Starting phenix.real_space_refine on Sun Apr 14 14:29:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qhd_18408/04_2024/8qhd_18408.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qhd_18408/04_2024/8qhd_18408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qhd_18408/04_2024/8qhd_18408.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qhd_18408/04_2024/8qhd_18408.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qhd_18408/04_2024/8qhd_18408.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qhd_18408/04_2024/8qhd_18408.pdb" } resolution = 3.6 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= 0.003 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 504 5.16 5 C 61404 2.51 5 N 16050 2.21 5 O 17390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ASP 26": "OD1" <-> "OD2" Residue "D TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 275": "OE1" <-> "OE2" Residue "D PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 728": "OE1" <-> "OE2" Residue "D GLU 772": "OE1" <-> "OE2" Residue "D GLU 796": "OE1" <-> "OE2" Residue "D ASP 910": "OD1" <-> "OD2" Residue "D TYR 1013": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1016": "OD1" <-> "OD2" Residue "D PHE 1406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1422": "OE1" <-> "OE2" Residue "D ASP 1446": "OD1" <-> "OD2" Residue "D PHE 1458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1523": "OD1" <-> "OD2" Residue "D TYR 1543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1860": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 2063": "NH1" <-> "NH2" Residue "D PHE 2069": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2086": "OE1" <-> "OE2" Residue "B TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 26": "OD1" <-> "OD2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 75": "OE1" <-> "OE2" Residue "B GLU 129": "OE1" <-> "OE2" Residue "B TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 602": "NH1" <-> "NH2" Residue "B TYR 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 894": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 911": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1040": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1091": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1260": "OD1" <-> "OD2" Residue "B PHE 1347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1583": "OE1" <-> "OE2" Residue "B ASP 1676": "OD1" <-> "OD2" Residue "B ASP 1865": "OD1" <-> "OD2" Residue "B TYR 2064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2082": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2121": "OE1" <-> "OE2" Residue "C TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 185": "NH1" <-> "NH2" Residue "C TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 707": "NH1" <-> "NH2" Residue "C GLU 851": "OE1" <-> "OE2" Residue "C GLU 909": "OE1" <-> "OE2" Residue "C ASP 972": "OD1" <-> "OD2" Residue "C ASP 1217": "OD1" <-> "OD2" Residue "C ASP 1285": "OD1" <-> "OD2" Residue "C GLU 1346": "OE1" <-> "OE2" Residue "C PHE 1349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1422": "OE1" <-> "OE2" Residue "C PHE 1436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1545": "OE1" <-> "OE2" Residue "C PHE 1733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 26": "OD1" <-> "OD2" Residue "F TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 275": "OE1" <-> "OE2" Residue "F PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 728": "OE1" <-> "OE2" Residue "F GLU 772": "OE1" <-> "OE2" Residue "F GLU 796": "OE1" <-> "OE2" Residue "F ASP 910": "OD1" <-> "OD2" Residue "F TYR 1013": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 1016": "OD1" <-> "OD2" Residue "F PHE 1406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1422": "OE1" <-> "OE2" Residue "F ASP 1446": "OD1" <-> "OD2" Residue "F PHE 1458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 1523": "OD1" <-> "OD2" Residue "F TYR 1543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1860": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 2063": "NH1" <-> "NH2" Residue "F PHE 2069": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 2086": "OE1" <-> "OE2" Residue "A TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 26": "OD1" <-> "OD2" Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A GLU 129": "OE1" <-> "OE2" Residue "A TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 602": "NH1" <-> "NH2" Residue "A TYR 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 894": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 911": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1040": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1091": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1260": "OD1" <-> "OD2" Residue "A PHE 1347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1583": "OE1" <-> "OE2" Residue "A ASP 1676": "OD1" <-> "OD2" Residue "A ASP 1865": "OD1" <-> "OD2" Residue "A TYR 2064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2082": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2121": "OE1" <-> "OE2" Residue "E TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 185": "NH1" <-> "NH2" Residue "E TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 202": "OE1" <-> "OE2" Residue "E PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 707": "NH1" <-> "NH2" Residue "E GLU 851": "OE1" <-> "OE2" Residue "E GLU 909": "OE1" <-> "OE2" Residue "E ASP 972": "OD1" <-> "OD2" Residue "E ASP 1217": "OD1" <-> "OD2" Residue "E ASP 1285": "OD1" <-> "OD2" Residue "E GLU 1346": "OE1" <-> "OE2" Residue "E PHE 1349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1422": "OE1" <-> "OE2" Residue "E PHE 1436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1545": "OE1" <-> "OE2" Residue "E PHE 1733": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 95348 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 16400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2030, 16400 Classifications: {'peptide': 2030} Link IDs: {'PTRANS': 70, 'TRANS': 1959} Chain breaks: 6 Chain: "B" Number of atoms: 15128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1873, 15128 Classifications: {'peptide': 1873} Link IDs: {'PTRANS': 69, 'TRANS': 1803} Chain breaks: 9 Chain: "C" Number of atoms: 16146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1999, 16146 Classifications: {'peptide': 1999} Link IDs: {'PTRANS': 70, 'TRANS': 1928} Chain breaks: 10 Chain: "F" Number of atoms: 16400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2030, 16400 Classifications: {'peptide': 2030} Link IDs: {'PTRANS': 70, 'TRANS': 1959} Chain breaks: 6 Chain: "A" Number of atoms: 15128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1873, 15128 Classifications: {'peptide': 1873} Link IDs: {'PTRANS': 69, 'TRANS': 1803} Chain breaks: 9 Chain: "E" Number of atoms: 16146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1999, 16146 Classifications: {'peptide': 1999} Link IDs: {'PTRANS': 70, 'TRANS': 1928} Chain breaks: 10 Time building chain proxies: 36.06, per 1000 atoms: 0.38 Number of scatterers: 95348 At special positions: 0 Unit cell: (272.675, 270.997, 180.385, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 504 16.00 O 17390 8.00 N 16050 7.00 C 61404 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 28.86 Conformation dependent library (CDL) restraints added in 12.6 seconds 23384 Ramachandran restraints generated. 11692 Oldfield, 0 Emsley, 11692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 22556 Finding SS restraints... Secondary structure from input PDB file: 548 helices and 110 sheets defined 58.2% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.58 Creating SS restraints... Processing helix chain 'D' and resid 1 through 12 Processing helix chain 'D' and resid 20 through 48 Processing helix chain 'D' and resid 56 through 64 Processing helix chain 'D' and resid 67 through 76 removed outlier: 3.715A pdb=" N ILE D 71 " --> pdb=" O PRO D 67 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS D 76 " --> pdb=" O THR D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 94 Processing helix chain 'D' and resid 116 through 146 removed outlier: 5.115A pdb=" N ALA D 130 " --> pdb=" O LEU D 126 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N GLY D 131 " --> pdb=" O LYS D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 172 Processing helix chain 'D' and resid 176 through 197 removed outlier: 3.578A pdb=" N VAL D 180 " --> pdb=" O ARG D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 202 No H-bonds generated for 'chain 'D' and resid 200 through 202' Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 239 through 252 removed outlier: 3.739A pdb=" N LEU D 243 " --> pdb=" O ASN D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 282 Processing helix chain 'D' and resid 306 through 322 removed outlier: 3.880A pdb=" N ARG D 316 " --> pdb=" O ILE D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 343 Processing helix chain 'D' and resid 345 through 352 Processing helix chain 'D' and resid 379 through 391 Processing helix chain 'D' and resid 409 through 429 Processing helix chain 'D' and resid 450 through 458 Processing helix chain 'D' and resid 458 through 463 Processing helix chain 'D' and resid 463 through 469 removed outlier: 4.310A pdb=" N LYS D 469 " --> pdb=" O ASP D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 490 removed outlier: 3.936A pdb=" N HIS D 474 " --> pdb=" O THR D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 491 through 496 removed outlier: 4.747A pdb=" N LYS D 496 " --> pdb=" O LEU D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 572 Processing helix chain 'D' and resid 572 through 593 Processing helix chain 'D' and resid 597 through 614 Processing helix chain 'D' and resid 616 through 635 removed outlier: 3.867A pdb=" N TYR D 628 " --> pdb=" O ASP D 624 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE D 630 " --> pdb=" O LEU D 626 " (cutoff:3.500A) Proline residue: D 631 - end of helix Processing helix chain 'D' and resid 639 through 649 removed outlier: 3.637A pdb=" N LEU D 643 " --> pdb=" O GLY D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 675 removed outlier: 3.648A pdb=" N VAL D 658 " --> pdb=" O SER D 654 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN D 675 " --> pdb=" O LEU D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 726 removed outlier: 4.001A pdb=" N LEU D 716 " --> pdb=" O HIS D 712 " (cutoff:3.500A) Processing helix chain 'D' and resid 730 through 733 Processing helix chain 'D' and resid 734 through 760 Processing helix chain 'D' and resid 760 through 767 removed outlier: 3.585A pdb=" N VAL D 764 " --> pdb=" O GLY D 760 " (cutoff:3.500A) Processing helix chain 'D' and resid 769 through 777 Processing helix chain 'D' and resid 786 through 802 removed outlier: 3.810A pdb=" N VAL D 800 " --> pdb=" O GLU D 796 " (cutoff:3.500A) Processing helix chain 'D' and resid 804 through 814 Processing helix chain 'D' and resid 820 through 828 removed outlier: 3.557A pdb=" N SER D 823 " --> pdb=" O PRO D 820 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN D 824 " --> pdb=" O TYR D 821 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N THR D 825 " --> pdb=" O PHE D 822 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG D 826 " --> pdb=" O SER D 823 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN D 827 " --> pdb=" O GLN D 824 " (cutoff:3.500A) Processing helix chain 'D' and resid 848 through 859 Processing helix chain 'D' and resid 864 through 872 Processing helix chain 'D' and resid 898 through 917 Processing helix chain 'D' and resid 918 through 920 No H-bonds generated for 'chain 'D' and resid 918 through 920' Processing helix chain 'D' and resid 930 through 948 removed outlier: 4.273A pdb=" N ALA D 934 " --> pdb=" O LYS D 930 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE D 935 " --> pdb=" O LYS D 931 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY D 948 " --> pdb=" O ARG D 944 " (cutoff:3.500A) Processing helix chain 'D' and resid 983 through 991 removed outlier: 4.312A pdb=" N ARG D 987 " --> pdb=" O ALA D 983 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE D 988 " --> pdb=" O LYS D 984 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N MET D 991 " --> pdb=" O ARG D 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 999 through 1013 removed outlier: 3.813A pdb=" N ASN D1003 " --> pdb=" O ASN D 999 " (cutoff:3.500A) Processing helix chain 'D' and resid 1020 through 1029 Processing helix chain 'D' and resid 1034 through 1044 removed outlier: 3.688A pdb=" N PHE D1044 " --> pdb=" O PHE D1040 " (cutoff:3.500A) Processing helix chain 'D' and resid 1061 through 1084 Processing helix chain 'D' and resid 1114 through 1126 Processing helix chain 'D' and resid 1127 through 1132 removed outlier: 5.879A pdb=" N HIS D1130 " --> pdb=" O GLY D1127 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TRP D1131 " --> pdb=" O HIS D1128 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE D1132 " --> pdb=" O LEU D1129 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1127 through 1132' Processing helix chain 'D' and resid 1138 through 1153 removed outlier: 3.535A pdb=" N GLY D1153 " --> pdb=" O ILE D1149 " (cutoff:3.500A) Processing helix chain 'D' and resid 1168 through 1181 Processing helix chain 'D' and resid 1184 through 1195 removed outlier: 4.031A pdb=" N ILE D1188 " --> pdb=" O PRO D1184 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU D1193 " --> pdb=" O LEU D1189 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N SER D1194 " --> pdb=" O LEU D1190 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASP D1195 " --> pdb=" O GLY D1191 " (cutoff:3.500A) Processing helix chain 'D' and resid 1200 through 1219 Processing helix chain 'D' and resid 1221 through 1241 Processing helix chain 'D' and resid 1249 through 1253 Processing helix chain 'D' and resid 1272 through 1279 Processing helix chain 'D' and resid 1282 through 1297 Processing helix chain 'D' and resid 1302 through 1319 Processing helix chain 'D' and resid 1322 through 1326 Processing helix chain 'D' and resid 1349 through 1353 removed outlier: 3.637A pdb=" N MET D1352 " --> pdb=" O PHE D1349 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TYR D1353 " --> pdb=" O ALA D1350 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1349 through 1353' Processing helix chain 'D' and resid 1354 through 1365 Processing helix chain 'D' and resid 1366 through 1370 Processing helix chain 'D' and resid 1375 through 1388 removed outlier: 4.027A pdb=" N ILE D1381 " --> pdb=" O ASP D1377 " (cutoff:3.500A) Processing helix chain 'D' and resid 1389 through 1397 Processing helix chain 'D' and resid 1402 through 1412 removed outlier: 4.404A pdb=" N PHE D1406 " --> pdb=" O LEU D1402 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG D1407 " --> pdb=" O GLN D1403 " (cutoff:3.500A) Processing helix chain 'D' and resid 1425 through 1439 removed outlier: 3.728A pdb=" N ASN D1439 " --> pdb=" O SER D1435 " (cutoff:3.500A) Processing helix chain 'D' and resid 1443 through 1455 Processing helix chain 'D' and resid 1463 through 1470 Processing helix chain 'D' and resid 1502 through 1512 Processing helix chain 'D' and resid 1514 through 1525 Processing helix chain 'D' and resid 1527 through 1529 No H-bonds generated for 'chain 'D' and resid 1527 through 1529' Processing helix chain 'D' and resid 1530 through 1546 Processing helix chain 'D' and resid 1552 through 1564 Proline residue: D1561 - end of helix Processing helix chain 'D' and resid 1581 through 1592 Processing helix chain 'D' and resid 1612 through 1642 removed outlier: 4.066A pdb=" N ARG D1616 " --> pdb=" O SER D1612 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LYS D1617 " --> pdb=" O ILE D1613 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN D1622 " --> pdb=" O GLU D1618 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN D1623 " --> pdb=" O ASP D1619 " (cutoff:3.500A) Processing helix chain 'D' and resid 1645 through 1651 Processing helix chain 'D' and resid 1660 through 1671 Processing helix chain 'D' and resid 1675 through 1677 No H-bonds generated for 'chain 'D' and resid 1675 through 1677' Processing helix chain 'D' and resid 1678 through 1690 Processing helix chain 'D' and resid 1693 through 1704 removed outlier: 3.595A pdb=" N GLN D1697 " --> pdb=" O TYR D1693 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D1704 " --> pdb=" O ALA D1700 " (cutoff:3.500A) Processing helix chain 'D' and resid 1759 through 1778 removed outlier: 3.501A pdb=" N LEU D1763 " --> pdb=" O GLN D1759 " (cutoff:3.500A) Processing helix chain 'D' and resid 1820 through 1823 Processing helix chain 'D' and resid 1867 through 1871 Processing helix chain 'D' and resid 1888 through 1894 Processing helix chain 'D' and resid 1896 through 1903 Processing helix chain 'D' and resid 1909 through 1918 Processing helix chain 'D' and resid 1923 through 1937 Processing helix chain 'D' and resid 2034 through 2041 Processing helix chain 'D' and resid 2054 through 2069 removed outlier: 3.686A pdb=" N ILE D2059 " --> pdb=" O PRO D2055 " (cutoff:3.500A) Processing helix chain 'D' and resid 2080 through 2092 removed outlier: 3.518A pdb=" N GLU D2086 " --> pdb=" O TYR D2082 " (cutoff:3.500A) Processing helix chain 'D' and resid 2094 through 2099 removed outlier: 3.766A pdb=" N VAL D2098 " --> pdb=" O TRP D2094 " (cutoff:3.500A) Processing helix chain 'D' and resid 2102 through 2116 removed outlier: 3.615A pdb=" N ASN D2115 " --> pdb=" O ASN D2111 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS D2116 " --> pdb=" O MET D2112 " (cutoff:3.500A) Processing helix chain 'D' and resid 2130 through 2142 Processing helix chain 'D' and resid 2145 through 2151 removed outlier: 4.239A pdb=" N SER D2149 " --> pdb=" O ASP D2145 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 13 removed outlier: 3.805A pdb=" N GLU B 13 " --> pdb=" O ASN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 48 removed outlier: 4.168A pdb=" N ILE B 43 " --> pdb=" O VAL B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 64 Processing helix chain 'B' and resid 67 through 75 Processing helix chain 'B' and resid 87 through 93 Processing helix chain 'B' and resid 116 through 146 removed outlier: 4.087A pdb=" N GLY B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 172 Processing helix chain 'B' and resid 176 through 197 Processing helix chain 'B' and resid 200 through 202 No H-bonds generated for 'chain 'B' and resid 200 through 202' Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 239 through 252 removed outlier: 3.992A pdb=" N LEU B 243 " --> pdb=" O ASN B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 282 Processing helix chain 'B' and resid 306 through 322 Processing helix chain 'B' and resid 328 through 343 Processing helix chain 'B' and resid 345 through 353 Processing helix chain 'B' and resid 374 through 378 Processing helix chain 'B' and resid 379 through 391 Processing helix chain 'B' and resid 409 through 428 removed outlier: 3.569A pdb=" N GLN B 413 " --> pdb=" O SER B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 463 removed outlier: 4.610A pdb=" N GLN B 460 " --> pdb=" O GLN B 456 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LYS B 461 " --> pdb=" O ASN B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 469 removed outlier: 4.312A pdb=" N LYS B 469 " --> pdb=" O ASP B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 490 removed outlier: 3.938A pdb=" N HIS B 474 " --> pdb=" O THR B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 571 Processing helix chain 'B' and resid 572 through 593 Processing helix chain 'B' and resid 597 through 614 Processing helix chain 'B' and resid 616 through 635 removed outlier: 3.852A pdb=" N TYR B 628 " --> pdb=" O ASP B 624 " (cutoff:3.500A) Proline residue: B 631 - end of helix removed outlier: 3.631A pdb=" N SER B 635 " --> pdb=" O PRO B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 643 Processing helix chain 'B' and resid 644 through 648 Processing helix chain 'B' and resid 654 through 678 removed outlier: 4.032A pdb=" N LYS B 676 " --> pdb=" O ALA B 672 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA B 677 " --> pdb=" O GLN B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 725 removed outlier: 4.084A pdb=" N LEU B 716 " --> pdb=" O HIS B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 733 Processing helix chain 'B' and resid 734 through 760 removed outlier: 3.502A pdb=" N GLU B 738 " --> pdb=" O ASN B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 766 removed outlier: 3.769A pdb=" N VAL B 764 " --> pdb=" O GLY B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 777 removed outlier: 3.843A pdb=" N LEU B 773 " --> pdb=" O MET B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 802 removed outlier: 3.892A pdb=" N VAL B 800 " --> pdb=" O GLU B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 814 Processing helix chain 'B' and resid 824 through 828 Processing helix chain 'B' and resid 848 through 859 Processing helix chain 'B' and resid 864 through 872 Processing helix chain 'B' and resid 898 through 919 removed outlier: 4.637A pdb=" N ASN B 918 " --> pdb=" O ALA B 914 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE B 919 " --> pdb=" O ILE B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 947 Processing helix chain 'B' and resid 983 through 991 removed outlier: 4.184A pdb=" N ARG B 987 " --> pdb=" O ALA B 983 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE B 988 " --> pdb=" O LYS B 984 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N MET B 991 " --> pdb=" O ARG B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 999 through 1013 Processing helix chain 'B' and resid 1020 through 1028 Processing helix chain 'B' and resid 1034 through 1044 removed outlier: 3.617A pdb=" N PHE B1044 " --> pdb=" O PHE B1040 " (cutoff:3.500A) Processing helix chain 'B' and resid 1061 through 1083 Processing helix chain 'B' and resid 1114 through 1126 Processing helix chain 'B' and resid 1128 through 1135 removed outlier: 4.527A pdb=" N SER B1133 " --> pdb=" O HIS B1130 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN B1135 " --> pdb=" O PHE B1132 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1152 removed outlier: 3.858A pdb=" N SER B1141 " --> pdb=" O GLU B1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 1168 through 1181 Processing helix chain 'B' and resid 1184 through 1192 removed outlier: 4.080A pdb=" N ILE B1188 " --> pdb=" O PRO B1184 " (cutoff:3.500A) Processing helix chain 'B' and resid 1199 through 1219 removed outlier: 3.951A pdb=" N ASP B1203 " --> pdb=" O LEU B1199 " (cutoff:3.500A) Processing helix chain 'B' and resid 1221 through 1241 Processing helix chain 'B' and resid 1249 through 1253 removed outlier: 3.690A pdb=" N ALA B1252 " --> pdb=" O HIS B1249 " (cutoff:3.500A) Processing helix chain 'B' and resid 1272 through 1279 Processing helix chain 'B' and resid 1282 through 1297 removed outlier: 3.789A pdb=" N LEU B1288 " --> pdb=" O SER B1284 " (cutoff:3.500A) Processing helix chain 'B' and resid 1304 through 1319 removed outlier: 3.742A pdb=" N LEU B1308 " --> pdb=" O MET B1304 " (cutoff:3.500A) Processing helix chain 'B' and resid 1326 through 1330 removed outlier: 3.721A pdb=" N PHE B1330 " --> pdb=" O LEU B1327 " (cutoff:3.500A) Processing helix chain 'B' and resid 1355 through 1366 Processing helix chain 'B' and resid 1375 through 1389 removed outlier: 4.361A pdb=" N ILE B1381 " --> pdb=" O ASP B1377 " (cutoff:3.500A) Processing helix chain 'B' and resid 1389 through 1397 Processing helix chain 'B' and resid 1402 through 1412 removed outlier: 4.028A pdb=" N PHE B1406 " --> pdb=" O LEU B1402 " (cutoff:3.500A) Processing helix chain 'B' and resid 1425 through 1439 removed outlier: 3.609A pdb=" N ASN B1439 " --> pdb=" O SER B1435 " (cutoff:3.500A) Processing helix chain 'B' and resid 1443 through 1456 Processing helix chain 'B' and resid 1458 through 1469 Processing helix chain 'B' and resid 1502 through 1511 Processing helix chain 'B' and resid 1514 through 1525 Processing helix chain 'B' and resid 1527 through 1529 No H-bonds generated for 'chain 'B' and resid 1527 through 1529' Processing helix chain 'B' and resid 1530 through 1546 Processing helix chain 'B' and resid 1552 through 1564 Proline residue: B1561 - end of helix Processing helix chain 'B' and resid 1581 through 1592 Processing helix chain 'B' and resid 1625 through 1642 Processing helix chain 'B' and resid 1645 through 1651 Processing helix chain 'B' and resid 1660 through 1671 Processing helix chain 'B' and resid 1675 through 1677 No H-bonds generated for 'chain 'B' and resid 1675 through 1677' Processing helix chain 'B' and resid 1678 through 1690 Processing helix chain 'B' and resid 1693 through 1704 removed outlier: 3.815A pdb=" N GLN B1697 " --> pdb=" O TYR B1693 " (cutoff:3.500A) Processing helix chain 'B' and resid 1838 through 1840 No H-bonds generated for 'chain 'B' and resid 1838 through 1840' Processing helix chain 'B' and resid 1867 through 1871 removed outlier: 3.743A pdb=" N VAL B1871 " --> pdb=" O TYR B1868 " (cutoff:3.500A) Processing helix chain 'B' and resid 1888 through 1894 Processing helix chain 'B' and resid 1896 through 1902 Processing helix chain 'B' and resid 1909 through 1917 removed outlier: 3.654A pdb=" N MET B1917 " --> pdb=" O TYR B1913 " (cutoff:3.500A) Processing helix chain 'B' and resid 1926 through 1937 removed outlier: 4.090A pdb=" N LEU B1935 " --> pdb=" O ASP B1931 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE B1936 " --> pdb=" O LEU B1932 " (cutoff:3.500A) Processing helix chain 'B' and resid 2035 through 2042 removed outlier: 3.590A pdb=" N LYS B2040 " --> pdb=" O VAL B2036 " (cutoff:3.500A) Processing helix chain 'B' and resid 2054 through 2069 Processing helix chain 'B' and resid 2080 through 2092 removed outlier: 3.942A pdb=" N THR B2085 " --> pdb=" O PRO B2081 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU B2086 " --> pdb=" O TYR B2082 " (cutoff:3.500A) Processing helix chain 'B' and resid 2094 through 2098 removed outlier: 3.786A pdb=" N CYS B2097 " --> pdb=" O TRP B2094 " (cutoff:3.500A) Processing helix chain 'B' and resid 2102 through 2116 removed outlier: 3.723A pdb=" N LYS B2116 " --> pdb=" O MET B2112 " (cutoff:3.500A) Processing helix chain 'B' and resid 2130 through 2142 Processing helix chain 'B' and resid 2146 through 2151 Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 20 through 48 Processing helix chain 'C' and resid 56 through 64 Processing helix chain 'C' and resid 67 through 76 removed outlier: 3.660A pdb=" N ILE C 71 " --> pdb=" O PRO C 67 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS C 76 " --> pdb=" O THR C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 94 removed outlier: 3.588A pdb=" N PHE C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 146 removed outlier: 5.050A pdb=" N ALA C 130 " --> pdb=" O LEU C 126 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLY C 131 " --> pdb=" O LYS C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 172 Processing helix chain 'C' and resid 176 through 197 Processing helix chain 'C' and resid 200 through 202 No H-bonds generated for 'chain 'C' and resid 200 through 202' Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 239 through 253 removed outlier: 3.962A pdb=" N ARG C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 282 removed outlier: 3.641A pdb=" N PHE C 268 " --> pdb=" O GLY C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 322 Processing helix chain 'C' and resid 328 through 343 Processing helix chain 'C' and resid 345 through 353 Processing helix chain 'C' and resid 379 through 391 Processing helix chain 'C' and resid 409 through 427 Processing helix chain 'C' and resid 450 through 463 removed outlier: 4.228A pdb=" N PHE C 454 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLN C 460 " --> pdb=" O GLN C 456 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LYS C 461 " --> pdb=" O ASN C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 468 Processing helix chain 'C' and resid 470 through 490 removed outlier: 3.848A pdb=" N HIS C 474 " --> pdb=" O THR C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 496 removed outlier: 4.602A pdb=" N LYS C 496 " --> pdb=" O LEU C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 543 removed outlier: 3.510A pdb=" N ASN C 542 " --> pdb=" O ASP C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 572 removed outlier: 3.529A pdb=" N ILE C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 592 Processing helix chain 'C' and resid 597 through 614 Processing helix chain 'C' and resid 616 through 635 removed outlier: 3.909A pdb=" N TYR C 628 " --> pdb=" O ASP C 624 " (cutoff:3.500A) Proline residue: C 631 - end of helix Processing helix chain 'C' and resid 639 through 646 removed outlier: 3.718A pdb=" N LEU C 643 " --> pdb=" O GLY C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 649 No H-bonds generated for 'chain 'C' and resid 647 through 649' Processing helix chain 'C' and resid 654 through 674 removed outlier: 3.608A pdb=" N ASN C 674 " --> pdb=" O ALA C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 677 No H-bonds generated for 'chain 'C' and resid 675 through 677' Processing helix chain 'C' and resid 712 through 725 removed outlier: 3.996A pdb=" N LEU C 716 " --> pdb=" O HIS C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 733 Processing helix chain 'C' and resid 734 through 760 removed outlier: 3.796A pdb=" N LYS C 740 " --> pdb=" O ASN C 736 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 767 Processing helix chain 'C' and resid 769 through 777 Processing helix chain 'C' and resid 786 through 802 removed outlier: 3.888A pdb=" N VAL C 800 " --> pdb=" O GLU C 796 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 814 Processing helix chain 'C' and resid 820 through 824 removed outlier: 3.618A pdb=" N SER C 823 " --> pdb=" O PRO C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 859 Processing helix chain 'C' and resid 864 through 872 Processing helix chain 'C' and resid 898 through 918 removed outlier: 4.316A pdb=" N ASN C 918 " --> pdb=" O ALA C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 932 through 948 removed outlier: 3.692A pdb=" N GLY C 948 " --> pdb=" O ARG C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 992 removed outlier: 4.395A pdb=" N ARG C 987 " --> pdb=" O ALA C 983 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE C 988 " --> pdb=" O LYS C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 999 through 1012 Processing helix chain 'C' and resid 1020 through 1028 removed outlier: 3.608A pdb=" N ASP C1028 " --> pdb=" O ARG C1024 " (cutoff:3.500A) Processing helix chain 'C' and resid 1033 through 1044 removed outlier: 3.568A pdb=" N ILE C1037 " --> pdb=" O LEU C1033 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE C1044 " --> pdb=" O PHE C1040 " (cutoff:3.500A) Processing helix chain 'C' and resid 1061 through 1084 Processing helix chain 'C' and resid 1113 through 1127 removed outlier: 4.559A pdb=" N PHE C1117 " --> pdb=" O GLY C1113 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY C1127 " --> pdb=" O GLN C1123 " (cutoff:3.500A) Processing helix chain 'C' and resid 1128 through 1134 Processing helix chain 'C' and resid 1137 through 1152 removed outlier: 3.919A pdb=" N SER C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1168 through 1181 Processing helix chain 'C' and resid 1184 through 1195 removed outlier: 4.033A pdb=" N ILE C1188 " --> pdb=" O PRO C1184 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU C1193 " --> pdb=" O LEU C1189 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER C1194 " --> pdb=" O LEU C1190 " (cutoff:3.500A) Processing helix chain 'C' and resid 1200 through 1218 Processing helix chain 'C' and resid 1221 through 1241 Processing helix chain 'C' and resid 1249 through 1253 Processing helix chain 'C' and resid 1257 through 1261 removed outlier: 3.620A pdb=" N THR C1261 " --> pdb=" O HIS C1258 " (cutoff:3.500A) Processing helix chain 'C' and resid 1272 through 1279 Processing helix chain 'C' and resid 1282 through 1297 removed outlier: 3.533A pdb=" N LYS C1286 " --> pdb=" O GLY C1282 " (cutoff:3.500A) Processing helix chain 'C' and resid 1302 through 1319 removed outlier: 3.630A pdb=" N ASP C1319 " --> pdb=" O MET C1315 " (cutoff:3.500A) Processing helix chain 'C' and resid 1354 through 1365 Processing helix chain 'C' and resid 1366 through 1370 Processing helix chain 'C' and resid 1375 through 1388 removed outlier: 3.841A pdb=" N ILE C1381 " --> pdb=" O ASP C1377 " (cutoff:3.500A) Processing helix chain 'C' and resid 1389 through 1397 removed outlier: 3.633A pdb=" N THR C1397 " --> pdb=" O VAL C1393 " (cutoff:3.500A) Processing helix chain 'C' and resid 1401 through 1413 removed outlier: 3.767A pdb=" N ARG C1405 " --> pdb=" O PRO C1401 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE C1406 " --> pdb=" O LEU C1402 " (cutoff:3.500A) Processing helix chain 'C' and resid 1425 through 1439 removed outlier: 3.948A pdb=" N ASN C1439 " --> pdb=" O SER C1435 " (cutoff:3.500A) Processing helix chain 'C' and resid 1443 through 1457 Processing helix chain 'C' and resid 1458 through 1470 Processing helix chain 'C' and resid 1502 through 1512 Processing helix chain 'C' and resid 1514 through 1525 Processing helix chain 'C' and resid 1527 through 1529 No H-bonds generated for 'chain 'C' and resid 1527 through 1529' Processing helix chain 'C' and resid 1530 through 1546 removed outlier: 3.652A pdb=" N TYR C1543 " --> pdb=" O LYS C1539 " (cutoff:3.500A) Processing helix chain 'C' and resid 1552 through 1558 removed outlier: 3.631A pdb=" N MET C1556 " --> pdb=" O LEU C1552 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG C1558 " --> pdb=" O ASP C1554 " (cutoff:3.500A) Processing helix chain 'C' and resid 1581 through 1592 Processing helix chain 'C' and resid 1622 through 1642 Processing helix chain 'C' and resid 1645 through 1651 Processing helix chain 'C' and resid 1660 through 1671 Processing helix chain 'C' and resid 1675 through 1677 No H-bonds generated for 'chain 'C' and resid 1675 through 1677' Processing helix chain 'C' and resid 1678 through 1689 Processing helix chain 'C' and resid 1693 through 1704 removed outlier: 3.668A pdb=" N GLN C1697 " --> pdb=" O TYR C1693 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA C1704 " --> pdb=" O ALA C1700 " (cutoff:3.500A) Processing helix chain 'C' and resid 1759 through 1778 Processing helix chain 'C' and resid 1820 through 1823 Processing helix chain 'C' and resid 1838 through 1840 No H-bonds generated for 'chain 'C' and resid 1838 through 1840' Processing helix chain 'C' and resid 1888 through 1894 Processing helix chain 'C' and resid 1896 through 1902 Processing helix chain 'C' and resid 1909 through 1918 removed outlier: 3.550A pdb=" N ASN C1918 " --> pdb=" O SER C1914 " (cutoff:3.500A) Processing helix chain 'C' and resid 1923 through 1937 Processing helix chain 'C' and resid 2034 through 2043 removed outlier: 3.658A pdb=" N TRP C2042 " --> pdb=" O LEU C2038 " (cutoff:3.500A) Processing helix chain 'C' and resid 2054 through 2069 removed outlier: 3.658A pdb=" N ILE C2059 " --> pdb=" O PRO C2055 " (cutoff:3.500A) Processing helix chain 'C' and resid 2080 through 2092 removed outlier: 3.550A pdb=" N GLU C2086 " --> pdb=" O TYR C2082 " (cutoff:3.500A) Processing helix chain 'C' and resid 2102 through 2116 Processing helix chain 'C' and resid 2130 through 2142 Processing helix chain 'C' and resid 2145 through 2151 removed outlier: 4.037A pdb=" N SER C2149 " --> pdb=" O ASP C2145 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 12 Processing helix chain 'F' and resid 20 through 48 Processing helix chain 'F' and resid 56 through 64 Processing helix chain 'F' and resid 67 through 76 removed outlier: 3.715A pdb=" N ILE F 71 " --> pdb=" O PRO F 67 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS F 76 " --> pdb=" O THR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 94 Processing helix chain 'F' and resid 116 through 146 removed outlier: 5.115A pdb=" N ALA F 130 " --> pdb=" O LEU F 126 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N GLY F 131 " --> pdb=" O LYS F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 172 Processing helix chain 'F' and resid 176 through 197 removed outlier: 3.578A pdb=" N VAL F 180 " --> pdb=" O ARG F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 202 No H-bonds generated for 'chain 'F' and resid 200 through 202' Processing helix chain 'F' and resid 203 through 216 Processing helix chain 'F' and resid 239 through 252 removed outlier: 3.739A pdb=" N LEU F 243 " --> pdb=" O ASN F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 282 Processing helix chain 'F' and resid 306 through 322 removed outlier: 3.880A pdb=" N ARG F 316 " --> pdb=" O ILE F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 343 Processing helix chain 'F' and resid 345 through 352 Processing helix chain 'F' and resid 379 through 391 Processing helix chain 'F' and resid 409 through 429 Processing helix chain 'F' and resid 450 through 458 Processing helix chain 'F' and resid 458 through 463 Processing helix chain 'F' and resid 463 through 469 removed outlier: 4.310A pdb=" N LYS F 469 " --> pdb=" O ASP F 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 470 through 490 removed outlier: 3.936A pdb=" N HIS F 474 " --> pdb=" O THR F 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 491 through 496 removed outlier: 4.747A pdb=" N LYS F 496 " --> pdb=" O LEU F 492 " (cutoff:3.500A) Processing helix chain 'F' and resid 563 through 572 Processing helix chain 'F' and resid 572 through 593 Processing helix chain 'F' and resid 597 through 614 Processing helix chain 'F' and resid 616 through 635 removed outlier: 3.867A pdb=" N TYR F 628 " --> pdb=" O ASP F 624 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE F 630 " --> pdb=" O LEU F 626 " (cutoff:3.500A) Proline residue: F 631 - end of helix Processing helix chain 'F' and resid 639 through 649 removed outlier: 3.637A pdb=" N LEU F 643 " --> pdb=" O GLY F 639 " (cutoff:3.500A) Processing helix chain 'F' and resid 654 through 675 removed outlier: 3.648A pdb=" N VAL F 658 " --> pdb=" O SER F 654 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN F 675 " --> pdb=" O LEU F 671 " (cutoff:3.500A) Processing helix chain 'F' and resid 712 through 726 removed outlier: 4.001A pdb=" N LEU F 716 " --> pdb=" O HIS F 712 " (cutoff:3.500A) Processing helix chain 'F' and resid 730 through 733 Processing helix chain 'F' and resid 734 through 760 Processing helix chain 'F' and resid 760 through 767 removed outlier: 3.585A pdb=" N VAL F 764 " --> pdb=" O GLY F 760 " (cutoff:3.500A) Processing helix chain 'F' and resid 769 through 777 Processing helix chain 'F' and resid 786 through 802 removed outlier: 3.810A pdb=" N VAL F 800 " --> pdb=" O GLU F 796 " (cutoff:3.500A) Processing helix chain 'F' and resid 804 through 814 Processing helix chain 'F' and resid 820 through 828 removed outlier: 3.557A pdb=" N SER F 823 " --> pdb=" O PRO F 820 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN F 824 " --> pdb=" O TYR F 821 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N THR F 825 " --> pdb=" O PHE F 822 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG F 826 " --> pdb=" O SER F 823 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN F 827 " --> pdb=" O GLN F 824 " (cutoff:3.500A) Processing helix chain 'F' and resid 848 through 859 Processing helix chain 'F' and resid 864 through 872 Processing helix chain 'F' and resid 898 through 917 Processing helix chain 'F' and resid 918 through 920 No H-bonds generated for 'chain 'F' and resid 918 through 920' Processing helix chain 'F' and resid 930 through 948 removed outlier: 4.273A pdb=" N ALA F 934 " --> pdb=" O LYS F 930 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE F 935 " --> pdb=" O LYS F 931 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY F 948 " --> pdb=" O ARG F 944 " (cutoff:3.500A) Processing helix chain 'F' and resid 983 through 991 removed outlier: 4.312A pdb=" N ARG F 987 " --> pdb=" O ALA F 983 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE F 988 " --> pdb=" O LYS F 984 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N MET F 991 " --> pdb=" O ARG F 987 " (cutoff:3.500A) Processing helix chain 'F' and resid 999 through 1013 removed outlier: 3.813A pdb=" N ASN F1003 " --> pdb=" O ASN F 999 " (cutoff:3.500A) Processing helix chain 'F' and resid 1020 through 1029 Processing helix chain 'F' and resid 1034 through 1044 removed outlier: 3.688A pdb=" N PHE F1044 " --> pdb=" O PHE F1040 " (cutoff:3.500A) Processing helix chain 'F' and resid 1061 through 1084 Processing helix chain 'F' and resid 1114 through 1126 Processing helix chain 'F' and resid 1127 through 1132 removed outlier: 5.879A pdb=" N HIS F1130 " --> pdb=" O GLY F1127 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TRP F1131 " --> pdb=" O HIS F1128 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE F1132 " --> pdb=" O LEU F1129 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1127 through 1132' Processing helix chain 'F' and resid 1138 through 1153 removed outlier: 3.535A pdb=" N GLY F1153 " --> pdb=" O ILE F1149 " (cutoff:3.500A) Processing helix chain 'F' and resid 1168 through 1181 Processing helix chain 'F' and resid 1184 through 1195 removed outlier: 4.031A pdb=" N ILE F1188 " --> pdb=" O PRO F1184 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU F1193 " --> pdb=" O LEU F1189 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N SER F1194 " --> pdb=" O LEU F1190 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASP F1195 " --> pdb=" O GLY F1191 " (cutoff:3.500A) Processing helix chain 'F' and resid 1200 through 1219 Processing helix chain 'F' and resid 1221 through 1241 Processing helix chain 'F' and resid 1249 through 1253 Processing helix chain 'F' and resid 1272 through 1279 Processing helix chain 'F' and resid 1282 through 1297 Processing helix chain 'F' and resid 1302 through 1319 Processing helix chain 'F' and resid 1322 through 1326 Processing helix chain 'F' and resid 1349 through 1353 removed outlier: 3.637A pdb=" N MET F1352 " --> pdb=" O PHE F1349 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TYR F1353 " --> pdb=" O ALA F1350 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1349 through 1353' Processing helix chain 'F' and resid 1354 through 1365 Processing helix chain 'F' and resid 1366 through 1370 Processing helix chain 'F' and resid 1375 through 1388 removed outlier: 4.027A pdb=" N ILE F1381 " --> pdb=" O ASP F1377 " (cutoff:3.500A) Processing helix chain 'F' and resid 1389 through 1397 Processing helix chain 'F' and resid 1402 through 1412 removed outlier: 4.404A pdb=" N PHE F1406 " --> pdb=" O LEU F1402 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG F1407 " --> pdb=" O GLN F1403 " (cutoff:3.500A) Processing helix chain 'F' and resid 1425 through 1439 removed outlier: 3.728A pdb=" N ASN F1439 " --> pdb=" O SER F1435 " (cutoff:3.500A) Processing helix chain 'F' and resid 1443 through 1455 Processing helix chain 'F' and resid 1463 through 1470 Processing helix chain 'F' and resid 1502 through 1512 Processing helix chain 'F' and resid 1514 through 1525 Processing helix chain 'F' and resid 1527 through 1529 No H-bonds generated for 'chain 'F' and resid 1527 through 1529' Processing helix chain 'F' and resid 1530 through 1546 Processing helix chain 'F' and resid 1552 through 1564 Proline residue: F1561 - end of helix Processing helix chain 'F' and resid 1581 through 1592 Processing helix chain 'F' and resid 1612 through 1642 removed outlier: 4.066A pdb=" N ARG F1616 " --> pdb=" O SER F1612 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LYS F1617 " --> pdb=" O ILE F1613 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN F1622 " --> pdb=" O GLU F1618 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN F1623 " --> pdb=" O ASP F1619 " (cutoff:3.500A) Processing helix chain 'F' and resid 1645 through 1651 Processing helix chain 'F' and resid 1660 through 1671 Processing helix chain 'F' and resid 1675 through 1677 No H-bonds generated for 'chain 'F' and resid 1675 through 1677' Processing helix chain 'F' and resid 1678 through 1690 Processing helix chain 'F' and resid 1693 through 1704 removed outlier: 3.595A pdb=" N GLN F1697 " --> pdb=" O TYR F1693 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA F1704 " --> pdb=" O ALA F1700 " (cutoff:3.500A) Processing helix chain 'F' and resid 1759 through 1778 removed outlier: 3.501A pdb=" N LEU F1763 " --> pdb=" O GLN F1759 " (cutoff:3.500A) Processing helix chain 'F' and resid 1820 through 1823 Processing helix chain 'F' and resid 1867 through 1871 Processing helix chain 'F' and resid 1888 through 1894 Processing helix chain 'F' and resid 1896 through 1903 Processing helix chain 'F' and resid 1909 through 1918 Processing helix chain 'F' and resid 1923 through 1937 Processing helix chain 'F' and resid 2034 through 2041 Processing helix chain 'F' and resid 2054 through 2069 removed outlier: 3.686A pdb=" N ILE F2059 " --> pdb=" O PRO F2055 " (cutoff:3.500A) Processing helix chain 'F' and resid 2080 through 2092 removed outlier: 3.518A pdb=" N GLU F2086 " --> pdb=" O TYR F2082 " (cutoff:3.500A) Processing helix chain 'F' and resid 2094 through 2099 removed outlier: 3.766A pdb=" N VAL F2098 " --> pdb=" O TRP F2094 " (cutoff:3.500A) Processing helix chain 'F' and resid 2102 through 2116 removed outlier: 3.615A pdb=" N ASN F2115 " --> pdb=" O ASN F2111 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS F2116 " --> pdb=" O MET F2112 " (cutoff:3.500A) Processing helix chain 'F' and resid 2130 through 2142 Processing helix chain 'F' and resid 2145 through 2151 removed outlier: 4.239A pdb=" N SER F2149 " --> pdb=" O ASP F2145 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 13 removed outlier: 3.805A pdb=" N GLU A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 48 removed outlier: 4.168A pdb=" N ILE A 43 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 64 Processing helix chain 'A' and resid 67 through 75 Processing helix chain 'A' and resid 87 through 93 Processing helix chain 'A' and resid 116 through 146 removed outlier: 4.087A pdb=" N GLY A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 176 through 197 Processing helix chain 'A' and resid 200 through 202 No H-bonds generated for 'chain 'A' and resid 200 through 202' Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 239 through 252 removed outlier: 3.992A pdb=" N LEU A 243 " --> pdb=" O ASN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 282 Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 328 through 343 Processing helix chain 'A' and resid 345 through 353 Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 379 through 391 Processing helix chain 'A' and resid 409 through 428 removed outlier: 3.569A pdb=" N GLN A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 463 removed outlier: 4.610A pdb=" N GLN A 460 " --> pdb=" O GLN A 456 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LYS A 461 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 469 removed outlier: 4.312A pdb=" N LYS A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 490 removed outlier: 3.938A pdb=" N HIS A 474 " --> pdb=" O THR A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 571 Processing helix chain 'A' and resid 572 through 593 Processing helix chain 'A' and resid 597 through 614 Processing helix chain 'A' and resid 616 through 635 removed outlier: 3.852A pdb=" N TYR A 628 " --> pdb=" O ASP A 624 " (cutoff:3.500A) Proline residue: A 631 - end of helix removed outlier: 3.631A pdb=" N SER A 635 " --> pdb=" O PRO A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 643 Processing helix chain 'A' and resid 644 through 648 Processing helix chain 'A' and resid 654 through 678 removed outlier: 4.032A pdb=" N LYS A 676 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA A 677 " --> pdb=" O GLN A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 725 removed outlier: 4.084A pdb=" N LEU A 716 " --> pdb=" O HIS A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 733 Processing helix chain 'A' and resid 734 through 760 removed outlier: 3.502A pdb=" N GLU A 738 " --> pdb=" O ASN A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 766 removed outlier: 3.769A pdb=" N VAL A 764 " --> pdb=" O GLY A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 777 removed outlier: 3.843A pdb=" N LEU A 773 " --> pdb=" O MET A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 802 removed outlier: 3.892A pdb=" N VAL A 800 " --> pdb=" O GLU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 814 Processing helix chain 'A' and resid 824 through 828 Processing helix chain 'A' and resid 848 through 859 Processing helix chain 'A' and resid 864 through 872 Processing helix chain 'A' and resid 898 through 919 removed outlier: 4.637A pdb=" N ASN A 918 " --> pdb=" O ALA A 914 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE A 919 " --> pdb=" O ILE A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 947 Processing helix chain 'A' and resid 983 through 991 removed outlier: 4.184A pdb=" N ARG A 987 " --> pdb=" O ALA A 983 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE A 988 " --> pdb=" O LYS A 984 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N MET A 991 " --> pdb=" O ARG A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1013 Processing helix chain 'A' and resid 1020 through 1028 Processing helix chain 'A' and resid 1034 through 1044 removed outlier: 3.617A pdb=" N PHE A1044 " --> pdb=" O PHE A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1083 Processing helix chain 'A' and resid 1114 through 1126 Processing helix chain 'A' and resid 1128 through 1135 removed outlier: 4.527A pdb=" N SER A1133 " --> pdb=" O HIS A1130 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN A1135 " --> pdb=" O PHE A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1152 removed outlier: 3.858A pdb=" N SER A1141 " --> pdb=" O GLU A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1168 through 1181 Processing helix chain 'A' and resid 1184 through 1192 removed outlier: 4.080A pdb=" N ILE A1188 " --> pdb=" O PRO A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1219 removed outlier: 3.951A pdb=" N ASP A1203 " --> pdb=" O LEU A1199 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1241 Processing helix chain 'A' and resid 1249 through 1253 removed outlier: 3.690A pdb=" N ALA A1252 " --> pdb=" O HIS A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1272 through 1279 Processing helix chain 'A' and resid 1282 through 1297 removed outlier: 3.789A pdb=" N LEU A1288 " --> pdb=" O SER A1284 " (cutoff:3.500A) Processing helix chain 'A' and resid 1304 through 1319 removed outlier: 3.742A pdb=" N LEU A1308 " --> pdb=" O MET A1304 " (cutoff:3.500A) Processing helix chain 'A' and resid 1326 through 1330 removed outlier: 3.721A pdb=" N PHE A1330 " --> pdb=" O LEU A1327 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1366 Processing helix chain 'A' and resid 1375 through 1389 removed outlier: 4.361A pdb=" N ILE A1381 " --> pdb=" O ASP A1377 " (cutoff:3.500A) Processing helix chain 'A' and resid 1389 through 1397 Processing helix chain 'A' and resid 1402 through 1412 removed outlier: 4.028A pdb=" N PHE A1406 " --> pdb=" O LEU A1402 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1439 removed outlier: 3.609A pdb=" N ASN A1439 " --> pdb=" O SER A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1443 through 1456 Processing helix chain 'A' and resid 1458 through 1469 Processing helix chain 'A' and resid 1502 through 1511 Processing helix chain 'A' and resid 1514 through 1525 Processing helix chain 'A' and resid 1527 through 1529 No H-bonds generated for 'chain 'A' and resid 1527 through 1529' Processing helix