outlier: 4.102A pdb=" N ARG E 39 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU E 40 " --> pdb=" O ASP E 36 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE E 41 " --> pdb=" O ASN E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 53 through 69 removed outlier: 3.549A pdb=" N ASN E 61 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP E 69 " --> pdb=" O LYS E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 91 removed outlier: 3.521A pdb=" N LEU E 90 " --> pdb=" O ILE E 86 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ALA E 91 " --> pdb=" O CYS E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 110 Processing helix chain 'E' and resid 114 through 122 Processing helix chain 'E' and resid 125 through 133 removed outlier: 4.430A pdb=" N ALA E 130 " --> pdb=" O TYR E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 156 removed outlier: 3.512A pdb=" N GLN E 145 " --> pdb=" O VAL E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 160 No H-bonds generated for 'chain 'E' and resid 158 through 160' Processing helix chain 'E' and resid 163 through 174 Processing helix chain 'E' and resid 185 through 197 removed outlier: 3.924A pdb=" N ILE E 190 " --> pdb=" O ALA E 186 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU E 193 " --> pdb=" O ALA E 189 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN E 197 " --> pdb=" O GLU E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 204 Processing helix chain 'E' and resid 207 through 217 removed outlier: 3.658A pdb=" N ILE E 211 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE E 216 " --> pdb=" O LEU E 212 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP E 217 " --> pdb=" O LYS E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 234 removed outlier: 3.671A pdb=" N ILE E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 243 No H-bonds generated for 'chain 'E' and resid 241 through 243' Processing helix chain 'E' and resid 250 through 258 removed outlier: 3.616A pdb=" N ILE E 253 " --> pdb=" O LEU E 250 " (cutoff:3.500A) Proline residue: E 256 - end of helix Processing helix chain 'E' and resid 273 through 292 removed outlier: 3.603A pdb=" N GLU E 278 " --> pdb=" O LYS E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 298 No H-bonds generated for 'chain 'E' and resid 295 through 298' Processing helix chain 'E' and resid 300 through 302 No H-bonds generated for 'chain 'E' and resid 300 through 302' Processing helix chain 'E' and resid 308 through 317 removed outlier: 3.742A pdb=" N LEU E 316 " --> pdb=" O LEU E 312 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N CYS E 317 " --> pdb=" O ILE E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 335 removed outlier: 3.677A pdb=" N GLU E 329 " --> pdb=" O ARG E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 350 Processing helix chain 'E' and resid 360 through 362 No H-bonds generated for 'chain 'E' and resid 360 through 362' Processing helix chain 'E' and resid 370 through 376 removed outlier: 4.237A pdb=" N THR E 375 " --> pdb=" O ALA E 371 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE E 376 " --> pdb=" O GLU E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 402 Processing helix chain 'E' and resid 404 through 413 Processing helix chain 'E' and resid 417 through 437 removed outlier: 3.662A pdb=" N VAL E 421 " --> pdb=" O ASP E 417 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ARG E 422 " --> pdb=" O HIS E 418 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR E 436 " --> pdb=" O HIS E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 443 No H-bonds generated for 'chain 'E' and resid 440 through 443' Processing helix chain 'E' and resid 450 through 454 Processing helix chain 'E' and resid 463 through 485 removed outlier: 3.534A pdb=" N HIS E 480 " --> pdb=" O LEU E 476 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU E 481 " --> pdb=" O LYS E 477 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET E 482 " --> pdb=" O ARG E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 506 removed outlier: 3.644A pdb=" N ILE E 497 " --> pdb=" O HIS E 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 535 Processing helix chain 'E' and resid 548 through 555 removed outlier: 3.840A pdb=" N THR E 553 " --> pdb=" O ASN E 549 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE E 554 " --> pdb=" O LEU E 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 568 through 580 removed outlier: 3.903A pdb=" N PHE E 580 " --> pdb=" O ARG E 576 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 614 removed outlier: 3.777A pdb=" N PHE E 611 " --> pdb=" O GLN E 607 " (cutoff:3.500A) Processing helix chain 'E' and resid 620 through 637 removed outlier: 3.767A pdb=" N ASP E 625 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU E 626 " --> pdb=" O TYR E 622 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP E 629 " --> pdb=" O ASP E 625 " (cutoff:3.500A) Processing helix chain 'E' and resid 648 through 653 Processing helix chain 'E' and resid 655 through 657 No H-bonds generated for 'chain 'E' and resid 655 through 657' Processing helix chain 'E' and resid 660 through 667 removed outlier: 3.804A pdb=" N LEU E 666 " --> pdb=" O PHE E 662 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER E 667 " --> pdb=" O ILE E 663 " (cutoff:3.500A) Processing helix chain 'E' and resid 670 through 679 removed outlier: 3.948A pdb=" N LYS E 674 " --> pdb=" O PRO E 670 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET E 675 " --> pdb=" O HIS E 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 682 through 689 removed outlier: 3.630A pdb=" N CYS E 689 " --> pdb=" O LEU E 685 " (cutoff:3.500A) Processing helix chain 'E' and resid 696 through 702 removed outlier: 3.511A pdb=" N THR E 701 " --> pdb=" O LEU E 697 " (cutoff:3.500A) Processing helix chain 'E' and resid 712 through 722 removed outlier: 3.639A pdb=" N LEU E 717 " --> pdb=" O ALA E 713 " (cutoff:3.500A) Processing helix chain 'E' and resid 726 through 736 Processing helix chain 'E' and resid 738 through 741 No H-bonds generated for 'chain 'E' and resid 738 through 741' Processing helix chain 'E' and resid 747 through 760 removed outlier: 4.772A pdb=" N ILE E 752 " --> pdb=" O ASN E 748 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU E 753 " --> pdb=" O ASN E 749 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU E 754 " --> pdb=" O TRP E 750 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR E 757 " --> pdb=" O GLU E 753 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HIS E 760 " --> pdb=" O VAL E 756 " (cutoff:3.500A) Processing helix chain 'E' and resid 764 through 779 removed outlier: 3.618A pdb=" N GLU E 776 " --> pdb=" O ASP E 772 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU E 779 " --> pdb=" O ASP E 775 " (cutoff:3.500A) Processing helix chain 'E' and resid 781 through 790 Processing helix chain 'E' and resid 799 through 810 removed outlier: 3.737A pdb=" N ARG E 807 " --> pdb=" O LEU E 803 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N PHE E 808 " --> pdb=" O LEU E 804 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LEU E 809 " --> pdb=" O LEU E 805 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N SER E 810 " --> pdb=" O LEU E 806 " (cutoff:3.500A) Processing helix chain 'E' and resid 812 through 820 removed outlier: 3.535A pdb=" N TYR E 817 " --> pdb=" O LYS E 813 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU E 820 " --> pdb=" O SER E 816 " (cutoff:3.500A) Processing helix chain 'E' and resid 824 through 833 Processing helix chain 'E' and resid 838 through 850 Processing helix chain 'E' and resid 882 through 885 No H-bonds generated for 'chain 'E' and resid 882 through 885' Processing helix chain 'E' and resid 890 through 898 removed outlier: 3.723A pdb=" N LEU E 895 " --> pdb=" O THR E 891 " (cutoff:3.500A) Processing helix chain 'E' and resid 902 through 910 removed outlier: 3.619A pdb=" N ASN E 908 " --> pdb=" O GLU E 904 " (cutoff:3.500A) Processing helix chain 'E' and resid 917 through 935 removed outlier: 3.836A pdb=" N LYS E 921 " --> pdb=" O TRP E 917 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS E 922 " --> pdb=" O GLU E 918 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA E 929 " --> pdb=" O ALA E 925 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN E 932 " --> pdb=" O TRP E 928 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE E 933 " --> pdb=" O ALA E 929 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER E 935 " --> pdb=" O GLY E 931 " (cutoff:3.500A) Processing helix chain 'E' and resid 937 through 940 No H-bonds generated for 'chain 'E' and resid 937 through 940' Processing helix chain 'E' and resid 949 through 957 removed outlier: 3.537A pdb=" N LYS E 957 " --> pdb=" O LEU E 953 " (cutoff:3.500A) Processing helix chain 'E' and resid 962 through 977 removed outlier: 3.900A pdb=" N VAL E 969 " --> pdb=" O ARG E 965 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR E 970 " --> pdb=" O GLY E 966 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU E 974 " --> pdb=" O TYR E 970 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE E 975 " --> pdb=" O VAL E 971 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA E 976 " --> pdb=" O LEU E 972 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS E 977 " --> pdb=" O GLY E 973 " (cutoff:3.500A) Processing helix chain 'E' and resid 979 through 988 removed outlier: 3.563A pdb=" N ILE E 984 " --> pdb=" O GLN E 980 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS E 988 " --> pdb=" O ILE E 984 " (cutoff:3.500A) Processing helix chain 'E' and resid 1433 through 1435 No H-bonds generated for 'chain 'E' and resid 1433 through 1435' Processing helix chain 'E' and resid 1480 through 1486 removed outlier: 4.097A pdb=" N GLN E1485 " --> pdb=" O HIS E1481 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLN E1486 " --> pdb=" O LEU E1482 " (cutoff:3.500A) Processing helix chain 'E' and resid 1489 through 1493 removed outlier: 3.769A pdb=" N MET E1493 " --> pdb=" O LEU E1489 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1489 through 1493' Processing helix chain 'E' and resid 1523 through 1525 No H-bonds generated for 'chain 'E' and resid 1523 through 1525' Processing helix chain 'E' and resid 1610 through 1624 removed outlier: 3.934A pdb=" N LYS E1614 " --> pdb=" O ILE E1610 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU E1615 " --> pdb=" O LEU E1611 " (cutoff:3.500A) Processing helix chain 'E' and resid 1629 through 1642 removed outlier: 3.598A pdb=" N ILE E1639 " --> pdb=" O GLY E1635 " (cutoff:3.500A) Processing helix chain 'E' and resid 1650 through 1662 removed outlier: 3.606A pdb=" N SER E1661 " --> pdb=" O SER E1657 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS E1662 " --> pdb=" O HIS E1658 " (cutoff:3.500A) Processing helix chain 'E' and resid 1667 through 1672 Processing helix chain 'E' and resid 1683 through 1693 Processing helix chain 'G' and resid 7 through 20 removed outlier: 3.551A pdb=" N ALA G 12 " --> pdb=" O THR G 8 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL G 19 " --> pdb=" O ARG G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 30 No H-bonds generated for 'chain 'G' and resid 27 through 30' Processing helix chain 'G' and resid 33 through 35 No H-bonds generated for 'chain 'G' and resid 33 through 35' Processing helix chain 'G' and resid 85 through 99 removed outlier: 3.901A pdb=" N GLU G 96 " --> pdb=" O ARG G 92 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASN G 99 " --> pdb=" O LYS G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 123 removed outlier: 3.812A pdb=" N LEU G 123 " --> pdb=" O LEU G 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 360 through 363 No H-bonds generated for 'chain 'I' and resid 360 through 363' Processing helix chain 'I' and resid 385 through 394 Processing helix chain 'J' and resid 360 through 363 No H-bonds generated for 'chain 'J' and resid 360 through 363' Processing helix chain 'J' and resid 385 through 394 Processing sheet with id= A, first strand: chain 'B' and resid 2120 through 2122 Processing sheet with id= B, first strand: chain 'B' and resid 2181 through 2183 removed outlier: 3.644A pdb=" N PHE B2182 " --> pdb=" O LEU B2174 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER B2155 " --> pdb=" O MET B2175 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 2184 through 2188 removed outlier: 3.541A pdb=" N LYS B2187 " --> pdb=" O GLY B2235 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY B2235 " --> pdb=" O LYS B2187 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 2243 through 2245 removed outlier: 3.537A pdb=" N ASP B2244 " --> pdb=" O LEU B2346 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 315 through 321 removed outlier: 7.303A pdb=" N ALA D 18 " --> pdb=" O VAL D 316 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU D 318 " --> pdb=" O ALA D 16 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA D 16 " --> pdb=" O LEU D 318 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N PHE D 320 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ILE D 14 " --> pdb=" O PHE D 320 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLY D 19 " --> pdb=" O THR D 23 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N THR D 23 " --> pdb=" O GLY D 19 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG D 36 " --> pdb=" O PHE D 26 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 47 through 50 removed outlier: 4.122A pdb=" N ALA D 47 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA D 60 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE D 79 " --> pdb=" O MET D 67 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 124 through 126 removed outlier: 4.143A pdb=" N THR D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 162 through 166 removed outlier: 4.905A pdb=" N ALA D 151 " --> pdb=" O ASP D 147 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP D 147 " --> pdb=" O ALA D 151 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N CYS D 133 " --> pdb=" O GLY D 146 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 173 through 178 removed outlier: 7.092A pdb=" N VAL D 188 " --> pdb=" O THR D 174 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ALA D 176 " --> pdb=" O ALA D 186 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ALA D 186 " --> pdb=" O ALA D 176 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N CYS D 194 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE D 216 " --> pdb=" O CYS D 194 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR