Starting phenix.real_space_refine on Wed Oct 28 12:17:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y6h_72562/10_2026/9y6h_72562.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y6h_72562/10_2026/9y6h_72562.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9y6h_72562/10_2026/9y6h_72562.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y6h_72562/10_2026/9y6h_72562.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y6h_72562/10_2026/9y6h_72562.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y6h_72562/10_2026/9y6h_72562.map" } resolution = 4.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.068 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 183 5.16 5 C 17496 2.51 5 N 4518 2.21 5 O 5253 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27450 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9150 Classifications: {'peptide': 1175} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 1124} Chain breaks: 5 Chain: "B" Number of atoms: 9150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9150 Classifications: {'peptide': 1175} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 1124} Chain breaks: 5 Chain: "C" Number of atoms: 9150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9150 Classifications: {'peptide': 1175} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 1124} Chain breaks: 5 Time building chain proxies: 5.63, per 1000 atoms: 0.21 Number of scatterers: 27450 At special positions: 0 Unit cell: (154.5, 154.5, 171, 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 183 16.00 O 5253 8.00 N 4518 7.00 C 17496 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=63, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 197 " distance=2.03 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 256 " distance=2.03 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 300 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 368 " distance=2.03 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 398 " - pdb=" SG CYS A 614 " distance=2.03 Simple disulfide: pdb=" SG CYS A 491 " - pdb=" SG CYS A 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 499 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 548 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 578 " distance=2.03 Simple disulfide: pdb=" SG CYS A 591 " - pdb=" SG CYS A 597 " distance=2.03 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 683 " distance=2.03 Simple disulfide: pdb=" SG CYS A 708 " - pdb=" SG CYS A 733 " distance=2.03 Simple disulfide: pdb=" SG CYS A 748 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 826 " - pdb=" SG CYS A 848 " distance=2.03 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS A 837 " distance=2.03 Simple disulfide: pdb=" SG CYS A 938 " - pdb=" SG CYS A 949 " distance=2.03 Simple disulfide: pdb=" SG CYS A1126 " - pdb=" SG CYS A1137 " distance=2.04 Simple disulfide: pdb=" SG CYS A1176 " - pdb=" SG CYS A1221 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 169 " distance=2.04 Simple disulfide: pdb=" SG CYS B 164 " - pdb=" SG CYS B 197 " distance=2.03 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 256 " distance=2.03 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 300 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 368 " distance=2.03 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 398 " - pdb=" SG CYS B 614 " distance=2.03 Simple disulfide: pdb=" SG CYS B 491 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS B 499 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 548 " distance=2.03 Simple disulfide: pdb=" SG CYS B 571 " - pdb=" SG CYS B 578 " distance=2.03 Simple disulfide: pdb=" SG CYS B 591 " - pdb=" SG CYS B 597 " distance=2.03 Simple disulfide: pdb=" SG CYS B 630 " - pdb=" SG CYS B 683 " distance=2.03 Simple disulfide: pdb=" SG CYS B 708 " - pdb=" SG CYS B 733 " distance=2.03 Simple disulfide: pdb=" SG CYS B 748 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 826 " - pdb=" SG CYS B 848 " distance=2.03 Simple disulfide: pdb=" SG CYS B 831 " - pdb=" SG CYS B 837 " distance=2.03 Simple disulfide: pdb=" SG CYS B 938 " - pdb=" SG CYS B 949 " distance=2.03 Simple disulfide: pdb=" SG CYS B1126 " - pdb=" SG CYS B1137 " distance=2.04 Simple disulfide: pdb=" SG CYS B1176 " - pdb=" SG CYS B1221 " distance=2.03 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 169 " distance=2.04 Simple disulfide: pdb=" SG CYS C 164 " - pdb=" SG CYS C 197 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 256 " distance=2.03 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 300 " distance=2.03 Simple disulfide: pdb=" SG CYS C 343 " - pdb=" SG CYS C 368 " distance=2.03 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 439 " distance=2.03 Simple disulfide: pdb=" SG CYS C 398 " - pdb=" SG CYS C 614 " distance=2.03 Simple disulfide: pdb=" SG CYS C 491 " - pdb=" SG CYS C 561 " distance=2.03 Simple disulfide: pdb=" SG CYS C 499 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 548 " distance=2.03 Simple disulfide: pdb=" SG CYS C 571 " - pdb=" SG CYS C 578 " distance=2.03 Simple disulfide: pdb=" SG CYS C 591 " - pdb=" SG CYS C 597 " distance=2.03 Simple disulfide: pdb=" SG CYS C 630 " - pdb=" SG CYS C 683 " distance=2.03 Simple disulfide: pdb=" SG CYS C 708 " - pdb=" SG CYS C 733 " distance=2.03 Simple disulfide: pdb=" SG CYS C 748 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 826 " - pdb=" SG CYS C 848 " distance=2.03 Simple disulfide: pdb=" SG CYS C 831 " - pdb=" SG CYS C 837 " distance=2.03 Simple disulfide: pdb=" SG CYS C 938 " - pdb=" SG CYS C 949 " distance=2.03 Simple disulfide: pdb=" SG CYS C1126 " - pdb=" SG CYS C1137 " distance=2.04 Simple disulfide: pdb=" SG CYS C1176 " - pdb=" SG CYS C1221 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 1.2 seconds 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6588 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 73 sheets defined 24.1% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 344 through 350 removed outlier: 3.815A pdb=" N TRP A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 379 removed outlier: 3.779A pdb=" N LEU A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N SER A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A 379 " --> pdb=" O LEU A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 394 removed outlier: 3.537A pdb=" N LYS A 393 " --> pdb=" O ASP A 390 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE A 394 " --> pdb=" O ALA A 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 390 through 394' Processing helix chain 'A' and resid 423 through 429 Processing helix chain 'A' and resid 446 through 450 removed outlier: 3.538A pdb=" N ASN A 449 " --> pdb=" O PRO A 446 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 450 " --> pdb=" O ALA A 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 446 through 450' Processing helix chain 'A' and resid 458 through 464 removed outlier: 3.821A pdb=" N LYS A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE A 464 " --> pdb=" O TRP A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 472 Processing helix chain 'A' and resid 707 through 716 Processing helix chain 'A' and resid 826 through 831 Processing helix chain 'A' and resid 834 through 841 removed outlier: 3.624A pdb=" N GLN A 840 " --> pdb=" O ALA A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 874 removed outlier: 4.099A pdb=" N CYS A 848 " --> pdb=" O TYR A 844 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N MET A 874 " --> pdb=" O ALA A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 885 removed outlier: 3.723A pdb=" N ASP A 885 " --> pdb=" O LYS A 882 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 882 through 885' Processing helix chain 'A' and resid 914 through 922 Processing helix chain 'A' and resid 927 through 936 removed