chain 'A' and resid 1530 through 1546 Processing helix chain 'A' and resid 1552 through 1564 Proline residue: A1561 - end of helix Processing helix chain 'A' and resid 1581 through 1592 Processing helix chain 'A' and resid 1625 through 1642 Processing helix chain 'A' and resid 1645 through 1651 Processing helix chain 'A' and resid 1660 through 1671 Processing helix chain 'A' and resid 1675 through 1677 No H-bonds generated for 'chain 'A' and resid 1675 through 1677' Processing helix chain 'A' and resid 1678 through 1690 Processing helix chain 'A' and resid 1693 through 1704 removed outlier: 3.815A pdb=" N GLN A1697 " --> pdb=" O TYR A1693 " (cutoff:3.500A) Processing helix chain 'A' and resid 1838 through 1840 No H-bonds generated for 'chain 'A' and resid 1838 through 1840' Processing helix chain 'A' and resid 1867 through 1871 removed outlier: 3.743A pdb=" N VAL A1871 " --> pdb=" O TYR A1868 " (cutoff:3.500A) Processing helix chain 'A' and resid 1888 through 1894 Processing helix chain 'A' and resid 1896 through 1902 Processing helix chain 'A' and resid 1909 through 1917 removed outlier: 3.654A pdb=" N MET A1917 " --> pdb=" O TYR A1913 " (cutoff:3.500A) Processing helix chain 'A' and resid 1926 through 1937 removed outlier: 4.090A pdb=" N LEU A1935 " --> pdb=" O ASP A1931 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE A1936 " --> pdb=" O LEU A1932 " (cutoff:3.500A) Processing helix chain 'A' and resid 2035 through 2042 removed outlier: 3.590A pdb=" N LYS A2040 " --> pdb=" O VAL A2036 " (cutoff:3.500A) Processing helix chain 'A' and resid 2054 through 2069 Processing helix chain 'A' and resid 2080 through 2092 removed outlier: 3.942A pdb=" N THR A2085 " --> pdb=" O PRO A2081 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU A2086 " --> pdb=" O TYR A2082 " (cutoff:3.500A) Processing helix chain 'A' and resid 2094 through 2098 removed outlier: 3.786A pdb=" N CYS A2097 " --> pdb=" O TRP A2094 " (cutoff:3.500A) Processing helix chain 'A' and resid 2102 through 2116 removed outlier: 3.723A pdb=" N LYS A2116 " --> pdb=" O MET A2112 " (cutoff:3.500A) Processing helix chain 'A' and resid 2130 through 2142 Processing helix chain 'A' and resid 2146 through 2151 Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 20 through 48 Processing helix chain 'E' and resid 56 through 64 Processing helix chain 'E' and resid 67 through 76 removed outlier: 3.660A pdb=" N ILE E 71 " --> pdb=" O PRO E 67 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS E 76 " --> pdb=" O THR E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 94 removed outlier: 3.588A pdb=" N PHE E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 146 removed outlier: 5.050A pdb=" N ALA E 130 " --> pdb=" O LEU E 126 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLY E 131 " --> pdb=" O LYS E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 172 Processing helix chain 'E' and resid 176 through 197 Processing helix chain 'E' and resid 200 through 202 No H-bonds generated for 'chain 'E' and resid 200 through 202' Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 239 through 253 removed outlier: 3.962A pdb=" N ARG E 253 " --> pdb=" O ASP E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 282 removed outlier: 3.641A pdb=" N PHE E 268 " --> pdb=" O GLY E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 322 Processing helix chain 'E' and resid 328 through 343 Processing helix chain 'E' and resid 345 through 353 Processing helix chain 'E' and resid 379 through 391 Processing helix chain 'E' and resid 409 through 427 Processing helix chain 'E' and resid 450 through 463 removed outlier: 4.228A pdb=" N PHE E 454 " --> pdb=" O VAL E 450 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLN E 460 " --> pdb=" O GLN E 456 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LYS E 461 " --> pdb=" O ASN E 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 468 Processing helix chain 'E' and resid 470 through 490 removed outlier: 3.848A pdb=" N HIS E 474 " --> pdb=" O THR E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 491 through 496 removed outlier: 4.602A pdb=" N LYS E 496 " --> pdb=" O LEU E 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 539 through 543 removed outlier: 3.510A pdb=" N ASN E 542 " --> pdb=" O ASP E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 563 through 572 removed outlier: 3.529A pdb=" N ILE E 572 " --> pdb=" O LEU E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 592 Processing helix chain 'E' and resid 597 through 614 Processing helix chain 'E' and resid 616 through 635 removed outlier: 3.909A pdb=" N TYR E 628 " --> pdb=" O ASP E 624 " (cutoff:3.500A) Proline residue: E 631 - end of helix Processing helix chain 'E' and resid 639 through 646 removed outlier: 3.718A pdb=" N LEU E 643 " --> pdb=" O GLY E 639 " (cutoff:3.500A) Processing helix chain 'E' and resid 647 through 649 No H-bonds generated for 'chain 'E' and resid 647 through 649' Processing helix chain 'E' and resid 654 through 674 removed outlier: 3.608A pdb=" N ASN E 674 " --> pdb=" O ALA E 670 " (cutoff:3.500A) Processing helix chain 'E' and resid 675 through 677 No H-bonds generated for 'chain 'E' and resid 675 through 677' Processing helix chain 'E' and resid 712 through 725 removed outlier: 3.996A pdb=" N LEU E 716 " --> pdb=" O HIS E 712 " (cutoff:3.500A) Processing helix chain 'E' and resid 730 through 733 Processing helix chain 'E' and resid 734 through 760 removed outlier: 3.796A pdb=" N LYS E 740 " --> pdb=" O ASN E 736 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) Processing helix chain 'E' and resid 760 through 767 Processing helix chain 'E' and resid 769 through 777 Processing helix chain 'E' and resid 786 through 802 removed outlier: 3.888A pdb=" N VAL E 800 " --> pdb=" O GLU E 796 " (cutoff:3.500A) Processing helix chain 'E' and resid 804 through 814 Processing helix chain 'E' and resid 820 through 824 removed outlier: 3.618A pdb=" N SER E 823 " --> pdb=" O PRO E 820 " (cutoff:3.500A) Processing helix chain 'E' and resid 848 through 859 Processing helix chain 'E' and resid 864 through 872 Processing helix chain 'E' and resid 898 through 918 removed outlier: 4.316A pdb=" N ASN E 918 " --> pdb=" O ALA E 914 " (cutoff:3.500A) Processing helix chain 'E' and resid 932 through 948 removed outlier: 3.692A pdb=" N GLY E 948 " --> pdb=" O ARG E 944 " (cutoff:3.500A) Processing helix chain 'E' and resid 983 through 992 removed outlier: 4.395A pdb=" N ARG E 987 " --> pdb=" O ALA E 983 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE E 988 " --> pdb=" O LYS E 984 " (cutoff:3.500A) Processing helix chain 'E' and resid 999 through 1012 Processing helix chain 'E' and resid 1020 through 1028 removed outlier: 3.608A pdb=" N ASP E1028 " --> pdb=" O ARG E1024 " (cutoff:3.500A) Processing helix chain 'E' and resid 1033 through 1044 removed outlier: 3.568A pdb=" N ILE E1037 " --> pdb=" O LEU E1033 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE E1044 " --> pdb=" O PHE E1040 " (cutoff:3.500A) Processing helix chain 'E' and resid 1061 through 1084 Processing helix chain 'E' and resid 1113 through 1127 removed outlier: 4.559A pdb=" N PHE E1117 " --> pdb=" O GLY E1113 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY E1127 " --> pdb=" O GLN E1123 " (cutoff:3.500A) Processing helix chain 'E' and resid 1128 through 1134 Processing helix chain 'E' and resid 1137 through 1152 removed outlier: 3.919A pdb=" N SER E1141 " --> pdb=" O GLU E1137 " (cutoff:3.500A) Processing helix chain 'E' and resid 1168 through 1181 Processing helix chain 'E' and resid 1184 through 1195 removed outlier: 4.033A pdb=" N ILE E1188 " --> pdb=" O PRO E1184 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU E1193 " --> pdb=" O LEU E1189 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER E1194 " --> pdb=" O LEU E1190 " (cutoff:3.500A) Processing helix chain 'E' and resid 1200 through 1218 Processing helix chain 'E' and resid 1221 through 1241 Processing helix chain 'E' and resid 1249 through 1253 Processing helix chain 'E' and resid 1257 through 1261 removed outlier: 3.620A pdb=" N THR E1261 " --> pdb=" O HIS E1258 " (cutoff:3.500A) Processing helix chain 'E' and resid 1272 through 1279 Processing helix chain 'E' and resid 1282 through 1297 removed outlier: 3.533A pdb=" N LYS E1286 " --> pdb=" O GLY E1282 " (cutoff:3.500A) Processing helix chain 'E' and resid 1302 through 1319 removed outlier: 3.630A pdb=" N ASP E1319 " --> pdb=" O MET E1315 " (cutoff:3.500A) Processing helix chain 'E' and resid 1354 through 1365 Processing helix chain 'E' and resid 1366 through 1370 Processing helix chain 'E' and resid 1375 through 1388 removed outlier: 3.841A pdb=" N ILE E1381 " --> pdb=" O ASP E1377 " (cutoff:3.500A) Processing helix chain 'E' and resid 1389 through 1397 removed outlier: 3.633A pdb=" N THR E1397 " --> pdb=" O VAL E1393 " (cutoff:3.500A) Processing helix chain 'E' and resid 1401 through 1413 removed outlier: 3.767A pdb=" N ARG E1405 " --> pdb=" O PRO E1401 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE E1406 " --> pdb=" O LEU E1402 " (cutoff:3.500A) Processing helix chain 'E' and resid 1425 through 1439 removed outlier: 3.948A pdb=" N ASN E1439 " --> pdb=" O SER E1435 " (cutoff:3.500A) Processing helix chain 'E' and resid 1443 through 1457 Processing helix chain 'E' and resid 1458 through 1470 Processing helix chain 'E' and resid 1502 through 1512 Processing helix chain 'E' and resid 1514 through 1525 Processing helix chain 'E' and resid 1527 through 1529 No H-bonds generated for 'chain 'E' and resid 1527 through 1529' Processing helix chain 'E' and resid 1530 through 1546 removed outlier: 3.652A pdb=" N TYR E1543 " --> pdb=" O LYS E1539 " (cutoff:3.500A) Processing helix chain 'E' and resid 1552 through 1558 removed outlier: 3.631A pdb=" N MET E1556 " --> pdb=" O LEU E1552 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG E1558 " --> pdb=" O ASP E1554 " (cutoff:3.500A) Processing helix chain 'E' and resid 1581 through 1592 Processing helix chain 'E' and resid 1622 through 1642 Processing helix chain 'E' and resid 1645 through 1651 Processing helix chain 'E' and resid 1660 through 1671 Processing helix chain 'E' and resid 1675 through 1677 No H-bonds generated for 'chain 'E' and resid 1675 through 1677' Processing helix chain 'E' and resid 1678 through 1689 Processing helix chain 'E' and resid 1693 through 1704 removed outlier: 3.668A pdb=" N GLN E1697 " --> pdb=" O TYR E1693 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA E1704 " --> pdb=" O ALA E1700 " (cutoff:3.500A) Processing helix chain 'E' and resid 1759 through 1778 Processing helix chain 'E' and resid 1820 through 1823 Processing helix chain 'E' and resid 1838 through 1840 No H-bonds generated for 'chain 'E' and resid 1838 through 1840' Processing helix chain 'E' and resid 1888 through 1894 Processing helix chain 'E' and resid 1896 through 1902 Processing helix chain 'E' and resid 1909 through 1918 removed outlier: 3.550A pdb=" N ASN E1918 " --> pdb=" O SER E1914 " (cutoff:3.500A) Processing helix chain 'E' and resid 1923 through 1937 Processing helix chain 'E' and resid 2034 through 2043 removed outlier: 3.658A pdb=" N TRP E2042 " --> pdb=" O LEU E2038 " (cutoff:3.500A) Processing helix chain 'E' and resid 2054 through 2069 removed outlier: 3.658A pdb=" N ILE E2059 " --> pdb=" O PRO E2055 " (cutoff:3.500A) Processing helix chain 'E' and resid 2080 through 2092 removed outlier: 3.550A pdb=" N GLU E2086 " --> pdb=" O TYR E2082 " (cutoff:3.500A) Processing helix chain 'E' and resid 2102 through 2116 Processing helix chain 'E' and resid 2130 through 2142 Processing helix chain 'E' and resid 2145 through 2151 removed outlier: 4.037A pdb=" N SER E2149 " --> pdb=" O ASP E2145 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 98 through 102 removed outlier: 3.984A pdb=" N ASN D 98 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL D 109 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL D 159 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR D 112 " --> pdb=" O VAL D 159 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 260 through 261 removed outlier: 3.608A pdb=" N PHE D1090 " --> pdb=" O GLY D1105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 260 through 261 removed outlier: 3.710A pdb=" N SER D 950 " --> pdb=" O MET D 962 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 284 through 285 Processing sheet with id=AA5, first strand: chain 'D' and resid 499 through 503 Processing sheet with id=AA6, first strand: chain 'D' and resid 499 through 503 removed outlier: 3.657A pdb=" N PHE D 527 " --> pdb=" O MET D 560 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 683 through 685 Processing sheet with id=AA8, first strand: chain 'D' and resid 701 through 702 Processing sheet with id=AA9, first strand: chain 'D' and resid 832 through 837 removed outlier: 5.158A pdb=" N SER D 844 " --> pdb=" O GLY D 835 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 895 through 897 removed outlier: 4.874A pdb=" N ILE D 881 " --> pdb=" O PHE D1018 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 1417 through 1419 removed outlier: 3.734A pdb=" N GLU D1422 " --> pdb=" O LEU D1419 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 1473 through 1476 removed outlier: 4.206A pdb=" N THR D1598 " --> pdb=" O ILE D1476 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 1486 through 1490 removed outlier: 3.613A pdb=" N ARG D1570 " --> pdb=" O PHE D1490 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 1658 through 1659 Processing sheet with id=AB6, first strand: chain 'D' and resid 1706 through 1710 removed outlier: 4.854A pdb=" N GLY D1707 " --> pdb=" O ASN D1734 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASN D1734 " --> pdb=" O GLY D1707 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU D1729 " --> pdb=" O ILE D1744 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP D1738 " --> pdb=" O PHE D1735 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N VAL D1817 " --> pdb=" O TYR D1751 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU D1753 " --> pdb=" O VAL D1817 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 1717 through 1719 Processing sheet with id=AB8, first strand: chain 'D' and resid 1783 through 1786 removed outlier: 3.551A pdb=" N VAL D1786 " --> pdb=" O CYS D1810 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE D1811 " --> pdb=" O LYS D1796 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU D1794 " --> pdb=" O TYR D1813 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY D1804 " --> pdb=" O VAL D1793 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 1833 through 1837 removed outlier: 3.633A pdb=" N MET D1833 " --> pdb=" O GLN D1846 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN D1846 " --> pdb=" O MET D1833 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ALA D1845 " --> pdb=" O LEU D1855 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LEU D1855 " --> pdb=" O ALA D1845 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 1878 through 1881 Processing sheet with id=AC2, first strand: chain 'B' and resid 98 through 102 removed outlier: 3.592A pdb=" N VAL B 159 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR B 112 " --> pdb=" O VAL B 159 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 260 through 261 Processing sheet with id=AC4, first strand: chain 'B' and resid 284 through 285 Processing sheet with id=AC5, first strand: chain 'B' and resid 296 through 297 Processing sheet with id=AC6, first strand: chain 'B' and resid 499 through 503 removed outlier: 4.976A pdb=" N THR B 529 " --> pdb=" O SER B 557 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 499 through 503 Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 702 removed outlier: 3.606A pdb=" N TYR B 701 " --> pdb=" O TYR B 710 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 832 through 837 removed outlier: 5.879A pdb=" N SER B 844 " --> pdb=" O GLY B 835 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 895 through 896 removed outlier: 5.694A pdb=" N ILE B 881 " --> pdb=" O PHE B1018 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 950 through 953 Processing sheet with id=AD3, first strand: chain 'B' and resid 950 through 953 Processing sheet with id=AD4, first strand: chain 'B' and resid 1417 through 1419 Processing sheet with id=AD5, first strand: chain 'B' and resid 1473 through 1476 removed outlier: 4.174A pdb=" N THR B1598 " --> pdb=" O ILE B1476 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1486 through 1489 Processing sheet with id=AD7, first strand: chain 'B' and resid 1658 through 1659 Processing sheet with id=AD8, first strand: chain 'B' and resid 1833 through 1837 removed outlier: 3.868A pdb=" N MET B1833 " --> pdb=" O GLN B1846 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN B1846 " --> pdb=" O MET B1833 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG B1842 " --> pdb=" O LYS B1837 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ALA B1845 " --> pdb=" O LEU B1855 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N LEU B1855 " --> pdb=" O ALA B1845 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1878 through 1881 Processing sheet with id=AE1, first strand: chain 'C' and resid 98 through 102 removed outlier: 3.939A pdb=" N ASN C 98 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL C 109 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL C 159 " --> pdb=" O GLU C 110 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR C 112 " --> pdb=" O VAL C 159 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 260 through 261 Processing sheet with id=AE3, first strand: chain 'C' and resid 284 through 285 Processing sheet with id=AE4, first strand: chain 'C' and resid 499 through 503 Processing sheet with id=AE5, first strand: chain 'C' and resid 499 through 503 Processing sheet with id=AE6, first strand: chain 'C' and resid 683 through 685 Processing sheet with id=AE7, first strand: chain 'C' and resid 832 through 837 removed outlier: 5.675A pdb=" N SER C 844 " --> pdb=" O GLY C 835 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 895 through 897 removed outlier: 4.281A pdb=" N ALA C 877 " --> pdb=" O LYS C1014 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE C 881 " --> pdb=" O PHE C1018 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 950 through 954 removed outlier: 3.766A pdb=" N SER C 950 " --> pdb=" O MET C 962 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS C 958 " --> pdb=" O LEU C 954 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 950 through 954 removed outlier: 3.766A pdb=" N SER C 950 " --> pdb=" O MET C 962 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS C 958 " --> pdb=" O LEU C 954 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1417 through 1418 Processing sheet with id=AF3, first strand: chain 'C' and resid 1473 through 1479 Processing sheet with id=AF4, first strand: chain 'C' and resid 1488 through 1489 Processing sheet with id=AF5, first strand: chain 'C' and resid 1658 through 1659 Processing sheet with id=AF6, first strand: chain 'C' and resid 1709 through 1710 removed outlier: 3.687A pdb=" N GLN C1709 " --> pdb=" O THR C1732 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU C1729 " --> pdb=" O ILE C1744 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N VAL C1817 " --> pdb=" O TYR C1751 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU C1753 " --> pdb=" O VAL C1817 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1717 through 1719 Processing sheet with id=AF8, first strand: chain 'C' and resid 1783 through 1786 removed outlier: 3.869A pdb=" N ILE C1811 " --> pdb=" O LYS C1796 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU C1794 " --> pdb=" O TYR C1813 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1833 through 1837 removed outlier: 5.976A pdb=" N ALA C1845 " --> pdb=" O LEU C1855 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LEU C1855 " --> pdb=" O ALA C1845 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 1878 through 1881 Processing sheet with id=AG2, first strand: chain 'F' and resid 98 through 102 removed outlier: 3.984A pdb=" N ASN F 98 " --> pdb=" O VAL F 109 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL F 109 " --> pdb=" O ASN F 98 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL F 159 " --> pdb=" O GLU F 110 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR F 112 " --> pdb=" O VAL F 159 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 260 through 261 removed outlier: 3.608A pdb=" N PHE F1090 " --> pdb=" O GLY F1105 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 260 through 261 removed outlier: 3.710A pdb=" N SER F 950 " --> pdb=" O MET F 962 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 284 through 285 Processing sheet with id=AG6, first strand: chain 'F' and resid 499 through 503 Processing sheet with id=AG7, first strand: chain 'F' and resid 499 through 503 removed outlier: 3.657A pdb=" N PHE F 527 " --> pdb=" O MET F 560 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 683 through 685 Processing sheet with id=AG9, first strand: chain 'F' and resid 701 through 702 Processing sheet with id=AH1, first strand: chain 'F' and resid 832 through 837 removed outlier: 5.158A pdb=" N SER F 844 " --> pdb=" O GLY F 835 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 895 through 897 removed outlier: 4.874A pdb=" N ILE F 881 " --> pdb=" O PHE F1018 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 1417 through 1419 removed outlier: 3.734A pdb=" N GLU F1422 " --> pdb=" O LEU F1419 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 1473 through 1476 removed outlier: 4.206A pdb=" N THR F1598 " --> pdb=" O ILE F1476 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 1486 through 1490 removed outlier: 3.613A pdb=" N ARG F1570 " --> pdb=" O PHE F1490 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'F' and resid 1658 through 1659 Processing sheet with id=AH7, first strand: chain 'F' and resid 1706 through 1710 removed outlier: 4.854A pdb=" N GLY F1707 " --> pdb=" O ASN F1734 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASN F1734 " --> pdb=" O GLY F1707 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU F1729 " --> pdb=" O ILE F1744 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP F1738 " --> pdb=" O PHE F1735 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N VAL F1817 " --> pdb=" O TYR F1751 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU F1753 " --> pdb=" O VAL F1817 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'F' and resid 1717 through 1719 Processing sheet with id=AH9, first strand: chain 'F' and resid 1783 through 1786 removed outlier: 3.551A pdb=" N VAL F1786 " --> pdb=" O CYS F1810 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE F1811 " --> pdb=" O LYS F1796 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU F1794 " --> pdb=" O TYR F1813 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY F1804 " --> pdb=" O VAL F1793 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'F' and resid 1833 through 1837 removed outlier: 3.633A pdb=" N MET F1833 " --> pdb=" O GLN F1846 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN F1846 " --> pdb=" O MET F1833 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ALA F1845 " --> pdb=" O LEU F1855 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LEU F1855 " --> pdb=" O ALA F1845 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'F' and resid 1878 through 1881 Processing sheet with id=AI3, first strand: chain 'A' and resid 98 through 102 removed outlier: 3.592A pdb=" N VAL A 159 " --> pdb=" O GLU A 110 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 112 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'A' and resid 260 through 261 Processing sheet with id=AI5, first strand: chain 'A' and resid 284 through 285 Processing sheet with id=AI6, first strand: chain 'A' and resid 296 through 297 Processing sheet with id=AI7, first strand: chain 'A' and resid 499 through 503 removed outlier: 4.976A pdb=" N THR A 529 " --> pdb=" O SER A 557 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'A' and resid 499 through 503 Processing sheet with id=AI9, first strand: chain 'A' and resid 701 through 702 removed outlier: 3.606A pdb=" N TYR A 701 " --> pdb=" O TYR A 710 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'A' and resid 832 through 837 removed outlier: 5.879A pdb=" N SER A 844 " --> pdb=" O GLY A 835 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'A' and resid 895 through 896 removed outlier: 5.694A pdb=" N ILE A 881 " --> pdb=" O PHE A1018 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'A' and resid 950 through 953 Processing sheet with id=AJ4, first strand: chain 'A' and resid 950 through 953 Processing sheet with id=AJ5, first strand: chain 'A' and resid 1417 through 1419 Processing sheet with id=AJ6, first strand: chain 'A' and resid 1473 through 1476 removed outlier: 4.174A pdb=" N THR A1598 " --> pdb=" O ILE A1476 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'A' and resid 1486 through 1489 Processing sheet with id=AJ8, first strand: chain 'A' and resid 1658 through 1659 Processing sheet with id=AJ9, first strand: chain 'A' and resid 1833 through 1837 removed outlier: 3.868A pdb=" N MET A1833 " --> pdb=" O GLN A1846 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN A1846 " --> pdb=" O MET A1833 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG A1842 " --> pdb=" O LYS A1837 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ALA A1845 " --> pdb=" O LEU A1855 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N LEU A1855 " --> pdb=" O ALA A1845 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'A' and resid 1878 through 1881 Processing sheet with id=AK2, first strand: chain 'E' and resid 98 through 102 removed outlier: 3.939A pdb=" N ASN E 98 " --> pdb=" O VAL E 109 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL E 109 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL E 159 " --> pdb=" O GLU E 110 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR E 112 " --> pdb=" O VAL E 159 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'E' and resid 260 through 261 Processing sheet with id=AK4, first strand: chain 'E' and resid 284 through 285 Processing sheet with id=AK5, first strand: chain 'E' and resid 499 through 503 Processing sheet with id=AK6, first strand: chain 'E' and resid 499 through 503 Processing sheet with id=AK7, first strand: chain 'E' and resid 683 through 685 Processing sheet with id=AK8, first strand: chain 'E' and resid 832 through 837 removed outlier: 5.675A pdb=" N SER E 844 " --> pdb=" O GLY E 835 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'E' and resid 895 through 897 removed outlier: 4.281A pdb=" N ALA E 877 " --> pdb=" O LYS E1014 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE E 881 " --> pdb=" O PHE E1018 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'E' and resid 950 through 954 removed outlier: 3.766A pdb=" N SER E 950 " --> pdb=" O MET E 962 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS E 958 " --> pdb=" O LEU E 954 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'E' and resid 950 through 954 removed outlier: 3.766A pdb=" N SER E 950 " --> pdb=" O MET E 962 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS E 958 " --> pdb=" O LEU E 954 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'E' and resid 1417 through 1418 Processing sheet with id=AL4, first strand: chain 'E' and resid 1473 through 1479 Processing sheet with id=AL5, first strand: chain 'E' and resid 1488 through 1489 Processing sheet with id=AL6, first strand: chain 'E' and resid 1658 through 1659 Processing sheet with id=AL7, first strand: chain 'E' and resid 1709 through 1710 removed outlier: 3.687A pdb=" N GLN E1709 " --> pdb=" O THR E1732 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU E1729 " --> pdb=" O ILE E1744 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N VAL E1817 " --> pdb=" O TYR E1751 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU E1753 " --> pdb=" O VAL E1817 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'E' and resid 1717 through 1719 Processing sheet with id=AL9, first strand: chain 'E' and resid 1783 through 1786 removed outlier: 3.869A pdb=" N ILE E1811 " --> pdb=" O LYS E1796 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU E1794 " --> pdb=" O TYR E1813 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'E' and resid 1833 through 1837 removed outlier: 5.976A pdb=" N ALA E1845 " --> pdb=" O LEU E1855 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LEU E1855 " --> pdb=" O ALA E1845 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'E' and resid 1878 through 1881 5207 hydrogen bonds defined for protein. 