D 214 " --> pdb=" O VAL D 196 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ASN D 198 " --> pdb=" O PRO D 212 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 226 through 228 removed outlier: 3.569A pdb=" N LYS D 245 " --> pdb=" O THR D 237 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR D 256 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ARG D 248 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU D 254 " --> pdb=" O ARG D 248 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 306 through 308 removed outlier: 3.603A pdb=" N ARG D 306 " --> pdb=" O LEU D 296 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 990 through 992 Processing sheet with id= M, first strand: chain 'A' and resid 2120 through 2122 Processing sheet with id= N, first strand: chain 'A' and resid 2181 through 2183 removed outlier: 3.643A pdb=" N PHE A2182 " --> pdb=" O LEU A2174 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER A2155 " --> pdb=" O MET A2175 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 2184 through 2188 removed outlier: 3.542A pdb=" N LYS A2187 " --> pdb=" O GLY A2235 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY A2235 " --> pdb=" O LYS A2187 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 2243 through 2245 removed outlier: 3.537A pdb=" N ASP A2244 " --> pdb=" O LEU A2346 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 315 through 321 removed outlier: 7.303A pdb=" N ALA C 18 " --> pdb=" O VAL C 316 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU C 318 " --> pdb=" O ALA C 16 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA C 16 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N PHE C 320 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ILE C 14 " --> pdb=" O PHE C 320 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLY C 19 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N THR C 23 " --> pdb=" O GLY C 19 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG C 36 " --> pdb=" O PHE C 26 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 47 through 50 removed outlier: 4.123A pdb=" N ALA C 47 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA C 60 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE C 79 " --> pdb=" O MET C 67 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 124 through 126 removed outlier: 4.143A pdb=" N THR C 108 " --> pdb=" O GLY C 104 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 162 through 166 removed outlier: 4.905A pdb=" N ALA C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP C 147 " --> pdb=" O ALA C 151 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS C 133 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 173 through 178 removed outlier: 7.092A pdb=" N VAL C 188 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ALA C 176 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA C 186 " --> pdb=" O ALA C 176 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N CYS C 194 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE C 216 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR C 214 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASN C 198 " --> pdb=" O PRO C 212 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 226 through 228 removed outlier: 3.568A pdb=" N LYS C 245 " --> pdb=" O THR C 237 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR C 256 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ARG C 248 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU C 254 " --> pdb=" O ARG C 248 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 306 through 308 removed outlier: 3.603A pdb=" N ARG C 306 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 990 through 992 Processing sheet with id= Y, first strand: chain 'I' and resid 329 through 333 Processing sheet with id= Z, first strand: chain 'I' and resid 342 through 344 Processing sheet with id= AA, first strand: chain 'J' and resid 329 through 333 Processing sheet with id= AB, first strand: chain 'J' and resid 342 through 344 2564 hydrogen bonds defined for protein. 7314 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: 22.85 Time building geometry restraints manager: 18.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 19666 1.34 - 1.46: 12678 1.46 - 1.58: 26756 1.58 - 1.70: 12 1.70 - 1.81: 546 Bond restraints: 59658 Sorted by residual: bond pdb=" O12 IHP B2601 " pdb=" P2 IHP B2601 " ideal model delta sigma weight residual 1.675 1.598 0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" O12 IHP A2601 " pdb=" P2 IHP A2601 " ideal model delta sigma weight residual 1.675 1.598 0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" O14 IHP A2601 " pdb=" P4 IHP A2601 " ideal model delta sigma weight residual 1.671 1.601 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" O14 IHP B2601 " pdb=" P4 IHP B2601 " ideal model delta sigma weight residual 1.671 1.601 0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" O15 IHP B2601 " pdb=" P5 IHP B2601 " ideal model delta sigma weight residual 1.675 1.619 0.056 2.00e-02 2.50e+03 7.94e+00 ... (remaining 59653 not shown) Histogram of bond angle deviations from ideal: 100.29 - 107.04: 1677 107.04 - 113.79: 34233 113.79 - 120.54: 24297 120.54 - 127.29: 20064 127.29 - 134.04: 721 Bond angle restraints: 80992 Sorted by residual: angle pdb=" N VAL B1081 " pdb=" CA VAL B1081 " pdb=" C VAL B1081 " ideal model delta sigma weight residual 113.53 107.67 5.86 9.80e-01 1.04e+00 3.57e+01 angle pdb=" N VAL A1081 " pdb=" CA VAL A1081 " pdb=" C VAL A1081 " ideal model delta sigma weight residual 113.53 107.69 5.84 9.80e-01 1.04e+00 3.56e+01 angle pdb=" N ALA E 91 " pdb=" CA ALA E 91 " pdb=" C ALA E 91 " ideal model delta sigma weight residual 114.56 109.67 4.89 1.27e+00 6.20e-01 1.48e+01 angle pdb=" N THR B1934 " pdb=" CA THR B1934 " pdb=" C THR B1934 " ideal model delta sigma weight residual 114.56 109.70 4.86 1.27e+00 6.20e-01 1.46e+01 angle pdb=" N THR A1934 " pdb=" CA THR A1934 " pdb=" C THR A1934 " ideal model delta sigma weight residual 114.56 109.70 4.86 1.27e+00 6.20e-01 1.46e+01 ... (remaining 80987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 34752 17.98 - 35.95: 1151 35.95 - 53.93: 157 53.93 - 71.91: 22 71.91 - 89.88: 12 Dihedral angle restraints: 36094 sinusoidal: 13684 harmonic: 22410 Sorted by residual: dihedral pdb=" CA TRP E 557 " pdb=" C TRP E 557 " pdb=" N PRO E 558 " pdb=" CA PRO E 558 " ideal model delta harmonic sigma weight residual -180.00 -159.39 -20.61 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA TRP F 557 " pdb=" C TRP F 557 " pdb=" N PRO F 558 " pdb=" CA PRO F 558 " ideal model delta harmonic sigma weight residual 180.00 -159.44 -20.56 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA ARG E 833 " pdb=" C ARG E 833 " pdb=" N GLU E 834 " pdb=" CA GLU E 834 " ideal model delta harmonic sigma weight residual -180.00 -162.73 -17.27 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 36091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 8356 0.057 - 0.113: 994 0.113 - 0.170: 44 0.170 - 0.226: 2 0.226 - 0.283: 4 Chirality restraints: 9400 Sorted by residual: chirality pdb=" C1 IHP A2601 " pdb=" C2 IHP A2601 " pdb=" C6 IHP A2601 " pdb=" O11 IHP A2601 " both_signs ideal model delta sigma weight residual False 2.32 2.60 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C1 IHP B2601 " pdb=" C2 IHP B2601 " pdb=" C6 IHP B2601 " pdb=" O11 IHP B2601 " both_signs ideal model delta sigma weight residual False 2.32 2.60 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" C3 IHP A2601 " pdb=" C2 IHP A2601 " pdb=" C4 IHP A2601 " pdb=" O13 IHP A2601 " both_signs ideal model delta sigma weight residual False -2.34 -2.59 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 9397 not shown) Planarity restraints: 10390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A1689 " -0.036 5.00e-02 4.00e+02 5.47e-02 4.79e+00 pdb=" N PRO A1690 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A1690 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A1690 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B1689 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.76e+00 pdb=" N PRO B1690 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B1690 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B1690 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A1645 " 0.024 5.00e-02 4.00e+02 3.59e-02 2.06e+00 pdb=" N PRO A1646 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A1646 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A1646 " 0.020 5.00e-02 4.00e+02 ... (remaining 10387 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 5500 2.74 - 3.28: 59864 3.28 - 3.82: 91251 3.82 - 4.36: 109679 4.36 - 4.90: 187538 Nonbonded interactions: 453832 Sorted by model distance: nonbonded pdb=" OG1 THR C 51 " pdb=" O MET C 56 " model vdw 2.205 2.440 nonbonded pdb=" OG1 THR D 51 " pdb=" O MET D 56 " model vdw 2.205 2.440 nonbonded pdb=" O LEU B1343 " pdb=" OG SER B1347 " model vdw 2.215 2.440 nonbonded pdb=" O LEU A1343 " pdb=" OG SER A1347 " model vdw 2.216 2.440 nonbonded pdb=" OE2 GLU B2526 " pdb=" NZ LYS B2530 " model vdw 2.234 2.520 ... (remaining 453827 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 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.690 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: 0.050 Extract box with map and model: 22.470 Check model and map are aligned: 0.620 Set scattering table: 0.410 Process input model: 128.270 Find NCS groups from input model: 2.680 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 161.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 59658 Z= 0.141 Angle : 0.458 8.794 80992 Z= 0.248 Chirality : 0.037 0.283 9400 Planarity : 0.003 0.055 10390 Dihedral : 9.059 89.885 21474 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.33 % Favored : 96.62 % Rotamer: Outliers : 0.98 % Allowed : 4.03 % Favored : 94.99 % 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: -0.02 (0.10), residues: 7536 helix: 0.57 (0.08), residues: 4588 sheet: 0.12 (0.28), residues: 358 loop : -0.95 (0.12), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 750 HIS 0.003 0.000 HIS E 445 PHE 0.011 0.001 PHE B1122 TYR 0.010 0.001 TYR E 835 ARG 0.003 0.000 ARG E 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1568 residues out of total 6766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 1510 time to evaluate : 4.898 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 631 THR cc_start: 0.7795 (OUTLIER) cc_final: 0.7053 (p) REVERT: B 725 PHE cc_start: 0.6807 (m-80) cc_final: 0.6582 (m-80) REVERT: B 772 MET cc_start: 0.8535 (mmp) cc_final: 0.8279 (mmm) REVERT: B 827 MET cc_start: 0.8418 (mtt) cc_final: 0.8211 (mtp) REVERT: B 956 MET cc_start: 0.8343 (mmm) cc_final: 0.7973 (mmm) REVERT: B 1227 GLU cc_start: 0.8042 (tp30) cc_final: 0.7776 (tt0) REVERT: B 1285 ARG cc_start: 0.7246 (ptm-80) cc_final: 0.7020 (ttp80) REVERT: B 1377 ASP cc_start: 0.6038 (t70) cc_final: 0.5694 (t70) REVERT: B 1539 ASP cc_start: 0.7792 (t0) cc_final: 0.7497 (t0) REVERT: B 1654 LEU cc_start: 0.8776 (mt) cc_final: 0.8541 (mt) REVERT: B 1726 GLN cc_start: 0.8651 (mp-120) cc_final: 0.8434 (mp10) REVERT: B 1747 MET cc_start: 0.8685 (mmm) cc_final: 0.8340 (mmm) REVERT: B 1757 TRP cc_start: 0.8660 (m-10) cc_final: 0.8375 (m-10) REVERT: B 1876 THR cc_start: 0.8152 (p) cc_final: 0.7669 (p) REVERT: B 1899 ASN cc_start: 0.8649 (p0) cc_final: 0.8171 (p0) REVERT: B 2063 GLN cc_start: 0.7578 (mp10) cc_final: 0.7285 (mp10) REVERT: B 2102 ASP cc_start: 0.7892 (t0) cc_final: 0.7466 (t0) REVERT: B 2135 ASP cc_start: 0.8468 (t0) cc_final: 0.8168 (t0) REVERT: B 2240 VAL cc_start: 0.9108 (OUTLIER) cc_final: 0.8864 (m) REVERT: B 2514 SER cc_start: 0.7706 (t) cc_final: 0.7368 (p) REVERT: D 69 ASP cc_start: 0.7833 (t0) cc_final: 0.7432 (p0) REVERT: D 94 HIS cc_start: 0.6281 (t-90) cc_final: 0.5667 (t70) REVERT: D 124 ILE cc_start: 0.6939 (mt) cc_final: 0.6579 (mm) REVERT: D 166 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8088 (mt) REVERT: D 168 GLU cc_start: 0.7630 (pt0) cc_final: 0.7385 (pt0) REVERT: D 254 LEU cc_start: 0.8664 (mt) cc_final: 0.8414 (tp) REVERT: D 278 PHE cc_start: 0.7559 (m-80) cc_final: 0.7168 (m-10) REVERT: D 284 TYR cc_start: 0.6947 (m-80) cc_final: 0.6337 (m-80) REVERT: F 60 LEU cc_start: 0.7513 (mt) cc_final: 0.7094 (mt) REVERT: F 104 LEU cc_start: 0.8045 (mt) cc_final: 0.7595 (mm) REVERT: F 177 LEU cc_start: 0.8657 (tp) cc_final: 0.8452 (mp) REVERT: F 251 GLU cc_start: 0.7934 (mp0) cc_final: 0.7716 (mp0) REVERT: F 433 MET cc_start: 0.8189 (ttm) cc_final: 0.7976 (ttm) REVERT: F 482 MET cc_start: 0.8148 (ttp) cc_final: 0.7877 (ttm) REVERT: F 746 PHE cc_start: 0.7472 (m-10) cc_final: 0.7046 (m-10) REVERT: H 94 ARG cc_start: 0.7991 (ttm110) cc_final: 0.7720 (ttm170) REVERT: A 680 ASP cc_start: 0.8097 (p0) cc_final: 0.7769 (t0) REVERT: A 796 ASN cc_start: 0.8061 (m-40) cc_final: 0.7767 (m-40) REVERT: A 1269 TRP cc_start: 0.7854 (m100) cc_final: 0.7519 (m100) REVERT: A 1332 ASP cc_start: 0.8156 (m-30) cc_final: 0.7811 (p0) REVERT: A 1350 ILE cc_start: 0.8360 (mp) cc_final: 0.7826 (tp) REVERT: A 1391 ARG cc_start: 0.7642 (mmt90) cc_final: 0.7207 (mtp85) REVERT: A 1503 LEU cc_start: 0.7919 (pt) cc_final: 0.7682 (pp) REVERT: A 1724 MET cc_start: 0.9062 (mmp) cc_final: 0.8579 (mmm) REVERT: A 1739 HIS cc_start: 0.7726 (t-90) cc_final: 0.7408 (t-90) REVERT: A 1960 LEU cc_start: 0.8739 (pp) cc_final: 0.8483 (pp) REVERT: A 2356 ILE cc_start: 0.8921 (pt) cc_final: 0.8701 (pt) REVERT: A 2404 MET cc_start: 0.8538 (mmt) cc_final: 0.8089 (tpt) REVERT: A 2514 SER cc_start: 0.7638 (t) cc_final: 0.7269 (p) REVERT: C 41 GLN cc_start: 0.7980 (tp40) cc_final: 0.7758 (pm20) REVERT: C 51 THR cc_start: 0.7458 (OUTLIER) cc_final: 0.7250 (p) REVERT: C 81 TYR cc_start: 0.7082 (m-80) cc_final: 0.6750 (m-80) REVERT: C 184 TYR cc_start: 0.5114 (m-80) cc_final: 0.4908 (m-80) REVERT: C 213 LYS cc_start: 0.7587 (tptm) cc_final: 0.6868 (ttmt) REVERT: C 255 MET cc_start: 0.7465 (tpt) cc_final: 0.6835 (mmt) REVERT: C 305 LYS cc_start: 0.8622 (tptt) cc_final: 0.8296 (tptt) REVERT: E 38 LEU cc_start: 0.8588 (mt) cc_final: 0.8101 (tp) REVERT: E 42 LEU cc_start: 0.8854 (mt) cc_final: 0.8464 (mt) REVERT: E 83 ASP cc_start: 0.7613 (m-30) cc_final: 0.7027 (t70) REVERT: E 153 MET cc_start: 0.8490 (mtp) cc_final: 0.7948 (ttm) REVERT: E 240 THR cc_start: 0.9429 (OUTLIER) cc_final: 0.9061 (p) REVERT: E 249 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7208 (tp30) REVERT: E 414 ASN cc_start: 0.8200 (t0) cc_final: 0.7831 (t0) REVERT: E 495 ASP cc_start: 0.7451 (t0) cc_final: 0.7102 (t0) REVERT: E 592 ASP cc_start: 0.7764 (t0) cc_final: 0.7450 (p0) REVERT: E 1683 LEU cc_start: 0.8987 (tp) cc_final: 0.8720 (pp) REVERT: G 6 ASN cc_start: 0.8383 (p0) cc_final: 0.8108 (m-40) REVERT: G 90 LEU cc_start: 0.6736 (tp) cc_final: 0.5920 (tt) REVERT: I 329 LYS cc_start: 0.7935 (ttmt) cc_final: 0.7535 (ttpp) REVERT: I 331 PHE cc_start: 0.7183 (m-10) cc_final: 0.6754 (m-10) REVERT: I 366 MET cc_start: 0.7454 (tpt) cc_final: 0.7094 (tpp) REVERT: I 391 LEU cc_start: 0.9383 (mt) cc_final: 0.9156 (tp) REVERT: J 326 TYR cc_start: 0.6937 (p90) cc_final: 0.6277 (p90) REVERT: J 333 ILE cc_start: 0.6870 (tp) cc_final: 0.6119 (tp) REVERT: J 375 VAL cc_start: 0.7578 (p) cc_final: 0.7306 (m) outliers start: 58 outliers final: 13 residues processed: 1549 average time/residue: 0.5879 time to fit residues: 1490.7144 Evaluate side-chains 798 residues out of total 6766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 780 time to evaluate : 4.