outlier: 3.720A pdb=" N TYR A 935 " --> pdb=" O PHE A 931 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN A 936 " --> pdb=" O VAL A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 955 Processing helix chain 'A' and resid 964 through 978 removed outlier: 3.612A pdb=" N PHE A 968 " --> pdb=" O SER A 964 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA A 978 " --> pdb=" O ALA A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1002 Processing helix chain 'A' and resid 1008 through 1012 removed outlier: 3.542A pdb=" N SER A1011 " --> pdb=" O ASP A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1030 Processing helix chain 'A' and resid 1036 through 1058 removed outlier: 3.569A pdb=" N GLN A1058 " --> pdb=" O ASN A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1062 removed outlier: 3.626A pdb=" N ASN A1062 " --> pdb=" O GLN A1059 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1059 through 1062' Processing helix chain 'A' and resid 1070 through 1078 Processing helix chain 'A' and resid 1079 through 1127 removed outlier: 4.090A pdb=" N ALA A1085 " --> pdb=" O LEU A1081 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 181 Processing helix chain 'B' and resid 293 through 303 Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 371 through 376 removed outlier: 3.721A pdb=" N LEU B 375 " --> pdb=" O ASN B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 394 removed outlier: 3.557A pdb=" N LYS B 393 " --> pdb=" O ASP B 390 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE B 394 " --> pdb=" O ALA B 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 390 through 394' Processing helix chain 'B' and resid 413 through 418 removed outlier: 3.630A pdb=" N LEU B 417 " --> pdb=" O LYS B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 429 Processing helix chain 'B' and resid 446 through 450 removed outlier: 3.585A pdb=" N ASN B 449 " --> pdb=" O PRO B 446 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 450 " --> pdb=" O ALA B 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 446 through 450' Processing helix chain 'B' and resid 458 through 464 removed outlier: 3.942A pdb=" N LYS B 462 " --> pdb=" O SER B 458 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE B 464 " --> pdb=" O TRP B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 472 Processing helix chain 'B' and resid 707 through 716 Processing helix chain 'B' and resid 826 through 831 Processing helix chain 'B' and resid 834 through 841 removed outlier: 3.641A pdb=" N GLN B 840 " --> pdb=" O ALA B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 874 removed outlier: 4.118A pdb=" N CYS B 848 " --> pdb=" O TYR B 844 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N MET B 874 " --> pdb=" O ALA B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 882 through 885 removed outlier: 3.650A pdb=" N ASP B 885 " --> pdb=" O LYS B 882 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 882 through 885' Processing helix chain 'B' and resid 914 through 922 Processing helix chain 'B' and resid 927 through 935 removed outlier: 3.712A pdb=" N TYR B 935 " --> pdb=" O PHE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 936 through 938 No H-bonds generated for 'chain 'B' and resid 936 through 938' Processing helix chain 'B' and resid 946 through 955 removed outlier: 3.595A pdb=" N GLY B 955 " --> pdb=" O GLN B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 978 removed outlier: 3.624A pdb=" N PHE B 968 " --> pdb=" O SER B 964 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B 978 " --> pdb=" O ALA B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1002 Processing helix chain 'B' and resid 1008 through 1012 removed outlier: 3.716A pdb=" N SER B1011 " --> pdb=" O ASP B1008 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1030 Processing helix chain 'B' and resid 1036 through 1058 removed outlier: 3.596A pdb=" N GLN B1058 " --> pdb=" O ASN B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1059 through 1062 removed outlier: 3.658A pdb=" N ASN B1062 " --> pdb=" O GLN B1059 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1059 through 1062' Processing helix chain 'B' and resid 1070 through 1078 Processing helix chain 'B' and resid 1079 through 1127 removed outlier: 4.100A pdb=" N ALA B1085 " --> pdb=" O LEU B1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 303 Processing helix chain 'C' and resid 345 through 350 Processing helix chain 'C' and resid 357 through 360 removed outlier: 4.001A pdb=" N TRP C 360 " --> pdb=" O PRO C 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 357 through 360' Processing helix chain 'C' and resid 371 through 376 removed outlier: 3.784A pdb=" N LEU C 375 " --> pdb=" O ASN C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 394 removed outlier: 3.728A pdb=" N ILE C 394 " --> pdb=" O ALA C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 429 Processing helix chain 'C' and resid 446 through 450 removed outlier: 3.580A pdb=" N ASN C 449 " --> pdb=" O PRO C 446 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 450 " --> pdb=" O ALA C 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 446 through 450' Processing helix chain 'C' and resid 458 through 464 removed outlier: 3.777A pdb=" N LYS C 462 " --> pdb=" O SER C 458 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE C 464 " --> pdb=" O TRP C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 472 Processing helix chain 'C' and resid 707 through 716 Processing helix chain 'C' and resid 826 through 831 Processing helix chain 'C' and resid 834 through 841 removed outlier: 3.635A pdb=" N GLN C 840 " --> pdb=" O ALA C 836 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 841 " --> pdb=" O CYS C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 874 removed outlier: 4.134A pdb=" N CYS C 848 " --> pdb=" O TYR C 844 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N MET C 874 " --> pdb=" O ALA C 870 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 885 removed outlier: 3.729A pdb=" N ASP C 885 " --> pdb=" O LYS C 882 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 882 through 885' Processing helix chain 'C' and resid 914 through 922 Processing helix chain 'C' and resid 927 through 936 removed outlier: 3.737A pdb=" N TYR C 935 " --> pdb=" O PHE C 931 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASN C 936 " --> pdb=" O VAL C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 955 Processing helix chain 'C' and resid 964 through 978 removed outlier: 3.626A pdb=" N PHE C 968 " --> pdb=" O SER C 964 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA C 978 " --> pdb=" O ALA C 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 1002 Processing helix chain 'C' and resid 1008 through 1012 removed outlier: 3.771A pdb=" N SER C1011 " --> pdb=" O ASP C1008 " (cutoff:3.500A) Processing helix chain 'C' and resid 1013 through 1029 Processing helix chain 'C' and resid 1036 through 1058 removed outlier: 3.620A pdb=" N GLN C1058 " --> pdb=" O ASN C1054 " (cutoff:3.500A) Processing helix chain 'C' and resid 1059 through 1062 removed outlier: 3.597A pdb=" N ASN C1062 " --> pdb=" O GLN C1059 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1059 through 1062' Processing helix chain 'C' and resid 1070 through 1078 Processing helix chain 'C' and resid 1079 through 1127 removed outlier: 4.096A pdb=" N ALA C1085 " --> pdb=" O LEU C1081 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 40 removed outlier: 4.844A pdb=" N TYR A 75 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N THR A 74 " --> pdb=" O PRO A 268 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU A 263 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A 216 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA A 105 " --> pdb=" O PHE A 214 