14925 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: 61.95 Time building geometry restraints manager: 31.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 30374 1.34 - 1.46: 22840 1.46 - 1.58: 43430 1.58 - 1.70: 0 1.70 - 1.82: 832 Bond restraints: 97476 Sorted by residual: bond pdb=" CE1 HIS D 197 " pdb=" NE2 HIS D 197 " ideal model delta sigma weight residual 1.321 1.363 -0.042 1.00e-02 1.00e+04 1.72e+01 bond pdb=" CE1 HIS F 197 " pdb=" NE2 HIS F 197 " ideal model delta sigma weight residual 1.321 1.363 -0.042 1.00e-02 1.00e+04 1.72e+01 bond pdb=" CA SER E 638 " pdb=" CB SER E 638 " ideal model delta sigma weight residual 1.530 1.481 0.049 1.36e-02 5.41e+03 1.28e+01 bond pdb=" CA SER C 638 " pdb=" CB SER C 638 " ideal model delta sigma weight residual 1.530 1.481 0.049 1.36e-02 5.41e+03 1.28e+01 bond pdb=" N HIS D1298 " pdb=" CA HIS D1298 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.29e-02 6.01e+03 8.61e+00 ... (remaining 97471 not shown) Histogram of bond angle deviations from ideal: 95.82 - 103.48: 1060 103.48 - 111.14: 38622 111.14 - 118.81: 39620 118.81 - 126.47: 51006 126.47 - 134.13: 1432 Bond angle restraints: 131740 Sorted by residual: angle pdb=" N THR E 163 " pdb=" CA THR E 163 " pdb=" C THR E 163 " ideal model delta sigma weight residual 112.34 121.10 -8.76 1.30e+00 5.92e-01 4.54e+01 angle pdb=" N THR C 163 " pdb=" CA THR C 163 " pdb=" C THR C 163 " ideal model delta sigma weight residual 112.34 121.10 -8.76 1.30e+00 5.92e-01 4.54e+01 angle pdb=" C MET E1766 " pdb=" N MET E1767 " pdb=" CA MET E1767 " ideal model delta sigma weight residual 120.72 112.56 8.16 1.67e+00 3.59e-01 2.39e+01 angle pdb=" C MET C1766 " pdb=" N MET C1767 " pdb=" CA MET C1767 " ideal model delta sigma weight residual 120.72 112.56 8.16 1.67e+00 3.59e-01 2.39e+01 angle pdb=" C SER F1706 " pdb=" CA SER F1706 " pdb=" CB SER F1706 " ideal model delta sigma weight residual 115.79 110.23 5.56 1.19e+00 7.06e-01 2.19e+01 ... (remaining 131735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 51594 17.97 - 35.93: 5574 35.93 - 53.90: 1201 53.90 - 71.87: 244 71.87 - 89.84: 97 Dihedral angle restraints: 58710 sinusoidal: 23926 harmonic: 34784 Sorted by residual: dihedral pdb=" CD ARG E1919 " pdb=" NE ARG E1919 " pdb=" CZ ARG E1919 " pdb=" NH1 ARG E1919 " ideal model delta sinusoidal sigma weight residual 0.00 -79.64 79.64 1 1.00e+01 1.00e-02 7.87e+01 dihedral pdb=" CD ARG C1919 " pdb=" NE ARG C1919 " pdb=" CZ ARG C1919 " pdb=" NH1 ARG C1919 " ideal model delta sinusoidal sigma weight residual 0.00 -79.64 79.64 1 1.00e+01 1.00e-02 7.87e+01 dihedral pdb=" CD ARG E 707 " pdb=" NE ARG E 707 " pdb=" CZ ARG E 707 " pdb=" NH1 ARG E 707 " ideal model delta sinusoidal sigma weight residual 0.00 -77.24 77.24 1 1.00e+01 1.00e-02 7.48e+01 ... (remaining 58707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 12608 0.059 - 0.118: 1874 0.118 - 0.177: 164 0.177 - 0.236: 22 0.236 - 0.295: 10 Chirality restraints: 14678 Sorted by residual: chirality pdb=" CB VAL A1366 " pdb=" CA VAL A1366 " pdb=" CG1 VAL A1366 " pdb=" CG2 VAL A1366 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CB VAL B1366 " pdb=" CA VAL B1366 " pdb=" CG1 VAL B1366 " pdb=" CG2 VAL B1366 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA ASN C1918 " pdb=" N ASN C1918 " pdb=" C ASN C1918 " pdb=" CB ASN C1918 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 14675 not shown) Planarity restraints: 16602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C1919 " -1.090 9.50e-02 1.11e+02 4.88e-01 1.44e+02 pdb=" NE ARG C1919 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG C1919 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG C1919 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG C1919 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E1919 " 1.090 9.50e-02 1.11e+02 4.88e-01 1.44e+02 pdb=" NE ARG E1919 " -0.064 2.00e-02 2.50e+03 pdb=" CZ ARG E1919 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG E1919 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG E1919 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 707 " -1.072 9.50e-02 1.11e+02 4.80e-01 1.39e+02 pdb=" NE ARG C 707 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG C 707 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG C 707 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG C 707 " -0.020 2.00e-02 2.50e+03 ... (remaining 16599 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 12436 2.75 - 3.29: 96072 3.29 - 3.82: 163040 3.82 - 4.36: 187193 4.36 - 4.90: 323538 Nonbonded interactions: 782279 Sorted by model distance: nonbonded pdb=" O LEU B1653 " pdb=" OG1 THR B1659 " model vdw 2.212 2.440 nonbonded pdb=" O LEU A1653 " pdb=" OG1 THR A1659 " model vdw 2.212 2.440 nonbonded pdb=" OG1 THR D 362 " pdb=" O VAL D 365 " model vdw 2.215 2.440 nonbonded pdb=" OG1 THR F 362 " pdb=" O VAL F 365 " model vdw 2.215 2.440 nonbonded pdb=" OD1 ASP A1549 " pdb=" OG SER A1551 " model vdw 2.216 2.440 ... (remaining 782274 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' and (resid 1 through 216 or resid 226 through 1340 or resid 1345 thro \ ugh 1491 or resid 1499 through 1606 or resid 1609 or resid 1624 through 2151)) selection = (chain 'B' and (resid 1 through 216 or resid 226 through 1340 or resid 1345 thro \ ugh 1491 or resid 1499 through 1606 or resid 1609 or resid 1624 through 2151)) selection = (chain 'C' and (resid 1 through 216 or resid 226 through 683 or resid 687 or res \ id 700 through 925 or resid 932 through 1606 or resid 1623 through 1704 or resid \ 1830 through 1948 or resid 2035 through 2151)) selection = (chain 'D' and (resid 1 through 683 or resid 699 through 885 or resid 893 throug \ h 925 or resid 932 through 1340 or resid 1345 through 1491 or resid 1499 through \ 1606 or resid 1609 or resid 1617 or resid 1625 through 1704 or resid 1830 throu \ gh 1948 or resid 2035 through 2151)) selection = (chain 'E' and (resid 1 through 216 or resid 226 through 683 or resid 687 or res \ id 700 through 925 or resid 932 through 1606 or resid 1623 through 1704 or resid \ 1830 through 1948 or resid 2035 through 2151)) selection = (chain 'F' and (resid 1 through 683 or resid 699 through 885 or resid 893 throug \ h 925 or resid 932 through 1340 or resid 1345 through 1491 or resid 1499 through \ 1606 or resid 1609 or resid 1617 or resid 1625 through 1704 or resid 1830 throu \ gh 1948 or resid 2035 through 2151)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 28.900 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: 0.080 Extract box with map and model: 67.120 Check model and map are aligned: 1.080 Set scattering table: 0.660 Process input model: 219.890 Find NCS groups from input model: 7.030 Set up NCS constraints: 0.380 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 327.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6463 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 97476 Z= 0.269 Angle : 0.595 10.717 131740 Z= 0.329 Chirality : 0.043 0.295 14678 Planarity : 0.012 0.488 16602 Dihedral : 15.697 89.837 36154 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.34 % Favored : 95.64 % Rotamer: Outliers : 0.50 % Allowed : 14.77 % Favored : 84.73 % Cbeta Deviations : 0.02 % 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: 0.70 (0.08), residues: 11692 helix: 1.52 (0.07), residues: 6230 sheet: 0.23 (0.17), residues: 1014 loop : -0.98 (0.09), residues: 4448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A1636 HIS 0.008 0.001 HIS B1036 PHE 0.022 0.001 PHE F 371 TYR 0.025 0.001 TYR B2064 ARG 0.014 0.000 ARG B2132 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23384 Ramachandran restraints generated. 11692 Oldfield, 0 Emsley, 11692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23384 Ramachandran restraints generated. 11692 Oldfield, 0 Emsley, 11692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1191 residues out of total 10516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 1138 time to evaluate : 8.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1748 LYS cc_start: 0.7008 (mttt) cc_final: 0.6551 (ttpt) REVERT: B 183 TYR cc_start: 0.8572 (t80) cc_final: 0.7918 (t80) REVERT: B 197 HIS cc_start: 0.8927 (t-90) cc_final: 0.8687 (t-170) REVERT: B 2092 ARG cc_start: 0.8293 (ttp-110) cc_final: 0.8045 (ttp-110) REVERT: C 11 LEU cc_start: 0.9041 (mt) cc_final: 0.8834 (mt) REVERT: C 108 PHE cc_start: 0.8245 (m-80) cc_final: 0.7496 (m-80) REVERT: C 193 TYR cc_start: 0.8839 (t80) cc_final: 0.8517 (t80) REVERT: C 418 SER cc_start: 0.6689 (m) cc_final: 0.6029 (p) REVERT: C 1650 PHE cc_start: 0.8364 (m-80) cc_final: 0.8109 (m-80) REVERT: F 1274 MET cc_start: 0.3057 (mmm) cc_final: 0.2782 (mmm) REVERT: F 1779 MET cc_start: -0.0581 (pmm) cc_final: -0.1243 (ppp) REVERT: A 110 GLU cc_start: 0.6024 (tp30) cc_final: 0.5783 (tm-30) REVERT: A 331 SER cc_start: 0.8319 (p) cc_final: 0.8089 (p) REVERT: A 769 MET cc_start: 0.8592 (mmm) cc_final: 0.8221 (mmm) REVERT: A 800 VAL cc_start: 0.7667 (t) cc_final: 0.7378 (p) REVERT: A 1013 TYR cc_start: 0.8052 (t80) cc_final: 0.7838 (t80) REVERT: A 1362 SER cc_start: 0.8979 (m) cc_final: 0.8733 (p) REVERT: A 1550 ILE cc_start: 0.8663 (mm) cc_final: 0.8423 (mm) REVERT: A 1556 MET cc_start: 0.8265 (tpt) cc_final: 0.8057 (tpt) REVERT: A 2092 ARG cc_start: 0.8049 (ttp-110) cc_final: 0.7785 (ttm110) REVERT: E 11 LEU cc_start: 0.9186 (mt) cc_final: 0.8972 (mt) REVERT: E 198 LEU cc_start: 0.8269 (mt) cc_final: 0.7836 (mt) REVERT: E 332 TYR cc_start: 0.8258 (m-80) cc_final: 0.8000 (m-10) REVERT: E 1538 MET cc_start: 0.8326 (mmp) cc_final: 0.8093 (mmp) outliers start: 53 outliers final: 17 residues processed: 1172 average time/residue: 0.8794 time to fit residues: 1762.1232 Evaluate side-chains 856 residues out of total 10516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 839 time to evaluate : 8.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1298 HIS Chi-restraints excluded: chain D residue 1617 LYS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 680 TYR Chi-restraints excluded: chain B residue 1118 LEU Chi-restraints excluded: chain B residue 1316 LYS Chi-restraints excluded: chain B residue 1613 ILE Chi-restraints excluded: chain C residue 1034 ASP Chi-restraints excluded: chain C residue 1298 HIS Chi-restraints excluded: chain C residue 1356 LYS Chi-restraints excluded: chain F residue 1617 LYS Chi-restraints excluded: chain A residue 680 TYR Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1316 LYS Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain E residue 1034 ASP Chi-restraints excluded: chain E residue 1298 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1178 random chunks: chunk 994 optimal weight: 20.0000 chunk 892 optimal weight: 0.8980 chunk 495 optimal weight: 1.9990 chunk 305 optimal weight: 0.0980 chunk 602 optimal weight: 30.0000 chunk 477 optimal weight: 0.2980 chunk 923 optimal weight: 0.9990 chunk 357 optimal weight: 6.9990 chunk 561 optimal weight: 6.9990 chunk 687 optimal weight: 30.0000 chunk 1069 optimal weight: 0.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 608 HIS D1409 GLN D1615 ASN D1623 GLN D1899 ASN ** B1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1078 GLN B1255 GLN B2133 HIS C 323 ASN C 410 HIS C 625 ASN ** C 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1036 HIS ** C1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1364 GLN C1451 GLN ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 608 HIS F1409 GLN F1615 ASN F1623 GLN A 625 ASN ** A1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1255 GLN A1287 ASN E 335 HIS ** E 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1036 HIS ** E1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1403 GLN E1451 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 97476 Z= 0.181 Angle : 0.554 11.728 131740 Z= 0.282 Chirality : 0.040 0.245 14678 Planarity : 0.004 0.064 16602 Dihedral : 4.108 56.550 12836 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.92 % Favored : 96.07 % Rotamer: Outliers : 1.94 % Allowed : 16.61 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.08), residues: 11692 helix: 1.64 (0.07), residues: 6282 sheet: 0.40 (0.17), residues: 1034 loop : -0.98 (0.09), residues: 4376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A1636 HIS 0.008 0.001 HIS A1036 PHE 0.025 0.001 PHE E1929 TYR 0.018 0.001 TYR E 193 ARG 0.009 0.000 ARG F 286 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23384 Ramachandran restraints generated. 11692 Oldfield, 0 Emsley, 11692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23384 Ramachandran restraints generated. 11692 Oldfield, 0 Emsley, 11692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1094 residues out of total 10516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 890 time to evaluate : 8.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 284 MET cc_start: 0.2989 (mmp) cc_final: 0.1797 (tpp) REVERT: B 32 TYR cc_start: 0.7681 (m-80) cc_final: 0.7479 (m-80) REVERT: B 183 TYR cc_start: 0.8563 (t80) cc_final: 0.7900 (t80) REVERT: B 993 HIS cc_start: 0.3998 (OUTLIER) cc_final: 0.3655 (t-170) REVERT: B 1518 MET cc_start: 0.8413 (tpp) cc_final: 0.8094 (tpp) REVERT: B 1658 LYS cc_start: 0.7808 (mtmm) cc_final: 0.7540 (mtmm) REVERT: B 1685 MET cc_start: 0.8894 (tpt) cc_final: 0.8506 (tpt) REVERT: B 1898 GLU cc_start: 0.8690 (tt0) cc_final: 0.8328 (tm-30) REVERT: B 2118 ILE cc_start: 0.6657 (OUTLIER) cc_final: 0.6171 (pt) REVERT: C 11 LEU cc_start: 0.9045 (mt) cc_final: 0.8775 (mt) REVERT: C 108 PHE cc_start: 0.8368 (m-80) cc_final: 0.7555 (m-80) REVERT: C 418 SER cc_start: 0.6602 (OUTLIER) cc_final: 0.6199 (p) REVERT: C 1302 LYS cc_start: 0.6716 (OUTLIER) cc_final: 0.6350 (tppt) REVERT: C 1304 MET cc_start: 0.8720 (mmp) cc_final: 0.8500 (mmp) REVERT: C 1482 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7953 (mp10) REVERT: C 1605 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7635 (pttm) REVERT: C 1766 MET cc_start: 0.7779 (mmm) cc_final: 0.7379 (mmm) REVERT: C 1928 MET cc_start: 0.8516 (tmm) cc_final: 0.8266 (tmm) REVERT: F 284 MET cc_start: 0.3058 (mmp) cc_final: 0.1819 (tpp) REVERT: F 286 ARG cc_start: 0.3302 (OUTLIER) cc_final: 0.1694 (mmp-170) REVERT: F 1274 MET cc_start: 0.3282 (mmm) cc_final: 0.3029 (mmt) REVERT: F 1779 MET cc_start: -0.1008 (pmm) cc_final: -0.1273 (ppp) REVERT: A 36 HIS cc_start: 0.7779 (t-90) cc_final: 0.7456 (t70) REVERT: A 110 GLU cc_start: 0.6147 (tp30) cc_final: 0.5876 (tm-30) REVERT: A 141 LYS cc_start: 0.8934 (pptt) cc_final: 0.8496 (tptp) REVERT: A 792 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7932 (mm) REVERT: A 800 VAL cc_start: 0.7794 (t) cc_final: 0.7490 (p) REVERT: A 1283 MET cc_start: 0.8016 (tpt) cc_final: 0.7788 (tpt) REVERT: A 1518 MET cc_start: 0.8468 (tpp) cc_final: 0.8250 (tpp) REVERT: A 2092 ARG cc_start: 0.8008 (ttp-110) cc_final: 0.7700 (ttm110) REVERT: E 11 LEU cc_start: 0.9201 (mt) cc_final: 0.8965 (mt) REVERT: E 418 SER cc_start: 0.6319 (OUTLIER) cc_final: 0.5884 (p) REVERT: E 625 ASN cc_start: 0.8677 (t0) cc_final: 0.8244 (t0) REVERT: E 1283 MET cc_start: 0.8776 (tpt) cc_final: 0.8255 (tpt) REVERT: E 1605 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7230 (pttm) REVERT: E 1655 PHE cc_start: 0.8630 (t80) cc_final: 0.7273 (t80) REVERT: E 1685 MET cc_start: 0.7337 (mmm) cc_final: 0.6989 (mmp) REVERT: E 1766 MET cc_start: 0.7597 (mmm) cc_final: 0.7250 (mmm) REVERT: E 1928 MET cc_start: 0.8646 (tmm) cc_final: 0.8381 (tmm) outliers start: 204 outliers final: 92 residues processed: 1032 average time/residue: 0.8773 time to fit residues: 1591.8863 Evaluate side-chains 916 residues out of total 10516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 814 time to evaluate : 8.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1465 LYS Chi-restraints excluded: chain D residue 1768 ASP Chi-restraints excluded: chain D residue 2052 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 680 TYR Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 993 HIS Chi-restraints excluded: chain B residue 1012 VAL Chi-restraints excluded: chain B residue 1084 PHE Chi-restraints excluded: chain B residue 1118 LEU Chi-restraints excluded: chain B residue 1347 PHE Chi-restraints excluded: chain B residue 1439 ASN Chi-restraints excluded: chain B residue 1548 LEU Chi-restraints excluded: chain B residue 1572 VAL Chi-restraints excluded: chain B residue 2089 SER Chi-restraints excluded: chain B residue 2118 ILE Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 867 LYS Chi-restraints excluded: chain C residue 894 PHE Chi-restraints excluded: chain C residue 1034 ASP Chi-restraints excluded: chain C residue 1134 VAL Chi-restraints excluded: chain C residue 1160 LYS Chi-restraints excluded: chain C residue 1164 VAL Chi-restraints excluded: chain C residue 1174 THR Chi-restraints excluded: chain C residue 1302 LYS Chi-restraints excluded: chain C residue 1482 GLN Chi-restraints excluded: chain C residue 1568 LYS Chi-restraints excluded: chain C residue 1593 MET Chi-restraints excluded: chain C residue 1601 VAL Chi-restraints excluded: chain C residue 1605 LYS Chi-restraints excluded: chain C residue 2089 SER Chi-restraints excluded: chain C residue 2098 VAL Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 617 MET Chi-restraints excluded: chain F residue 1298 HIS Chi-restraints excluded: chain F residue 2052 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 1084 PHE Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1347 PHE Chi-restraints excluded: chain A residue 1369 ASP Chi-restraints excluded: chain A residue 1439 ASN Chi-restraints excluded: chain A residue 1548 LEU Chi-restraints excluded: chain A residue 1572 VAL Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain E residue 197 HIS Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 357 ILE Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain E residue 556 VAL Chi-restraints excluded: chain E residue 694 THR Chi-restraints excluded: chain E residue 743 LEU Chi-restraints excluded: chain E residue 867 LYS Chi-restraints excluded: chain E residue 1034 ASP Chi-restraints excluded: chain E residue 1134 VAL Chi-restraints excluded: chain E residue 1160 LYS Chi-restraints excluded: chain E residue 1164 VAL Chi-restraints excluded: chain E residue 1174 THR Chi-restraints excluded: chain E residue 1203 ASP Chi-restraints excluded: chain E residue 1568 LYS Chi-restraints excluded: chain E residue 1593 MET Chi-restraints excluded: chain E residue 1601 VAL Chi-restraints excluded: chain E residue 1605 LYS Chi-restraints excluded: chain E residue 1654 TRP Chi-restraints excluded: chain E residue 1698 LEU Chi-restraints excluded: chain E residue 2105 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1178 random chunks: chunk 594 optimal weight: 30.0000 chunk 332 optimal weight: 0.4980 chunk 890 optimal weight: 0.9990 chunk 728 optimal weight: 7.9990 chunk 295 optimal weight: 2.9990 chunk 1071 optimal weight: 2.9990 chunk 1157 optimal weight: 20.0000 chunk 954 optimal weight: 5.9990 chunk 1062 optimal weight: 1.9990 chunk 365 optimal weight: 9.9990 chunk 859 optimal weight: 0.2980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 625 ASN ** B1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1301 GLN ** C 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1699 GLN ** C1918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 625 ASN F2133 HIS ** A1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1403 GLN E1409 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 97476 Z= 0.247 Angle : 0.552 10.252 131740 Z= 0.282 Chirality : 0.041 0.420 14678 Planarity : 0.004 0.057 16602 Dihedral : 3.967 55.281 12804 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.20 % Favored : 95.77 % Rotamer: Outliers : 2.76 % Allowed : 16.59 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.08), residues: 11692 helix: 1.66 (0.07), residues: 6286 sheet: 0.44 (0.17), residues: 1002 loop : -1.00 (0.09), residues: 4404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 172 HIS 0.008 0.001 HIS B1036 PHE 0.030 0.001 PHE C1929 TYR 0.023 0.001 TYR A 32 ARG 0.006 0.000 ARG F 286 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23384 Ramachandran restraints generated. 11692 Oldfield, 0 Emsley, 11692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23384 Ramachandran restraints generated. 11692 Oldfield, 0 Emsley, 11692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1131 residues out of total 10516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 290 poor density : 841 time to evaluate : 8.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 LEU cc_start: 0.8940 (mp) cc_final: 0.8652 (pp) REVERT: B 183 TYR cc_start: 0.8547 (t80) cc_final: 0.7906 (t80) REVERT: B 197 HIS cc_start: 0.8857 (t-170) cc_final: 0.8646 (t-170) REVERT: B 210 MET cc_start: 0.7941 (ptp) cc_final: 0.7698 (mtp) REVERT: B 993 HIS cc_start: 0.4036 (OUTLIER) cc_final: 0.3324 (t70) REVERT: B 1518 MET cc_start: 0.8474 (tpp) cc_final: 0.8075 (tpp) REVERT: B 1658 LYS cc_start: 0.7866 (mtmm) cc_final: 0.7615 (mtmm) REVERT: B 1898 GLU cc_start: 0.8680 (tt0) cc_final: 0.8394 (tm-30) REVERT: B 1913 TYR cc_start: 0.9003 (t80) cc_final: 0.8748 (t80) REVERT: B 2118 ILE cc_start: 0.6985 (OUTLIER) cc_final: 0.6523 (pt) REVERT: C 11 LEU cc_start: 0.9062 (mt) cc_final: 0.8848 (mt) REVERT: C 108 PHE cc_start: 0.8389 (m-80) cc_final: 0.7614 (m-80) REVERT: C 345 THR cc_start: 0.8629 (p) cc_final: 0.8426 (p) REVERT: C 418 SER cc_start: 0.6708 (OUTLIER) cc_final: 0.6311 (p) REVERT: C 1302 LYS cc_start: 0.6841 (OUTLIER) cc_final: 0.6219 (ttmp) REVERT: C 1605 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7659 (pttm) REVERT: C 1655 PHE cc_start: 0.8794 (t80) cc_final: 0.7434 (t80) REVERT: C 1766 MET cc_start: 0.7852 (mmm) cc_final: 0.7429 (mmm) REVERT: C 1928 MET cc_start: 0.8949 (tmm) cc_final: 0.8689 (tmm) REVERT: F 286 ARG cc_start: 0.3028 (OUTLIER) cc_final: 0.1385 (mmp-170) REVERT: F 510 LEU cc_start: 0.5230 (OUTLIER) cc_final: 0.5012 (tp) REVERT: F 1274 MET cc_start: 0.3324 (mmm) cc_final: 0.2377 (tmm) REVERT: F 1779 MET cc_start: -0.0970 (pmm) cc_final: -0.1256 (ppp) REVERT: A 36 HIS cc_start: 0.7810 (t-90) cc_final: 0.7488 (t70) REVERT: A 110 GLU cc_start: 0.6429 (tp30) cc_final: 0.6101 (tm-30) REVERT: A 141 LYS cc_start: 0.9001 (pptt) cc_final: 0.8606 (tptp) REVERT: A 792 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8248 (mm) REVERT: A 800 VAL cc_start: 0.7883 (t) cc_final: 0.7579 (p) REVERT: A 993 HIS cc_start: 0.4627 (OUTLIER) cc_final: 0.4270 (t-90) REVERT: A 1283 MET cc_start: 0.8055 (tpt) cc_final: 0.7835 (tpt) REVERT: A 1518 MET cc_start: 0.8486 (tpp) cc_final: 0.8158 (tpp) REVERT: A 1608 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8527 (mt) REVERT: E 11 LEU cc_start: 0.9189 (mt) cc_final: 0.8986 (mt) REVERT: E 415 GLU cc_start: 0.6541 (tt0) cc_final: 0.6226 (mt-10) REVERT: E 1283 MET cc_start: 0.8773 (tpt) cc_final: 0.8244 (tpt) REVERT: E 1605 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7149 (pttm) REVERT: E 1655 PHE cc_start: 0.8514 (t80) cc_final: 0.8286 (t80) REVERT: E 1685 MET cc_start: 0.7492 (mmm) cc_final: 0.7109 (mmp) REVERT: E 1766 MET cc_start: 0.7662 (mmm) cc_final: 0.7311 (mmm) REVERT: E 1928 MET cc_start: 0.8976 (tmm) cc_final: 0.8764 (tmm) outliers start: 290 outliers final: 154 residues processed: 1052 average time/residue: 0.8278 time to fit residues: 1533.9521 Evaluate side-chains 957 residues out of total 10516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 792 time to evaluate : 8.