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 1644 VAL Chi-restraints excluded: chain B residue 2240 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1048 ILE Chi-restraints excluded: chain A residue 1644 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 1003 VAL Chi-restraints excluded: chain E residue 1664 THR Chi-restraints excluded: chain J residue 309 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 641 optimal weight: 1.9990 chunk 576 optimal weight: 0.9990 chunk 319 optimal weight: 2.9990 chunk 196 optimal weight: 5.9990 chunk 388 optimal weight: 10.0000 chunk 307 optimal weight: 0.9990 chunk 595 optimal weight: 0.4980 chunk 230 optimal weight: 10.0000 chunk 362 optimal weight: 3.9990 chunk 443 optimal weight: 0.0970 chunk 690 optimal weight: 0.6980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 HIS ** B 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 967 HIS B 992 GLN B1084 HIS B1157 HIS B1207 GLN B1308 GLN B1355 GLN B1439 HIS ** B1554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1561 GLN B1693 HIS B1741 GLN B1791 HIS B1915 HIS B1970 GLN B2106 HIS B2319 ASN ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 HIS ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 GLN ** F 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN H 88 GLN A 763 ASN A 967 HIS ** A1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1157 HIS ** A1207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1308 GLN A1355 GLN ** A1729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1765 ASN A2106 HIS ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 474 ASN E 496 HIS E 540 HIS ** E 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 832 HIS ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN ** I 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 59658 Z= 0.180 Angle : 0.559 14.680 80992 Z= 0.284 Chirality : 0.040 0.213 9400 Planarity : 0.004 0.050 10390 Dihedral : 3.971 58.735 8295 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.20 % Favored : 96.75 % Rotamer: Outliers : 2.50 % Allowed : 11.20 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.10), residues: 7536 helix: 1.03 (0.08), residues: 4582 sheet: 0.01 (0.28), residues: 342 loop : -0.97 (0.12), residues: 2612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 750 HIS 0.020 0.001 HIS A2189 PHE 0.030 0.001 PHE F1531 TYR 0.028 0.001 TYR E 731 ARG 0.008 0.000 ARG H 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1011 residues out of total 6766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 863 time to evaluate : 5.059 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: B 655 VAL cc_start: 0.7933 (OUTLIER) cc_final: 0.7727 (p) REVERT: B 725 PHE cc_start: 0.7011 (m-80) cc_final: 0.6766 (m-80) REVERT: B 772 MET cc_start: 0.8531 (mmp) cc_final: 0.8239 (mmm) REVERT: B 1227 GLU cc_start: 0.8121 (tp30) cc_final: 0.7818 (tt0) REVERT: B 1285 ARG cc_start: 0.7321 (ptm-80) cc_final: 0.7013 (ttp80) REVERT: B 1539 ASP cc_start: 0.7818 (t0) cc_final: 0.7493 (t0) REVERT: B 1654 LEU cc_start: 0.8738 (mt) cc_final: 0.8537 (mt) REVERT: B 1726 GLN cc_start: 0.8653 (mp-120) cc_final: 0.8241 (mp10) REVERT: B 2047 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7430 (ttp) REVERT: B 2135 ASP cc_start: 0.8328 (t0) cc_final: 0.8079 (t0) REVERT: B 2274 ASP cc_start: 0.7329 (p0) cc_final: 0.7007 (p0) REVERT: B 2357 ASP cc_start: 0.8101 (t0) cc_final: 0.7787 (t0) REVERT: D 62 TYR cc_start: 0.7595 (t80) cc_final: 0.7297 (t80) REVERT: D 69 ASP cc_start: 0.7871 (t0) cc_final: 0.7635 (p0) REVERT: D 134 VAL cc_start: 0.8769 (t) cc_final: 0.8390 (p) REVERT: D 137 HIS cc_start: 0.6005 (t70) cc_final: 0.5561 (t70) REVERT: D 255 MET cc_start: 0.7948 (mtp) cc_final: 0.7333 (mtp) REVERT: F 54 MET cc_start: 0.6293 (tmm) cc_final: 0.5957 (tmm) REVERT: F 76 LYS cc_start: 0.8295 (mttp) cc_final: 0.8059 (mtmm) REVERT: F 132 CYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8484 (t) REVERT: F 177 LEU cc_start: 0.8703 (tp) cc_final: 0.8487 (mp) REVERT: F 247 ASP cc_start: 0.7559 (m-30) cc_final: 0.7295 (m-30) REVERT: F 251 GLU cc_start: 0.7887 (mp0) cc_final: 0.7542 (mp0) REVERT: F 482 MET cc_start: 0.8319 (ttp) cc_final: 0.7867 (ttt) REVERT: F 894 HIS cc_start: 0.7995 (t70) cc_final: 0.7570 (t-90) REVERT: F 907 ARG cc_start: 0.8266 (tpp-160) cc_final: 0.7969 (ttm110) REVERT: F 1633 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7056 (mp0) REVERT: H 94 ARG cc_start: 0.7948 (ttm110) cc_final: 0.7628 (ttm170) REVERT: A 610 PHE cc_start: 0.7476 (p90) cc_final: 0.7045 (p90) REVERT: A 617 GLU cc_start: 0.6868 (tm-30) cc_final: 0.6437 (mt-10) REVERT: A 654 ASP cc_start: 0.8159 (t0) cc_final: 0.7934 (t0) REVERT: A 668 ASP cc_start: 0.7410 (p0) cc_final: 0.7115 (p0) REVERT: A 710 LEU cc_start: 0.8329 (tp) cc_final: 0.8120 (mt) REVERT: A 796 ASN cc_start: 0.8129 (m-40) cc_final: 0.7899 (m-40) REVERT: A 1174 MET cc_start: 0.6944 (mmt) cc_final: 0.6615 (tpp) REVERT: A 1269 TRP cc_start: 0.7529 (m100) cc_final: 0.6782 (m-10) REVERT: A 1503 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7673 (pp) REVERT: A 1947 ASP cc_start: 0.7396 (p0) cc_final: 0.7150 (p0) REVERT: A 2404 MET cc_start: 0.8514 (mmt) cc_final: 0.8311 (tpt) REVERT: A 2424 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.8128 (m-30) REVERT: C 41 GLN cc_start: 0.8025 (tp40) cc_final: 0.7805 (pm20) REVERT: C 184 TYR cc_start: 0.5125 (m-80) cc_final: 0.4883 (m-10) REVERT: C 213 LYS cc_start: 0.7505 (tptm) cc_final: 0.6743 (ttmt) REVERT: C 255 MET cc_start: 0.7550 (tpt) cc_final: 0.6906 (mmt) REVERT: C 273 MET cc_start: 0.7428 (ttp) cc_final: 0.7110 (ttp) REVERT: E 38 LEU cc_start: 0.8625 (mt) cc_final: 0.8355 (tp) REVERT: E 42 LEU cc_start: 0.8817 (mt) cc_final: 0.8509 (mt) REVERT: E 83 ASP cc_start: 0.7596 (m-30) cc_final: 0.7170 (t70) REVERT: E 153 MET cc_start: 0.8424 (mtp) cc_final: 0.8083 (ttm) REVERT: E 200 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8329 (tp30) REVERT: E 240 THR cc_start: 0.9464 (OUTLIER) cc_final: 0.9091 (p) REVERT: E 249 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7291 (mm-30) REVERT: E 414 ASN cc_start: 0.8189 (t0) cc_final: 0.7652 (t0) REVERT: E 453 MET cc_start: 0.8643 (tpp) cc_final: 0.8405 (mmt) REVERT: E 529 LEU cc_start: 0.8124 (mt) cc_final: 0.7241 (pp) REVERT: E 592 ASP cc_start: 0.7667 (t0) cc_final: 0.7378 (p0) REVERT: E 790 MET cc_start: 0.7776 (mtp) cc_final: 0.7558 (mpp) REVERT: G 6 ASN cc_start: 0.8463 (p0) cc_final: 0.8101 (m-40) REVERT: I 319 LEU cc_start: 0.7957 (tt) cc_final: 0.7323 (tp) REVERT: I 329 LYS cc_start: 0.7838 (ttmt) cc_final: 0.7509 (ttpp) REVERT: I 331 PHE cc_start: 0.6755 (m-10) cc_final: 0.6226 (m-10) REVERT: I 391 LEU cc_start: 0.9376 (mt) cc_final: 0.9122 (tp) outliers start: 148 outliers final: 83 residues processed: 964 average time/residue: 0.5425 time to fit residues: 888.8469 Evaluate side-chains 788 residues out of total 6766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 699 time to evaluate : 5.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 944 ASP Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1172 THR Chi-restraints excluded: chain B residue 1293 LYS Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1542 ASP Chi-restraints excluded: chain B residue 1607 LEU Chi-restraints excluded: chain B residue 1644 VAL Chi-restraints excluded: chain B residue 2021 ILE Chi-restraints excluded: chain B residue 2047 MET Chi-restraints excluded: chain B residue 2151 ILE Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 132 CYS Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 460 ASP Chi-restraints excluded: chain F residue 463 LYS Chi-restraints excluded: chain F residue 495 ASP Chi-restraints excluded: chain F residue 524 THR Chi-restraints excluded: chain F residue 663 ILE Chi-restraints excluded: chain F residue 687 ASN Chi-restraints excluded: chain F residue 712 LEU Chi-restraints excluded: chain F residue 720 ILE Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1621 ILE Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 686 HIS Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1341 ILE Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1542 ASP Chi-restraints excluded: chain A residue 1644 VAL Chi-restraints excluded: chain A residue 1765 ASN Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain A residue 2307 SER Chi-restraints excluded: chain A residue 2424 ASP Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain E residue 231 ILE Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 451 THR Chi-restraints excluded: chain E residue 606 CYS Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain E residue 653 THR Chi-restraints excluded: chain E residue 693 ASN Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain E residue 978 THR Chi-restraints excluded: chain E residue 1003 VAL Chi-restraints excluded: chain E residue 1628 SER Chi-restraints excluded: chain E residue 1654 SER Chi-restraints excluded: chain E residue 1656 VAL Chi-restraints excluded: chain E residue 1664 THR Chi-restraints excluded: chain E residue 1669 CYS Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 35 ASP Chi-restraints excluded: chain I residue 384 ASP Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain J residue 305 ASN Chi-restraints excluded: chain J residue 309 VAL Chi-restraints excluded: chain J residue 310 LEU Chi-restraints excluded: chain J residue 331 PHE Chi-restraints excluded: chain J residue 383 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 383 optimal weight: 30.0000 chunk 214 optimal weight: 2.9990 chunk 574 optimal weight: 0.9980 chunk 469 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 chunk 691 optimal weight: 0.9990 chunk 746 optimal weight: 2.9990 chunk 615 optimal weight: 8.9990 chunk 685 optimal weight: 7.9990 chunk 235 optimal weight: 10.0000 chunk 554 optimal weight: 0.0010 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 HIS ** B 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1509 GLN B1554 GLN ** B1726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1762 GLN D 87 ASN ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 HIS D 242 GLN ** F 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 657 GLN ** F 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 827 GLN ** F 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 932 ASN F 988 HIS ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1084 HIS A1308 GLN A1509 GLN A1729 GLN A1989 ASN C 39 GLN C 41 GLN ** C 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 GLN E 435 ASN ** E 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 827 GLN ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 59658 Z= 0.231 Angle : 0.552 14.213 80992 Z= 0.278 Chirality : 0.041 0.213 9400 Planarity : 0.004 0.046 10390 Dihedral : 4.027 56.830 8286 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.86 % Favored : 96.09 % Rotamer: Outliers : 3.15 % Allowed : 12.55 % Favored : 84.29 % 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: 0.48 (0.10), residues: 7536 helix: 1.15 (0.08), residues: 4576 sheet: -0.16 (0.27), residues: 370 loop : -1.06 (0.12), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 197 HIS 0.026 0.001 HIS E 72 PHE 0.033 0.001 PHE F1531 TYR 0.021 0.001 TYR E 731 ARG 0.011 0.000 ARG G 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 923 residues out of total 6766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 736 time to evaluate : 4.995 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: B 733 MET cc_start: 0.7272 (tpp) cc_final: 0.7016 (tpp) REVERT: B 772 MET cc_start: 0.8490 (mmp) cc_final: 0.8235 (mmm) REVERT: B 1227 GLU cc_start: 0.8149 (tp30) cc_final: 0.7847 (tt0) REVERT: B 1285 ARG cc_start: 0.7409 (ptm-80) cc_final: 0.7047 (mtp-110) REVERT: B 1477 MET cc_start: 0.8430 (ppp) cc_final: 0.7777 (ppp) REVERT: B 1539 ASP cc_start: 0.7849 (t0) cc_final: 0.7508 (t0) REVERT: B 1757 TRP cc_start: 0.8740 (m-10) cc_final: 0.8507 (m-90) REVERT: B 2135 ASP cc_start: 0.8493 (t0) cc_final: 0.8228 (t0) REVERT: B 2274 ASP cc_start: 0.7635 (p0) cc_final: 0.7386 (p0) REVERT: B 2281 MET cc_start: 0.7954 (tpp) cc_final: 0.7659 (tpp) REVERT: B 2357 ASP cc_start: 0.8239 (t0) cc_final: 0.7930 (t0) REVERT: D 137 HIS cc_start: 0.6387 (t70) cc_final: 0.5747 (t70) REVERT: D 297 TRP cc_start: 0.8078 (m100) cc_final: 0.7667 (m-10) REVERT: F 247 ASP cc_start: 0.7417 (m-30) cc_final: 0.6962 (m-30) REVERT: F 251 GLU cc_start: 0.7947 (mp0) cc_final: 0.7531 (mt-10) REVERT: F 495 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8433 (m-30) REVERT: F 594 ASP cc_start: 0.8168 (m-30) cc_final: 0.7585 (t0) REVERT: F 806 LEU cc_start: 0.8559 (mt) cc_final: 0.8065 (tt) REVERT: F 1633 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7097 (mp0) REVERT: H 24 THR cc_start: 0.8564 (m) cc_final: 0.8358 (m) REVERT: H 36 VAL cc_start: 0.6117 (m) cc_final: 0.5695 (p) REVERT: H 94 ARG cc_start: 0.7876 (ttm110) cc_final: 0.7584 (ttm170) REVERT: A 617 GLU cc_start: 0.6959 (tm-30) cc_final: 0.6577 (mt-10) REVERT: A 654 ASP cc_start: 0.8414 (t0) cc_final: 0.8129 (t0) REVERT: A 668 ASP cc_start: 0.7454 (p0) cc_final: 0.7144 (p0) REVERT: A 796 ASN cc_start: 0.8146 (m-40) cc_final: 0.7940 (m-40) REVERT: A 1269 TRP cc_start: 0.7664 (m100) cc_final: 0.6868 (m-10) REVERT: A 1289 LEU cc_start: 0.8507 (mm) cc_final: 0.8305 (mt) REVERT: A 1503 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7915 (pp) REVERT: A 1515 MET cc_start: 0.8498 (mpp) cc_final: 0.8282 (mtp) REVERT: A 2143 THR cc_start: 0.9107 (OUTLIER) cc_final: 0.8906 (p) REVERT: A 2161 GLN cc_start: 0.7709 (tm-30) cc_final: 0.7237 (tm-30) REVERT: A 2387 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7978 (mtm) REVERT: A 2424 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8202 (m-30) REVERT: C 41 GLN cc_start: 0.8080 (tp-100) cc_final: 0.7678 (pm20) REVERT: C 51 THR cc_start: 0.7440 (OUTLIER) cc_final: 0.7174 (p) REVERT: C 67 MET cc_start: 0.7515 (mtt) cc_final: 0.7272 (mtm) REVERT: C 255 MET cc_start: 0.7373 (tpt) cc_final: 0.6668 (mmt) REVERT: E 38 LEU cc_start: 0.8542 (mt) cc_final: 0.8284 (tp) REVERT: E 42 LEU cc_start: 0.8795 (mt) cc_final: 0.8514 (mt) REVERT: E 72 HIS cc_start: 0.6937 (OUTLIER) cc_final: 0.6721 (p-80) REVERT: E 83 ASP cc_start: 0.7546 (m-30) cc_final: 0.7124 (t70) REVERT: E 213 LYS cc_start: 0.8272 (mtmt) cc_final: 0.7534 (tttm) REVERT: E 240 THR cc_start: 0.9492 (OUTLIER) cc_final: 0.9087 (p) REVERT: E 249 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7370 (mm-30) REVERT: E 414 ASN cc_start: 0.8358 (t0) cc_final: 0.7971 (t0) REVERT: E 529 LEU cc_start: 0.8152 (mt) cc_final: 0.7288 (pp) REVERT: E 542 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6517 (pm20) REVERT: E 675 MET cc_start: 0.7352 (tmm) cc_final: 0.7089 (tmm) REVERT: E 831 TRP cc_start: 0.7529 (m100) cc_final: 0.7279 (m100) REVERT: G 6 ASN cc_start: 0.8410 (OUTLIER) cc_final: 0.8097 (m-40) REVERT: G 92 ARG cc_start: 0.8615 (ttm110) cc_final: 0.8328 (ttp-110) REVERT: G 103 CYS cc_start: 0.7781 (t) cc_final: 0.6865 (t) REVERT: I 329 LYS cc_start: 0.8009 (ttmt) cc_final: 0.7621 (ttpp) REVERT: I 331 PHE cc_start: 0.6621 (m-10) cc_final: 0.5959 (m-10) REVERT: I 374 SER cc_start: 0.6163 (t) cc_final: 0.5656 (t) REVERT: J 366 MET cc_start: 0.7358 (tpp) cc_final: 0.7055 (tpp) outliers start: 187 outliers final: 110 residues processed: 872 average time/residue: 0.5276 time to fit residues: 789.1549 Evaluate side-chains 775 residues out of total 6766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 655 time to evaluate : 5.