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 214 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR A 213 " --> pdb=" O THR A 228 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR A 228 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ALA A 225 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 56 removed outlier: 6.018A pdb=" N VAL A 56 " --> pdb=" O TYR C 660 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR C 667 " --> pdb=" O ILE C 680 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE C 669 " --> pdb=" O PHE C 678 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N THR C 677 " --> pdb=" O VAL C 647 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL C 647 " --> pdb=" O THR C 677 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY C 640 " --> pdb=" O TYR C 633 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL C 333 " --> pdb=" O ASN C 632 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG C 335 " --> pdb=" O ASP C 634 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 61 through 68 removed outlier: 3.675A pdb=" N LEU A 64 " --> pdb=" O TYR A 274 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY A 66 " --> pdb=" O ARG A 272 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 272 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASN A 286 " --> pdb=" O ALA A 277 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 81 through 82 removed outlier: 3.528A pdb=" N GLY A 82 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N THR A 255 " --> pdb=" O PRO A 172 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR A 174 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 10.487A pdb=" N TYR A 171 " --> pdb=" O HIS A 189 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N HIS A 189 " --> pdb=" O TYR A 171 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 187 " --> pdb=" O GLN A 173 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 97 through 98 removed outlier: 3.757A pdb=" N SER A 97 " --> pdb=" O TYR A 249 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N CYS A 164 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 139 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N GLY A 157 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N THR A 204 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU A 159 " --> pdb=" O ASN A 202 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASN A 202 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL A 161 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LYS A 200 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL A 163 " --> pdb=" O LEU A 198 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 110 through 114 removed outlier: 3.897A pdb=" N THR A 110 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU A 121 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 112 " --> pdb=" O TYR A 119 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR A 119 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 310 through 313 removed outlier: 3.684A pdb=" N GLY A 310 " --> pdb=" O PHE A 692 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR A 312 " --> pdb=" O ALA A 690 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.772A pdb=" N TYR A 325 " --> pdb=" O GLY A 686 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY A 686 " --> pdb=" O TYR A 325 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 332 through 335 removed outlier: 3.570A pdb=" N VAL A 333 " --> pdb=" O ASN A 632 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 335 " --> pdb=" O ASP A 634 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY A 640 " --> pdb=" O TYR A 633 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 647 " --> pdb=" O THR A 677 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N THR A 677 " --> pdb=" O VAL A 647 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE A 669 " --> pdb=" O PHE A 678 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N TYR A 667 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR A 660 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 353 through 355 removed outlier: 3.581A pdb=" N SER A 453 " --> pdb=" O VAL A 354 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 361 through 365 removed outlier: 4.036A pdb=" N GLU A 361 " --> pdb=" O LYS A 406 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS A 406 " --> pdb=" O GLU A 361 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A 363 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A 404 " --> pdb=" O LYS A 363 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR A 443 " --> pdb=" O ILE A 599 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU A 441 " --> pdb=" O ALA A 601 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER A 438 " --> pdb=" O ASN A 387 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 383 " --> pdb=" O TYR A 442 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 369 through 370 removed outlier: 3.953A pdb=" N PHE A 370 " --> pdb=" O CYS A 614 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 485 through 488 removed outlier: 3.660A pdb=" N ASP A 589 " --> pdb=" O VAL A 485 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR A 487 " --> pdb=" O SER A 587 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 492 through 493 removed outlier: 3.585A pdb=" N THR A 551 " --> pdb=" O LYS A 493 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 565 through 566 removed outlier: 3.839A pdb=" N ALA A 565 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 571 through 572 Processing sheet with id=AB9, first strand: chain 'A' and resid 726 through 727 removed outlier: 3.847A pdb=" N PHE A 727 " --> pdb=" O VAL A 734 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 738 through 745 removed outlier: 6.688A pdb=" N PHE A 776 " --> pdb=" O ASN A 739 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR A 741 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASN A 778 " --> pdb=" O THR A 741 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE A 743 " --> pdb=" O ASN A 778 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG A 775 " --> pdb=" O ASP A 759 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP A 759 " --> pdb=" O ARG A 775 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TYR A 756 " --> pdb=" O VAL A 752 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU A 750 " --> pdb=" O VAL A 758 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 785 through 787 removed outlier: 6.285A pdb=" N ASN A 785 " --> pdb=" O LEU B 879 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 798 through 803 Processing sheet with id=AC4, first strand: chain 'A' and resid 806 through 816 removed outlier: 3.652A pdb=" N GLU A 813 " --> pdb=" O PHE A1156 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 815 " --> pdb=" O LEU A1154 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A1154 " --> pdb=" O ILE A 815 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A1153 " --> pdb=" O ALA A1150 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A1159 " --> pdb=" O ILE A1144 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE A1144 " --> pdb=" O PHE A1159 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TYR A1161 " --> pdb=" O HIS A1142 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N HIS A1142 " --> pdb=" O TYR A1161 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 821 through 824 removed outlier: 4.576A pdb=" N LYS A 821 " --> pdb=" O LEU A 959 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS A 957 " --> pdb=" O THR A 823 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 878 through 880 Processing sheet with id=AC7, first strand: chain 'A' and resid 890 through 891 Processing sheet with id=AC8, first strand: chain 'A' and resid 1182 through 1183 removed outlier: 3.888A pdb=" N