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 1298 HIS Chi-restraints excluded: chain D residue 1304 MET Chi-restraints excluded: chain D residue 1465 LYS Chi-restraints excluded: chain D residue 1607 VAL Chi-restraints excluded: chain D residue 1891 ILE Chi-restraints excluded: chain D residue 2052 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 680 TYR Chi-restraints excluded: chain B residue 860 ARG Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 905 LEU Chi-restraints excluded: chain B residue 993 HIS Chi-restraints excluded: chain B residue 1012 VAL Chi-restraints excluded: chain B residue 1084 PHE Chi-restraints excluded: chain B residue 1118 LEU Chi-restraints excluded: chain B residue 1154 SER Chi-restraints excluded: chain B residue 1347 PHE Chi-restraints excluded: chain B residue 1439 ASN Chi-restraints excluded: chain B residue 1495 LYS Chi-restraints excluded: chain B residue 1548 LEU Chi-restraints excluded: chain B residue 1572 VAL Chi-restraints excluded: chain B residue 1578 VAL Chi-restraints excluded: chain B residue 1598 THR Chi-restraints excluded: chain B residue 1613 ILE Chi-restraints excluded: chain B residue 2049 ILE Chi-restraints excluded: chain B residue 2089 SER Chi-restraints excluded: chain B residue 2118 ILE Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 743 LEU Chi-restraints excluded: chain C residue 816 ASN Chi-restraints excluded: chain C residue 837 VAL Chi-restraints excluded: chain C residue 867 LYS Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 894 PHE Chi-restraints excluded: chain C residue 1034 ASP Chi-restraints excluded: chain C residue 1160 LYS Chi-restraints excluded: chain C residue 1164 VAL Chi-restraints excluded: chain C residue 1174 THR Chi-restraints excluded: chain C residue 1298 HIS Chi-restraints excluded: chain C residue 1302 LYS Chi-restraints excluded: chain C residue 1354 THR Chi-restraints excluded: chain C residue 1397 THR Chi-restraints excluded: chain C residue 1402 LEU Chi-restraints excluded: chain C residue 1447 MET Chi-restraints excluded: chain C residue 1529 ASP Chi-restraints excluded: chain C residue 1546 LEU Chi-restraints excluded: chain C residue 1568 LYS Chi-restraints excluded: chain C residue 1593 MET Chi-restraints excluded: chain C residue 1601 VAL Chi-restraints excluded: chain C residue 1605 LYS Chi-restraints excluded: chain C residue 1698 LEU Chi-restraints excluded: chain C residue 1872 ASP Chi-restraints excluded: chain C residue 1888 LEU Chi-restraints excluded: chain C residue 2098 VAL Chi-restraints excluded: chain F residue 284 MET Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 617 MET Chi-restraints excluded: chain F residue 1034 ASP Chi-restraints excluded: chain F residue 1298 HIS Chi-restraints excluded: chain F residue 1556 MET Chi-restraints excluded: chain F residue 1607 VAL Chi-restraints excluded: chain F residue 2049 ILE Chi-restraints excluded: chain F residue 2052 VAL Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 680 TYR Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 993 HIS Chi-restraints excluded: chain A residue 1084 PHE Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1154 SER Chi-restraints excluded: chain A residue 1316 LYS Chi-restraints excluded: chain A residue 1347 PHE Chi-restraints excluded: chain A residue 1369 ASP Chi-restraints excluded: chain A residue 1439 ASN Chi-restraints excluded: chain A residue 1548 LEU Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 2049 ILE Chi-restraints excluded: chain A residue 2052 VAL Chi-restraints excluded: chain A residue 2089 SER Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 226 TYR Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 357 ILE Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 556 VAL Chi-restraints excluded: chain E residue 694 THR Chi-restraints excluded: chain E residue 743 LEU Chi-restraints excluded: chain E residue 816 ASN Chi-restraints excluded: chain E residue 837 VAL Chi-restraints excluded: chain E residue 867 LYS Chi-restraints excluded: chain E residue 872 THR Chi-restraints excluded: chain E residue 1034 ASP Chi-restraints excluded: chain E residue 1134 VAL Chi-restraints excluded: chain E residue 1160 LYS Chi-restraints excluded: chain E residue 1164 VAL Chi-restraints excluded: chain E residue 1174 THR Chi-restraints excluded: chain E residue 1203 ASP Chi-restraints excluded: chain E residue 1298 HIS Chi-restraints excluded: chain E residue 1358 LEU Chi-restraints excluded: chain E residue 1397 THR Chi-restraints excluded: chain E residue 1475 VAL Chi-restraints excluded: chain E residue 1529 ASP Chi-restraints excluded: chain E residue 1546 LEU Chi-restraints excluded: chain E residue 1554 ASP Chi-restraints excluded: chain E residue 1568 LYS Chi-restraints excluded: chain E residue 1593 MET Chi-restraints excluded: chain E residue 1601 VAL Chi-restraints excluded: chain E residue 1605 LYS Chi-restraints excluded: chain E residue 1698 LEU Chi-restraints excluded: chain E residue 1872 ASP Chi-restraints excluded: chain E residue 2098 VAL Chi-restraints excluded: chain E residue 2105 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1178 random chunks: chunk 1058 optimal weight: 3.9990 chunk 805 optimal weight: 4.9990 chunk 556 optimal weight: 6.9990 chunk 118 optimal weight: 20.0000 chunk 511 optimal weight: 0.2980 chunk 719 optimal weight: 30.0000 chunk 1075 optimal weight: 0.5980 chunk 1138 optimal weight: 9.9990 chunk 561 optimal weight: 3.9990 chunk 1019 optimal weight: 0.6980 chunk 306 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 GLN ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1497 GLN B 69 ASN ** B1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1082 ASN ** B1697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 504 ASN ** C 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1378 ASN C1815 ASN ** C1918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 GLN F 594 GLN ** F 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1497 GLN A 994 ASN ** A1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1301 GLN ** A1697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 HIS E 456 GLN ** E 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1378 ASN E1403 GLN E1815 ASN E1918 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 97476 Z= 0.261 Angle : 0.554 12.382 131740 Z= 0.282 Chirality : 0.041 0.289 14678 Planarity : 0.004 0.054 16602 Dihedral : 4.003 54.617 12804 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.37 % Favored : 95.58 % Rotamer: Outliers : 2.90 % Allowed : 17.41 % Favored : 79.69 % 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 (0.08), residues: 11692 helix: 1.63 (0.07), residues: 6308 sheet: 0.42 (0.17), residues: 1006 loop : -1.02 (0.09), residues: 4378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C2094 HIS 0.010 0.001 HIS F1298 PHE 0.056 0.001 PHE C1929 TYR 0.024 0.001 TYR F1543 ARG 0.007 0.000 ARG E1703 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23384 Ramachandran restraints generated. 11692 Oldfield, 0 Emsley, 11692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23384 Ramachandran restraints generated. 11692 Oldfield, 0 Emsley, 11692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1126 residues out of total 10516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 305 poor density : 821 time to evaluate : 8.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1779 MET cc_start: 0.0879 (pmm) cc_final: 0.0627 (ppp) REVERT: B 183 TYR cc_start: 0.8598 (t80) cc_final: 0.7939 (t80) REVERT: B 197 HIS cc_start: 0.8872 (t-170) cc_final: 0.8640 (t-170) REVERT: B 210 MET cc_start: 0.8024 (ptp) cc_final: 0.7787 (mtp) REVERT: B 962 MET cc_start: 0.5346 (mmt) cc_final: 0.5135 (mmt) REVERT: B 993 HIS cc_start: 0.3986 (OUTLIER) cc_final: 0.2942 (t70) REVERT: B 1414 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7390 (mtm) REVERT: B 1518 MET cc_start: 0.8462 (tpp) cc_final: 0.8037 (tpp) REVERT: B 1898 GLU cc_start: 0.8683 (tt0) cc_final: 0.8376 (tm-30) REVERT: B 1913 TYR cc_start: 0.9036 (t80) cc_final: 0.8770 (t80) REVERT: B 2118 ILE cc_start: 0.7077 (OUTLIER) cc_final: 0.6650 (pt) REVERT: C 108 PHE cc_start: 0.8396 (m-80) cc_final: 0.7602 (m-80) REVERT: C 198 LEU cc_start: 0.8372 (mp) cc_final: 0.7856 (mt) REVERT: C 332 TYR cc_start: 0.8364 (m-80) cc_final: 0.8158 (m-10) REVERT: C 345 THR cc_start: 0.8652 (p) cc_final: 0.8449 (p) REVERT: C 418 SER cc_start: 0.6805 (m) cc_final: 0.6445 (p) REVERT: C 1302 LYS cc_start: 0.6830 (OUTLIER) cc_final: 0.6197 (ttmp) REVERT: C 1465 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8153 (ttpt) REVERT: C 1482 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7938 (mp10) REVERT: C 1605 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7596 (pttm) REVERT: C 1655 PHE cc_start: 0.8551 (t80) cc_final: 0.8334 (t80) REVERT: C 1766 MET cc_start: 0.8009 (mmm) cc_final: 0.7622 (mmm) REVERT: F 286 ARG cc_start: 0.3181 (OUTLIER) cc_final: 0.2226 (mmm160) REVERT: F 1298 HIS cc_start: 0.3730 (OUTLIER) cc_final: 0.2561 (p90) REVERT: A 63 PHE cc_start: 0.8751 (m-10) cc_final: 0.8538 (m-10) REVERT: A 110 GLU cc_start: 0.6615 (tp30) cc_final: 0.6160 (tm-30) REVERT: A 141 LYS cc_start: 0.9041 (pptt) cc_final: 0.8701 (tptp) REVERT: A 284 MET cc_start: 0.7780 (tpp) cc_final: 0.6779 (mmt) REVERT: A 792 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8459 (mm) REVERT: A 1150 LEU cc_start: 0.8901 (mt) cc_final: 0.8691 (mt) REVERT: A 1283 MET cc_start: 0.8113 (tpt) cc_final: 0.7797 (tpt) REVERT: A 1398 MET cc_start: 0.6252 (mtm) cc_final: 0.6010 (mtm) REVERT: A 1518 MET cc_start: 0.8476 (tpp) cc_final: 0.8141 (tpp) REVERT: E 207 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8767 (mm) REVERT: E 386 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8655 (mm) REVERT: E 664 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.8058 (mt) REVERT: E 1283 MET cc_start: 0.8727 (tpt) cc_final: 0.8178 (tpt) REVERT: E 1465 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8053 (tttm) REVERT: E 1605 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7108 (pttm) REVERT: E 1655 PHE cc_start: 0.8447 (t80) cc_final: 0.8208 (t80) REVERT: E 1685 MET cc_start: 0.7784 (mmm) cc_final: 0.7481 (mmp) REVERT: E 1766 MET cc_start: 0.7761 (mmm) cc_final: 0.7456 (mmm) outliers start: 305 outliers final: 183 residues processed: 1048 average time/residue: 0.8225 time to fit residues: 1522.1646 Evaluate side-chains 968 residues out of total 10516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 770 time to evaluate : 8.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 377 MET Chi-restraints excluded: chain D residue 1304 MET Chi-restraints excluded: chain D residue 1465 LYS Chi-restraints excluded: chain D residue 1546 LEU Chi-restraints excluded: chain D residue 1607 VAL Chi-restraints excluded: chain D residue 1901 MET Chi-restraints excluded: chain D residue 2052 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 680 TYR Chi-restraints excluded: chain B residue 834 SER Chi-restraints excluded: chain B residue 847 VAL Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 974 THR Chi-restraints excluded: chain B residue 993 HIS Chi-restraints excluded: chain B residue 1012 VAL Chi-restraints excluded: chain B residue 1084 PHE Chi-restraints excluded: chain B residue 1118 LEU Chi-restraints excluded: chain B residue 1165 SER Chi-restraints excluded: chain B residue 1297 SER Chi-restraints excluded: chain B residue 1316 LYS Chi-restraints excluded: chain B residue 1347 PHE Chi-restraints excluded: chain B residue 1414 MET Chi-restraints excluded: chain B residue 1439 ASN Chi-restraints excluded: chain B residue 1486 VAL Chi-restraints excluded: chain B residue 1495 LYS Chi-restraints excluded: chain B residue 1546 LEU Chi-restraints excluded: chain B residue 1548 LEU Chi-restraints excluded: chain B residue 1572 VAL Chi-restraints excluded: chain B residue 1578 VAL Chi-restraints excluded: chain B residue 1598 THR Chi-restraints excluded: chain B residue 1607 VAL Chi-restraints excluded: chain B residue 1613 ILE Chi-restraints excluded: chain B residue 1935 LEU Chi-restraints excluded: chain B residue 2049 ILE Chi-restraints excluded: chain B residue 2052 VAL Chi-restraints excluded: chain B residue 2083 ASP Chi-restraints excluded: chain B residue 2089 SER Chi-restraints excluded: chain B residue 2118 ILE Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 226 TYR Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 743 LEU Chi-restraints excluded: chain C residue 816 ASN Chi-restraints excluded: chain C residue 837 VAL Chi-restraints excluded: chain C residue 866 LEU Chi-restraints excluded: chain C residue 867 LYS Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 878 MET Chi-restraints excluded: chain C residue 894 PHE Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1160 LYS Chi-restraints excluded: chain C residue 1164 VAL Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1174 THR Chi-restraints excluded: chain C residue 1193 LEU Chi-restraints excluded: chain C residue 1203 ASP Chi-restraints excluded: chain C residue 1298 HIS Chi-restraints excluded: chain C residue 1302 LYS Chi-restraints excluded: chain C residue 1354 THR Chi-restraints excluded: chain C residue 1397 THR Chi-restraints excluded: chain C residue 1402 LEU Chi-restraints excluded: chain C residue 1465 LYS Chi-restraints excluded: chain C residue 1482 GLN Chi-restraints excluded: chain C residue 1529 ASP Chi-restraints excluded: chain C residue 1546 LEU Chi-restraints excluded: chain C residue 1554 ASP Chi-restraints excluded: chain C residue 1568 LYS Chi-restraints excluded: chain C residue 1593 MET Chi-restraints excluded: chain C residue 1601 VAL Chi-restraints excluded: chain C residue 1605 LYS Chi-restraints excluded: chain C residue 1698 LEU Chi-restraints excluded: chain C residue 1888 LEU Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 617 MET Chi-restraints excluded: chain F residue 1019 MET Chi-restraints excluded: chain F residue 1034 ASP Chi-restraints excluded: chain F residue 1298 HIS Chi-restraints excluded: chain F residue 1321 THR Chi-restraints excluded: chain F residue 1607 VAL Chi-restraints excluded: chain F residue 2049 ILE Chi-restraints excluded: chain F residue 2052 VAL Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 674 ASN Chi-restraints excluded: chain A residue 680 TYR Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 994 ASN Chi-restraints excluded: chain A residue 1084 PHE Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1154 SER Chi-restraints excluded: chain A residue 1316 LYS Chi-restraints excluded: chain A residue 1347 PHE Chi-restraints excluded: chain A residue 1369 ASP Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1439 ASN Chi-restraints excluded: chain A residue 1486 VAL Chi-restraints excluded: chain A residue 1548 LEU Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 2049 ILE Chi-restraints excluded: chain A residue 2083 ASP Chi-restraints excluded: chain A residue 2089 SER Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 226 TYR Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 357 ILE Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 428 GLU Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 556 VAL Chi-restraints excluded: chain E residue 664 ILE Chi-restraints excluded: chain E residue 694 THR Chi-restraints excluded: chain E residue 743 LEU Chi-restraints excluded: chain E residue 816 ASN Chi-restraints excluded: chain E residue 837 VAL Chi-restraints excluded: chain E residue 866 LEU Chi-restraints excluded: chain E residue 867 LYS Chi-restraints excluded: chain E residue 872 THR Chi-restraints excluded: chain E residue 931 LYS Chi-restraints excluded: chain E residue 1160 LYS Chi-restraints excluded: chain E residue 1164 VAL Chi-restraints excluded: chain E residue 1165 SER Chi-restraints excluded: chain E residue 1174 THR Chi-restraints excluded: chain E residue 1193 LEU Chi-restraints excluded: chain E residue 1203 ASP Chi-restraints excluded: chain E residue 1298 HIS Chi-restraints excluded: chain E residue 1352 MET Chi-restraints excluded: chain E residue 1354 THR Chi-restraints excluded: chain E residue 1358 LEU Chi-restraints excluded: chain E residue 1367 THR Chi-restraints excluded: chain E residue 1397 THR Chi-restraints excluded: chain E residue 1465 LYS Chi-restraints excluded: chain E residue 1475 VAL Chi-restraints excluded: chain E residue 1529 ASP Chi-restraints excluded: chain E residue 1546 LEU Chi-restraints excluded: chain E residue 1554 ASP Chi-restraints excluded: chain E residue 1568 LYS Chi-restraints excluded: chain E residue 1593 MET Chi-restraints excluded: chain E residue 1601 VAL Chi-restraints excluded: chain E residue 1605 LYS Chi-restraints excluded: chain E residue 1698 LEU Chi-restraints excluded: chain E residue 1703 ARG Chi-restraints excluded: chain E residue 1872 ASP Chi-restraints excluded: chain E residue 1900 PHE Chi-restraints excluded: chain E residue 2098 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1178 random chunks: chunk 948 optimal weight: 3.9990 chunk 646 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 847 optimal weight: 0.9980 chunk 469 optimal weight: 2.9990 chunk 971 optimal weight: 8.9990 chunk 787 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 581 optimal weight: 6.9990 chunk 1022 optimal weight: 0.8980 chunk 287 optimal weight: 0.3980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 274 ASN ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN ** B1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1082 ASN ** B1697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1364 GLN ** C1918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN F 571 ASN F 776 ASN ** F 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1469 ASN ** A 993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 GLN A1082 ASN A1301 GLN ** A1697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 HIS E 323 ASN E 410 HIS E 457 ASN ** E 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 97476 Z= 0.252 Angle : 0.549 10.930 131740 Z= 0.278 Chirality : 0.040 0.313 14678 Planarity : 0.004 0.051 16602 Dihedral : 3.918 41.554 12798 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.30 % Favored : 95.65 % Rotamer: Outliers : 3.04 % Allowed : 17.71 % Favored : 79.25 % 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: 0.85 (0.08), residues: 11692 helix: 1.63 (0.07), residues: 6310 sheet: 0.40 (0.17), residues: 996 loop : -0.99 (0.09), residues: 4386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B1636 HIS 0.011 0.001 HIS A 993 PHE 0.036 0.001 PHE C1929 TYR 0.024 0.001 TYR A 32 ARG 0.010 0.000 ARG D 286 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23384 Ramachandran restraints generated. 11692 Oldfield, 0 Emsley, 11692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23384 Ramachandran restraints generated. 11692 Oldfield, 0 Emsley, 11692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1118 residues out of total 10516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 320 poor density : 798 time to evaluate : 8.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1246 MET cc_start: 0.3954 (ppp) cc_final: 0.3635 (ppp) REVERT: B 63 PHE cc_start: 0.8647 (m-10) cc_final: 0.8406 (m-10) REVERT: B 183 TYR cc_start: 0.8596 (t80) cc_final: 0.7937 (t80) REVERT: B 197 HIS cc_start: 0.8871 (t-170) cc_final: 0.8645 (t-170) REVERT: B 210 MET cc_start: 0.8134 (ptp) cc_final: 0.7881 (mtp) REVERT: B 962 MET cc_start: 0.5346 (mmt) cc_final: 0.5139 (mmt) REVERT: B 993 HIS cc_start: 0.4013 (OUTLIER) cc_final: 0.3021 (t70) REVERT: B 1398 MET cc_start: 0.5929 (mtm) cc_final: 0.5198 (mtm) REVERT: B 1414 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7357 (mtm) REVERT: B 1518 MET cc_start: 0.8498 (tpp) cc_final: 0.8069 (tpp) REVERT: B 1685 MET cc_start: 0.8885 (tpt) cc_final: 0.8346 (ttm) REVERT: B 1898 GLU cc_start: 0.8689 (tt0) cc_final: 0.8387 (tm-30) REVERT: B 1913 TYR cc_start: 0.9038 (t80) cc_final: 0.8781 (t80) REVERT: B 2118 ILE cc_start: 0.7045 (OUTLIER) cc_final: 0.6619 (pt) REVERT: C 108 PHE cc_start: 0.8405 (m-80) cc_final: 0.7692 (m-80) REVERT: C 198 LEU cc_start: 0.8336 (mp) cc_final: 0.7843 (mt) REVERT: C 332 TYR cc_start: 0.8393 (m-80) cc_final: 0.8171 (m-10) REVERT: C 345 THR cc_start: 0.8652 (p) cc_final: 0.8450 (p) REVERT: C 418 SER cc_start: 0.6870 (OUTLIER) cc_final: 0.6539 (p) REVERT: C 650 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7559 (mtt-85) REVERT: C 667 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7664 (tp) REVERT: C 818 GLU cc_start: 0.6207 (mt-10) cc_final: 0.5905 (mt-10) REVERT: C 940 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7221 (mt-10) REVERT: C 1302 LYS cc_start: 0.6819 (OUTLIER) cc_final: 0.6191 (tttp) REVERT: C 1465 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8147 (ttpt) REVERT: C 1482 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7947 (mp10) REVERT: C 1605 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7608 (pttm) REVERT: C 1655 PHE cc_start: 0.8615 (t80) cc_final: 0.8378 (t80) REVERT: C 1766 MET cc_start: 0.8020 (mmm) cc_final: 0.7597 (mmm) REVERT: F 286 ARG cc_start: 0.3350 (OUTLIER) cc_final: 0.2426 (mmm160) REVERT: F 967 MET cc_start: -0.1403 (tpt) cc_final: -0.2182 (tpt) REVERT: F 1298 HIS cc_start: 0.4001 (OUTLIER) cc_final: 0.2882 (p90) REVERT: A 63 PHE cc_start: 0.8752 (m-10) cc_final: 0.8521 (m-10) REVERT: A 110 GLU cc_start: 0.6734 (tp30) cc_final: 0.6250 (tm-30) REVERT: A 141 LYS cc_start: 0.9028 (pptt) cc_final: 0.8713 (tptp) REVERT: A 560 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7653 (mtp) REVERT: A 792 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8488 (mm) REVERT: A 881 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8827 (tp) REVERT: A 1150 LEU cc_start: 0.8932 (mt) cc_final: 0.8711 (mt) REVERT: A 1283 MET cc_start: 0.8122 (tpt) cc_final: 0.7715 (tpt) REVERT: A 1518 MET cc_start: 0.8435 (tpp) cc_final: 0.8134 (tpp) REVERT: A 2092 ARG cc_start: 0.8178 (ttp-110) cc_final: 0.7910 (ttm110) REVERT: E 193 TYR cc_start: 0.8549 (t80) cc_final: 0.8094 (t80) REVERT: E 207 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8683 (mm) REVERT: E 386 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8623 (mm) REVERT: E 544 ASP cc_start: 0.8143 (t0) cc_final: 0.7892 (t0) REVERT: E 664 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.8042 (mt) REVERT: E 1283 MET cc_start: 0.8687 (tpt) cc_final: 0.8173 (tpt) REVERT: E 1465 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8026 (tttm) REVERT: E 1482 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7673 (mp10) REVERT: E 1605 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7251 (pttm) REVERT: E 1654 TRP cc_start: 0.8842 (t-100) cc_final: 0.8617 (t-100) REVERT: E 1685 MET cc_start: 0.7758 (mmm) cc_final: 0.7453 (mmp) REVERT: E 1766 MET cc_start: 0.7781 (mmm) cc_final: 0.7425 (mmm) outliers start: 320 outliers final: 220 residues processed: 1041 average time/residue: 0.8235 time to fit residues: 1523.0971 Evaluate side-chains 997 residues out of total 10516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 755 time to evaluate : 8.