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 944 ASP Chi-restraints excluded: chain B residue 961 ASP Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1075 ILE Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1172 THR Chi-restraints excluded: chain B residue 1313 MET Chi-restraints excluded: chain B residue 1377 ASP Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1465 LYS Chi-restraints excluded: chain B residue 1542 ASP Chi-restraints excluded: chain B residue 1552 LEU Chi-restraints excluded: chain B residue 1607 LEU Chi-restraints excluded: chain B residue 1644 VAL Chi-restraints excluded: chain B residue 1660 CYS Chi-restraints excluded: chain B residue 2047 MET Chi-restraints excluded: chain B residue 2150 ILE Chi-restraints excluded: chain B residue 2151 ILE Chi-restraints excluded: chain B residue 2172 LEU Chi-restraints excluded: chain B residue 2240 VAL Chi-restraints excluded: chain B residue 2349 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 397 SER Chi-restraints excluded: chain F residue 460 ASP Chi-restraints excluded: chain F residue 463 LYS Chi-restraints excluded: chain F residue 495 ASP Chi-restraints excluded: chain F residue 524 THR Chi-restraints excluded: chain F residue 554 ILE Chi-restraints excluded: chain F residue 663 ILE Chi-restraints excluded: chain F residue 687 ASN Chi-restraints excluded: chain F residue 689 CYS Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1621 ILE Chi-restraints excluded: chain F residue 1634 THR Chi-restraints excluded: chain H residue 6 ASN Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1048 ILE Chi-restraints excluded: chain A residue 1051 THR Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1277 LYS Chi-restraints excluded: chain A residue 1341 ILE Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1437 MET Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1542 ASP Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1558 SER Chi-restraints excluded: chain A residue 1644 VAL Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2057 MET Chi-restraints excluded: chain A residue 2143 THR Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain A residue 2387 MET Chi-restraints excluded: chain A residue 2424 ASP Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 451 THR Chi-restraints excluded: chain E residue 542 GLU Chi-restraints excluded: chain E residue 606 CYS Chi-restraints excluded: chain E residue 693 ASN Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain E residue 978 THR Chi-restraints excluded: chain E residue 1516 THR Chi-restraints excluded: chain E residue 1654 SER Chi-restraints excluded: chain E residue 1656 VAL Chi-restraints excluded: chain E residue 1664 THR Chi-restraints excluded: chain E residue 1669 CYS Chi-restraints excluded: chain G residue 6 ASN Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 35 ASP Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain I residue 380 VAL Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain J residue 305 ASN Chi-restraints excluded: chain J residue 309 VAL Chi-restraints excluded: chain J residue 310 LEU Chi-restraints excluded: chain J residue 331 PHE Chi-restraints excluded: chain J residue 383 VAL Chi-restraints excluded: chain J residue 401 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 683 optimal weight: 5.9990 chunk 519 optimal weight: 1.9990 chunk 358 optimal weight: 0.0670 chunk 76 optimal weight: 1.9990 chunk 329 optimal weight: 2.9990 chunk 464 optimal weight: 3.9990 chunk 693 optimal weight: 0.8980 chunk 734 optimal weight: 8.9990 chunk 362 optimal weight: 2.9990 chunk 657 optimal weight: 0.6980 chunk 197 optimal weight: 4.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 HIS ** B 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2028 HIS D 87 ASN ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 GLN ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 758 GLN ** F 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1509 GLN C 41 GLN C 164 GLN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS ** E 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 59658 Z= 0.194 Angle : 0.521 11.444 80992 Z= 0.260 Chirality : 0.040 0.183 9400 Planarity : 0.003 0.048 10390 Dihedral : 3.985 53.840 8284 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.68 % Favored : 96.28 % Rotamer: Outliers : 3.19 % Allowed : 13.66 % Favored : 83.15 % 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: 0.63 (0.10), residues: 7536 helix: 1.32 (0.08), residues: 4548 sheet: -0.19 (0.28), residues: 350 loop : -1.05 (0.12), residues: 2638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 99 HIS 0.010 0.001 HIS A2189 PHE 0.023 0.001 PHE F1531 TYR 0.027 0.001 TYR C 101 ARG 0.005 0.000 ARG A1683 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 906 residues out of total 6766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 717 time to evaluate : 5.000 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: B 721 MET cc_start: 0.8366 (mmm) cc_final: 0.7961 (mtp) REVERT: B 772 MET cc_start: 0.8515 (mmp) cc_final: 0.8210 (mmm) REVERT: B 821 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.8126 (t80) REVERT: B 827 MET cc_start: 0.8458 (mtm) cc_final: 0.8211 (mtp) REVERT: B 1285 ARG cc_start: 0.7463 (ptm-80) cc_final: 0.7060 (mtp-110) REVERT: B 1477 MET cc_start: 0.8361 (ppp) cc_final: 0.7834 (ppp) REVERT: B 1539 ASP cc_start: 0.7812 (t0) cc_final: 0.7460 (t0) REVERT: B 1757 TRP cc_start: 0.8909 (m-10) cc_final: 0.8697 (m-90) REVERT: B 1955 ARG cc_start: 0.7847 (ptm160) cc_final: 0.7497 (ptm-80) REVERT: B 2058 MET cc_start: 0.9050 (mtp) cc_final: 0.8849 (mtp) REVERT: B 2135 ASP cc_start: 0.8471 (t0) cc_final: 0.8161 (t0) REVERT: B 2274 ASP cc_start: 0.7669 (p0) cc_final: 0.7392 (p0) REVERT: B 2357 ASP cc_start: 0.8293 (t0) cc_final: 0.7875 (t0) REVERT: D 137 HIS cc_start: 0.6765 (t70) cc_final: 0.6338 (t70) REVERT: D 297 TRP cc_start: 0.8156 (m100) cc_final: 0.7604 (m-10) REVERT: F 177 LEU cc_start: 0.8795 (tp) cc_final: 0.8564 (mp) REVERT: F 594 ASP cc_start: 0.8142 (m-30) cc_final: 0.7595 (t0) REVERT: F 1633 GLU cc_start: 0.7605 (mt-10) cc_final: 0.6996 (mp0) REVERT: H 15 ARG cc_start: 0.7973 (mtt90) cc_final: 0.7770 (mtt90) REVERT: H 94 ARG cc_start: 0.7944 (ttm110) cc_final: 0.7723 (ttm170) REVERT: H 104 LYS cc_start: 0.8064 (ttmm) cc_final: 0.7825 (ttpp) REVERT: A 617 GLU cc_start: 0.7008 (tm-30) cc_final: 0.6639 (mt-10) REVERT: A 668 ASP cc_start: 0.7564 (p0) cc_final: 0.7206 (p0) REVERT: A 1269 TRP cc_start: 0.7649 (m100) cc_final: 0.6963 (m100) REVERT: A 1503 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7980 (pp) REVERT: A 1515 MET cc_start: 0.8465 (mpp) cc_final: 0.8210 (mtp) REVERT: A 1745 LYS cc_start: 0.9054 (mtmm) cc_final: 0.8776 (mtmm) REVERT: A 1904 LEU cc_start: 0.8833 (tp) cc_final: 0.8556 (mt) REVERT: A 2135 ASP cc_start: 0.7949 (t0) cc_final: 0.7608 (t0) REVERT: A 2424 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.8223 (m-30) REVERT: C 51 THR cc_start: 0.7544 (OUTLIER) cc_final: 0.7261 (p) REVERT: C 255 MET cc_start: 0.7465 (tpt) cc_final: 0.6729 (mmt) REVERT: E 38 LEU cc_start: 0.8536 (mt) cc_final: 0.8310 (tp) REVERT: E 42 LEU cc_start: 0.8778 (mt) cc_final: 0.8500 (mt) REVERT: E 83 ASP cc_start: 0.7543 (m-30) cc_final: 0.7136 (t70) REVERT: E 213 LYS cc_start: 0.8220 (mtmt) cc_final: 0.7559 (tttm) REVERT: E 240 THR cc_start: 0.9491 (OUTLIER) cc_final: 0.9109 (p) REVERT: E 249 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7387 (mm-30) REVERT: E 366 ASP cc_start: 0.7810 (m-30) cc_final: 0.7223 (t0) REVERT: E 414 ASN cc_start: 0.8378 (t0) cc_final: 0.8090 (t0) REVERT: E 520 ILE cc_start: 0.5754 (OUTLIER) cc_final: 0.5527 (mt) REVERT: E 529 LEU cc_start: 0.8149 (mt) cc_final: 0.7261 (pp) REVERT: E 675 MET cc_start: 0.7359 (tmm) cc_final: 0.7128 (tmm) REVERT: E 678 LYS cc_start: 0.9114 (mmmt) cc_final: 0.8248 (ttpt) REVERT: E 790 MET cc_start: 0.7902 (mpp) cc_final: 0.7636 (mpp) REVERT: G 6 ASN cc_start: 0.8477 (OUTLIER) cc_final: 0.8161 (m-40) REVERT: G 103 CYS cc_start: 0.7609 (t) cc_final: 0.6657 (t) REVERT: I 328 ARG cc_start: 0.6035 (mmm160) cc_final: 0.5658 (mmp-170) REVERT: I 329 LYS cc_start: 0.8100 (ttmt) cc_final: 0.7687 (ttpp) REVERT: I 331 PHE cc_start: 0.6519 (m-10) cc_final: 0.5925 (m-10) REVERT: I 391 LEU cc_start: 0.9242 (mt) cc_final: 0.8919 (tp) REVERT: I 402 GLU cc_start: 0.5849 (mm-30) cc_final: 0.5483 (tp30) REVERT: J 366 MET cc_start: 0.7273 (tpp) cc_final: 0.6995 (tpp) outliers start: 189 outliers final: 118 residues processed: 846 average time/residue: 0.5368 time to fit residues: 780.7322 Evaluate side-chains 774 residues out of total 6766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 649 time to evaluate : 4.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 752 GLN Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 944 ASP Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1075 ILE Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1172 THR Chi-restraints excluded: chain B residue 1213 ILE Chi-restraints excluded: chain B residue 1313 MET Chi-restraints excluded: chain B residue 1338 ILE Chi-restraints excluded: chain B residue 1377 ASP Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1552 LEU Chi-restraints excluded: chain B residue 1607 LEU Chi-restraints excluded: chain B residue 1638 MET Chi-restraints excluded: chain B residue 1644 VAL Chi-restraints excluded: chain B residue 1660 CYS Chi-restraints excluded: chain B residue 2150 ILE Chi-restraints excluded: chain B residue 2151 ILE Chi-restraints excluded: chain B residue 2172 LEU Chi-restraints excluded: chain B residue 2240 VAL Chi-restraints excluded: chain B residue 2349 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 397 SER Chi-restraints excluded: chain F residue 460 ASP Chi-restraints excluded: chain F residue 463 LYS Chi-restraints excluded: chain F residue 524 THR Chi-restraints excluded: chain F residue 554 ILE Chi-restraints excluded: chain F residue 663 ILE Chi-restraints excluded: chain F residue 687 ASN Chi-restraints excluded: chain F residue 689 CYS Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1621 ILE Chi-restraints excluded: chain F residue 1634 THR Chi-restraints excluded: chain H residue 5 ASP Chi-restraints excluded: chain H residue 6 ASN Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1236 MET Chi-restraints excluded: chain A residue 1277 LYS Chi-restraints excluded: chain A residue 1341 ILE Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1437 MET Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1535 MET Chi-restraints excluded: chain A residue 1542 ASP Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1569 ASP Chi-restraints excluded: chain A residue 1644 VAL Chi-restraints excluded: chain A residue 1759 LEU Chi-restraints excluded: chain A residue 1998 MET Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2057 MET Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain A residue 2424 ASP Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain A residue 2548 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 460 ASP Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 606 CYS Chi-restraints excluded: chain E residue 663 ILE Chi-restraints excluded: chain E residue 686 LEU Chi-restraints excluded: chain E residue 693 ASN Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain E residue 796 HIS Chi-restraints excluded: chain E residue 940 LEU Chi-restraints excluded: chain E residue 978 THR Chi-restraints excluded: chain E residue 1516 THR Chi-restraints excluded: chain E residue 1607 MET Chi-restraints excluded: chain E residue 1628 SER Chi-restraints excluded: chain E residue 1654 SER Chi-restraints excluded: chain E residue 1656 VAL Chi-restraints excluded: chain E residue 1664 THR Chi-restraints excluded: chain E residue 1669 CYS Chi-restraints excluded: chain G residue 6 ASN Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 35 ASP Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain I residue 384 ASP Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain J residue 305 ASN Chi-restraints excluded: chain J residue 309 VAL Chi-restraints excluded: chain J residue 310 LEU Chi-restraints excluded: chain J residue 331 PHE Chi-restraints excluded: chain J residue 383 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 611 optimal weight: 3.9990 chunk 417 optimal weight: 0.7980 chunk 10 optimal weight: 30.0000 chunk 546 optimal weight: 1.9990 chunk 303 optimal weight: 0.7980 chunk 626 optimal weight: 1.9990 chunk 507 optimal weight: 0.0470 chunk 0 optimal weight: 50.0000 chunk 375 optimal weight: 9.9990 chunk 659 optimal weight: 4.9990 chunk 185 optimal weight: 5.