ILE A1183 " --> pdb=" O LEU A1175 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU A1175 " --> pdb=" O ILE A1183 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 1188 through 1192 removed outlier: 3.807A pdb=" N THR A1200 " --> pdb=" O TYR A1189 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 26 through 27 Processing sheet with id=AD2, first strand: chain 'B' and resid 36 through 40 removed outlier: 5.069A pdb=" N TYR B 75 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N THR B 74 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU B 263 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE B 216 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA B 105 " --> pdb=" O PHE B 214 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE B 214 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR B 213 " --> pdb=" O THR B 228 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR B 228 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR B 217 " --> pdb=" O TYR B 224 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ALA B 225 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 61 through 68 removed outlier: 3.775A pdb=" N LEU B 64 " --> pdb=" O TYR B 274 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B 66 " --> pdb=" O ARG B 272 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASN B 286 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 81 through 82 removed outlier: 3.564A pdb=" N GLY B 82 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N THR B 255 " --> pdb=" O PRO B 172 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N THR B 174 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 10.509A pdb=" N TYR B 171 " --> pdb=" O HIS B 189 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N HIS B 189 " --> pdb=" O TYR B 171 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 187 " --> pdb=" O GLN B 173 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 97 through 98 removed outlier: 3.766A pdb=" N SER B 97 " --> pdb=" O TYR B 249 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS B 164 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL B 139 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N GLY B 157 " --> pdb=" O THR B 204 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N THR B 204 " --> pdb=" O GLY B 157 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU B 159 " --> pdb=" O ASN B 202 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASN B 202 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL B 161 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS B 200 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL B 163 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 110 through 114 removed outlier: 3.856A pdb=" N THR B 110 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU B 121 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL B 112 " --> pdb=" O TYR B 119 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR B 119 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 310 through 313 removed outlier: 3.676A pdb=" N GLY B 310 " --> pdb=" O PHE B 692 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR B 312 " --> pdb=" O ALA B 690 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.811A pdb=" N TYR B 325 " --> pdb=" O GLY B 686 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY B 686 " --> pdb=" O TYR B 325 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'B' and resid 334 through 335 removed outlier: 3.742A pdb=" N ARG B 335 " --> pdb=" O ASP B 634 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY B 640 " --> pdb=" O TYR B 633 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 647 " --> pdb=" O THR B 677 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR B 677 " --> pdb=" O VAL B 647 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE B 669 " --> pdb=" O PHE B 678 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N TYR B 667 " --> pdb=" O ILE B 680 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY B 668 " --> pdb=" O LEU B 659 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR B 660 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 353 through 355 removed outlier: 3.572A pdb=" N SER B 453 " --> pdb=" O VAL B 354 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 361 through 365 removed outlier: 4.050A pdb=" N GLU B 361 " --> pdb=" O LYS B 406 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS B 406 " --> pdb=" O GLU B 361 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS B 363 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE B 404 " --> pdb=" O LYS B 363 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER B 401 " --> pdb=" O HIS B 606 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS B 606 " --> pdb=" O SER B 401 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE B 407 " --> pdb=" O PHE B 600 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR B 443 " --> pdb=" O ILE B 599 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 441 " --> pdb=" O ALA B 601 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER B 438 " --> pdb=" O ASN B 387 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR B 385 " --> pdb=" O GLN B 440 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER B 383 " --> pdb=" O TYR B 442 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 369 through 370 removed outlier: 3.952A pdb=" N PHE B 370 " --> pdb=" O CYS B 614 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 485 through 488 removed outlier: 3.648A pdb=" N ASP B 589 " --> pdb=" O VAL B 485 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR B 487 " --> pdb=" O SER B 587 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 492 through 493 removed outlier: 3.615A pdb=" N THR B 551 " --> pdb=" O LYS B 493 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 565 through 566 removed outlier: 3.831A pdb=" N ALA B 565 " --> pdb=" O LEU B 584 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 571 through 572 Processing sheet with id=AE8, first strand: chain 'B' and resid 726 through 727 removed outlier: 3.863A pdb=" N PHE B 727 " --> pdb=" O VAL B 734 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 738 through 745 removed outlier: 6.646A pdb=" N PHE B 776 " --> pdb=" O ASN B 739 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASN B 778 " --> pdb=" O THR B 741 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE B 743 " --> pdb=" O ASN B 778 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG B 775 " --> pdb=" O ASP B 759 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP B 759 " --> pdb=" O ARG B 775 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TYR B 756 " --> pdb=" O VAL B 752 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU B 750 " --> pdb=" O VAL B 758 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 785 through 787 removed outlier: 6.524A pdb=" N ASN B 785 " --> pdb=" O LEU C 879 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'B' and resid 798 through 816 removed outlier: 6.521A pdb=" N LYS B1165 " --> pdb=" O SER B 804 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N PHE B 806 " --> pdb=" O PRO B1163 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ILE B 808 " --> pdb=" O TYR B1161 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N TYR B1161 " --> pdb=" O ILE B 808 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASN B 810 " --> pdb=" O PHE B1159 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N PHE B1159 " --> pdb=" O ASN B 810 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL B 812 " --> pdb=" O ILE B1157 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ILE B1157 " --> pdb=" O VAL B 812 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N PHE B 814 " --> pdb=" O TYR B1155 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N