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 286 ARG Chi-restraints excluded: chain D residue 377 MET Chi-restraints excluded: chain D residue 1164 VAL Chi-restraints excluded: chain D residue 1298 HIS Chi-restraints excluded: chain D residue 1304 MET Chi-restraints excluded: chain D residue 1399 GLN Chi-restraints excluded: chain D residue 1425 THR Chi-restraints excluded: chain D residue 1465 LYS Chi-restraints excluded: chain D residue 1546 LEU Chi-restraints excluded: chain D residue 1556 MET Chi-restraints excluded: chain D residue 1607 VAL Chi-restraints excluded: chain D residue 1891 ILE Chi-restraints excluded: chain D residue 1901 MET Chi-restraints excluded: chain D residue 2052 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 680 TYR Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 834 SER Chi-restraints excluded: chain B residue 847 VAL Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 974 THR Chi-restraints excluded: chain B residue 993 HIS Chi-restraints excluded: chain B residue 1012 VAL Chi-restraints excluded: chain B residue 1084 PHE Chi-restraints excluded: chain B residue 1118 LEU Chi-restraints excluded: chain B residue 1122 GLN Chi-restraints excluded: chain B residue 1165 SER Chi-restraints excluded: chain B residue 1259 THR Chi-restraints excluded: chain B residue 1294 LEU Chi-restraints excluded: chain B residue 1297 SER Chi-restraints excluded: chain B residue 1316 LYS Chi-restraints excluded: chain B residue 1347 PHE Chi-restraints excluded: chain B residue 1372 ILE Chi-restraints excluded: chain B residue 1414 MET Chi-restraints excluded: chain B residue 1439 ASN Chi-restraints excluded: chain B residue 1486 VAL Chi-restraints excluded: chain B residue 1495 LYS Chi-restraints excluded: chain B residue 1546 LEU Chi-restraints excluded: chain B residue 1548 LEU Chi-restraints excluded: chain B residue 1572 VAL Chi-restraints excluded: chain B residue 1578 VAL Chi-restraints excluded: chain B residue 1598 THR Chi-restraints excluded: chain B residue 1613 ILE Chi-restraints excluded: chain B residue 1866 ILE Chi-restraints excluded: chain B residue 1935 LEU Chi-restraints excluded: chain B residue 2049 ILE Chi-restraints excluded: chain B residue 2083 ASP Chi-restraints excluded: chain B residue 2089 SER Chi-restraints excluded: chain B residue 2118 ILE Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 226 TYR Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 650 ARG Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 743 LEU Chi-restraints excluded: chain C residue 816 ASN Chi-restraints excluded: chain C residue 837 VAL Chi-restraints excluded: chain C residue 866 LEU Chi-restraints excluded: chain C residue 867 LYS Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 878 MET Chi-restraints excluded: chain C residue 894 PHE Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 940 GLU Chi-restraints excluded: chain C residue 1160 LYS Chi-restraints excluded: chain C residue 1164 VAL Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1174 THR Chi-restraints excluded: chain C residue 1193 LEU Chi-restraints excluded: chain C residue 1203 ASP Chi-restraints excluded: chain C residue 1218 LEU Chi-restraints excluded: chain C residue 1298 HIS Chi-restraints excluded: chain C residue 1302 LYS Chi-restraints excluded: chain C residue 1354 THR Chi-restraints excluded: chain C residue 1367 THR Chi-restraints excluded: chain C residue 1397 THR Chi-restraints excluded: chain C residue 1402 LEU Chi-restraints excluded: chain C residue 1465 LYS Chi-restraints excluded: chain C residue 1482 GLN Chi-restraints excluded: chain C residue 1529 ASP Chi-restraints excluded: chain C residue 1546 LEU Chi-restraints excluded: chain C residue 1568 LYS Chi-restraints excluded: chain C residue 1593 MET Chi-restraints excluded: chain C residue 1601 VAL Chi-restraints excluded: chain C residue 1605 LYS Chi-restraints excluded: chain C residue 1698 LEU Chi-restraints excluded: chain C residue 1872 ASP Chi-restraints excluded: chain C residue 1888 LEU Chi-restraints excluded: chain C residue 2071 LEU Chi-restraints excluded: chain C residue 2098 VAL Chi-restraints excluded: chain F residue 284 MET Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 617 MET Chi-restraints excluded: chain F residue 1019 MET Chi-restraints excluded: chain F residue 1034 ASP Chi-restraints excluded: chain F residue 1164 VAL Chi-restraints excluded: chain F residue 1298 HIS Chi-restraints excluded: chain F residue 1425 THR Chi-restraints excluded: chain F residue 1546 LEU Chi-restraints excluded: chain F residue 1607 VAL Chi-restraints excluded: chain F residue 2049 ILE Chi-restraints excluded: chain F residue 2052 VAL Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 680 TYR Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 994 ASN Chi-restraints excluded: chain A residue 1084 PHE Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1154 SER Chi-restraints excluded: chain A residue 1183 ILE Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1297 SER Chi-restraints excluded: chain A residue 1316 LYS Chi-restraints excluded: chain A residue 1347 PHE Chi-restraints excluded: chain A residue 1369 ASP Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1439 ASN Chi-restraints excluded: chain A residue 1548 LEU Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1607 VAL Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1936 ILE Chi-restraints excluded: chain A residue 2049 ILE Chi-restraints excluded: chain A residue 2052 VAL Chi-restraints excluded: chain A residue 2083 ASP Chi-restraints excluded: chain A residue 2089 SER Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 226 TYR Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 357 ILE Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 428 GLU Chi-restraints excluded: chain E residue 556 VAL Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 664 ILE Chi-restraints excluded: chain E residue 694 THR Chi-restraints excluded: chain E residue 743 LEU Chi-restraints excluded: chain E residue 816 ASN Chi-restraints excluded: chain E residue 833 MET Chi-restraints excluded: chain E residue 837 VAL Chi-restraints excluded: chain E residue 866 LEU Chi-restraints excluded: chain E residue 867 LYS Chi-restraints excluded: chain E residue 872 THR Chi-restraints excluded: chain E residue 931 LYS Chi-restraints excluded: chain E residue 1034 ASP Chi-restraints excluded: chain E residue 1108 GLU Chi-restraints excluded: chain E residue 1160 LYS Chi-restraints excluded: chain E residue 1164 VAL Chi-restraints excluded: chain E residue 1165 SER Chi-restraints excluded: chain E residue 1174 THR Chi-restraints excluded: chain E residue 1203 ASP Chi-restraints excluded: chain E residue 1298 HIS Chi-restraints excluded: chain E residue 1352 MET Chi-restraints excluded: chain E residue 1354 THR Chi-restraints excluded: chain E residue 1358 LEU Chi-restraints excluded: chain E residue 1367 THR Chi-restraints excluded: chain E residue 1397 THR Chi-restraints excluded: chain E residue 1402 LEU Chi-restraints excluded: chain E residue 1465 LYS Chi-restraints excluded: chain E residue 1475 VAL Chi-restraints excluded: chain E residue 1482 GLN Chi-restraints excluded: chain E residue 1529 ASP Chi-restraints excluded: chain E residue 1546 LEU Chi-restraints excluded: chain E residue 1564 TYR Chi-restraints excluded: chain E residue 1568 LYS Chi-restraints excluded: chain E residue 1593 MET Chi-restraints excluded: chain E residue 1601 VAL Chi-restraints excluded: chain E residue 1605 LYS Chi-restraints excluded: chain E residue 1698 LEU Chi-restraints excluded: chain E residue 1703 ARG Chi-restraints excluded: chain E residue 1872 ASP Chi-restraints excluded: chain E residue 1900 PHE Chi-restraints excluded: chain E residue 2098 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1178 random chunks: chunk 383 optimal weight: 4.9990 chunk 1025 optimal weight: 0.4980 chunk 225 optimal weight: 0.9980 chunk 668 optimal weight: 9.9990 chunk 281 optimal weight: 5.9990 chunk 1139 optimal weight: 10.0000 chunk 946 optimal weight: 3.9990 chunk 527 optimal weight: 0.6980 chunk 94 optimal weight: 50.0000 chunk 377 optimal weight: 9.9990 chunk 598 optimal weight: 6.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 776 ASN ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1651 GLN ** D1697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1881 HIS B 69 ASN B 274 ASN B 827 ASN ** B1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 ASN ** C 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1651 GLN F1869 GLN A 827 ASN ** A 993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 994 ASN ** A1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1301 GLN ** A1697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2133 HIS ** E 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 HIS E 311 GLN E 504 ASN ** E 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2111 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 97476 Z= 0.356 Angle : 0.596 11.800 131740 Z= 0.304 Chirality : 0.042 0.323 14678 Planarity : 0.004 0.053 16602 Dihedral : 4.100 50.739 12798 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.90 % Favored : 95.04 % Rotamer: Outliers : 3.41 % Allowed : 18.29 % Favored : 78.30 % 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: 0.69 (0.08), residues: 11692 helix: 1.50 (0.07), residues: 6308 sheet: 0.34 (0.17), residues: 980 loop : -1.05 (0.09), residues: 4404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 172 HIS 0.009 0.001 HIS D1298 PHE 0.036 0.002 PHE C1660 TYR 0.022 0.001 TYR C1543 ARG 0.006 0.000 ARG D 286 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23384 Ramachandran restraints generated. 11692 Oldfield, 0 Emsley, 11692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23384 Ramachandran restraints generated. 11692 Oldfield, 0 Emsley, 11692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1122 residues out of total 10516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 359 poor density : 763 time to evaluate : 8.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1274 MET cc_start: 0.5337 (tmm) cc_final: 0.3774 (mmt) REVERT: B 32 TYR cc_start: 0.7971 (m-80) cc_final: 0.7557 (m-80) REVERT: B 183 TYR cc_start: 0.8623 (t80) cc_final: 0.7956 (t80) REVERT: B 197 HIS cc_start: 0.8917 (t-170) cc_final: 0.8685 (t-170) REVERT: B 210 MET cc_start: 0.8121 (ptp) cc_final: 0.7815 (mtp) REVERT: B 560 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7492 (mtp) REVERT: B 881 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8655 (tp) REVERT: B 1398 MET cc_start: 0.5980 (mtm) cc_final: 0.5236 (mtm) REVERT: B 1414 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7520 (mtm) REVERT: B 1518 MET cc_start: 0.8592 (tpp) cc_final: 0.8211 (tpp) REVERT: B 1583 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7597 (mm-30) REVERT: B 1913 TYR cc_start: 0.9071 (t80) cc_final: 0.8788 (t80) REVERT: B 2112 MET cc_start: 0.9015 (mpp) cc_final: 0.8804 (mpp) REVERT: B 2118 ILE cc_start: 0.7182 (OUTLIER) cc_final: 0.6719 (pt) REVERT: C 108 PHE cc_start: 0.8470 (m-80) cc_final: 0.7791 (m-80) REVERT: C 295 GLN cc_start: 0.9170 (OUTLIER) cc_final: 0.8550 (mt0) REVERT: C 332 TYR cc_start: 0.8513 (m-80) cc_final: 0.8261 (m-10) REVERT: C 345 THR cc_start: 0.8684 (p) cc_final: 0.8460 (p) REVERT: C 418 SER cc_start: 0.6973 (OUTLIER) cc_final: 0.6671 (p) REVERT: C 424 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7471 (mp) REVERT: C 650 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7597 (mtt-85) REVERT: C 667 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7701 (tp) REVERT: C 818 GLU cc_start: 0.6062 (mt-10) cc_final: 0.5750 (mt-10) REVERT: C 940 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7308 (mt-10) REVERT: C 1302 LYS cc_start: 0.6971 (OUTLIER) cc_final: 0.6420 (tttp) REVERT: C 1465 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8154 (ttpt) REVERT: C 1605 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7590 (pttm) REVERT: C 1654 TRP cc_start: 0.9034 (t60) cc_final: 0.8818 (t-100) REVERT: C 1766 MET cc_start: 0.8060 (mmm) cc_final: 0.7560 (mmm) REVERT: F 1271 MET cc_start: 0.0755 (tmm) cc_final: 0.0478 (tmm) REVERT: F 1298 HIS cc_start: 0.3906 (OUTLIER) cc_final: 0.2704 (p90) REVERT: F 1539 LYS cc_start: 0.7807 (tppt) cc_final: 0.7388 (mmtt) REVERT: A 63 PHE cc_start: 0.8787 (m-10) cc_final: 0.8534 (m-10) REVERT: A 110 GLU cc_start: 0.7076 (tp30) cc_final: 0.6454 (tm-30) REVERT: A 560 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7638 (mtp) REVERT: A 792 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8578 (mm) REVERT: A 805 SER cc_start: 0.1792 (OUTLIER) cc_final: 0.0445 (t) REVERT: A 845 SER cc_start: 0.8164 (m) cc_final: 0.7894 (p) REVERT: A 881 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8859 (tp) REVERT: A 993 HIS cc_start: 0.4508 (OUTLIER) cc_final: 0.3516 (t-90) REVERT: A 1021 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7854 (mpp80) REVERT: A 1150 LEU cc_start: 0.9139 (mt) cc_final: 0.8884 (mt) REVERT: A 1294 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8450 (mm) REVERT: A 1398 MET cc_start: 0.5925 (mtm) cc_final: 0.5603 (mtm) REVERT: A 1493 ARG cc_start: 0.7154 (tmt170) cc_final: 0.6936 (tmt170) REVERT: A 1518 MET cc_start: 0.8408 (tpp) cc_final: 0.8108 (tpp) REVERT: A 2092 ARG cc_start: 0.8260 (ttp-110) cc_final: 0.8047 (ttp-110) REVERT: E 386 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8729 (mm) REVERT: E 415 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6563 (mt-10) REVERT: E 544 ASP cc_start: 0.8203 (t0) cc_final: 0.7950 (t0) REVERT: E 650 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7760 (mtt-85) REVERT: E 970 SER cc_start: 0.9061 (OUTLIER) cc_final: 0.8806 (t) REVERT: E 1283 MET cc_start: 0.8710 (tpt) cc_final: 0.8206 (tpt) REVERT: E 1465 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.7973 (tmmt) REVERT: E 1482 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.7718 (mp10) REVERT: E 1605 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7543 (pttm) REVERT: E 1685 MET cc_start: 0.7729 (mmm) cc_final: 0.7403 (mmp) REVERT: E 1766 MET cc_start: 0.7829 (mmm) cc_final: 0.7430 (mmm) outliers start: 359 outliers final: 248 residues processed: 1039 average time/residue: 0.8902 time to fit residues: 1646.4212 Evaluate side-chains 1008 residues out of total 10516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 732 time to evaluate : 8.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 286 ARG Chi-restraints excluded: chain D residue 377 MET Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 1164 VAL Chi-restraints excluded: chain D residue 1304 MET Chi-restraints excluded: chain D residue 1398 MET Chi-restraints excluded: chain D residue 1399 GLN Chi-restraints excluded: chain D residue 1414 MET Chi-restraints excluded: chain D residue 1465 LYS Chi-restraints excluded: chain D residue 1546 LEU Chi-restraints excluded: chain D residue 1556 MET Chi-restraints excluded: chain D residue 1607 VAL Chi-restraints excluded: chain D residue 1891 ILE Chi-restraints excluded: chain D residue 1915 LEU Chi-restraints excluded: chain D residue 2052 VAL Chi-restraints excluded: chain D residue 2076 VAL Chi-restraints excluded: chain D residue 2097 CYS Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 560 MET Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 594 GLN Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 680 TYR Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 834 SER Chi-restraints excluded: chain B residue 847 VAL Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 881 ILE Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 974 THR Chi-restraints excluded: chain B residue 993 HIS Chi-restraints excluded: chain B residue 1012 VAL Chi-restraints excluded: chain B residue 1084 PHE Chi-restraints excluded: chain B residue 1118 LEU Chi-restraints excluded: chain B residue 1165 SER Chi-restraints excluded: chain B residue 1259 THR Chi-restraints excluded: chain B residue 1294 LEU Chi-restraints excluded: chain B residue 1297 SER Chi-restraints excluded: chain B residue 1316 LYS Chi-restraints excluded: chain B residue 1317 LEU Chi-restraints excluded: chain B residue 1340 ILE Chi-restraints excluded: chain B residue 1347 PHE Chi-restraints excluded: chain B residue 1372 ILE Chi-restraints excluded: chain B residue 1414 MET Chi-restraints excluded: chain B residue 1439 ASN Chi-restraints excluded: chain B residue 1486 VAL Chi-restraints excluded: chain B residue 1495 LYS Chi-restraints excluded: chain B residue 1546 LEU Chi-restraints excluded: chain B residue 1548 LEU Chi-restraints excluded: chain B residue 1572 VAL Chi-restraints excluded: chain B residue 1578 VAL Chi-restraints excluded: chain B residue 1581 THR Chi-restraints excluded: chain B residue 1583 GLU Chi-restraints excluded: chain B residue 1598 THR Chi-restraints excluded: chain B residue 1607 VAL Chi-restraints excluded: chain B residue 1613 ILE Chi-restraints excluded: chain B residue 1664 LEU Chi-restraints excluded: chain B residue 1866 ILE Chi-restraints excluded: chain B residue 1924 VAL Chi-restraints excluded: chain B residue 1935 LEU Chi-restraints excluded: chain B residue 2083 ASP Chi-restraints excluded: chain B residue 2089 SER Chi-restraints excluded: chain B residue 2118 ILE Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 226 TYR Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 650 ARG Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 743 LEU Chi-restraints excluded: chain C residue 816 ASN Chi-restraints excluded: chain C residue 837 VAL Chi-restraints excluded: chain C residue 866 LEU Chi-restraints excluded: chain C residue 867 LYS Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 878 MET Chi-restraints excluded: chain C residue 894 PHE Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 940 GLU Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 989 THR Chi-restraints excluded: chain C residue 1034 ASP Chi-restraints excluded: chain C residue 1112 ASP Chi-restraints excluded: chain C residue 1160 LYS Chi-restraints excluded: chain C residue 1164 VAL Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1193 LEU Chi-restraints excluded: chain C residue 1203 ASP Chi-restraints excluded: chain C residue 1255 GLN Chi-restraints excluded: chain C residue 1298 HIS Chi-restraints excluded: chain C residue 1302 LYS Chi-restraints excluded: chain C residue 1354 THR Chi-restraints excluded: chain C residue 1397 THR Chi-restraints excluded: chain C residue 1402 LEU Chi-restraints excluded: chain C residue 1465 LYS Chi-restraints excluded: chain C residue 1500 GLN Chi-restraints excluded: chain C residue 1529 ASP Chi-restraints excluded: chain C residue 1546 LEU Chi-restraints excluded: chain C residue 1554 ASP Chi-restraints excluded: chain C residue 1568 LYS Chi-restraints excluded: chain C residue 1593 MET Chi-restraints excluded: chain C residue 1601 VAL Chi-restraints excluded: chain C residue 1605 LYS Chi-restraints excluded: chain C residue 1698 LEU Chi-restraints excluded: chain C residue 1872 ASP Chi-restraints excluded: chain C residue 1888 LEU Chi-restraints excluded: chain C residue 2071 LEU Chi-restraints excluded: chain C residue 2098 VAL Chi-restraints excluded: chain F residue 284 MET Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 406 ASN Chi-restraints excluded: chain F residue 617 MET Chi-restraints excluded: chain F residue 1019 MET Chi-restraints excluded: chain F residue 1034 ASP Chi-restraints excluded: chain F residue 1164 VAL Chi-restraints excluded: chain F residue 1298 HIS Chi-restraints excluded: chain F residue 1398 MET Chi-restraints excluded: chain F residue 1425 THR Chi-restraints excluded: chain F residue 1546 LEU Chi-restraints excluded: chain F residue 1607 VAL Chi-restraints excluded: chain F residue 2049 ILE Chi-restraints excluded: chain F residue 2052 VAL Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 680 TYR Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 993 HIS Chi-restraints excluded: chain A residue 1021 ARG Chi-restraints excluded: chain A residue 1084 PHE Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1154 SER Chi-restraints excluded: chain A residue 1183 ILE Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1297 SER Chi-restraints excluded: chain A residue 1316 LYS Chi-restraints excluded: chain A residue 1347 PHE Chi-restraints excluded: chain A residue 1369 ASP Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1439 ASN Chi-restraints excluded: chain A residue 1486 VAL Chi-restraints excluded: chain A residue 1548 LEU Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1607 VAL Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1901 MET Chi-restraints excluded: chain A residue 1936 ILE Chi-restraints excluded: chain A residue 2052 VAL Chi-restraints excluded: chain A residue 2083 ASP Chi-restraints excluded: chain A residue 2089 SER Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 226 TYR Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 357 ILE Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 428 GLU Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 556 VAL Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 634 THR Chi-restraints excluded: chain E residue 650 ARG Chi-restraints excluded: chain E residue 694 THR Chi-restraints excluded: chain E residue 705 MET Chi-restraints excluded: chain E residue 743 LEU Chi-restraints excluded: chain E residue 816 ASN Chi-restraints excluded: chain E residue 837 VAL Chi-restraints excluded: chain E residue 866 LEU Chi-restraints excluded: chain E residue 867 LYS Chi-restraints excluded: chain E residue 872 THR Chi-restraints excluded: chain E residue 931 LYS Chi-restraints excluded: chain E residue 970 SER Chi-restraints excluded: chain E residue 974 THR Chi-restraints excluded: chain E residue 989 THR Chi-restraints excluded: chain E residue 1034 ASP Chi-restraints excluded: chain E residue 1160 LYS Chi-restraints excluded: chain E residue 1164 VAL Chi-restraints excluded: chain E residue 1165 SER Chi-restraints excluded: chain E residue 1174 THR Chi-restraints excluded: chain E residue 1203 ASP Chi-restraints excluded: chain E residue 1297 SER Chi-restraints excluded: chain E residue 1298 HIS Chi-restraints excluded: chain E residue 1354 THR Chi-restraints excluded: chain E residue 1358 LEU Chi-restraints excluded: chain E residue 1397 THR Chi-restraints excluded: chain E residue 1402 LEU Chi-restraints excluded: chain E residue 1441 SER Chi-restraints excluded: chain E residue 1465 LYS Chi-restraints excluded: chain E residue 1475 VAL Chi-restraints excluded: chain E residue 1482 GLN Chi-restraints excluded: chain E residue 1529 ASP Chi-restraints excluded: chain E residue 1546 LEU Chi-restraints excluded: chain E residue 1562 MET Chi-restraints excluded: chain E residue 1564 TYR Chi-restraints excluded: chain E residue 1568 LYS Chi-restraints excluded: chain E residue 1601 VAL Chi-restraints excluded: chain E residue 1605 LYS Chi-restraints excluded: chain E residue 1662 GLU Chi-restraints excluded: chain E residue 1698 LEU Chi-restraints excluded: chain E residue 1703 ARG Chi-restraints excluded: chain E residue 1872 ASP Chi-restraints excluded: chain E residue 1900 PHE Chi-restraints excluded: chain E residue 2098 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1178 random chunks: chunk 1098 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 649 optimal weight: 50.0000 chunk 832 optimal weight: 0.9980 chunk 644 optimal weight: 30.0000 chunk 959 optimal weight: 0.4980 chunk 636 optimal weight: 40.0000 chunk 1135 optimal weight: 6.9990 chunk 710 optimal weight: 5.9990 chunk 692 optimal weight: 50.0000 chunk 524 optimal weight: 3.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN ** B1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1497 GLN ** B1697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2070 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 457 ASN ** C 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 571 ASN ** F 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1881 HIS A 608 HIS ** A 993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1301 GLN ** A1697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 HIS E 277 ASN ** E 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1095 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 97476 Z= 0.388 Angle : 0.616 12.440 131740 Z= 0.313 Chirality : 0.042 0.364 14678 Planarity : 0.004 0.055 16602 Dihedral : 4.178 42.683 12798 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.86 % Favored : 95.07 % Rotamer: Outliers : 3.39 % Allowed : 18.88 % Favored : 77.73 % 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: 0.60 (0.08), residues: 11692 helix: 1.43 (0.07), residues: 6296 sheet: 0.23 (0.17), residues: 962 loop : -1.07 (0.09), residues: 4434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E2094 HIS 0.009 0.001 HIS D1298 PHE 0.031 0.002 PHE E1929 TYR 0.036 0.002 TYR F1543 ARG 0.006 0.000 ARG D 286 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23384 Ramachandran restraints generated. 11692 Oldfield, 0 Emsley, 11692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23384 Ramachandran restraints generated. 11692 Oldfield, 0 Emsley, 11692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1107 residues out of total 10516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 357 poor density : 750 time to evaluate : 8.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1274 MET cc_start: 0.5384 (tmm) cc_final: 0.3894 (mmt) REVERT: D 1298 HIS cc_start: 0.4296 (OUTLIER) cc_final: 0.2463 (p90) REVERT: B 77 LYS cc_start: 0.8012 (ttmm) cc_final: 0.7803 (ttmm) REVERT: B 183 TYR cc_start: 0.8653 (t80) cc_final: 0.7945 (t80) REVERT: B 197 HIS cc_start: 0.8918 (t-170) cc_final: 0.8694 (t-170) REVERT: B 210 MET cc_start: 0.8141 (ptp) cc_final: 0.7849 (mtp) REVERT: B 560 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7539 (mtp) REVERT: B 769 MET cc_start: 0.8643 (mmm) cc_final: 0.8389 (mmm) REVERT: B 881 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8665 (tp) REVERT: B 993 HIS cc_start: 0.4026 (OUTLIER) cc_final: 0.2898 (t70) REVERT: B 1021 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7835 (tpp80) REVERT: B 1398 MET cc_start: 0.5974 (mtm) cc_final: 0.5335 (mtm) REVERT: B 1414 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7573 (mtm) REVERT: B 1518 MET cc_start: 0.8564 (tpp) cc_final: 0.8194 (tpp) REVERT: B 1583 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7565 (mm-30) REVERT: B 1913 TYR cc_start: 0.9091 (t80) cc_final: 0.8802 (t80) REVERT: B 2118 ILE cc_start: 0.7315 (OUTLIER) cc_final: 0.6868 (pt) REVERT: C 108 PHE cc_start: 0.8475 (m-80) cc_final: 0.7824 (m-80) REVERT: C 295 GLN cc_start: 0.9167 (OUTLIER) cc_final: 0.8564 (mt0) REVERT: C 345 THR cc_start: 0.8695 (p) cc_final: 0.8472 (p) REVERT: C 418 SER cc_start: 0.6918 (OUTLIER) cc_final: 0.6628 (p) REVERT: C 424 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7498 (mp) REVERT: C 650 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7580 (mtt-85) REVERT: C 667 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7708 (tp) REVERT: C 940 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7350 (mt-10) REVERT: C 1302 LYS cc_start: 0.7018 (OUTLIER) cc_final: 0.6585 (tttp) REVERT: C 1465 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8122 (ttpt) REVERT: C 1605 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7560 (pttm) REVERT: C 1654 TRP cc_start: 0.9061 (t60) cc_final: 0.8809 (t-100) REVERT: C 1766 MET cc_start: 0.8135 (mmm) cc_final: 0.7649 (mmm) REVERT: F 233 MET cc_start: -0.2458 (mtt) cc_final: -0.2696 (mtp) REVERT: A 63 PHE cc_start: 0.8789 (m-10) cc_final: 0.8551 (m-10) REVERT: A 110 GLU cc_start: 0.7312 (tp30) cc_final: 0.6565 (tm-30) REVERT: A 560 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.7626 (mtp) REVERT: A 805 SER cc_start: 0.1970 (OUTLIER) cc_final: 0.0819 (t) REVERT: A 881 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8840 (tp) REVERT: A 993 HIS cc_start: 0.4360 (OUTLIER) cc_final: 0.3662 (t-170) REVERT: A 1150 LEU cc_start: 0.9229 (mt) cc_final: 0.8972 (mt) REVERT: A 1294 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8429 (mm) REVERT: A 1398 MET cc_start: 0.5913 (mtm) cc_final: 0.5530 (mtm) REVERT: A 1518 MET cc_start: 0.8424 (tpp) cc_final: 0.8130 (tpp) REVERT: E 94 MET cc_start: 0.1254 (ppp) cc_final: 0.0875 (ppp) REVERT: E 415 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6364 (mt-10) REVERT: E 544 ASP cc_start: 0.8209 (t0) cc_final: 0.7935 (t0) REVERT: E 650 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7727 (mtt-85) REVERT: E 970 SER cc_start: 0.9088 (OUTLIER) cc_final: 0.8857 (t) REVERT: E 1283 MET cc_start: 0.8707 (tpt) cc_final: 0.8267 (tpt) REVERT: E 1465 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.7967 (tttm) REVERT: E 1482 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7791 (mp10) REVERT: E 1605 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7568 (pttm) REVERT: E 1685 MET cc_start: 0.7849 (mmm) cc_final: 0.7503 (mmp) REVERT: E 1766 MET cc_start: 0.7905 (mmm) cc_final: 0.7517 (mmm) outliers start: 357 outliers final: 259 residues processed: 1027 average time/residue: 0.8324 time to fit residues: 1513.4093 Evaluate side-chains 1014 residues out of total 10516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 728 time to evaluate : 8.