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1355 GLN D 64 HIS ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 ASN ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2001 HIS C 164 GLN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 219 GLN ** E 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 59658 Z= 0.194 Angle : 0.522 11.437 80992 Z= 0.259 Chirality : 0.039 0.165 9400 Planarity : 0.003 0.049 10390 Dihedral : 3.958 52.660 8284 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.97 % Favored : 95.98 % Rotamer: Outliers : 3.26 % Allowed : 14.32 % Favored : 82.42 % 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: 0.69 (0.10), residues: 7536 helix: 1.38 (0.08), residues: 4570 sheet: -0.10 (0.28), residues: 340 loop : -1.11 (0.12), residues: 2626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A2429 HIS 0.008 0.001 HIS A2189 PHE 0.019 0.001 PHE F1531 TYR 0.023 0.001 TYR F1653 ARG 0.006 0.000 ARG A1683 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 6766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 678 time to evaluate : 4.983 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 721 MET cc_start: 0.8386 (mmm) cc_final: 0.7995 (mtp) REVERT: B 821 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.8105 (t80) REVERT: B 827 MET cc_start: 0.8494 (mtm) cc_final: 0.8218 (mtp) REVERT: B 1285 ARG cc_start: 0.7498 (ptm-80) cc_final: 0.7076 (mtp-110) REVERT: B 1291 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8179 (mm) REVERT: B 1565 ASP cc_start: 0.7987 (m-30) cc_final: 0.7370 (m-30) REVERT: B 1726 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8267 (mm-40) REVERT: B 2274 ASP cc_start: 0.7804 (p0) cc_final: 0.7510 (p0) REVERT: B 2357 ASP cc_start: 0.8293 (t0) cc_final: 0.7895 (t0) REVERT: D 137 HIS cc_start: 0.6760 (t70) cc_final: 0.6347 (t70) REVERT: D 245 LYS cc_start: 0.6959 (mmtt) cc_final: 0.6669 (mmtt) REVERT: D 297 TRP cc_start: 0.8144 (m100) cc_final: 0.7516 (m-10) REVERT: F 594 ASP cc_start: 0.8142 (m-30) cc_final: 0.7632 (t0) REVERT: F 913 ASP cc_start: 0.7015 (OUTLIER) cc_final: 0.6471 (p0) REVERT: H 91 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7631 (mp0) REVERT: H 94 ARG cc_start: 0.7955 (ttm110) cc_final: 0.7659 (ttm170) REVERT: H 104 LYS cc_start: 0.7986 (ttmm) cc_final: 0.7744 (ttpp) REVERT: A 617 GLU cc_start: 0.7108 (tm-30) cc_final: 0.6696 (mp0) REVERT: A 668 ASP cc_start: 0.7482 (p0) cc_final: 0.7184 (p0) REVERT: A 1066 GLU cc_start: 0.7529 (pt0) cc_final: 0.7269 (pt0) REVERT: A 1269 TRP cc_start: 0.7657 (m100) cc_final: 0.6962 (m100) REVERT: A 1313 MET cc_start: 0.8931 (tmm) cc_final: 0.7854 (tmm) REVERT: A 1503 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8081 (pp) REVERT: A 1515 MET cc_start: 0.8519 (mpp) cc_final: 0.8268 (mtp) REVERT: A 1539 ASP cc_start: 0.7968 (t0) cc_final: 0.7667 (t0) REVERT: A 1650 MET cc_start: 0.7796 (mtm) cc_final: 0.7567 (ttp) REVERT: A 1798 PHE cc_start: 0.9049 (t80) cc_final: 0.8687 (t80) REVERT: A 1904 LEU cc_start: 0.8870 (tp) cc_final: 0.8597 (mt) REVERT: A 2135 ASP cc_start: 0.7925 (t0) cc_final: 0.7562 (t0) REVERT: A 2161 GLN cc_start: 0.7591 (tm-30) cc_final: 0.7175 (tm-30) REVERT: A 2424 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8271 (m-30) REVERT: C 51 THR cc_start: 0.7601 (OUTLIER) cc_final: 0.7338 (p) REVERT: C 305 LYS cc_start: 0.8820 (mmmt) cc_final: 0.8427 (mmtm) REVERT: E 38 LEU cc_start: 0.8558 (mt) cc_final: 0.8310 (tp) REVERT: E 42 LEU cc_start: 0.8789 (mt) cc_final: 0.8500 (mt) REVERT: E 83 ASP cc_start: 0.7554 (m-30) cc_final: 0.7153 (t70) REVERT: E 213 LYS cc_start: 0.8222 (mtmt) cc_final: 0.7474 (tttm) REVERT: E 240 THR cc_start: 0.9511 (OUTLIER) cc_final: 0.9140 (p) REVERT: E 249 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7413 (mm-30) REVERT: E 366 ASP cc_start: 0.7862 (m-30) cc_final: 0.7259 (t0) REVERT: E 414 ASN cc_start: 0.8407 (t0) cc_final: 0.8135 (t0) REVERT: E 520 ILE cc_start: 0.5759 (OUTLIER) cc_final: 0.5437 (mt) REVERT: E 528 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7208 (mp) REVERT: E 529 LEU cc_start: 0.8236 (mt) cc_final: 0.7344 (pp) REVERT: E 678 LYS cc_start: 0.9156 (mmmt) cc_final: 0.8293 (ttpt) REVERT: E 725 THR cc_start: 0.7347 (OUTLIER) cc_final: 0.7088 (p) REVERT: E 790 MET cc_start: 0.7816 (mpp) cc_final: 0.6877 (mpp) REVERT: G 6 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.8178 (m-40) REVERT: G 103 CYS cc_start: 0.7529 (t) cc_final: 0.6619 (t) REVERT: I 329 LYS cc_start: 0.7996 (ttmt) cc_final: 0.7598 (tttm) REVERT: I 331 PHE cc_start: 0.6534 (m-10) cc_final: 0.5907 (m-10) REVERT: I 391 LEU cc_start: 0.9269 (mt) cc_final: 0.8929 (tt) REVERT: I 402 GLU cc_start: 0.6059 (mm-30) cc_final: 0.5774 (tp30) REVERT: J 371 PHE cc_start: 0.7842 (m-80) cc_final: 0.7554 (m-80) outliers start: 193 outliers final: 131 residues processed: 815 average time/residue: 0.5307 time to fit residues: 742.5469 Evaluate side-chains 775 residues out of total 6766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 633 time to evaluate : 4.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 702 ASP Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 725 PHE Chi-restraints excluded: chain B residue 752 GLN Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 944 ASP Chi-restraints excluded: chain B residue 961 ASP Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1075 ILE Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1172 THR Chi-restraints excluded: chain B residue 1213 ILE Chi-restraints excluded: chain B residue 1221 THR Chi-restraints excluded: chain B residue 1291 LEU Chi-restraints excluded: chain B residue 1313 MET Chi-restraints excluded: chain B residue 1338 ILE Chi-restraints excluded: chain B residue 1377 ASP Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1552 LEU Chi-restraints excluded: chain B residue 1607 LEU Chi-restraints excluded: chain B residue 1638 MET Chi-restraints excluded: chain B residue 1644 VAL Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 2143 THR Chi-restraints excluded: chain B residue 2150 ILE Chi-restraints excluded: chain B residue 2151 ILE Chi-restraints excluded: chain B residue 2172 LEU Chi-restraints excluded: chain B residue 2240 VAL Chi-restraints excluded: chain B residue 2349 LEU Chi-restraints excluded: chain B residue 2375 ILE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 397 SER Chi-restraints excluded: chain F residue 460 ASP Chi-restraints excluded: chain F residue 524 THR Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain F residue 554 ILE Chi-restraints excluded: chain F residue 663 ILE Chi-restraints excluded: chain F residue 687 ASN Chi-restraints excluded: chain F residue 689 CYS Chi-restraints excluded: chain F residue 720 ILE Chi-restraints excluded: chain F residue 783 ASN Chi-restraints excluded: chain F residue 913 ASP Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1621 ILE Chi-restraints excluded: chain F residue 1634 THR Chi-restraints excluded: chain H residue 6 ASN Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1048 ILE Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1236 MET Chi-restraints excluded: chain A residue 1277 LYS Chi-restraints excluded: chain A residue 1341 ILE Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1542 ASP Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1590 MET Chi-restraints excluded: chain A residue 1644 VAL Chi-restraints excluded: chain A residue 1759 LEU Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2057 MET Chi-restraints excluded: chain A residue 2091 SER Chi-restraints excluded: chain A residue 2147 ASN Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain A residue 2424 ASP Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain A residue 2548 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 451 THR Chi-restraints excluded: chain E residue 460 ASP Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 551 ILE Chi-restraints excluded: chain E residue 606 CYS Chi-restraints excluded: chain E residue 663 ILE Chi-restraints excluded: chain E residue 693 ASN Chi-restraints excluded: chain E residue 725 THR Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain E residue 796 HIS Chi-restraints excluded: chain E residue 940 LEU Chi-restraints excluded: chain E residue 978 THR Chi-restraints excluded: chain E residue 1003 VAL Chi-restraints excluded: chain E residue 1516 THR Chi-restraints excluded: chain E residue 1607 MET Chi-restraints excluded: chain E residue 1628 SER Chi-restraints excluded: chain E residue 1654 SER Chi-restraints excluded: chain E residue 1656 VAL Chi-restraints excluded: chain E residue 1664 THR Chi-restraints excluded: chain E residue 1669 CYS Chi-restraints excluded: chain G residue 6 ASN Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 29 MET Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain I residue 382 HIS Chi-restraints excluded: chain I residue 384 ASP Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain J residue 305 ASN Chi-restraints excluded: chain J residue 310 LEU Chi-restraints excluded: chain J residue 331 PHE Chi-restraints excluded: chain J residue 383 VAL Chi-restraints excluded: chain J residue 400 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 247 optimal weight: 9.9990 chunk 661 optimal weight: 1.9990 chunk 145 optimal weight: 0.0170 chunk 431 optimal weight: 0.7980 chunk 181 optimal weight: 0.0970 chunk 735 optimal weight: 0.9980 chunk 610 optimal weight: 5.9990 chunk 340 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 243 optimal weight: 6.9990 chunk 386 optimal weight: 2.9990 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1355 GLN ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 ASN ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1634 GLN A2206 ASN C 164 GLN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 783 ASN ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 59658 Z= 0.138 Angle : 0.495 10.000 80992 Z= 0.244 Chirality : 0.038 0.360 9400 Planarity : 0.003 0.056 10390 Dihedral : 3.807 52.858 8283 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.48 % Favored : 96.47 % Rotamer: Outliers : 2.80 % Allowed : 15.38 % Favored : 81.82 % 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: 0.83 (0.10), residues: 7536 helix: 1.52 (0.08), residues: 4580 sheet: 0.01 (0.28), residues: 344 loop : -1.12 (0.12), residues: 2612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A2429 HIS 0.007 0.001 HIS A2189 PHE 0.015 0.001 PHE I 371 TYR 0.024 0.001 TYR B2542 ARG 0.007 0.000 ARG A1683 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 6766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 696 time to evaluate : 4.983 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: B 721 MET cc_start: 0.8336 (mmm) cc_final: 0.7938 (mtp) REVERT: B 821 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.8069 (t80) REVERT: B 827 MET cc_start: 0.8454 (mtm) cc_final: 0.8178 (mtp) REVERT: B 1285 ARG cc_start: 0.7470 (ptm-80) cc_final: 0.7039 (mtp-110) REVERT: B 1368 ASP cc_start: 0.8206 (p0) cc_final: 0.8005 (p0) REVERT: B 1565 ASP cc_start: 0.7939 (m-30) cc_final: 0.7315 (m-30) REVERT: B 1726 GLN cc_start: 0.8441 (mm-40) cc_final: 0.8209 (mm-40) REVERT: B 1743 LEU cc_start: 0.8616 (tt) cc_final: 0.8049 (tp) REVERT: B 1747 MET cc_start: 0.8549 (mmm) cc_final: 0.7658 (mpp) REVERT: B 2274 ASP cc_start: 0.7712 (p0) cc_final: 0.7448 (p0) REVERT: B 2357 ASP cc_start: 0.8290 (t0) cc_final: 0.7955 (t0) REVERT: D 245 LYS cc_start: 0.6813 (mmtt) cc_final: 0.6513 (mmtt) REVERT: D 297 TRP cc_start: 0.8122 (m100) cc_final: 0.7647 (m-10) REVERT: F 55 ARG cc_start: 0.8224 (mmm160) cc_final: 0.7843 (mmm160) REVERT: F 177 LEU cc_start: 0.8889 (tp) cc_final: 0.8570 (mp) REVERT: F 1633 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7190 (mp0) REVERT: H 6 ASN cc_start: 0.8511 (OUTLIER) cc_final: 0.7931 (m-40) REVERT: H 94 ARG cc_start: 0.7873 (ttm110) cc_final: 0.7365 (ttm170) REVERT: H 104 LYS cc_start: 0.8029 (ttmm) cc_final: 0.7764 (ttpp) REVERT: A 617 GLU cc_start: 0.6963 (tm-30) cc_final: 0.6639 (mp0) REVERT: A 668 ASP cc_start: 0.7561 (p0) cc_final: 0.7231 (p0) REVERT: A 721 MET cc_start: 0.8582 (mmm) cc_final: 0.8211 (mmm) REVERT: A 752 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7914 (mt0) REVERT: A 1066 GLU cc_start: 0.7484 (pt0) cc_final: 0.7228 (pt0) REVERT: A 1269 TRP cc_start: 0.7630 (m100) cc_final: 0.6954 (m100) REVERT: A 1313 MET cc_start: 0.8899 (tmm) cc_final: 0.7862 (tmm) REVERT: A 1478 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7959 (tt) REVERT: A 1503 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8130 (pp) REVERT: A 1515 MET cc_start: 0.8413 (mpp) cc_final: 0.8161 (mtp) REVERT: A 1904 LEU cc_start: 0.8818 (tp) cc_final: 0.8575 (mt) REVERT: A 2135 ASP cc_start: 0.7853 (t0) cc_final: 0.7516 (t0) REVERT: A 2297 ASP cc_start: 0.8624 (p0) cc_final: 0.8422 (p0) REVERT: A 2424 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8287 (m-30) REVERT: C 51 THR cc_start: 0.7623 (OUTLIER) cc_final: 0.7388 (p) REVERT: C 305 LYS cc_start: 0.8727 (mmmt) cc_final: 0.8460 (mmtm) REVERT: E 38 LEU cc_start: 0.8524 (mt) cc_final: 0.8284 (tp) REVERT: E 42 LEU cc_start: 0.8775 (mt) cc_final: 0.8481 (mt) REVERT: E 83 ASP cc_start: 0.7538 (m-30) cc_final: 0.7140 (t70) REVERT: E 213 LYS cc_start: 0.8211 (mtmt) cc_final: 0.7456 (tttm) REVERT: E 240 THR cc_start: 0.9483 (OUTLIER) cc_final: 0.9103 (p) REVERT: E 249 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7433 (mm-30) REVERT: E 366 ASP cc_start: 0.7817 (m-30) cc_final: 0.7272 (t0) REVERT: E 414 ASN cc_start: 0.8298 (t0) cc_final: 0.8038 (t0) REVERT: E 451 THR cc_start: 0.9406 (OUTLIER) cc_final: 0.9034 (p) REVERT: E 520 ILE cc_start: 0.5749 (OUTLIER) cc_final: 0.5412 (mt) REVERT: E 528 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7207 (mp) REVERT: E 529 LEU cc_start: 0.8240 (mt) cc_final: 0.7353 (pp) REVERT: E 573 PHE cc_start: 0.6771 (t80) cc_final: 0.6404 (t80) REVERT: E 678 LYS cc_start: 0.9220 (mmmt) cc_final: 0.8369 (ttpt) REVERT: E 725 THR cc_start: 0.7232 (OUTLIER) cc_final: 0.6973 (p) REVERT: E 790 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.6772 (mpp) REVERT: G 6 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.8171 (m-40) REVERT: G 103 CYS cc_start: 0.7540 (t) cc_final: 0.6691 (t) REVERT: I 329 LYS cc_start: 0.7845 (ttmt) cc_final: 0.7401 (tttm) REVERT: I 331 PHE cc_start: 0.6624 (m-10) cc_final: 0.5953 (m-10) REVERT: I 391 LEU cc_start: 0.9263 (mt) cc_final: 0.8927 (tp) REVERT: I 402 GLU cc_start: 0.6184 (mm-30) cc_final: 0.5937 (tp30) REVERT: J 366 MET cc_start: 0.7060 (tpp) cc_final: 0.6826 (tpp) REVERT: J 404 MET cc_start: 0.7354 (ttp) cc_final: 0.7015 (ppp) outliers start: 166 outliers final: 117 residues processed: 811 average time/residue: 0.5405 time to fit residues: 753.8515 Evaluate side-chains 766 residues out of total 6766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 635 time to evaluate : 5.