TYR B1155 " --> pdb=" O PHE B 814 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N GLN B 816 " --> pdb=" O GLY B1153 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY B1153 " --> pdb=" O GLN B 816 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY B1153 " --> pdb=" O ALA B1150 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE B1159 " --> pdb=" O ILE B1144 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE B1144 " --> pdb=" O PHE B1159 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N TYR B1161 " --> pdb=" O HIS B1142 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N HIS B1142 " --> pdb=" O TYR B1161 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 821 through 824 removed outlier: 4.500A pdb=" N LYS B 821 " --> pdb=" O LEU B 959 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS B 957 " --> pdb=" O THR B 823 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 890 through 891 Processing sheet with id=AF5, first strand: chain 'B' and resid 1175 through 1176 removed outlier: 4.254A pdb=" N LEU B1175 " --> pdb=" O ILE B1183 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE B1183 " --> pdb=" O LEU B1175 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'B' and resid 1188 through 1192 removed outlier: 3.811A pdb=" N THR B1200 " --> pdb=" O TYR B1189 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 26 through 27 Processing sheet with id=AF8, first strand: chain 'C' and resid 36 through 40 removed outlier: 5.177A pdb=" N TYR C 75 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N THR C 74 " --> pdb=" O PRO C 268 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLU C 263 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE C 216 " --> pdb=" O ILE C 103 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA C 105 " --> pdb=" O PHE C 214 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE C 214 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR C 213 " --> pdb=" O THR C 228 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ALA C 225 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N THR C 49 " --> pdb=" O THR C 234 " (cutoff:3.500A) removed outlier: 9.265A pdb=" N PHE C 236 " --> pdb=" O THR C 49 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 61 through 68 removed outlier: 3.656A pdb=" N LEU C 64 " --> pdb=" O TYR C 274 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY C 66 " --> pdb=" O ARG C 272 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 288 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASN C 286 " --> pdb=" O ALA C 277 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 81 through 82 removed outlier: 3.501A pdb=" N GLY C 82 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N THR C 255 " --> pdb=" O PRO C 172 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR C 174 " --> pdb=" O THR C 255 " (cutoff:3.500A) removed outlier: 10.454A pdb=" N TYR C 171 " --> pdb=" O HIS C 189 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N HIS C 189 " --> pdb=" O TYR C 171 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 97 through 98 removed outlier: 3.707A pdb=" N SER C 97 " --> pdb=" O TYR C 249 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N CYS C 164 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL C 139 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N GLY C 157 " --> pdb=" O THR C 204 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N THR C 204 " --> pdb=" O GLY C 157 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU C 159 " --> pdb=" O ASN C 202 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASN C 202 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL C 161 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS C 200 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL C 163 " --> pdb=" O LEU C 198 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 110 through 114 removed outlier: 3.904A pdb=" N THR C 110 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU C 121 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL C 112 " --> pdb=" O TYR C 119 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR C 119 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 310 through 313 removed outlier: 3.639A pdb=" N GLY C 310 " --> pdb=" O PHE C 692 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE C 692 " --> pdb=" O GLY C 310 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR C 312 " --> pdb=" O ALA C 690 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER C 689 " --> pdb=" O LEU C 702 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.876A pdb=" N TYR C 325 " --> pdb=" O GLY C 686 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY C 686 " --> pdb=" O TYR C 325 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'C' and resid 353 through 355 removed outlier: 3.554A pdb=" N SER C 453 " --> pdb=" O VAL C 354 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 361 through 365 removed outlier: 4.080A pdb=" N GLU C 361 " --> pdb=" O LYS C 406 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS C 406 " --> pdb=" O GLU C 361 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS C 363 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE C 404 " --> pdb=" O LYS C 363 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER C 401 " --> pdb=" O HIS C 606 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS C 606 " --> pdb=" O SER C 401 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE C 407 " --> pdb=" O PHE C 600 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR C 443 " --> pdb=" O ILE C 599 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU C 441 " --> pdb=" O ALA C 601 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER C 438 " --> pdb=" O ASN C 387 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER C 383 " --> pdb=" O TYR C 442 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 369 through 370 removed outlier: 3.937A pdb=" N PHE C 370 " --> pdb=" O CYS C 614 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 485 through 488 removed outlier: 3.621A pdb=" N ASP C 589 " --> pdb=" O VAL C 485 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR C 487 " --> pdb=" O SER C 587 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 492 through 493 removed outlier: 3.599A pdb=" N THR C 551 " --> pdb=" O LYS C 493 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 565 through 566 removed outlier: 3.743A pdb=" N ALA C 565 " --> pdb=" O LEU C 584 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 571 through 572 Processing sheet with id=AH4, first strand: chain 'C' and resid 726 through 728 removed outlier: 3.777A pdb=" N PHE C 727 " --> pdb=" O VAL C 734 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 744 through 745 removed outlier: 3.638A pdb=" N ARG C 775 " --> pdb=" O ASP C 759 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP C 759 " --> pdb=" O ARG C 775 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR C 756 " --> pdb=" O VAL C 752 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU C 750 " --> pdb=" O VAL C 758 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 798 through 816 removed outlier: 6.561A pdb=" N LYS C1165 " --> pdb=" O SER C 804 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE C 806 " --> pdb=" O PRO C1163 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ILE C 808 " --> pdb=" O TYR C1161 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N TYR C1161 " --> pdb=" O ILE C 808 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASN C 810 " --> pdb=" O PHE C1159 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE C1159 " --> pdb=" O ASN C 810 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL C 812 " --> pdb=" O ILE C1157 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ILE C1157 " --> pdb=" O VAL C 812 