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 286 ARG Chi-restraints excluded: chain D residue 377 MET Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 1164 VAL Chi-restraints excluded: chain D residue 1298 HIS Chi-restraints excluded: chain D residue 1304 MET Chi-restraints excluded: chain D residue 1367 THR Chi-restraints excluded: chain D residue 1398 MET Chi-restraints excluded: chain D residue 1414 MET Chi-restraints excluded: chain D residue 1425 THR Chi-restraints excluded: chain D residue 1465 LYS Chi-restraints excluded: chain D residue 1546 LEU Chi-restraints excluded: chain D residue 1556 MET Chi-restraints excluded: chain D residue 1607 VAL Chi-restraints excluded: chain D residue 1891 ILE Chi-restraints excluded: chain D residue 2052 VAL Chi-restraints excluded: chain D residue 2076 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 560 MET Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 594 GLN Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 680 TYR Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 834 SER Chi-restraints excluded: chain B residue 847 VAL Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 881 ILE Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 974 THR Chi-restraints excluded: chain B residue 993 HIS Chi-restraints excluded: chain B residue 994 ASN Chi-restraints excluded: chain B residue 1012 VAL Chi-restraints excluded: chain B residue 1021 ARG Chi-restraints excluded: chain B residue 1084 PHE Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain B residue 1118 LEU Chi-restraints excluded: chain B residue 1122 GLN Chi-restraints excluded: chain B residue 1154 SER Chi-restraints excluded: chain B residue 1165 SER Chi-restraints excluded: chain B residue 1259 THR Chi-restraints excluded: chain B residue 1294 LEU Chi-restraints excluded: chain B residue 1297 SER Chi-restraints excluded: chain B residue 1316 LYS Chi-restraints excluded: chain B residue 1317 LEU Chi-restraints excluded: chain B residue 1347 PHE Chi-restraints excluded: chain B residue 1371 ILE Chi-restraints excluded: chain B residue 1372 ILE Chi-restraints excluded: chain B residue 1414 MET Chi-restraints excluded: chain B residue 1439 ASN Chi-restraints excluded: chain B residue 1486 VAL Chi-restraints excluded: chain B residue 1495 LYS Chi-restraints excluded: chain B residue 1546 LEU Chi-restraints excluded: chain B residue 1548 LEU Chi-restraints excluded: chain B residue 1572 VAL Chi-restraints excluded: chain B residue 1578 VAL Chi-restraints excluded: chain B residue 1581 THR Chi-restraints excluded: chain B residue 1583 GLU Chi-restraints excluded: chain B residue 1598 THR Chi-restraints excluded: chain B residue 1607 VAL Chi-restraints excluded: chain B residue 1613 ILE Chi-restraints excluded: chain B residue 1866 ILE Chi-restraints excluded: chain B residue 1924 VAL Chi-restraints excluded: chain B residue 1935 LEU Chi-restraints excluded: chain B residue 2083 ASP Chi-restraints excluded: chain B residue 2089 SER Chi-restraints excluded: chain B residue 2118 ILE Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 226 TYR Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 650 ARG Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 743 LEU Chi-restraints excluded: chain C residue 837 VAL Chi-restraints excluded: chain C residue 866 LEU Chi-restraints excluded: chain C residue 867 LYS Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 878 MET Chi-restraints excluded: chain C residue 894 PHE Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 940 GLU Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 989 THR Chi-restraints excluded: chain C residue 1112 ASP Chi-restraints excluded: chain C residue 1160 LYS Chi-restraints excluded: chain C residue 1164 VAL Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1193 LEU Chi-restraints excluded: chain C residue 1255 GLN Chi-restraints excluded: chain C residue 1297 SER Chi-restraints excluded: chain C residue 1298 HIS Chi-restraints excluded: chain C residue 1302 LYS Chi-restraints excluded: chain C residue 1354 THR Chi-restraints excluded: chain C residue 1397 THR Chi-restraints excluded: chain C residue 1402 LEU Chi-restraints excluded: chain C residue 1424 VAL Chi-restraints excluded: chain C residue 1465 LYS Chi-restraints excluded: chain C residue 1500 GLN Chi-restraints excluded: chain C residue 1529 ASP Chi-restraints excluded: chain C residue 1530 SER Chi-restraints excluded: chain C residue 1536 LYS Chi-restraints excluded: chain C residue 1554 ASP Chi-restraints excluded: chain C residue 1568 LYS Chi-restraints excluded: chain C residue 1593 MET Chi-restraints excluded: chain C residue 1601 VAL Chi-restraints excluded: chain C residue 1605 LYS Chi-restraints excluded: chain C residue 1662 GLU Chi-restraints excluded: chain C residue 1872 ASP Chi-restraints excluded: chain C residue 1888 LEU Chi-restraints excluded: chain C residue 1896 LEU Chi-restraints excluded: chain C residue 1900 PHE Chi-restraints excluded: chain C residue 2034 GLU Chi-restraints excluded: chain C residue 2071 LEU Chi-restraints excluded: chain C residue 2098 VAL Chi-restraints excluded: chain F residue 284 MET Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 617 MET Chi-restraints excluded: chain F residue 1019 MET Chi-restraints excluded: chain F residue 1034 ASP Chi-restraints excluded: chain F residue 1164 VAL Chi-restraints excluded: chain F residue 1414 MET Chi-restraints excluded: chain F residue 1546 LEU Chi-restraints excluded: chain F residue 1607 VAL Chi-restraints excluded: chain F residue 2052 VAL Chi-restraints excluded: chain F residue 2076 VAL Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 680 TYR Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 993 HIS Chi-restraints excluded: chain A residue 994 ASN Chi-restraints excluded: chain A residue 1084 PHE Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1154 SER Chi-restraints excluded: chain A residue 1183 ILE Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1297 SER Chi-restraints excluded: chain A residue 1316 LYS Chi-restraints excluded: chain A residue 1340 ILE Chi-restraints excluded: chain A residue 1347 PHE Chi-restraints excluded: chain A residue 1369 ASP Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1439 ASN Chi-restraints excluded: chain A residue 1486 VAL Chi-restraints excluded: chain A residue 1548 LEU Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1581 THR Chi-restraints excluded: chain A residue 1607 VAL Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1901 MET Chi-restraints excluded: chain A residue 1924 VAL Chi-restraints excluded: chain A residue 1935 LEU Chi-restraints excluded: chain A residue 1936 ILE Chi-restraints excluded: chain A residue 2052 VAL Chi-restraints excluded: chain A residue 2083 ASP Chi-restraints excluded: chain A residue 2089 SER Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 226 TYR Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 357 ILE Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 428 GLU Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 556 VAL Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 634 THR Chi-restraints excluded: chain E residue 650 ARG Chi-restraints excluded: chain E residue 694 THR Chi-restraints excluded: chain E residue 705 MET Chi-restraints excluded: chain E residue 731 LEU Chi-restraints excluded: chain E residue 743 LEU Chi-restraints excluded: chain E residue 816 ASN Chi-restraints excluded: chain E residue 837 VAL Chi-restraints excluded: chain E residue 866 LEU Chi-restraints excluded: chain E residue 867 LYS Chi-restraints excluded: chain E residue 872 THR Chi-restraints excluded: chain E residue 931 LYS Chi-restraints excluded: chain E residue 970 SER Chi-restraints excluded: chain E residue 974 THR Chi-restraints excluded: chain E residue 989 THR Chi-restraints excluded: chain E residue 1034 ASP Chi-restraints excluded: chain E residue 1112 ASP Chi-restraints excluded: chain E residue 1160 LYS Chi-restraints excluded: chain E residue 1164 VAL Chi-restraints excluded: chain E residue 1165 SER Chi-restraints excluded: chain E residue 1174 THR Chi-restraints excluded: chain E residue 1203 ASP Chi-restraints excluded: chain E residue 1297 SER Chi-restraints excluded: chain E residue 1298 HIS Chi-restraints excluded: chain E residue 1354 THR Chi-restraints excluded: chain E residue 1358 LEU Chi-restraints excluded: chain E residue 1397 THR Chi-restraints excluded: chain E residue 1402 LEU Chi-restraints excluded: chain E residue 1465 LYS Chi-restraints excluded: chain E residue 1475 VAL Chi-restraints excluded: chain E residue 1482 GLN Chi-restraints excluded: chain E residue 1529 ASP Chi-restraints excluded: chain E residue 1536 LYS Chi-restraints excluded: chain E residue 1546 LEU Chi-restraints excluded: chain E residue 1562 MET Chi-restraints excluded: chain E residue 1564 TYR Chi-restraints excluded: chain E residue 1568 LYS Chi-restraints excluded: chain E residue 1601 VAL Chi-restraints excluded: chain E residue 1605 LYS Chi-restraints excluded: chain E residue 1698 LEU Chi-restraints excluded: chain E residue 1703 ARG Chi-restraints excluded: chain E residue 1872 ASP Chi-restraints excluded: chain E residue 1900 PHE Chi-restraints excluded: chain E residue 2098 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1178 random chunks: chunk 702 optimal weight: 4.9990 chunk 453 optimal weight: 0.9990 chunk 678 optimal weight: 20.0000 chunk 342 optimal weight: 0.7980 chunk 223 optimal weight: 3.9990 chunk 219 optimal weight: 0.5980 chunk 721 optimal weight: 2.9990 chunk 773 optimal weight: 7.9990 chunk 561 optimal weight: 8.9990 chunk 105 optimal weight: 50.0000 chunk 892 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1903 ASN D2075 GLN B 69 ASN ** B1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN C 816 ASN ** C 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1409 GLN C1716 GLN ** C1918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 571 ASN F 625 ASN ** F 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN ** A 993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 HIS ** E 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 97476 Z= 0.307 Angle : 0.597 15.650 131740 Z= 0.301 Chirality : 0.041 0.282 14678 Planarity : 0.004 0.053 16602 Dihedral : 4.108 42.761 12796 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.75 % Favored : 95.19 % Rotamer: Outliers : 3.20 % Allowed : 19.20 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.08), residues: 11692 helix: 1.45 (0.07), residues: 6290 sheet: 0.25 (0.17), residues: 964 loop : -1.02 (0.09), residues: 4438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B1636 HIS 0.010 0.001 HIS D1298 PHE 0.032 0.001 PHE B 156 TYR 0.036 0.001 TYR F1543 ARG 0.006 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23384 Ramachandran restraints generated. 11692 Oldfield, 0 Emsley, 11692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23384 Ramachandran restraints generated. 11692 Oldfield, 0 Emsley, 11692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1094 residues out of total 10516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 336 poor density : 758 time to evaluate : 8.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 233 MET cc_start: -0.1495 (mpp) cc_final: -0.1931 (pmm) REVERT: D 1274 MET cc_start: 0.5354 (tmm) cc_final: 0.4045 (mmt) REVERT: D 1298 HIS cc_start: 0.4189 (OUTLIER) cc_final: 0.2368 (p90) REVERT: B 32 TYR cc_start: 0.7943 (m-80) cc_final: 0.7569 (m-80) REVERT: B 77 LYS cc_start: 0.8067 (ttmm) cc_final: 0.7865 (ttmm) REVERT: B 197 HIS cc_start: 0.8905 (t-170) cc_final: 0.8653 (t-170) REVERT: B 210 MET cc_start: 0.8130 (ptp) cc_final: 0.7849 (mtp) REVERT: B 560 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7521 (mtp) REVERT: B 769 MET cc_start: 0.8594 (mmm) cc_final: 0.8362 (mmm) REVERT: B 993 HIS cc_start: 0.4109 (OUTLIER) cc_final: 0.3032 (t70) REVERT: B 1021 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7815 (tpp80) REVERT: B 1398 MET cc_start: 0.5887 (mtm) cc_final: 0.5237 (mtm) REVERT: B 1414 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7497 (mtm) REVERT: B 1518 MET cc_start: 0.8539 (tpp) cc_final: 0.8193 (tpp) REVERT: B 1524 THR cc_start: 0.9131 (t) cc_final: 0.8892 (p) REVERT: B 1685 MET cc_start: 0.8933 (tpt) cc_final: 0.8179 (mtt) REVERT: B 1913 TYR cc_start: 0.9074 (t80) cc_final: 0.8798 (t80) REVERT: B 2118 ILE cc_start: 0.7407 (OUTLIER) cc_final: 0.6980 (pt) REVERT: C 94 MET cc_start: 0.1262 (ppp) cc_final: 0.0918 (ppp) REVERT: C 108 PHE cc_start: 0.8472 (m-80) cc_final: 0.7829 (m-80) REVERT: C 295 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8532 (mt0) REVERT: C 345 THR cc_start: 0.8665 (p) cc_final: 0.8431 (p) REVERT: C 418 SER cc_start: 0.6922 (OUTLIER) cc_final: 0.6643 (p) REVERT: C 424 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7477 (mp) REVERT: C 650 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7570 (mtt-85) REVERT: C 667 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7701 (tp) REVERT: C 833 MET cc_start: 0.8377 (ttt) cc_final: 0.8153 (ttt) REVERT: C 940 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7278 (mt-10) REVERT: C 1302 LYS cc_start: 0.6957 (OUTLIER) cc_final: 0.6494 (tttp) REVERT: C 1405 ARG cc_start: 0.8188 (mmm160) cc_final: 0.7963 (mtp85) REVERT: C 1465 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8118 (ttpt) REVERT: C 1605 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7491 (pttm) REVERT: C 1654 TRP cc_start: 0.9150 (t60) cc_final: 0.8860 (t-100) REVERT: C 1766 MET cc_start: 0.8141 (mmm) cc_final: 0.7659 (mmm) REVERT: F 1298 HIS cc_start: 0.3797 (OUTLIER) cc_final: 0.1915 (p90) REVERT: F 1779 MET cc_start: 0.0773 (pmm) cc_final: -0.0022 (ppp) REVERT: A 63 PHE cc_start: 0.8783 (m-10) cc_final: 0.8543 (m-10) REVERT: A 110 GLU cc_start: 0.7317 (tp30) cc_final: 0.6660 (tm-30) REVERT: A 210 MET cc_start: 0.7652 (ptp) cc_final: 0.7322 (ptp) REVERT: A 560 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7596 (mtp) REVERT: A 805 SER cc_start: 0.2029 (OUTLIER) cc_final: 0.0883 (t) REVERT: A 881 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8803 (tp) REVERT: A 993 HIS cc_start: 0.4395 (OUTLIER) cc_final: 0.3806 (t-170) REVERT: A 1150 LEU cc_start: 0.9212 (mt) cc_final: 0.8939 (mt) REVERT: A 1294 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8403 (mm) REVERT: A 1398 MET cc_start: 0.5824 (mtm) cc_final: 0.5394 (mtm) REVERT: A 1518 MET cc_start: 0.8400 (tpp) cc_final: 0.8110 (tpp) REVERT: A 2092 ARG cc_start: 0.8437 (ttp-110) cc_final: 0.8057 (ttm110) REVERT: E 94 MET cc_start: 0.1438 (ppp) cc_final: 0.1086 (ppp) REVERT: E 386 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8710 (mm) REVERT: E 544 ASP cc_start: 0.8157 (t0) cc_final: 0.7922 (t0) REVERT: E 1283 MET cc_start: 0.8678 (tpt) cc_final: 0.8299 (tpt) REVERT: E 1465 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.7987 (tmmt) REVERT: E 1482 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7758 (mp10) REVERT: E 1685 MET cc_start: 0.7955 (mmm) cc_final: 0.7559 (mmp) REVERT: E 1766 MET cc_start: 0.7921 (mmm) cc_final: 0.7520 (mmm) REVERT: E 1928 MET cc_start: 0.9584 (ppp) cc_final: 0.9306 (ppp) outliers start: 336 outliers final: 266 residues processed: 1018 average time/residue: 0.8227 time to fit residues: 1482.7504 Evaluate side-chains 1024 residues out of total 10516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 290 poor density : 734 time to evaluate : 8.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 286 ARG Chi-restraints excluded: chain D residue 377 MET Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 1164 VAL Chi-restraints excluded: chain D residue 1298 HIS Chi-restraints excluded: chain D residue 1304 MET Chi-restraints excluded: chain D residue 1367 THR Chi-restraints excluded: chain D residue 1414 MET Chi-restraints excluded: chain D residue 1425 THR Chi-restraints excluded: chain D residue 1465 LYS Chi-restraints excluded: chain D residue 1546 LEU Chi-restraints excluded: chain D residue 1556 MET Chi-restraints excluded: chain D residue 1607 VAL Chi-restraints excluded: chain D residue 1891 ILE Chi-restraints excluded: chain D residue 1901 MET Chi-restraints excluded: chain D residue 2052 VAL Chi-restraints excluded: chain D residue 2076 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 560 MET Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 594 GLN Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 680 TYR Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 834 SER Chi-restraints excluded: chain B residue 847 VAL Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 974 THR Chi-restraints excluded: chain B residue 993 HIS Chi-restraints excluded: chain B residue 994 ASN Chi-restraints excluded: chain B residue 1012 VAL Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain B residue 1020 SER Chi-restraints excluded: chain B residue 1021 ARG Chi-restraints excluded: chain B residue 1084 PHE Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain B residue 1118 LEU Chi-restraints excluded: chain B residue 1122 GLN Chi-restraints excluded: chain B residue 1154 SER Chi-restraints excluded: chain B residue 1165 SER Chi-restraints excluded: chain B residue 1259 THR Chi-restraints excluded: chain B residue 1297 SER Chi-restraints excluded: chain B residue 1316 LYS Chi-restraints excluded: chain B residue 1317 LEU Chi-restraints excluded: chain B residue 1340 ILE Chi-restraints excluded: chain B residue 1347 PHE Chi-restraints excluded: chain B residue 1371 ILE Chi-restraints excluded: chain B residue 1372 ILE Chi-restraints excluded: chain B residue 1414 MET Chi-restraints excluded: chain B residue 1439 ASN Chi-restraints excluded: chain B residue 1486 VAL Chi-restraints excluded: chain B residue 1495 LYS Chi-restraints excluded: chain B residue 1546 LEU Chi-restraints excluded: chain B residue 1548 LEU Chi-restraints excluded: chain B residue 1572 VAL Chi-restraints excluded: chain B residue 1578 VAL Chi-restraints excluded: chain B residue 1598 THR Chi-restraints excluded: chain B residue 1607 VAL Chi-restraints excluded: chain B residue 1613 ILE Chi-restraints excluded: chain B residue 1866 ILE Chi-restraints excluded: chain B residue 1924 VAL Chi-restraints excluded: chain B residue 1935 LEU Chi-restraints excluded: chain B residue 2083 ASP Chi-restraints excluded: chain B residue 2089 SER Chi-restraints excluded: chain B residue 2118 ILE Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 226 TYR Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 650 ARG Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 743 LEU Chi-restraints excluded: chain C residue 837 VAL Chi-restraints excluded: chain C residue 866 LEU Chi-restraints excluded: chain C residue 867 LYS Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 878 MET Chi-restraints excluded: chain C residue 894 PHE Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 940 GLU Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 989 THR Chi-restraints excluded: chain C residue 1112 ASP Chi-restraints excluded: chain C residue 1160 LYS Chi-restraints excluded: chain C residue 1164 VAL Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1193 LEU Chi-restraints excluded: chain C residue 1203 ASP Chi-restraints excluded: chain C residue 1255 GLN Chi-restraints excluded: chain C residue 1257 LYS Chi-restraints excluded: chain C residue 1297 SER Chi-restraints excluded: chain C residue 1298 HIS Chi-restraints excluded: chain C residue 1302 LYS Chi-restraints excluded: chain C residue 1354 THR Chi-restraints excluded: chain C residue 1397 THR Chi-restraints excluded: chain C residue 1402 LEU Chi-restraints excluded: chain C residue 1424 VAL Chi-restraints excluded: chain C residue 1465 LYS Chi-restraints excluded: chain C residue 1491 THR Chi-restraints excluded: chain C residue 1500 GLN Chi-restraints excluded: chain C residue 1529 ASP Chi-restraints excluded: chain C residue 1530 SER Chi-restraints excluded: chain C residue 1536 LYS Chi-restraints excluded: chain C residue 1554 ASP Chi-restraints excluded: chain C residue 1568 LYS Chi-restraints excluded: chain C residue 1581 THR Chi-restraints excluded: chain C residue 1593 MET Chi-restraints excluded: chain C residue 1601 VAL Chi-restraints excluded: chain C residue 1605 LYS Chi-restraints excluded: chain C residue 1872 ASP Chi-restraints excluded: chain C residue 1900 PHE Chi-restraints excluded: chain C residue 2034 GLU Chi-restraints excluded: chain C residue 2071 LEU Chi-restraints excluded: chain C residue 2098 VAL Chi-restraints excluded: chain F residue 284 MET Chi-restraints excluded: chain F residue 406 ASN Chi-restraints excluded: chain F residue 617 MET Chi-restraints excluded: chain F residue 1019 MET Chi-restraints excluded: chain F residue 1034 ASP Chi-restraints excluded: chain F residue 1298 HIS Chi-restraints excluded: chain F residue 1367 THR Chi-restraints excluded: chain F residue 1414 MET Chi-restraints excluded: chain F residue 1425 THR Chi-restraints excluded: chain F residue 1448 ASP Chi-restraints excluded: chain F residue 1546 LEU Chi-restraints excluded: chain F residue 1607 VAL Chi-restraints excluded: chain F residue 1915 LEU Chi-restraints excluded: chain F residue 2052 VAL Chi-restraints excluded: chain F residue 2076 VAL Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 680 TYR Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 993 HIS Chi-restraints excluded: chain A residue 1084 PHE Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1154 SER Chi-restraints excluded: chain A residue 1183 ILE Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1297 SER Chi-restraints excluded: chain A residue 1316 LYS Chi-restraints excluded: chain A residue 1340 ILE Chi-restraints excluded: chain A residue 1347 PHE Chi-restraints excluded: chain A residue 1369 ASP Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1439 ASN Chi-restraints excluded: chain A residue 1486 VAL Chi-restraints excluded: chain A residue 1548 LEU Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1581 THR Chi-restraints excluded: chain A residue 1607 VAL Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1901 MET Chi-restraints excluded: chain A residue 1924 VAL Chi-restraints excluded: chain A residue 1935 LEU Chi-restraints excluded: chain A residue 1936 ILE Chi-restraints excluded: chain A residue 2052 VAL Chi-restraints excluded: chain A residue 2083 ASP Chi-restraints excluded: chain A residue 2089 SER Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 226 TYR Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 357 ILE Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 428 GLU Chi-restraints excluded: chain E residue 556 VAL Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 634 THR Chi-restraints excluded: chain E residue 694 THR Chi-restraints excluded: chain E residue 705 MET Chi-restraints excluded: chain E residue 743 LEU Chi-restraints excluded: chain E residue 816 ASN Chi-restraints excluded: chain E residue 837 VAL Chi-restraints excluded: chain E residue 866 LEU Chi-restraints excluded: chain E residue 867 LYS Chi-restraints excluded: chain E residue 872 THR Chi-restraints excluded: chain E residue 974 THR Chi-restraints excluded: chain E residue 989 THR Chi-restraints excluded: chain E residue 1112 ASP Chi-restraints excluded: chain E residue 1160 LYS Chi-restraints excluded: chain E residue 1164 VAL Chi-restraints excluded: chain E residue 1165 SER Chi-restraints excluded: chain E residue 1174 THR Chi-restraints excluded: chain E residue 1203 ASP Chi-restraints excluded: chain E residue 1297 SER Chi-restraints excluded: chain E residue 1298 HIS Chi-restraints excluded: chain E residue 1352 MET Chi-restraints excluded: chain E residue 1354 THR Chi-restraints excluded: chain E residue 1358 LEU Chi-restraints excluded: chain E residue 1397 THR Chi-restraints excluded: chain E residue 1402 LEU Chi-restraints excluded: chain E residue 1441 SER Chi-restraints excluded: chain E residue 1465 LYS Chi-restraints excluded: chain E residue 1475 VAL Chi-restraints excluded: chain E residue 1482 GLN Chi-restraints excluded: chain E residue 1529 ASP Chi-restraints excluded: chain E residue 1536 LYS Chi-restraints excluded: chain E residue 1546 LEU Chi-restraints excluded: chain E residue 1562 MET Chi-restraints excluded: chain E residue 1564 TYR Chi-restraints excluded: chain E residue 1568 LYS Chi-restraints excluded: chain E residue 1601 VAL Chi-restraints excluded: chain E residue 1698 LEU Chi-restraints excluded: chain E residue 1703 ARG Chi-restraints excluded: chain E residue 1872 ASP Chi-restraints excluded: chain E residue 1900 PHE Chi-restraints excluded: chain E residue 2098 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1178 random chunks: chunk 1032 optimal weight: 0.7980 chunk 1087 optimal weight: 0.8980 chunk 992 optimal weight: 20.0000 chunk 1058 optimal weight: 2.9990 chunk 636 optimal weight: 30.0000 chunk 460 optimal weight: 0.6980 chunk 830 optimal weight: 0.7980 chunk 324 optimal weight: 0.5980 chunk 956 optimal weight: 0.1980 chunk 1000 optimal weight: 2.9990 chunk 1054 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 625 ASN ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN B 274 ASN ** B1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1082 ASN ** B1697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 816 ASN ** C 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1403 GLN ** C1918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 ASN A 608 HIS ** A 993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1497 GLN ** A1697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 97476 Z= 0.168 Angle : 0.565 13.519 131740 Z= 0.281 Chirality : 0.040 0.378 14678 Planarity : 0.003 0.052 16602 Dihedral : 3.935 41.359 12796 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.10 % Favored : 95.86 % Rotamer: Outliers : 2.16 % Allowed : 20.38 % Favored : 77.46 % 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: 0.81 (0.08), residues: 11692 helix: 1.60 (0.07), residues: 6314 sheet: 0.24 (0.17), residues: 984 loop : -0.96 (0.09), residues: 4394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 172 HIS 0.011 0.001 HIS B 82 PHE 0.029 0.001 PHE B 156 TYR 0.040 0.001 TYR F1543 ARG 0.005 0.000 ARG D 286 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23384 Ramachandran restraints generated. 