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 725 PHE Chi-restraints excluded: chain B residue 752 GLN Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 944 ASP Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1136 LEU Chi-restraints excluded: chain B residue 1172 THR Chi-restraints excluded: chain B residue 1213 ILE Chi-restraints excluded: chain B residue 1221 THR Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1552 LEU Chi-restraints excluded: chain B residue 1638 MET Chi-restraints excluded: chain B residue 1660 CYS Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 2050 VAL Chi-restraints excluded: chain B residue 2150 ILE Chi-restraints excluded: chain B residue 2151 ILE Chi-restraints excluded: chain B residue 2172 LEU Chi-restraints excluded: chain B residue 2237 ILE Chi-restraints excluded: chain B residue 2240 VAL Chi-restraints excluded: chain B residue 2364 VAL Chi-restraints excluded: chain B residue 2375 ILE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 397 SER Chi-restraints excluded: chain F residue 460 ASP Chi-restraints excluded: chain F residue 463 LYS Chi-restraints excluded: chain F residue 524 THR Chi-restraints excluded: chain F residue 554 ILE Chi-restraints excluded: chain F residue 656 SER Chi-restraints excluded: chain F residue 663 ILE Chi-restraints excluded: chain F residue 783 ASN Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1621 ILE Chi-restraints excluded: chain H residue 6 ASN Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1155 ILE Chi-restraints excluded: chain A residue 1236 MET Chi-restraints excluded: chain A residue 1277 LYS Chi-restraints excluded: chain A residue 1341 ILE Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1437 MET Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1542 ASP Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1590 MET Chi-restraints excluded: chain A residue 1614 ILE Chi-restraints excluded: chain A residue 1644 VAL Chi-restraints excluded: chain A residue 1759 LEU Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2091 SER Chi-restraints excluded: chain A residue 2147 ASN Chi-restraints excluded: chain A residue 2172 LEU Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain A residue 2333 ILE Chi-restraints excluded: chain A residue 2424 ASP Chi-restraints excluded: chain A residue 2548 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 451 THR Chi-restraints excluded: chain E residue 460 ASP Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 551 ILE Chi-restraints excluded: chain E residue 606 CYS Chi-restraints excluded: chain E residue 725 THR Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain E residue 790 MET Chi-restraints excluded: chain E residue 796 HIS Chi-restraints excluded: chain E residue 940 LEU Chi-restraints excluded: chain E residue 1003 VAL Chi-restraints excluded: chain E residue 1516 THR Chi-restraints excluded: chain E residue 1607 MET Chi-restraints excluded: chain E residue 1628 SER Chi-restraints excluded: chain E residue 1654 SER Chi-restraints excluded: chain E residue 1656 VAL Chi-restraints excluded: chain E residue 1669 CYS Chi-restraints excluded: chain G residue 6 ASN Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 29 MET Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain I residue 384 ASP Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain J residue 305 ASN Chi-restraints excluded: chain J residue 331 PHE Chi-restraints excluded: chain J residue 383 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 708 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 418 optimal weight: 1.9990 chunk 536 optimal weight: 0.9990 chunk 416 optimal weight: 0.0000 chunk 618 optimal weight: 0.2980 chunk 410 optimal weight: 20.0000 chunk 732 optimal weight: 0.9990 chunk 458 optimal weight: 0.8980 chunk 446 optimal weight: 5.9990 chunk 338 optimal weight: 4.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 569 GLN F 687 ASN ** F 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 671 HIS ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 59658 Z= 0.140 Angle : 0.499 9.571 80992 Z= 0.244 Chirality : 0.038 0.152 9400 Planarity : 0.003 0.056 10390 Dihedral : 3.733 52.955 8281 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.69 % Favored : 96.26 % Rotamer: Outliers : 2.83 % Allowed : 15.77 % Favored : 81.39 % 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: 0.91 (0.10), residues: 7536 helix: 1.59 (0.08), residues: 4594 sheet: 0.08 (0.29), residues: 344 loop : -1.11 (0.12), residues: 2598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A2429 HIS 0.006 0.001 HIS A2189 PHE 0.017 0.001 PHE E 63 TYR 0.022 0.001 TYR F1653 ARG 0.007 0.000 ARG E 182 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 6766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 663 time to evaluate : 5.033 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: B 304 MET cc_start: 0.5851 (tmm) cc_final: 0.5450 (tmm) REVERT: B 706 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7360 (pt0) REVERT: B 721 MET cc_start: 0.8363 (mmm) cc_final: 0.7979 (mtp) REVERT: B 827 MET cc_start: 0.8447 (mtm) cc_final: 0.8159 (mtp) REVERT: B 853 TYR cc_start: 0.8037 (OUTLIER) cc_final: 0.6704 (t80) REVERT: B 1285 ARG cc_start: 0.7493 (ptm-80) cc_final: 0.7198 (mtp-110) REVERT: B 1291 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8061 (mm) REVERT: B 1481 MET cc_start: 0.8086 (mtt) cc_final: 0.7807 (mmm) REVERT: B 1565 ASP cc_start: 0.7873 (m-30) cc_final: 0.7182 (m-30) REVERT: B 1726 GLN cc_start: 0.8431 (mm-40) cc_final: 0.8198 (mm-40) REVERT: B 1743 LEU cc_start: 0.8667 (tt) cc_final: 0.8170 (tp) REVERT: B 1747 MET cc_start: 0.8437 (mmm) cc_final: 0.7659 (mpp) REVERT: B 2357 ASP cc_start: 0.8255 (t0) cc_final: 0.7918 (t0) REVERT: D 245 LYS cc_start: 0.6814 (mmtt) cc_final: 0.6503 (mmtt) REVERT: D 297 TRP cc_start: 0.8070 (m100) cc_final: 0.7596 (m-10) REVERT: F 177 LEU cc_start: 0.8836 (tp) cc_final: 0.8545 (mp) REVERT: F 594 ASP cc_start: 0.8068 (m-30) cc_final: 0.7554 (t0) REVERT: F 913 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.6854 (p0) REVERT: F 1633 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7004 (mp0) REVERT: H 94 ARG cc_start: 0.7854 (ttm110) cc_final: 0.7358 (ttm170) REVERT: H 104 LYS cc_start: 0.8094 (ttmm) cc_final: 0.7823 (ttpp) REVERT: A 617 GLU cc_start: 0.7057 (tm-30) cc_final: 0.6758 (mp0) REVERT: A 668 ASP cc_start: 0.7574 (p0) cc_final: 0.7238 (p0) REVERT: A 680 ASP cc_start: 0.8164 (p0) cc_final: 0.7753 (t0) REVERT: A 752 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7894 (mt0) REVERT: A 1066 GLU cc_start: 0.7420 (pt0) cc_final: 0.7066 (pt0) REVERT: A 1269 TRP cc_start: 0.7637 (m100) cc_final: 0.6957 (m100) REVERT: A 1313 MET cc_start: 0.8888 (tmm) cc_final: 0.7740 (tmm) REVERT: A 1458 ASP cc_start: 0.7476 (m-30) cc_final: 0.7158 (m-30) REVERT: A 1478 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7907 (tt) REVERT: A 1503 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8059 (pp) REVERT: A 1515 MET cc_start: 0.8387 (mpp) cc_final: 0.8138 (mtp) REVERT: A 1904 LEU cc_start: 0.8784 (tp) cc_final: 0.8535 (mt) REVERT: A 1947 ASP cc_start: 0.7296 (p0) cc_final: 0.7088 (p0) REVERT: A 2135 ASP cc_start: 0.7825 (t0) cc_final: 0.7481 (t0) REVERT: A 2424 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8297 (m-30) REVERT: C 51 THR cc_start: 0.7555 (p) cc_final: 0.7344 (p) REVERT: C 67 MET cc_start: 0.7314 (mtt) cc_final: 0.7087 (mtm) REVERT: E 38 LEU cc_start: 0.8561 (mt) cc_final: 0.8313 (tp) REVERT: E 42 LEU cc_start: 0.8786 (mt) cc_final: 0.8482 (mt) REVERT: E 83 ASP cc_start: 0.7736 (m-30) cc_final: 0.7381 (t70) REVERT: E 213 LYS cc_start: 0.8221 (mtmt) cc_final: 0.7440 (tttm) REVERT: E 225 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6963 (mt-10) REVERT: E 240 THR cc_start: 0.9492 (OUTLIER) cc_final: 0.9123 (p) REVERT: E 366 ASP cc_start: 0.7796 (m-30) cc_final: 0.7230 (t0) REVERT: E 414 ASN cc_start: 0.8295 (t0) cc_final: 0.7991 (t0) REVERT: E 520 ILE cc_start: 0.5595 (OUTLIER) cc_final: 0.5327 (mt) REVERT: E 528 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7197 (mp) REVERT: E 529 LEU cc_start: 0.8237 (mt) cc_final: 0.7346 (pp) REVERT: E 573 PHE cc_start: 0.6788 (t80) cc_final: 0.6467 (t80) REVERT: E 671 HIS cc_start: 0.6919 (p-80) cc_final: 0.6698 (p90) REVERT: E 678 LYS cc_start: 0.9204 (mmmt) cc_final: 0.8344 (ttpt) REVERT: E 725 THR cc_start: 0.7246 (OUTLIER) cc_final: 0.6972 (p) REVERT: E 790 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.6776 (mpp) REVERT: G 6 ASN cc_start: 0.8457 (OUTLIER) cc_final: 0.8153 (m-40) REVERT: G 103 CYS cc_start: 0.7458 (t) cc_final: 0.6631 (t) REVERT: I 329 LYS cc_start: 0.7759 (ttmt) cc_final: 0.7323 (tttm) REVERT: I 331 PHE cc_start: 0.6505 (m-10) cc_final: 0.6017 (m-10) REVERT: I 386 ARG cc_start: 0.9052 (mtp85) cc_final: 0.8670 (mtp85) REVERT: I 391 LEU cc_start: 0.9293 (mt) cc_final: 0.8971 (tp) REVERT: I 402 GLU cc_start: 0.6213 (mm-30) cc_final: 0.5893 (tp30) REVERT: J 366 MET cc_start: 0.6943 (tpp) cc_final: 0.6714 (tpp) outliers start: 168 outliers final: 127 residues processed: 780 average time/residue: 0.5354 time to fit residues: 716.4960 Evaluate side-chains 777 residues out of total 6766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 637 time to evaluate : 4.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 725 PHE Chi-restraints excluded: chain B residue 752 GLN Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 944 ASP Chi-restraints excluded: chain B residue 961 ASP Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1075 ILE Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1136 LEU Chi-restraints excluded: chain B residue 1172 THR Chi-restraints excluded: chain B residue 1213 ILE Chi-restraints excluded: chain B residue 1221 THR Chi-restraints excluded: chain B residue 1291 LEU Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1638 MET Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1692 VAL Chi-restraints excluded: chain B residue 2151 ILE Chi-restraints excluded: chain B residue 2172 LEU Chi-restraints excluded: chain B residue 2240 VAL Chi-restraints excluded: chain B residue 2364 VAL Chi-restraints excluded: chain B residue 2375 ILE Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 397 SER Chi-restraints excluded: chain F residue 433 MET Chi-restraints excluded: chain F residue 460 ASP Chi-restraints excluded: chain F residue 463 LYS Chi-restraints excluded: chain F residue 524 THR Chi-restraints excluded: chain F residue 554 ILE Chi-restraints excluded: chain F residue 663 ILE Chi-restraints excluded: chain F residue 689 CYS Chi-restraints excluded: chain F residue 693 ASN Chi-restraints excluded: chain F residue 783 ASN Chi-restraints excluded: chain F residue 913 ASP Chi-restraints excluded: chain F residue 1000 LEU Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1528 ILE Chi-restraints excluded: chain F residue 1621 ILE Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain H residue 107 GLN Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1155 ILE Chi-restraints excluded: chain A residue 1236 MET Chi-restraints excluded: chain A residue 1277 LYS Chi-restraints excluded: chain A residue 1341 ILE Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1437 MET Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1542 ASP Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1590 MET Chi-restraints excluded: chain A residue 1614 ILE Chi-restraints excluded: chain A residue 1644 VAL Chi-restraints excluded: chain A residue 1759 LEU Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2057 MET Chi-restraints excluded: chain A residue 2091 SER Chi-restraints excluded: chain A residue 2143 THR Chi-restraints excluded: chain A residue 2147 ASN Chi-restraints excluded: chain A residue 2172 LEU Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain A residue 2333 ILE Chi-restraints excluded: chain A residue 2424 ASP Chi-restraints excluded: chain A residue 2548 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 451 THR Chi-restraints excluded: chain E residue 460 ASP Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 551 ILE Chi-restraints excluded: chain E residue 606 CYS Chi-restraints excluded: chain E residue 693 ASN Chi-restraints excluded: chain E residue 725 THR Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain E residue 790 MET Chi-restraints excluded: chain E residue 796 HIS Chi-restraints excluded: chain E residue 940 LEU Chi-restraints excluded: chain E residue 978 THR Chi-restraints excluded: chain E residue 1003 VAL Chi-restraints excluded: chain E residue 1516 THR Chi-restraints excluded: chain E residue 1607 MET Chi-restraints excluded: chain E residue 1628 SER Chi-restraints excluded: chain E residue 1654 SER Chi-restraints excluded: chain E residue 1656 VAL Chi-restraints excluded: chain E residue 1669 CYS Chi-restraints excluded: chain G residue 6 ASN Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 29 MET Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain I residue 382 HIS Chi-restraints excluded: chain I residue 384 ASP Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain J residue 305 ASN Chi-restraints excluded: chain J residue 331 PHE Chi-restraints excluded: chain J residue 383 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 453 optimal weight: 0.0030 chunk 292 optimal weight: 1.9990 chunk 437 optimal weight: 0.9980 chunk 220 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 465 optimal weight: 0.9990 chunk 499 optimal weight: 1.9990 chunk 362 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 575 optimal weight: 0.9980 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 687 ASN ** F 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 59658 Z= 0.157 Angle : 0.506 9.378 80992 Z= 0.248 Chirality : 0.039 0.192 9400 Planarity : 0.003 0.058 10390 Dihedral : 3.718 53.154 8280 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.80 % Favored : 96.15 % Rotamer: Outliers : 3.04 % Allowed : 15.69 % Favored : 81.28 % 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: 0.94 (0.10), residues: 7536 helix: 1.61 (0.08), residues: 4596 sheet: 0.12 (0.29), residues: 354 loop : -1.11 (0.12), residues: 2586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A2429 HIS 0.006 0.001 HIS A2189 PHE 0.023 0.001 PHE B1322 TYR 0.036 0.001 TYR E 835 ARG 0.008 0.000 ARG E 182 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 