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N PHE C 814 " --> pdb=" O TYR C1155 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N TYR C1155 " --> pdb=" O PHE C 814 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLN C 816 " --> pdb=" O GLY C1153 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLY C1153 " --> pdb=" O GLN C 816 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY C1153 " --> pdb=" O ALA C1150 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE C1159 " --> pdb=" O ILE C1144 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE C1144 " --> pdb=" O PHE C1159 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N TYR C1161 " --> pdb=" O HIS C1142 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N HIS C1142 " --> pdb=" O TYR C1161 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'C' and resid 821 through 824 removed outlier: 4.486A pdb=" N LYS C 821 " --> pdb=" O LEU C 959 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS C 957 " --> pdb=" O THR C 823 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'C' and resid 890 through 891 Processing sheet with id=AH9, first strand: chain 'C' and resid 1182 through 1183 removed outlier: 3.679A pdb=" N ILE C1183 " --> pdb=" O LEU C1175 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU C1175 " --> pdb=" O ILE C1183 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'C' and resid 1188 through 1193 removed outlier: 3.923A pdb=" N THR C1200 " --> pdb=" O TYR C1189 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR C1196 " --> pdb=" O VAL C1193 " (cutoff:3.500A) 857 hydrogen bonds defined for protein. 2382 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: 6.79 Time building geometry restraints manager: 2.37 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: 8830 1.34 - 1.47: 7017 1.47 - 1.59: 11993 1.59 - 1.71: 0 1.71 - 1.83: 237 Bond restraints: 28077 Sorted by residual: bond pdb=" C SER A1103 " pdb=" O SER A1103 " ideal model delta sigma weight residual 1.237 1.250 -0.014 1.17e-02 7.31e+03 1.35e+00 bond pdb=" C SER C1103 " pdb=" O SER C1103 " ideal model delta sigma weight residual 1.237 1.250 -0.013 1.17e-02 7.31e+03 1.24e+00 bond pdb=" C ALA C1100 " pdb=" O ALA C1100 " ideal model delta sigma weight residual 1.237 1.249 -0.013 1.17e-02 7.31e+03 1.18e+00 bond pdb=" CA VAL A1127 " pdb=" CB VAL A1127 " ideal model delta sigma weight residual 1.545 1.535 0.010 9.10e-03 1.21e+04 1.15e+00 bond pdb=" C SER B1103 " pdb=" O SER B1103 " ideal model delta sigma weight residual 1.237 1.249 -0.012 1.17e-02 7.31e+03 1.14e+00 ... (remaining 28072 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 37422 1.57 - 3.15: 748 3.15 - 4.72: 52 4.72 - 6.30: 7 6.30 - 7.87: 3 Bond angle restraints: 38232 Sorted by residual: angle pdb=" C ARG B 719 " pdb=" CA ARG B 719 " pdb=" CB ARG B 719 " ideal model delta sigma weight residual 117.23 110.90 6.33 1.36e+00 5.41e-01 2.17e+01 angle pdb=" C GLY C1140 " pdb=" N ASN C1141 " pdb=" CA ASN C1141 " ideal model delta sigma weight residual 122.46 128.55 -6.09 1.41e+00 5.03e-01 1.87e+01 angle pdb=" C CYS B1126 " pdb=" N VAL B1127 " pdb=" CA VAL B1127 " ideal model delta sigma weight residual 122.97 118.74 4.23 9.80e-01 1.04e+00 1.86e+01 angle pdb=" C CYS C1126 " pdb=" N VAL C1127 " pdb=" CA VAL C1127 " ideal model delta sigma weight residual 122.97 118.76 4.21 9.80e-01 1.04e+00 1.85e+01 angle pdb=" C ASN C 387 " pdb=" N ASN C 388 " pdb=" CA ASN C 388 " ideal model delta sigma weight residual 121.54 129.41 -7.87 1.91e+00 2.74e-01 1.70e+01 ... (remaining 38227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.57: 15268 14.57 - 29.14: 1098 29.14 - 43.71: 255 43.71 - 58.28: 93 58.28 - 72.85: 20 Dihedral angle restraints: 16734 sinusoidal: 6429 harmonic: 10305 Sorted by residual: dihedral pdb=" CA ASN A 315 " pdb=" C ASN A 315 " pdb=" N GLY A 316 " pdb=" CA GLY A 316 " ideal model delta harmonic sigma weight residual 180.00 157.57 22.43 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA ASN B 315 " pdb=" C ASN B 315 " pdb=" N GLY B 316 " pdb=" CA GLY B 316 " ideal model delta harmonic sigma weight residual 180.00 158.60 21.40 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ASN C 315 " pdb=" C ASN C 315 " pdb=" N GLY C 316 " pdb=" CA GLY C 316 " ideal model delta harmonic sigma weight residual 180.00 159.31 20.69 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 16731 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2673 0.031 - 0.062: 961 0.062 - 0.094: 423 0.094 - 0.125: 221 0.125 - 0.156: 42 Chirality restraints: 4320 Sorted by residual: chirality pdb=" CA ASN C 388 " pdb=" N ASN C 388 " pdb=" C ASN C 388 " pdb=" CB ASN C 388 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" CA ASN B 388 " pdb=" N ASN B 388 " pdb=" C ASN B 388 " pdb=" CB ASN B 388 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA ILE C1157 " pdb=" N ILE C1157 " pdb=" C ILE C1157 " pdb=" CB ILE C1157 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 4317 not shown) Planarity restraints: 4938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 897 " 0.051 5.00e-02 4.00e+02 7.57e-02 9.17e+00 pdb=" N PRO B 898 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO B 898 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 898 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 897 " 0.050 5.00e-02 4.00e+02 7.55e-02 9.12e+00 pdb=" N PRO C 898 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO C 898 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 898 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 897 " -0.049 5.00e-02 4.00e+02 7.31e-02 8.56e+00 pdb=" N PRO A 898 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 898 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 898 " -0.041 5.00e-02 4.00e+02 ... (remaining 4935 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 8696 2.82 - 3.34: 21344 3.34 - 3.86: 42901 3.86 - 4.38: 43799 4.38 - 4.90: 79278 Nonbonded interactions: 196018 Sorted by model distance: nonbonded pdb=" OG SER A 356 " pdb=" OD1 ASN A 359 " model vdw 2.299 3.040 nonbonded pdb=" O PRO C 898 " pdb=" OG SER C 914 " model vdw 2.303 3.040 nonbonded pdb=" O PRO C 523 " pdb=" OG1 THR C 526 " model vdw 2.303 3.040 nonbonded pdb=" O PRO B 523 " pdb=" OG1 THR B 526 " model vdw 2.306 3.040 nonbonded pdb=" OG SER B 356 " pdb=" OD1 ASN B 359 " model vdw 2.309 3.040 ... (remaining 196013 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.100 Set scattering table: 0.050 Process input model: 25.670 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 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 0.047 28140 Z= 0.177 Angle : 0.553 7.872 38358 Z= 0.322 Chirality : 0.044 0.156 4320 Planarity : 0.005 0.076 4938 Dihedral : 11.640 72.851 9957 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 5.51 % Allowed : 5.71 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.13), residues: 3489 helix: -0.25 (0.18), residues: 690 sheet: -0.67 (0.21), residues: 582 loop : -1.89 (0.11), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 362 TYR 0.015 0.001 TYR C 633 PHE 0.015 0.002 PHE B 122 TRP 0.006 0.001 TRP B 348 HIS 0.004 0.001 HIS B1142 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 (28077) covalent geometry : angle 0.55211 / 0.32 (38232) SS BOND : bond 0.00223 / 0.15 ( 63) SS BOND : angle 0.83444 / 0.56 ( 126) hydrogen bonds : bond 0.25953 / 17.29 ( 857) hydrogen bonds : angle 7.56722 / 5.27 ( 2382) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 282 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.8481 (m-10) REVERT: A 53 LEU cc_start: 0.8812 (mt) cc_final: 0.8278 (pp) REVERT: A 56 VAL cc_start: 0.8789 (OUTLIER) cc_final: 0.8547 (m) REVERT: A 286 ASN cc_start: 0.9090 (t0) cc_final: 0.8704 (t0) REVERT: A 291 MET cc_start: 0.9400 (mmm) cc_final: 0.9126 (mmm) REVERT: A 295 MET cc_start: 0.8828 (tpt) cc_final: 