11692 Oldfield, 0 Emsley, 11692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23384 Ramachandran restraints generated. 11692 Oldfield, 0 Emsley, 11692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1023 residues out of total 10516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 796 time to evaluate : 8.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1274 MET cc_start: 0.5285 (tmm) cc_final: 0.4178 (mmt) REVERT: D 1298 HIS cc_start: 0.3941 (OUTLIER) cc_final: 0.2223 (p90) REVERT: B 77 LYS cc_start: 0.8082 (ttmm) cc_final: 0.7803 (ttmm) REVERT: B 184 MET cc_start: 0.8993 (ppp) cc_final: 0.8619 (ppp) REVERT: B 197 HIS cc_start: 0.8877 (t-170) cc_final: 0.8605 (t-170) REVERT: B 210 MET cc_start: 0.8146 (ptp) cc_final: 0.7883 (mtp) REVERT: B 560 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7434 (mtp) REVERT: B 993 HIS cc_start: 0.4085 (OUTLIER) cc_final: 0.3373 (t70) REVERT: B 1283 MET cc_start: 0.7950 (tpt) cc_final: 0.7612 (tpt) REVERT: B 1398 MET cc_start: 0.5714 (mtm) cc_final: 0.5063 (mtm) REVERT: B 1414 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7119 (mtm) REVERT: B 1518 MET cc_start: 0.8512 (tpp) cc_final: 0.8140 (tpp) REVERT: B 1898 GLU cc_start: 0.8710 (tt0) cc_final: 0.8368 (tm-30) REVERT: B 1913 TYR cc_start: 0.9034 (t80) cc_final: 0.8767 (t80) REVERT: B 2118 ILE cc_start: 0.7416 (OUTLIER) cc_final: 0.7018 (pt) REVERT: C 94 MET cc_start: 0.1268 (ppp) cc_final: 0.0959 (ppp) REVERT: C 108 PHE cc_start: 0.8434 (m-80) cc_final: 0.7784 (m-80) REVERT: C 424 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7390 (mp) REVERT: C 667 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7638 (tp) REVERT: C 940 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7175 (mt-10) REVERT: C 1302 LYS cc_start: 0.6939 (OUTLIER) cc_final: 0.6420 (tttp) REVERT: C 1405 ARG cc_start: 0.8148 (mmm160) cc_final: 0.7925 (ttt-90) REVERT: C 1465 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8099 (ttpt) REVERT: C 1482 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7996 (mp10) REVERT: C 1605 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7485 (pttm) REVERT: C 1653 LEU cc_start: 0.9047 (mp) cc_final: 0.8699 (mt) REVERT: C 1654 TRP cc_start: 0.9155 (t60) cc_final: 0.8909 (t-100) REVERT: C 1766 MET cc_start: 0.8283 (mmm) cc_final: 0.7806 (mmm) REVERT: F 1274 MET cc_start: 0.3498 (mmm) cc_final: 0.3242 (mmm) REVERT: F 1298 HIS cc_start: 0.3680 (OUTLIER) cc_final: 0.1930 (p90) REVERT: F 1779 MET cc_start: 0.0602 (pmm) cc_final: -0.0131 (ppp) REVERT: A 63 PHE cc_start: 0.8768 (m-10) cc_final: 0.8537 (m-10) REVERT: A 110 GLU cc_start: 0.7256 (tp30) cc_final: 0.6563 (tm-30) REVERT: A 560 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.7502 (mtp) REVERT: A 805 SER cc_start: 0.1871 (OUTLIER) cc_final: 0.1199 (t) REVERT: A 845 SER cc_start: 0.8199 (m) cc_final: 0.7918 (p) REVERT: A 962 MET cc_start: 0.5807 (tpp) cc_final: 0.5436 (mmt) REVERT: A 1150 LEU cc_start: 0.9078 (mt) cc_final: 0.8801 (mt) REVERT: A 1283 MET cc_start: 0.8103 (tpt) cc_final: 0.7817 (tpt) REVERT: A 1398 MET cc_start: 0.5616 (mtm) cc_final: 0.5217 (mtm) REVERT: A 1518 MET cc_start: 0.8411 (tpp) cc_final: 0.8118 (tpp) REVERT: A 2092 ARG cc_start: 0.8389 (ttp-110) cc_final: 0.7807 (ttm110) REVERT: E 94 MET cc_start: 0.1393 (ppp) cc_final: 0.1106 (ppp) REVERT: E 193 TYR cc_start: 0.8659 (t80) cc_final: 0.7992 (t80) REVERT: E 415 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6366 (mt-10) REVERT: E 867 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8507 (tttp) REVERT: E 1283 MET cc_start: 0.8613 (tpt) cc_final: 0.8310 (tpt) REVERT: E 1465 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8027 (tttm) REVERT: E 1482 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.7671 (mp10) REVERT: E 1605 LYS cc_start: 0.7731 (pttm) cc_final: 0.7299 (tppt) REVERT: E 1626 LEU cc_start: 0.9314 (mt) cc_final: 0.9087 (pp) REVERT: E 1685 MET cc_start: 0.7950 (mmm) cc_final: 0.7595 (mmp) REVERT: E 1766 MET cc_start: 0.7926 (mmm) cc_final: 0.7512 (mmm) REVERT: E 1928 MET cc_start: 0.9554 (ppp) cc_final: 0.9220 (ppp) outliers start: 227 outliers final: 173 residues processed: 963 average time/residue: 0.8403 time to fit residues: 1429.7842 Evaluate side-chains 946 residues out of total 10516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 755 time to evaluate : 8.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 286 ARG Chi-restraints excluded: chain D residue 377 MET Chi-restraints excluded: chain D residue 1019 MET Chi-restraints excluded: chain D residue 1298 HIS Chi-restraints excluded: chain D residue 1414 MET Chi-restraints excluded: chain D residue 1425 THR Chi-restraints excluded: chain D residue 1465 LYS Chi-restraints excluded: chain D residue 1546 LEU Chi-restraints excluded: chain D residue 1556 MET Chi-restraints excluded: chain D residue 1607 VAL Chi-restraints excluded: chain D residue 1891 ILE Chi-restraints excluded: chain D residue 1901 MET Chi-restraints excluded: chain D residue 2052 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 560 MET Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 680 TYR Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 834 SER Chi-restraints excluded: chain B residue 847 VAL Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 993 HIS Chi-restraints excluded: chain B residue 1012 VAL Chi-restraints excluded: chain B residue 1084 PHE Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain B residue 1118 LEU Chi-restraints excluded: chain B residue 1122 GLN Chi-restraints excluded: chain B residue 1165 SER Chi-restraints excluded: chain B residue 1259 THR Chi-restraints excluded: chain B residue 1297 SER Chi-restraints excluded: chain B residue 1347 PHE Chi-restraints excluded: chain B residue 1371 ILE Chi-restraints excluded: chain B residue 1372 ILE Chi-restraints excluded: chain B residue 1414 MET Chi-restraints excluded: chain B residue 1439 ASN Chi-restraints excluded: chain B residue 1495 LYS Chi-restraints excluded: chain B residue 1546 LEU Chi-restraints excluded: chain B residue 1548 LEU Chi-restraints excluded: chain B residue 1607 VAL Chi-restraints excluded: chain B residue 1613 ILE Chi-restraints excluded: chain B residue 1866 ILE Chi-restraints excluded: chain B residue 1935 LEU Chi-restraints excluded: chain B residue 2083 ASP Chi-restraints excluded: chain B residue 2092 ARG Chi-restraints excluded: chain B residue 2118 ILE Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 226 TYR Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 837 VAL Chi-restraints excluded: chain C residue 866 LEU Chi-restraints excluded: chain C residue 867 LYS Chi-restraints excluded: chain C residue 878 MET Chi-restraints excluded: chain C residue 882 VAL Chi-restraints excluded: chain C residue 894 PHE Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 940 GLU Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 1160 LYS Chi-restraints excluded: chain C residue 1164 VAL Chi-restraints excluded: chain C residue 1193 LEU Chi-restraints excluded: chain C residue 1298 HIS Chi-restraints excluded: chain C residue 1302 LYS Chi-restraints excluded: chain C residue 1354 THR Chi-restraints excluded: chain C residue 1397 THR Chi-restraints excluded: chain C residue 1465 LYS Chi-restraints excluded: chain C residue 1482 GLN Chi-restraints excluded: chain C residue 1491 THR Chi-restraints excluded: chain C residue 1536 LYS Chi-restraints excluded: chain C residue 1568 LYS Chi-restraints excluded: chain C residue 1581 THR Chi-restraints excluded: chain C residue 1593 MET Chi-restraints excluded: chain C residue 1601 VAL Chi-restraints excluded: chain C residue 1605 LYS Chi-restraints excluded: chain C residue 1872 ASP Chi-restraints excluded: chain C residue 2098 VAL Chi-restraints excluded: chain F residue 284 MET Chi-restraints excluded: chain F residue 406 ASN Chi-restraints excluded: chain F residue 617 MET Chi-restraints excluded: chain F residue 1019 MET Chi-restraints excluded: chain F residue 1034 ASP Chi-restraints excluded: chain F residue 1298 HIS Chi-restraints excluded: chain F residue 1367 THR Chi-restraints excluded: chain F residue 1414 MET Chi-restraints excluded: chain F residue 1607 VAL Chi-restraints excluded: chain F residue 1766 MET Chi-restraints excluded: chain F residue 2052 VAL Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 680 TYR Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 1084 PHE Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1122 GLN Chi-restraints excluded: chain A residue 1183 ILE Chi-restraints excluded: chain A residue 1297 SER Chi-restraints excluded: chain A residue 1340 ILE Chi-restraints excluded: chain A residue 1347 PHE Chi-restraints excluded: chain A residue 1369 ASP Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1439 ASN Chi-restraints excluded: chain A residue 1548 LEU Chi-restraints excluded: chain A residue 1607 VAL Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1901 MET Chi-restraints excluded: chain A residue 1935 LEU Chi-restraints excluded: chain A residue 1936 ILE Chi-restraints excluded: chain A residue 2083 ASP Chi-restraints excluded: chain A residue 2089 SER Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 226 TYR Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 357 ILE Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 556 VAL Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 634 THR Chi-restraints excluded: chain E residue 694 THR Chi-restraints excluded: chain E residue 743 LEU Chi-restraints excluded: chain E residue 816 ASN Chi-restraints excluded: chain E residue 837 VAL Chi-restraints excluded: chain E residue 866 LEU Chi-restraints excluded: chain E residue 867 LYS Chi-restraints excluded: chain E residue 1112 ASP Chi-restraints excluded: chain E residue 1160 LYS Chi-restraints excluded: chain E residue 1164 VAL Chi-restraints excluded: chain E residue 1174 THR Chi-restraints excluded: chain E residue 1203 ASP Chi-restraints excluded: chain E residue 1297 SER Chi-restraints excluded: chain E residue 1298 HIS Chi-restraints excluded: chain E residue 1397 THR Chi-restraints excluded: chain E residue 1465 LYS Chi-restraints excluded: chain E residue 1475 VAL Chi-restraints excluded: chain E residue 1482 GLN Chi-restraints excluded: chain E residue 1536 LYS Chi-restraints excluded: chain E residue 1568 LYS Chi-restraints excluded: chain E residue 1601 VAL Chi-restraints excluded: chain E residue 1703 ARG Chi-restraints excluded: chain E residue 1872 ASP Chi-restraints excluded: chain E residue 1900 PHE Chi-restraints excluded: chain E residue 2098 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1178 random chunks: chunk 694 optimal weight: 40.0000 chunk 1118 optimal weight: 0.8980 chunk 682 optimal weight: 30.0000 chunk 530 optimal weight: 0.6980 chunk 777 optimal weight: 0.9990 chunk 1173 optimal weight: 0.8980 chunk 1080 optimal weight: 3.9990 chunk 934 optimal weight: 0.7980 chunk 97 optimal weight: 30.0000 chunk 721 optimal weight: 5.9990 chunk 573 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 343 ASN ** D 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 625 ASN ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 ASN ** B1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 HIS C 413 GLN C 816 ASN ** C 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 571 ASN ** F 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2075 GLN ** A 993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1301 GLN ** A1697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 HIS ** E 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 97476 Z= 0.187 Angle : 0.576 20.971 131740 Z= 0.286 Chirality : 0.041 0.398 14678 Planarity : 0.003 0.049 16602 Dihedral : 3.907 42.475 12796 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.29 % Favored : 95.66 % Rotamer: Outliers : 1.94 % Allowed : 20.67 % Favored : 77.39 % 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: 0.84 (0.08), residues: 11692 helix: 1.61 (0.07), residues: 6324 sheet: 0.29 (0.17), residues: 1000 loop : -0.94 (0.09), residues: 4368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.001 TRP B1636 HIS 0.010 0.001 HIS E 82 PHE 0.029 0.001 PHE B 156 TYR 0.035 0.001 TYR D1543 ARG 0.005 0.000 ARG D 286 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23384 Ramachandran restraints generated. 11692 Oldfield, 0 Emsley, 11692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23384 Ramachandran restraints generated. 11692 Oldfield, 0 Emsley, 11692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 970 residues out of total 10516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 766 time to evaluate : 8.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1274 MET cc_start: 0.5295 (tmm) cc_final: 0.4305 (mmt) REVERT: D 1298 HIS cc_start: 0.3966 (OUTLIER) cc_final: 0.2305 (p90) REVERT: B 32 TYR cc_start: 0.7971 (m-80) cc_final: 0.7604 (m-80) REVERT: B 77 LYS cc_start: 0.8084 (ttmm) cc_final: 0.7814 (ttmm) REVERT: B 184 MET cc_start: 0.8984 (ppp) cc_final: 0.8588 (ppp) REVERT: B 197 HIS cc_start: 0.8854 (t-170) cc_final: 0.8582 (t-170) REVERT: B 210 MET cc_start: 0.8133 (ptp) cc_final: 0.7827 (mtp) REVERT: B 560 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7455 (mtp) REVERT: B 993 HIS cc_start: 0.4222 (OUTLIER) cc_final: 0.3515 (t70) REVERT: B 1283 MET cc_start: 0.7963 (tpt) cc_final: 0.7606 (tpt) REVERT: B 1398 MET cc_start: 0.5721 (mtm) cc_final: 0.5060 (mtm) REVERT: B 1518 MET cc_start: 0.8503 (tpp) cc_final: 0.8122 (tpp) REVERT: B 1685 MET cc_start: 0.8775 (tpt) cc_final: 0.8281 (mtt) REVERT: B 1898 GLU cc_start: 0.8700 (tt0) cc_final: 0.8396 (tm-30) REVERT: B 1913 TYR cc_start: 0.9037 (t80) cc_final: 0.8777 (t80) REVERT: B 2118 ILE cc_start: 0.7540 (OUTLIER) cc_final: 0.7173 (pt) REVERT: C 94 MET cc_start: 0.1391 (ppp) cc_final: 0.1115 (ppp) REVERT: C 108 PHE cc_start: 0.8446 (m-80) cc_final: 0.7788 (m-80) REVERT: C 424 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7345 (mp) REVERT: C 667 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7661 (tp) REVERT: C 867 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8731 (tttp) REVERT: C 1302 LYS cc_start: 0.6948 (OUTLIER) cc_final: 0.6430 (tttp) REVERT: C 1605 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7490 (pttm) REVERT: C 1653 LEU cc_start: 0.9050 (mp) cc_final: 0.8716 (mt) REVERT: C 1654 TRP cc_start: 0.9160 (t60) cc_final: 0.8914 (t-100) REVERT: C 1766 MET cc_start: 0.8251 (mmm) cc_final: 0.7798 (mmm) REVERT: F 967 MET cc_start: -0.0585 (tpt) cc_final: -0.1178 (tpt) REVERT: F 1271 MET cc_start: 0.0835 (tmm) cc_final: 0.0610 (tmm) REVERT: F 1274 MET cc_start: 0.3470 (mmm) cc_final: 0.3218 (mmm) REVERT: F 1298 HIS cc_start: 0.3593 (OUTLIER) cc_final: 0.1955 (p90) REVERT: A 63 PHE cc_start: 0.8789 (m-10) cc_final: 0.8579 (m-10) REVERT: A 110 GLU cc_start: 0.7240 (tp30) cc_final: 0.6536 (tm-30) REVERT: A 800 VAL cc_start: 0.8325 (t) cc_final: 0.8049 (p) REVERT: A 805 SER cc_start: 0.1887 (OUTLIER) cc_final: 0.1226 (t) REVERT: A 913 ASP cc_start: 0.8465 (t70) cc_final: 0.8092 (t0) REVERT: A 1150 LEU cc_start: 0.9088 (mt) cc_final: 0.8801 (mt) REVERT: A 1283 MET cc_start: 0.8101 (tpt) cc_final: 0.7835 (tpt) REVERT: A 1398 MET cc_start: 0.5615 (mtm) cc_final: 0.5225 (mtm) REVERT: A 1518 MET cc_start: 0.8402 (tpp) cc_final: 0.8109 (tpp) REVERT: A 2092 ARG cc_start: 0.8404 (ttp-110) cc_final: 0.7909 (ttm110) REVERT: E 94 MET cc_start: 0.1619 (ppp) cc_final: 0.1362 (ppp) REVERT: E 415 GLU cc_start: 0.7009 (mt-10) cc_final: 0.6400 (mt-10) REVERT: E 867 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8503 (tttp) REVERT: E 1283 MET cc_start: 0.8644 (tpt) cc_final: 0.8296 (tpt) REVERT: E 1465 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8024 (tttm) REVERT: E 1482 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7643 (mp10) REVERT: E 1605 LYS cc_start: 0.7782 (pttm) cc_final: 0.7249 (tppt) REVERT: E 1626 LEU cc_start: 0.9291 (mt) cc_final: 0.9080 (pp) REVERT: E 1654 TRP cc_start: 0.9134 (t60) cc_final: 0.8912 (t-100) REVERT: E 1685 MET cc_start: 0.7986 (mmm) cc_final: 0.7627 (mmp) REVERT: E 1766 MET cc_start: 0.8021 (mmm) cc_final: 0.7630 (mmm) REVERT: E 1928 MET cc_start: 0.9553 (ppp) cc_final: 0.9220 (ppp) outliers start: 204 outliers final: 176 residues processed: 920 average time/residue: 0.8421 time to fit residues: 1364.5640 Evaluate side-chains 938 residues out of total 10516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 748 time to evaluate : 8.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 286 ARG Chi-restraints excluded: chain D residue 1019 MET Chi-restraints excluded: chain D residue 1298 HIS Chi-restraints excluded: chain D residue 1367 THR Chi-restraints excluded: chain D residue 1414 MET Chi-restraints excluded: chain D residue 1425 THR Chi-restraints excluded: chain D residue 1465 LYS Chi-restraints excluded: chain D residue 1546 LEU Chi-restraints excluded: chain D residue 1556 MET Chi-restraints excluded: chain D residue 1607 VAL Chi-restraints excluded: chain D residue 1891 ILE Chi-restraints excluded: chain D residue 1901 MET Chi-restraints excluded: chain D residue 2052 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 560 MET Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 680 TYR Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 834 SER Chi-restraints excluded: chain B residue 847 VAL Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 993 HIS Chi-restraints excluded: chain B residue 994 ASN Chi-restraints excluded: chain B residue 1012 VAL Chi-restraints excluded: chain B residue 1084 PHE Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain B residue 1118 LEU Chi-restraints excluded: chain B residue 1122 GLN Chi-restraints excluded: chain B residue 1165 SER Chi-restraints excluded: chain B residue 1259 THR Chi-restraints excluded: chain B residue 1297 SER Chi-restraints excluded: chain B residue 1347 PHE Chi-restraints excluded: chain B residue 1371 ILE Chi-restraints excluded: chain B residue 1372 ILE Chi-restraints excluded: chain B residue 1439 ASN Chi-restraints excluded: chain B residue 1495 LYS Chi-restraints excluded: chain B residue 1546 LEU Chi-restraints excluded: chain B residue 1548 LEU Chi-restraints excluded: chain B residue 1572 VAL Chi-restraints excluded: chain B residue 1607 VAL Chi-restraints excluded: chain B residue 1613 ILE Chi-restraints excluded: chain B residue 1866 ILE Chi-restraints excluded: chain B residue 1924 VAL Chi-restraints excluded: chain B residue 1935 LEU Chi-restraints excluded: chain B residue 2083 ASP Chi-restraints excluded: chain B residue 2118 ILE Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 226 TYR Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 837 VAL Chi-restraints excluded: chain C residue 866 LEU Chi-restraints excluded: chain C residue 867 LYS Chi-restraints excluded: chain C residue 878 MET Chi-restraints excluded: chain C residue 882 VAL Chi-restraints excluded: chain C residue 894 PHE Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 1160 LYS Chi-restraints excluded: chain C residue 1164 VAL Chi-restraints excluded: chain C residue 1174 THR Chi-restraints excluded: chain C residue 1193 LEU Chi-restraints excluded: chain C residue 1298 HIS Chi-restraints excluded: chain C residue 1302 LYS Chi-restraints excluded: chain C residue 1354 THR Chi-restraints excluded: chain C residue 1397 THR Chi-restraints excluded: chain C residue 1491 THR Chi-restraints excluded: chain C residue 1536 LYS Chi-restraints excluded: chain C residue 1568 LYS Chi-restraints excluded: chain C residue 1593 MET Chi-restraints excluded: chain C residue 1601 VAL Chi-restraints excluded: chain C residue 1605 LYS Chi-restraints excluded: chain C residue 1872 ASP Chi-restraints excluded: chain C residue 2098 VAL Chi-restraints excluded: chain F residue 284 MET Chi-restraints excluded: chain F residue 406 ASN Chi-restraints excluded: chain F residue 617 MET Chi-restraints excluded: chain F residue 1019 MET Chi-restraints excluded: chain F residue 1034 ASP Chi-restraints excluded: chain F residue 1298 HIS Chi-restraints excluded: chain F residue 1367 THR Chi-restraints excluded: chain F residue 1414 MET Chi-restraints excluded: chain F residue 1425 THR Chi-restraints excluded: chain F residue 1607 VAL Chi-restraints excluded: chain F residue 1766 MET Chi-restraints excluded: chain F residue 2052 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 680 TYR Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 1084 PHE Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1122 GLN Chi-restraints excluded: chain A residue 1183 ILE Chi-restraints excluded: chain A residue 1340 ILE Chi-restraints excluded: chain A residue 1347 PHE Chi-restraints excluded: chain A residue 1369 ASP Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1439 ASN Chi-restraints excluded: chain A residue 1548 LEU Chi-restraints excluded: chain A residue 1607 VAL Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1901 MET Chi-restraints excluded: chain A residue 1924 VAL Chi-restraints excluded: chain A residue 1935 LEU Chi-restraints excluded: chain A residue 1936 ILE Chi-restraints excluded: chain A residue 2052 VAL Chi-restraints excluded: chain A residue 2083 ASP Chi-restraints excluded: chain A residue 2089 SER Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 226 TYR Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 357 ILE Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 556 VAL Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 634 THR Chi-restraints excluded: chain E residue 694 THR Chi-restraints excluded: chain E residue 743 LEU Chi-restraints excluded: chain E residue 816 ASN Chi-restraints excluded: chain E residue 837 VAL Chi-restraints excluded: chain E residue 866 LEU Chi-restraints excluded: chain E residue 867 LYS Chi-restraints excluded: chain E residue 1112 ASP Chi-restraints excluded: chain E residue 1160 LYS Chi-restraints excluded: chain E residue 1164 VAL Chi-restraints excluded: chain E residue 1174 THR Chi-restraints excluded: chain E residue 1203 ASP Chi-restraints excluded: chain E residue 1298 HIS Chi-restraints excluded: chain E residue 1397 THR Chi-restraints excluded: chain E residue 1465 LYS Chi-restraints excluded: chain E residue 1475 VAL Chi-restraints excluded: chain E residue 1482 GLN Chi-restraints excluded: chain E residue 1536 LYS Chi-restraints excluded: chain E residue 1568 LYS Chi-restraints excluded: chain E residue 1601 VAL Chi-restraints excluded: chain E residue 1703 ARG Chi-restraints excluded: chain E residue 1872 ASP Chi-restraints excluded: chain E residue 1900 PHE Chi-restraints excluded: chain E residue 2098 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1178 random chunks: chunk 742 optimal weight: 7.9990 chunk 995 optimal weight: 0.8980 chunk 286 optimal weight: 0.9980 chunk 861 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 259 optimal weight: 0.0470 chunk 936 optimal weight: 0.9980 chunk 391 optimal weight: 0.0570 chunk 961 optimal weight: 0.8980 chunk 118 optimal weight: 20.0000 chunk 172 optimal weight: 30.0000 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 ASN ** B1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 816 ASN ** C 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 571 ASN ** F 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 HIS ** A 993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1301 GLN ** A1697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 HIS ** E 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.153613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.127357 restraints weight = 301992.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.126225 restraints weight = 522308.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.127422 restraints weight = 360230.553| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 97476 Z= 0.163 Angle : 0.571 22.045 131740 Z= 0.283 Chirality : 0.040 0.401 14678 Planarity : 0.003 0.049 16602 Dihedral : 3.838 43.461 12796 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.06 % Favored : 95.89 % Rotamer: Outliers : 1.93 % Allowed : 20.85 % Favored : 77.22 % 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: 0.90 (0.08), residues: 11692 helix: 1.64 (0.07), residues: 6332 sheet: 0.33 (0.17), residues: 986 loop : -0.89 (0.09), residues: 4374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.001 TRP B1636 HIS 0.011 0.001 HIS E 82 PHE 0.028 0.001 PHE B 156 TYR 0.043 0.001 TYR F1543 ARG 0.006 0.000 ARG D 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23079.43 seconds wall clock time: 406 minutes 40.09 seconds (24400.09 seconds total)