6766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 678 time to evaluate : 4.944 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: B 304 MET cc_start: 0.5916 (tmm) cc_final: 0.5136 (tmm) REVERT: B 706 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7373 (pt0) REVERT: B 721 MET cc_start: 0.8361 (mmm) cc_final: 0.7971 (mtp) REVERT: B 827 MET cc_start: 0.8522 (mtm) cc_final: 0.8223 (mtp) REVERT: B 853 TYR cc_start: 0.8102 (OUTLIER) cc_final: 0.6733 (t80) REVERT: B 1291 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8096 (mm) REVERT: B 1481 MET cc_start: 0.8121 (mtt) cc_final: 0.7836 (mmm) REVERT: B 1565 ASP cc_start: 0.7930 (m-30) cc_final: 0.7261 (m-30) REVERT: B 1743 LEU cc_start: 0.8742 (tt) cc_final: 0.8283 (tp) REVERT: B 1747 MET cc_start: 0.8345 (mmm) cc_final: 0.7662 (mpp) REVERT: B 2357 ASP cc_start: 0.8250 (t0) cc_final: 0.8010 (t0) REVERT: D 158 LYS cc_start: 0.5902 (tptt) cc_final: 0.5205 (mmmm) REVERT: D 245 LYS cc_start: 0.6827 (mmtt) cc_final: 0.6506 (mmtt) REVERT: D 297 TRP cc_start: 0.8147 (m100) cc_final: 0.7662 (m-10) REVERT: F 177 LEU cc_start: 0.8801 (tp) cc_final: 0.8545 (mp) REVERT: F 594 ASP cc_start: 0.8114 (m-30) cc_final: 0.7541 (t0) REVERT: F 775 ASP cc_start: 0.8705 (t70) cc_final: 0.8505 (t0) REVERT: F 1621 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8814 (tp) REVERT: F 1633 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7027 (mp0) REVERT: H 94 ARG cc_start: 0.7835 (ttm110) cc_final: 0.7325 (ttm170) REVERT: H 104 LYS cc_start: 0.8136 (ttmm) cc_final: 0.7909 (ttpp) REVERT: A 617 GLU cc_start: 0.7168 (tm-30) cc_final: 0.6871 (mp0) REVERT: A 668 ASP cc_start: 0.7549 (p0) cc_final: 0.7246 (p0) REVERT: A 680 ASP cc_start: 0.8143 (p0) cc_final: 0.7797 (t0) REVERT: A 752 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7885 (mt0) REVERT: A 1066 GLU cc_start: 0.7476 (pt0) cc_final: 0.7126 (pt0) REVERT: A 1269 TRP cc_start: 0.7644 (m100) cc_final: 0.6964 (m100) REVERT: A 1313 MET cc_start: 0.8866 (tmm) cc_final: 0.7739 (tmm) REVERT: A 1458 ASP cc_start: 0.7484 (m-30) cc_final: 0.7175 (m-30) REVERT: A 1478 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7935 (tt) REVERT: A 1503 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8149 (pt) REVERT: A 1515 MET cc_start: 0.8428 (mpp) cc_final: 0.8129 (mtp) REVERT: A 1676 LEU cc_start: 0.9030 (mm) cc_final: 0.8338 (mp) REVERT: A 1904 LEU cc_start: 0.8795 (tp) cc_final: 0.8554 (mt) REVERT: A 1947 ASP cc_start: 0.7257 (p0) cc_final: 0.7050 (p0) REVERT: A 2135 ASP cc_start: 0.7802 (t0) cc_final: 0.7462 (t0) REVERT: A 2161 GLN cc_start: 0.7406 (tm-30) cc_final: 0.7159 (tm-30) REVERT: A 2424 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8424 (m-30) REVERT: E 38 LEU cc_start: 0.8571 (mt) cc_final: 0.8310 (tp) REVERT: E 42 LEU cc_start: 0.8760 (mt) cc_final: 0.8455 (mt) REVERT: E 83 ASP cc_start: 0.7757 (m-30) cc_final: 0.7405 (t70) REVERT: E 213 LYS cc_start: 0.8244 (mtmt) cc_final: 0.7462 (tttm) REVERT: E 225 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6987 (mt-10) REVERT: E 240 THR cc_start: 0.9496 (OUTLIER) cc_final: 0.9123 (p) REVERT: E 366 ASP cc_start: 0.7847 (m-30) cc_final: 0.7290 (t0) REVERT: E 414 ASN cc_start: 0.8324 (t0) cc_final: 0.8039 (t0) REVERT: E 520 ILE cc_start: 0.5573 (OUTLIER) cc_final: 0.5338 (mt) REVERT: E 528 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7220 (mp) REVERT: E 529 LEU cc_start: 0.8206 (mt) cc_final: 0.7296 (pp) REVERT: E 573 PHE cc_start: 0.6689 (t80) cc_final: 0.6407 (t80) REVERT: E 725 THR cc_start: 0.7167 (OUTLIER) cc_final: 0.6910 (p) REVERT: E 790 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.6764 (mpp) REVERT: G 6 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.8202 (m-40) REVERT: G 103 CYS cc_start: 0.7416 (t) cc_final: 0.6600 (t) REVERT: I 329 LYS cc_start: 0.7734 (ttmt) cc_final: 0.7308 (tttm) REVERT: I 331 PHE cc_start: 0.6446 (m-10) cc_final: 0.5922 (m-10) REVERT: I 391 LEU cc_start: 0.9291 (mt) cc_final: 0.8957 (tp) outliers start: 180 outliers final: 135 residues processed: 804 average time/residue: 0.5354 time to fit residues: 742.6405 Evaluate side-chains 789 residues out of total 6766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 641 time to evaluate : 5.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 725 PHE Chi-restraints excluded: chain B residue 752 GLN Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 944 ASP Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1075 ILE Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1136 LEU Chi-restraints excluded: chain B residue 1172 THR Chi-restraints excluded: chain B residue 1213 ILE Chi-restraints excluded: chain B residue 1221 THR Chi-restraints excluded: chain B residue 1291 LEU Chi-restraints excluded: chain B residue 1313 MET Chi-restraints excluded: chain B residue 1337 LEU Chi-restraints excluded: chain B residue 1338 ILE Chi-restraints excluded: chain B residue 1377 ASP Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1638 MET Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1692 VAL Chi-restraints excluded: chain B residue 1962 THR Chi-restraints excluded: chain B residue 2050 VAL Chi-restraints excluded: chain B residue 2057 MET Chi-restraints excluded: chain B residue 2151 ILE Chi-restraints excluded: chain B residue 2172 LEU Chi-restraints excluded: chain B residue 2240 VAL Chi-restraints excluded: chain B residue 2364 VAL Chi-restraints excluded: chain B residue 2375 ILE Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 397 SER Chi-restraints excluded: chain F residue 433 MET Chi-restraints excluded: chain F residue 460 ASP Chi-restraints excluded: chain F residue 524 THR Chi-restraints excluded: chain F residue 554 ILE Chi-restraints excluded: chain F residue 656 SER Chi-restraints excluded: chain F residue 663 ILE Chi-restraints excluded: chain F residue 687 ASN Chi-restraints excluded: chain F residue 689 CYS Chi-restraints excluded: chain F residue 693 ASN Chi-restraints excluded: chain F residue 783 ASN Chi-restraints excluded: chain F residue 795 SER Chi-restraints excluded: chain F residue 1000 LEU Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1621 ILE Chi-restraints excluded: chain H residue 6 ASN Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain H residue 107 GLN Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1155 ILE Chi-restraints excluded: chain A residue 1236 MET Chi-restraints excluded: chain A residue 1277 LYS Chi-restraints excluded: chain A residue 1341 ILE Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1437 MET Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1542 ASP Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1590 MET Chi-restraints excluded: chain A residue 1614 ILE Chi-restraints excluded: chain A residue 1644 VAL Chi-restraints excluded: chain A residue 1759 LEU Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2057 MET Chi-restraints excluded: chain A residue 2091 SER Chi-restraints excluded: chain A residue 2143 THR Chi-restraints excluded: chain A residue 2147 ASN Chi-restraints excluded: chain A residue 2172 LEU Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain A residue 2333 ILE Chi-restraints excluded: chain A residue 2424 ASP Chi-restraints excluded: chain A residue 2548 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 451 THR Chi-restraints excluded: chain E residue 460 ASP Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 551 ILE Chi-restraints excluded: chain E residue 606 CYS Chi-restraints excluded: chain E residue 693 ASN Chi-restraints excluded: chain E residue 725 THR Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain E residue 790 MET Chi-restraints excluded: chain E residue 796 HIS Chi-restraints excluded: chain E residue 978 THR Chi-restraints excluded: chain E residue 1003 VAL Chi-restraints excluded: chain E residue 1516 THR Chi-restraints excluded: chain E residue 1628 SER Chi-restraints excluded: chain E residue 1654 SER Chi-restraints excluded: chain E residue 1656 VAL Chi-restraints excluded: chain E residue 1669 CYS Chi-restraints excluded: chain G residue 6 ASN Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 29 MET Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain I residue 382 HIS Chi-restraints excluded: chain I residue 384 ASP Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain J residue 305 ASN Chi-restraints excluded: chain J residue 331 PHE Chi-restraints excluded: chain J residue 383 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 666 optimal weight: 0.1980 chunk 701 optimal weight: 4.9990 chunk 640 optimal weight: 0.9980 chunk 682 optimal weight: 0.8980 chunk 410 optimal weight: 20.0000 chunk 297 optimal weight: 2.9990 chunk 536 optimal weight: 0.9980 chunk 209 optimal weight: 0.9990 chunk 616 optimal weight: 9.9990 chunk 645 optimal weight: 1.9990 chunk 680 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 687 ASN ** F 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 59658 Z= 0.160 Angle : 0.518 10.938 80992 Z= 0.253 Chirality : 0.039 0.152 9400 Planarity : 0.003 0.056 10390 Dihedral : 3.721 53.192 8280 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.85 % Favored : 96.10 % Rotamer: Outliers : 2.70 % Allowed : 16.11 % Favored : 81.19 % 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: 0.99 (0.10), residues: 7536 helix: 1.65 (0.08), residues: 4584 sheet: 0.13 (0.29), residues: 344 loop : -1.08 (0.12), residues: 2608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP D 99 HIS 0.008 0.001 HIS D 94 PHE 0.017 0.001 PHE B1322 TYR 0.032 0.001 TYR E 835 ARG 0.008 0.000 ARG E 182 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 6766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 665 time to evaluate : 5.010 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 304 MET cc_start: 0.5930 (tmm) cc_final: 0.5162 (tmm) REVERT: B 706 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7386 (pt0) REVERT: B 721 MET cc_start: 0.8379 (mmm) cc_final: 0.8003 (mtp) REVERT: B 827 MET cc_start: 0.8553 (mtm) cc_final: 0.8167 (mtp) REVERT: B 853 TYR cc_start: 0.8141 (OUTLIER) cc_final: 0.6858 (t80) REVERT: B 1291 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8077 (mm) REVERT: B 1565 ASP cc_start: 0.7890 (m-30) cc_final: 0.7348 (m-30) REVERT: B 1743 LEU cc_start: 0.8742 (tt) cc_final: 0.8309 (tp) REVERT: B 1747 MET cc_start: 0.8383 (mmm) cc_final: 0.7698 (mpp) REVERT: D 158 LYS cc_start: 0.5911 (tptt) cc_final: 0.5210 (mmmm) REVERT: D 245 LYS cc_start: 0.6907 (mmtt) cc_final: 0.6592 (mmtt) REVERT: D 297 TRP cc_start: 0.8168 (m100) cc_final: 0.7709 (m-10) REVERT: F 177 LEU cc_start: 0.8776 (tp) cc_final: 0.8547 (mp) REVERT: F 594 ASP cc_start: 0.8112 (m-30) cc_final: 0.7448 (t0) REVERT: F 775 ASP cc_start: 0.8705 (t70) cc_final: 0.8503 (t0) REVERT: F 1621 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8800 (tp) REVERT: F 1633 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7052 (mp0) REVERT: H 94 ARG cc_start: 0.7837 (ttm110) cc_final: 0.7335 (ttm170) REVERT: H 104 LYS cc_start: 0.8152 (ttmm) cc_final: 0.7907 (ttpp) REVERT: A 668 ASP cc_start: 0.7562 (p0) cc_final: 0.7259 (p0) REVERT: A 680 ASP cc_start: 0.8189 (p0) cc_final: 0.7828 (t0) REVERT: A 752 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7890 (mt0) REVERT: A 1066 GLU cc_start: 0.7471 (pt0) cc_final: 0.7136 (pt0) REVERT: A 1269 TRP cc_start: 0.7650 (m100) cc_final: 0.6965 (m100) REVERT: A 1313 MET cc_start: 0.8858 (tmm) cc_final: 0.7725 (tmm) REVERT: A 1458 ASP cc_start: 0.7517 (m-30) cc_final: 0.7216 (m-30) REVERT: A 1478 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7947 (tt) REVERT: A 1503 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8161 (pt) REVERT: A 1515 MET cc_start: 0.8426 (mpp) cc_final: 0.8141 (mtp) REVERT: A 1904 LEU cc_start: 0.8793 (tp) cc_final: 0.8578 (mt) REVERT: A 1947 ASP cc_start: 0.7283 (p0) cc_final: 0.7063 (p0) REVERT: A 2135 ASP cc_start: 0.7799 (t0) cc_final: 0.7454 (t0) REVERT: A 2424 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8429 (m-30) REVERT: E 38 LEU cc_start: 0.8574 (mt) cc_final: 0.8312 (tp) REVERT: E 42 LEU cc_start: 0.8762 (mt) cc_final: 0.8459 (mt) REVERT: E 83 ASP cc_start: 0.7818 (m-30) cc_final: 0.7404 (t70) REVERT: E 213 LYS cc_start: 0.8273 (mtmt) cc_final: 0.7530 (tttm) REVERT: E 225 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6990 (mt-10) REVERT: E 240 THR cc_start: 0.9496 (OUTLIER) cc_final: 0.9118 (p) REVERT: E 366 ASP cc_start: 0.7835 (m-30) cc_final: 0.7255 (t0) REVERT: E 414 ASN cc_start: 0.8375 (t0) cc_final: 0.8110 (t0) REVERT: E 520 ILE cc_start: 0.5584 (OUTLIER) cc_final: 0.5289 (mt) REVERT: E 528 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7179 (mp) REVERT: E 529 LEU cc_start: 0.8202 (mt) cc_final: 0.7293 (pp) REVERT: E 573 PHE cc_start: 0.6702 (t80) cc_final: 0.6410 (t80) REVERT: E 671 HIS cc_start: 0.6972 (p-80) cc_final: 0.6521 (p-80) REVERT: E 725 THR cc_start: 0.7168 (OUTLIER) cc_final: 0.6910 (p) REVERT: E 790 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.6758 (mpp) REVERT: G 6 ASN cc_start: 0.8392 (OUTLIER) cc_final: 0.8105 (m-40) REVERT: G 103 CYS cc_start: 0.7470 (t) cc_final: 0.6717 (t) REVERT: I 331 PHE cc_start: 0.6293 (m-10) cc_final: 0.5484 (m-10) REVERT: I 391 LEU cc_start: 0.9291 (mt) cc_final: 0.8963 (tp) REVERT: J 366 MET cc_start: 0.7080 (tpp) cc_final: 0.6772 (tpp) outliers start: 160 outliers final: 134 residues processed: 781 average time/residue: 0.5753 time to fit residues: 775.9079 Evaluate side-chains 787 residues out of total 6766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 640 time to evaluate : 4.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 725 PHE Chi-restraints excluded: chain B residue 752 GLN Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 944 ASP Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1075 ILE Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1136 LEU Chi-restraints excluded: chain B residue 1172 THR Chi-restraints excluded: chain B residue 1213 ILE Chi-restraints excluded: chain B residue 1221 THR Chi-restraints excluded: chain B residue 1291 LEU Chi-restraints excluded: chain B residue 1313 MET Chi-restraints excluded: chain B residue 1337 LEU Chi-restraints excluded: chain B residue 1377 ASP Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1552 LEU Chi-restraints excluded: chain B residue 1638 MET Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1692 VAL Chi-restraints excluded: chain B residue 2050 VAL Chi-restraints excluded: chain B residue 2057 MET Chi-restraints excluded: chain B residue 2151 ILE Chi-restraints excluded: chain B residue 2172 LEU Chi-restraints excluded: chain B residue 2240 VAL Chi-restraints excluded: chain B residue 2364 VAL Chi-restraints excluded: chain B residue 2375 ILE Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 397 SER Chi-restraints excluded: chain F residue 433 MET Chi-restraints excluded: chain F residue 460 ASP Chi-restraints excluded: chain F residue 505 HIS Chi-restraints excluded: chain F residue 524 THR Chi-restraints excluded: chain F residue 554 ILE Chi-restraints excluded: chain F residue 656 SER Chi-restraints excluded: chain F residue 663 ILE Chi-restraints excluded: chain F residue 689 CYS Chi-restraints excluded: chain F residue 722 THR Chi-restraints excluded: chain F residue 783 ASN Chi-restraints excluded: chain F residue 795 SER Chi-restraints excluded: chain F residue 1000 LEU Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1621 ILE Chi-restraints excluded: chain H residue 6 ASN Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain H residue 107 GLN Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1048 ILE Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1155 ILE Chi-restraints excluded: chain A residue 1236 MET Chi-restraints excluded: chain A residue 1277 LYS Chi-restraints excluded: chain A residue 1341 ILE Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1542 ASP Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1590 MET Chi-restraints excluded: chain A residue 1614 ILE Chi-restraints excluded: chain A residue 1644 VAL Chi-restraints excluded: chain A residue 1663 SER Chi-restraints excluded: chain A residue 1759 LEU Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2057 MET Chi-restraints excluded: chain A residue 2091 SER Chi-restraints excluded: chain A residue 2143 THR Chi-restraints excluded: chain A residue 2147 ASN Chi-restraints excluded: chain A residue 2172 LEU Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain A residue 2424 ASP Chi-restraints excluded: chain A residue 2548 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 451 THR Chi-restraints excluded: chain E residue 460 ASP Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 551 ILE Chi-restraints excluded: chain E residue 606 CYS Chi-restraints excluded: chain E residue 693 ASN Chi-restraints excluded: chain E residue 725 THR Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain E residue 790 MET Chi-restraints excluded: chain E residue 796 HIS Chi-restraints excluded: chain E residue 940 LEU Chi-restraints excluded: chain E residue 978 THR Chi-restraints excluded: chain E residue 1003 VAL Chi-restraints excluded: chain E residue 1516 THR Chi-restraints excluded: chain E residue 1628 SER Chi-restraints excluded: chain E residue 1654 SER Chi-restraints excluded: chain E residue 1656 VAL Chi-restraints excluded: chain E residue 1669 CYS Chi-restraints excluded: chain G residue 6 ASN Chi-restraints excluded: chain G residue 29 MET Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain I residue 384 ASP Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain J residue 305 ASN Chi-restraints excluded: chain J residue 331 PHE Chi-restraints excluded: chain J residue 383 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 448 optimal weight: 0.9980 chunk 721 optimal weight: 0.6980 chunk 440 optimal weight: 0.6980 chunk 342 optimal weight: 0.0010 chunk 501 optimal weight: 0.8980 chunk 757 optimal weight: 5.9990 chunk 696 optimal weight: 4.9990 chunk 602 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 465 optimal weight: 2.9990 chunk 369 optimal weight: 40.0000 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 687 ASN ** F 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 671 HIS ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 59658 Z= 0.148 Angle : 0.517 11.126 80992 Z= 0.252 Chirality : 0.039 0.232 9400 Planarity : 0.003 0.053 10390 Dihedral : 3.693 53.625 8280 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.83 % Favored : 96.11 % Rotamer: Outliers : 2.56 % Allowed : 16.31 % Favored : 81.12 % 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: 1.01 (0.10), residues: 7536 helix: 1.67 (0.08), residues: 4586 sheet: 0.16 (0.29), residues: 344 loop : -1.08 (0.12), residues: 2606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP D 99 HIS 0.009 0.001 HIS G 34 PHE 0.018 0.001 PHE B1322 TYR 0.032 0.001 TYR E 835 ARG 0.009 0.000 ARG E 182 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 6766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 655 time to evaluate : 5.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 304 MET cc_start: 0.5911 (tmm) cc_final: 0.5252 (tmm) REVERT: B 706 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7355 (pt0) REVERT: B 721 MET cc_start: 0.8379 (mmm) cc_final: 0.8013 (mtp) REVERT: B 827 MET cc_start: 0.8524 (mtm) cc_final: 0.8137 (mtp) REVERT: B 853 TYR cc_start: 0.8155 (OUTLIER) cc_final: 0.6930 (t80) REVERT: B 1285 ARG cc_start: 0.7655 (ttt90) cc_final: 0.7332 (mtp-110) REVERT: B 1291 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8020 (mm) REVERT: B 1565 ASP cc_start: 0.7961 (m-30) cc_final: 0.7398 (m-30) REVERT: B 1743 LEU cc_start: 0.8708 (tt) cc_final: 0.8269 (tp) REVERT: B 1747 MET cc_start: 0.8591 (mmm) cc_final: 0.7790 (mpp) REVERT: D 67 MET cc_start: 0.7698 (ptp) cc_final: 0.7428 (ptp) REVERT: D 158 LYS cc_start: 0.6144 (tptt) cc_final: 0.5440 (mmmm) REVERT: D 245 LYS cc_start: 0.6929 (mmtt) cc_final: 0.6701 (mmtt) REVERT: D 297 TRP cc_start: 0.8156 (m100) cc_final: 0.7691 (m-10) REVERT: D 307 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7857 (pp20) REVERT: F 177 LEU cc_start: 0.8782 (tp) cc_final: 0.8539 (mp) REVERT: F 594 ASP cc_start: 0.8140 (m-30) cc_final: 0.7493 (t0) REVERT: F 1621 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8812 (tp) REVERT: H 91 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7914 (mp0) REVERT: H 94 ARG cc_start: 0.7867 (ttm110) cc_final: 0.7448 (ttm170) REVERT: A 668 ASP cc_start: 0.7552 (p0) cc_final: 0.7250 (p0) REVERT: A 680 ASP cc_start: 0.8210 (p0) cc_final: 0.7857 (t0) REVERT: A 752 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7921 (mt0) REVERT: A 1066 GLU cc_start: 0.7448 (pt0) cc_final: 0.7107 (pt0) REVERT: A 1269 TRP cc_start: 0.7629 (m100) cc_final: 0.6946 (m100) REVERT: A 1313 MET cc_start: 0.8846 (tmm) cc_final: 0.7710 (tmm) REVERT: A 1458 ASP cc_start: 0.7518 (m-30) cc_final: 0.7205 (m-30) REVERT: A 1478 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7943 (tt) REVERT: A 1503 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8175 (pt) REVERT: A 1515 MET cc_start: 0.8416 (mpp) cc_final: 0.8109 (mtp) REVERT: A 1947 ASP cc_start: 0.7254 (p0) cc_final: 0.7039 (p0) REVERT: A 2135 ASP cc_start: 0.7838 (t0) cc_final: 0.7491 (t0) REVERT: A 2424 ASP cc_start: 0.8626 (OUTLIER) cc_final: 0.8416 (m-30) REVERT: E 38 LEU cc_start: 0.8577 (mt) cc_final: 0.8312 (tp) REVERT: E 42 LEU cc_start: 0.8761 (mt) cc_final: 0.8457 (mt) REVERT: E 83 ASP cc_start: 0.7821 (m-30) cc_final: 0.7325 (t70) REVERT: E 213 LYS cc_start: 0.8240 (mtmt) cc_final: 0.7475 (tttm) REVERT: E 225 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6988 (mt-10) REVERT: E 240 THR cc_start: 0.9487 (OUTLIER) cc_final: 0.9105 (p) REVERT: E 366 ASP cc_start: 0.7829 (m-30) cc_final: 0.7271 (t0) REVERT: E 414 ASN cc_start: 0.8370 (t0) cc_final: 0.8110 (t0) REVERT: E 520 ILE cc_start: 0.5583 (OUTLIER) cc_final: 0.5290 (mt) REVERT: E 528 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7220 (mp) REVERT: E 529 LEU cc_start: 0.8196 (mt) cc_final: 0.7283 (pp) REVERT: E 671 HIS cc_start: 0.6676 (p90) cc_final: 0.6076 (p90) REVERT: E 725 THR cc_start: 0.7138 (OUTLIER) cc_final: 0.6886 (p) REVERT: E 790 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.6754 (mpp) REVERT: G 6 ASN cc_start: 0.8417 (OUTLIER) cc_final: 0.8124 (m-40) REVERT: G 103 CYS cc_start: 0.7460 (t) cc_final: 0.6715 (t) REVERT: I 331 PHE cc_start: 0.6495 (m-10) cc_final: 0.6062 (m-10) REVERT: I 391 LEU cc_start: 0.9288 (mt) cc_final: 0.8962 (tp) REVERT: J 366 MET cc_start: 0.7163 (tpp) cc_final: 0.6961 (tpp) outliers start: 152 outliers final: 127 residues processed: 761 average time/residue: 0.5333 time to fit residues: 699.0216 Evaluate side-chains 778 residues out of total 6766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 636 time to evaluate : 5.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 725 PHE Chi-restraints excluded: chain B residue 752 GLN Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 944 ASP Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1075 ILE Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1136 LEU Chi-restraints excluded: chain B residue 1172 THR Chi-restraints excluded: chain B residue 1213 ILE Chi-restraints excluded: chain B residue 1221 THR Chi-restraints excluded: chain B residue 1291 LEU Chi-restraints excluded: chain B residue 1313 MET Chi-restraints excluded: chain B residue 1337 LEU Chi-restraints excluded: chain B residue 1377 ASP Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1552 LEU Chi-restraints excluded: chain B residue 1638 MET Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1692 VAL Chi-restraints excluded: chain B residue 2050 VAL Chi-restraints excluded: chain B residue 2172 LEU Chi-restraints excluded: chain B residue 2240 VAL Chi-restraints excluded: chain B residue 2364 VAL Chi-restraints excluded: chain B residue 2375 ILE Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 307 GLU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 397 SER Chi-restraints excluded: chain F residue 433 MET Chi-restraints excluded: chain F residue 460 ASP Chi-restraints excluded: chain F residue 505 HIS Chi-restraints excluded: chain F residue 524 THR Chi-restraints excluded: chain F residue 554 ILE Chi-restraints excluded: chain F residue 656 SER Chi-restraints excluded: chain F residue 663 ILE Chi-restraints excluded: chain F residue 687 ASN Chi-restraints excluded: chain F residue 689 CYS Chi-restraints excluded: chain F residue 693 ASN Chi-restraints excluded: chain F residue 722 THR Chi-restraints excluded: chain F residue 783 ASN Chi-restraints excluded: chain F residue 795 SER Chi-restraints excluded: chain F residue 1000 LEU Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1621 ILE Chi-restraints excluded: chain H residue 6 ASN Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain H residue 107 GLN Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1155 ILE Chi-restraints excluded: chain A residue 1236 MET Chi-restraints excluded: chain A residue 1277 LYS Chi-restraints excluded: chain A residue 1341 ILE Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1542 ASP Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1590 MET Chi-restraints excluded: chain A residue 1614 ILE Chi-restraints excluded: chain A residue 1644 VAL Chi-restraints excluded: chain A residue 1663 SER Chi-restraints excluded: chain A residue 1759 LEU Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2091 SER Chi-restraints excluded: chain A residue 2147 ASN Chi-restraints excluded: chain A residue 2172 LEU Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain A residue 2333 ILE Chi-restraints excluded: chain A residue 2424 ASP Chi-restraints excluded: chain A residue 2548 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 451 THR Chi-restraints excluded: chain E residue 460 ASP Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 551 ILE Chi-restraints excluded: chain E residue 606 CYS Chi-restraints excluded: chain E residue 725 THR Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain E residue 790 MET Chi-restraints excluded: chain E residue 796 HIS Chi-restraints excluded: chain E residue 940 LEU Chi-restraints excluded: chain E residue 978 THR Chi-restraints excluded: chain E residue 1003 VAL Chi-restraints excluded: chain E residue 1516 THR Chi-restraints excluded: chain E residue 1628 SER Chi-restraints excluded: chain E residue 1654 SER Chi-restraints excluded: chain E residue 1656 VAL Chi-restraints excluded: chain E residue 1669 CYS Chi-restraints excluded: chain G residue 6 ASN Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 29 MET Chi-restraints excluded: chain G residue 34 HIS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain I residue 384 ASP Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain J residue 305 ASN Chi-restraints excluded: chain J residue 383 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.7995 > 50: distance: 57 - 62: 14.841 distance: 62 - 63: 6.599 distance: 63 - 64: 7.542 distance: 63 - 66: 27.484 distance: 64 - 65: 15.559 distance: 64 - 71: 23.730 distance: 66 - 67: 16.273 distance: 67 - 68: 15.910 distance: 68 - 69: 3.103 distance: 68 - 70: 45.035 distance: 71 - 72: 49.830 distance: 72 - 73: 41.564 distance: 72 - 75: 61.682 distance: 73 - 74: 8.463 distance: 73 - 79: 11.642 distance: 75 - 76: 61.164 distance: 76 - 77: 38.626 distance: 76 - 78: 36.779 distance: 79 - 80: 12.732 distance: 80 - 81: 18.766 distance: 80 - 83: 11.351 distance: 81 - 82: 20.349 distance: 81 - 90: 9.863 distance: 83 - 84: 13.426 distance: 84 - 85: 13.305 distance: 84 - 86: 7.411 distance: 85 - 87: 3.486 distance: 87 - 89: 9.329 distance: 88 - 89: 8.987 distance: 90 - 91: 7.638 distance: 91 - 92: 12.405 distance: 92 - 93: 12.146 distance: 92 - 94: 12.408 distance: 94 - 95: 23.995 distance: 95 - 96: 13.488 distance: 95 - 98: 8.343 distance: 96 - 97: 16.664 distance: 96 - 99: 9.935 distance: 99 - 100: 12.901 distance: 100 - 101: 22.312 distance: 100 - 103: 11.850 distance: 101 - 102: 11.351 distance: 101 - 107: 38.866 distance: 103 - 104: 23.247 distance: 104 - 105: 25.196 distance: 104 - 106: 18.944 distance: 107 - 108: 9.826 distance: 108 - 109: 16.364 distance: 108 - 111: 24.446 distance: 109 - 110: 17.723 distance: 109 - 115: 36.771 distance: 111 - 112: 18.071 distance: 112 - 113: 18.005 distance: 112 - 114: 41.977 distance: 115 - 116: 8.713 distance: 116 - 117: 36.161 distance: 116 - 119: 12.378 distance: 117 - 118: 22.857 distance: 117 - 123: 6.581 distance: 119 - 120: 34.957 distance: 120 - 121: 13.566 distance: 120 - 122: 11.141 distance: 123 - 124: 25.464 distance: 124 - 125: 23.721 distance: 124 - 127: 27.551 distance: 125 - 126: 15.886 distance: 125 - 131: 13.194 distance: 128 - 129: 28.604 distance: 128 - 130: 29.309 distance: 131 - 132: 38.798 distance: 132 - 133: 18.869 distance: 132 - 135: 8.712 distance: 133 - 134: 22.072 distance: 133 - 143: 22.624 distance: 135 - 136: 27.921 distance: 136 - 137: 56.003 distance: 136 - 138: 12.329 distance: 137 - 139: 19.855 distance: 138 - 140: 17.510 distance: 139 - 141: 15.542 distance: 140 - 141: 24.920 distance: 141 - 142: 6.696