0.8457 (tpp) REVERT: A 371 ASN cc_start: 0.4939 (OUTLIER) cc_final: 0.4009 (p0) REVERT: A 547 LYS cc_start: 0.9207 (ttpt) cc_final: 0.8947 (mmtt) REVERT: A 776 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.7726 (m-10) REVERT: A 789 ASP cc_start: 0.9101 (m-30) cc_final: 0.8695 (t70) REVERT: A 849 ASP cc_start: 0.9207 (m-30) cc_final: 0.8916 (m-30) REVERT: A 873 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9366 (tp) REVERT: A 877 VAL cc_start: 0.9456 (t) cc_final: 0.9206 (p) REVERT: A 888 ASN cc_start: 0.8942 (OUTLIER) cc_final: 0.7771 (t0) REVERT: A 889 PHE cc_start: 0.8303 (p90) cc_final: 0.8081 (m-10) REVERT: A 1007 MET cc_start: 0.8766 (mmm) cc_final: 0.8298 (mmm) REVERT: A 1109 SER cc_start: 0.9539 (t) cc_final: 0.9183 (p) REVERT: A 1112 VAL cc_start: 0.9704 (t) cc_final: 0.9379 (p) REVERT: B 51 TYR cc_start: 0.8868 (OUTLIER) cc_final: 0.8631 (m-10) REVERT: B 56 VAL cc_start: 0.9117 (OUTLIER) cc_final: 0.8902 (p) REVERT: B 78 MET cc_start: 0.9401 (mmm) cc_final: 0.9198 (mmt) REVERT: B 215 HIS cc_start: 0.9341 (OUTLIER) cc_final: 0.8937 (m-70) REVERT: B 262 LEU cc_start: 0.9481 (mt) cc_final: 0.9254 (mm) REVERT: B 291 MET cc_start: 0.9371 (mmm) cc_final: 0.9152 (mmm) REVERT: B 295 MET cc_start: 0.9082 (tpt) cc_final: 0.8626 (tpp) REVERT: B 303 GLN cc_start: 0.9366 (tt0) cc_final: 0.8795 (tm-30) REVERT: B 371 ASN cc_start: 0.3405 (OUTLIER) cc_final: 0.2619 (p0) REVERT: B 394 ILE cc_start: 0.9438 (OUTLIER) cc_final: 0.9061 (mt) REVERT: B 559 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8218 (mp0) REVERT: B 598 ASN cc_start: 0.9194 (OUTLIER) cc_final: 0.8344 (m-40) REVERT: B 776 PHE cc_start: 0.9141 (OUTLIER) cc_final: 0.8577 (m-10) REVERT: B 789 ASP cc_start: 0.8913 (m-30) cc_final: 0.8424 (t70) REVERT: B 849 ASP cc_start: 0.9295 (m-30) cc_final: 0.9070 (m-30) REVERT: B 863 ASP cc_start: 0.9016 (m-30) cc_final: 0.8783 (t0) REVERT: B 879 LEU cc_start: 0.9225 (mt) cc_final: 0.8927 (pt) REVERT: B 889 PHE cc_start: 0.8366 (p90) cc_final: 0.7870 (p90) REVERT: B 952 SER cc_start: 0.9463 (t) cc_final: 0.9172 (p) REVERT: B 971 TYR cc_start: 0.9357 (m-10) cc_final: 0.9109 (m-80) REVERT: B 1109 SER cc_start: 0.9674 (t) cc_final: 0.9164 (p) REVERT: B 1111 LEU cc_start: 0.9704 (OUTLIER) cc_final: 0.9478 (tt) REVERT: B 1112 VAL cc_start: 0.9612 (t) cc_final: 0.9315 (p) REVERT: C 56 VAL cc_start: 0.8916 (OUTLIER) cc_final: 0.8646 (m) REVERT: C 215 HIS cc_start: 0.9158 (OUTLIER) cc_final: 0.8800 (m90) REVERT: C 254 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8642 (tp) REVERT: C 274 TYR cc_start: 0.8833 (OUTLIER) cc_final: 0.7189 (t80) REVERT: C 286 ASN cc_start: 0.8915 (t0) cc_final: 0.8597 (t0) REVERT: C 291 MET cc_start: 0.9388 (mmm) cc_final: 0.9137 (mmm) REVERT: C 295 MET cc_start: 0.8919 (tpt) cc_final: 0.8538 (tpp) REVERT: C 303 GLN cc_start: 0.9347 (tt0) cc_final: 0.8535 (tm-30) REVERT: C 372 MET cc_start: 0.8732 (mmm) cc_final: 0.8155 (mmm) REVERT: C 547 LYS cc_start: 0.9180 (ttpt) cc_final: 0.8908 (mmtm) REVERT: C 608 VAL cc_start: 0.9191 (OUTLIER) cc_final: 0.8932 (t) REVERT: C 743 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8886 (tt) REVERT: C 789 ASP cc_start: 0.8876 (m-30) cc_final: 0.8263 (t0) REVERT: C 811 MET cc_start: 0.8686 (ttt) cc_final: 0.8233 (ttt) REVERT: C 849 ASP cc_start: 0.9112 (m-30) cc_final: 0.8833 (m-30) REVERT: C 850 ASN cc_start: 0.8517 (OUTLIER) cc_final: 0.8202 (t0) REVERT: C 863 ASP cc_start: 0.8975 (m-30) cc_final: 0.8697 (t0) REVERT: C 874 MET cc_start: 0.9245 (ptp) cc_final: 0.8894 (ptp) REVERT: C 877 VAL cc_start: 0.9515 (t) cc_final: 0.9263 (p) REVERT: C 888 ASN cc_start: 0.8775 (OUTLIER) cc_final: 0.7539 (t0) REVERT: C 917 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8564 (mt-10) REVERT: C 952 SER cc_start: 0.9524 (t) cc_final: 0.9305 (p) REVERT: C 971 TYR cc_start: 0.9390 (m-10) cc_final: 0.8744 (m-80) REVERT: C 1007 MET cc_start: 0.8694 (mmm) cc_final: 0.7699 (mmm) REVERT: C 1063 ARG cc_start: 0.8610 (mtt180) cc_final: 0.8355 (mtm-85) REVERT: C 1112 VAL cc_start: 0.9612 (t) cc_final: 0.9358 (p) outliers start: 169 outliers final: 59 residues processed: 444 average time/residue: 0.1388 time to fit residues: 107.6894 Evaluate side-chains 249 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 168 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.0040 chunk 298 optimal weight: 7.9990 overall best weight: 2.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 429 ASN A 598 ASN A 801 GLN A 810 ASN B 560 HIS B 801 GLN C 189 HIS ** C 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.070625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.053710 restraints weight = 89650.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.055913 restraints weight = 46084.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.057415 restraints weight = 29377.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.058512 restraints weight = 21550.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.059276 restraints weight = 17193.090| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28140 Z= 0.203 Angle : 0.594 8.553 38358 Z= 0.322 Chirality : 0.043 0.197 4320 Planarity : 0.004 0.051 4938 Dihedral : 4.591 23.518 3819 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.99 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.14), residues: 3489 helix: 1.09 (0.20), residues: 726 sheet: -0.60 (0.21), residues: 636 loop : -1.68 (0.12), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 913 TYR 0.031 0.002 TYR A 971 PHE 0.013 0.001 PHE A 407 TRP 0.014 0.001 TRP C 655 HIS 0.005 0.001 HIS B1142 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 (28077) covalent geometry : angle 0.59015 / 0.32 (38232) SS BOND : bond 0.00307 / 0.20 ( 63) SS BOND : angle 1.26809 / 0.93 ( 126) hydrogen bonds : bond 0.06981 / 4.51 ( 857) hydrogen bonds : angle 5.94608 / 4.14 ( 2382) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 ASN cc_start: 0.9329 (t0) cc_final: 0.9123 (t0) REVERT: A 291 MET cc_start: 0.9391 (mmm) cc_final: 0.9085 (mmm) REVERT: A 295 MET cc_start: 0.8795 (tpt) cc_final: 0.8386 (tpp) REVERT: A 750 LEU cc_start: 0.9342 (mp) cc_final: 0.8594 (mp) REVERT: A 849 ASP cc_start: 0.9220 (m-30) cc_final: 0.8945 (m-30) REVERT: A 865 THR cc_start: 0.9644 (m) cc_final: 0.9327 (p) REVERT: A 877 VAL cc_start: 0.9536 (t) cc_final: 0.9299 (p) REVERT: A 1051 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8807 (tm-30) REVERT: A 1109 SER cc_start: 0.9549 (t) cc_final: 0.9150 (p) REVERT: A 1112 VAL cc_start: 0.9674 (t) cc_final: 0.9379 (p) REVERT: B 78 MET cc_start: 0.9397 (mmm) cc_final: 0.9187 (mmp) REVERT: B 252 MET cc_start: 0.9102 (mtm) cc_final: 0.8696 (mtm) REVERT: B 291 MET cc_start: 0.9406 (mmm) cc_final: 0.9132 (mmm) REVERT: B 295 MET cc_start: 0.9005 (tpt) cc_final: 0.8579 (tpp) REVERT: B 849 ASP cc_start: 0.9294 (m-30) cc_final: 0.9057 (m-30) REVERT: B 863 ASP cc_start: 0.9057 (m-30) cc_final: 0.8803 (t0) REVERT: B 879 LEU cc_start: 0.9277 (mt) cc_final: 0.8919 (pt) REVERT: B 917 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8575 (mt-10) REVERT: B 952 SER cc_start: 0.9413 (t) cc_final: 0.9209 (p) REVERT: B 1109 SER cc_start: 0.9751 (t) cc_final: 0.9224 (p) REVERT: B 1112 VAL cc_start: 0.9664 (t) cc_final: 0.9402 (p) REVERT: B 1120 MET cc_start: 0.8950 (ttm) cc_final: 0.8214 (ttm) REVERT: B 1127 VAL cc_start: 0.8807 (t) cc_final: 0.8589 (t) REVERT: B 1198 MET cc_start: 0.7852 (mpp) cc_final: 0.7584 (mpp) REVERT: C 252 MET cc_start: 0.8926 (mtm) cc_final: 0.8507 (pmm) REVERT: C 291 MET cc_start: 0.9410 (mmm) cc_final: 0.9140 (mmm) REVERT: C 296 SER cc_start: 0.8939 (m) cc_final: 0.8606 (p) REVERT: C 397 MET cc_start: 0.8808 (mtm) cc_final: 0.8456 (mtm) REVERT: C 547 LYS cc_start: 0.9161 (ttpt) cc_final: 0.8932 (mmtm) REVERT: C 617 ASP cc_start: 0.7524 (m-30) cc_final: 0.7288 (m-30) REVERT: C 849 ASP cc_start: 0.9128 (m-30) cc_final: 0.8864 (m-30) REVERT: C 863 ASP cc_start: 0.9026 (m-30) cc_final: 0.8746 (t0) REVERT: C 874 MET cc_start: 0.8998 (ptm) cc_final: 0.8537 (ptp) REVERT: C 877 VAL cc_start: 0.9500 (t) cc_final: 0.9285 (p) REVERT: C 952 SER cc_start: 0.9564 (t) cc_final: 0.9333 (p) REVERT: C 971 TYR cc_start: 0.9428 (m-10) cc_final: 0.8782 (m-80) REVERT: C 1007 MET cc_start: 0.8347 (mmm) cc_final: 0.8082 (mmm) REVERT: C 1063 ARG cc_start: 0.8668 (mtt180) cc_final: 0.8379 (mtm-85) REVERT: C 1112 VAL cc_start: 0.9612 (t) cc_final: 0.9398 (p) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.1386 time to fit residues: 51.1552 Evaluate side-chains 137 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: [140, 248, 190, 93, 13, 286, 169, 182, 150, 133, 191] chunk 140 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 190 optimal weight: 20.0000 chunk 93 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 286 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 chunk 182 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 chunk 133 optimal weight: 8.9990 chunk 191 optimal weight: 0.6980 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN A 429 ASN A 449 ASN ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 598 ASN ** B 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 705 ASN B 859 ASN C 429 ASN C 609 ASN C 715 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.067451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.050553 restraints weight = 93165.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.052622 restraints weight = 49008.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.054055 restraints weight = 31773.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.055076 restraints weight = 23469.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.055800 restraints weight = 18947.567| |-----------------------------------------------------------------------------| r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 28140 Z= 0.334 Angle : 0.733 10.675 38358 Z= 0.384 Chirality : 0.046 0.293 4320 Planarity : 0.005 0.052 4938 Dihedral : 4.944 23.267 3819 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 0.10 % Allowed : 3.23 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.14), residues: 3489 helix: 1.23 (0.20), residues: 693 sheet: -0.72 (0.21), residues: 633 loop : -1.90 (0.12), residues: 2163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 272 TYR 0.037 0.002 TYR A 971 PHE 0.020 0.002 PHE A 776 TRP 0.015 0.002 TRP C 265 HIS 0.007 0.001 HIS C 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00749 / 0.33 (28077) covalent geometry : angle 0.72824 / 0.38 (38232) SS BOND : bond 0.00424 / 0.29 ( 63) SS BOND : angle 1.58242 / 1.10 ( 126) hydrogen bonds : bond 0.07313 / 4.77 ( 857) hydrogen bonds : angle 5.99223 / 4.19 ( 2382) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 151 time to evaluate : 1.109 Fit side-chains revert: symmetry clash REVERT: A 286 ASN cc_start: 0.9259 (t0) cc_final: 0.9031 (t0) REVERT: A 291 MET cc_start: 0.9399 (mmm) cc_final: 0.9114 (mmm) REVERT: A 295 MET cc_start: 0.8721 (tpt) cc_final: 0.8319 (tpp) REVERT: A 849 ASP cc_start: 0.9180 (m-30) cc_final: 0.8875 (m-30) REVERT: A 865 THR cc_start: 0.9676 (m) cc_final: 0.9376 (p) REVERT: A 877 VAL cc_start: 0.9562 (t) cc_final: 0.9350 (p) REVERT: A 1109 SER cc_start: 0.9644 (t) cc_final: 0.9284 (p) REVERT: B 118 MET cc_start: 0.9236 (mpp) cc_final: 0.8989 (mpp) REVERT: B 252 MET cc_start: 0.8967 (mtm) cc_final: 0.8688 (mtm) REVERT: B 291 MET cc_start: 0.9419 (mmm) cc_final: 0.9186 (mmm) REVERT: B 397 MET cc_start: 0.8563 (mtm) cc_final: 0.8303 (mtp) REVERT: B 849 ASP cc_start: 0.9279 (m-30) cc_final: 0.9022 (m-30) REVERT: B 863 ASP cc_start: 0.9092 (m-30) cc_final: 0.8829 (t0) REVERT: B 874 MET cc_start: 0.9185 (ptp) cc_final: 0.8893 (ptt) REVERT: B 889 PHE cc_start: 0.8258 (p90) cc_final: 0.7548 (p90) REVERT: B 917 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8618 (mt-10) REVERT: B 1109 SER cc_start: 0.9701 (t) cc_final: 0.9190 (p) REVERT: B 1120 MET cc_start: 0.8981 (ttm) cc_final: 0.8327 (ttm) REVERT: B 1198 MET cc_start: 0.8010 (mpp) cc_final: 0.7747 (mpp) REVERT: C 53 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8078 (pp) REVERT: C 118 MET cc_start: 0.9255 (mpp) cc_final: 0.9041 (mpp) REVERT: C 252 MET cc_start: 0.8993 (mtm) cc_final: 0.8391 (pmm) REVERT: C 291 MET cc_start: 0.9450 (mmm) cc_final: 0.9148 (mmm) REVERT: C 296 SER cc_start: 0.9070 (m) cc_final: 0.8720 (p) REVERT: C 397 MET cc_start: 0.8848 (mtm) cc_final: 0.8551 (mtm) REVERT: C 547 LYS cc_start: 0.9156 (ttpt) cc_final: 0.8913 (mmtm) REVERT: C 617 ASP cc_start: 0.7606 (m-30) cc_final: 0.7321 (m-30) REVERT: C 849 ASP cc_start: 0.9108 (m-30) cc_final: 0.8813 (m-30) REVERT: C 863 ASP cc_start: 0.9079 (m-30) cc_final: 0.8758 (t0) REVERT: C 874 MET cc_start: 0.9308 (ptm) cc_final: 0.8586 (ptp) REVERT: C 952 SER cc_start: 0.9652 (t) cc_final: 0.9437 (p) REVERT: C 971 TYR cc_start: 0.9451 (m-10) cc_final: 0.8755 (m-80) REVERT: C 1007 MET cc_start: 0.8370 (mmm) cc_final: 0.8121 (mmm) REVERT: C 1109 SER cc_start: 0.9615 (t) cc_final: 0.9281 (p) outliers start: 3 outliers final: 0 residues processed: 154 average time/residue: 0.1429 time to fit residues: 38.6603 Evaluate side-chains 117 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: [52, 183, 115, 234, 344, 268, 132, 69, 27, 118, 199] chunk 52 optimal weight: 9.9990 chunk 183 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 234 optimal weight: 8.9990 chunk 344 optimal weight: 2.9990 chunk 268 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 118 optimal weight: 9.9990 chunk 199 optimal weight: 7.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN A 609 ASN ** B 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1105 GLN C 303 GLN C 429 ASN C 705 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.068321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.051710 restraints weight = 88867.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.053872 restraints weight = 45367.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.055393 restraints weight = 28853.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.056403 restraints weight = 20961.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.057190 restraints weight = 16838.651| |-----------------------------------------------------------------------------| r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 28140 Z= 0.131 Angle : 0.513 8.804 38358 Z= 0.280 Chirality : 0.042 0.244 4320 Planarity : 0.004 0.048 4938 Dihedral : 4.461 28.606 3819 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.03 % Allowed : 1.86 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.14), residues: 3489 helix: 1.37 (0.20), residues: 729 sheet: -0.51 (0.21), residues: 603 loop : -1.76 (0.12), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 913 TYR 0.016 0.001 TYR C 738 PHE 0.014 0.001 PHE B 223 TRP 0.009 0.001 TRP B 655 HIS 0.004 0.001 HIS A1142 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (28077) covalent geometry : angle 0.50963 / 0.28 (38232) SS BOND : bond 0.00212 / 0.14 ( 63) SS BOND : angle 1.15760 / 0.82 ( 126) hydrogen bonds : bond 0.06260 / 4.04 ( 857) hydrogen bonds : angle 5.43426 / 3.79 ( 2382) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: A 252 MET cc_start: 0.9283 (mtm) cc_final: 0.8459 (pmm) REVERT: A 291 MET cc_start: 0.9383 (mmm) cc_final: 0.9070 (mmm) REVERT: A 295 MET cc_start: 0.8516 (tpt) cc_final: 0.8067 (tpp) REVERT: A 849 ASP cc_start: 0.9232 (m-30) cc_final: 0.8918 (m-30) REVERT: A 865 THR cc_start: 0.9641 (m) cc_final: 0.9313 (p) REVERT: A 877 VAL cc_start: 0.9578 (t) cc_final: 0.9359 (p) REVERT: A 1109 SER cc_start: 0.9614 (t) cc_final: 0.9198 (p) REVERT: A 1112 VAL cc_start: 0.9662 (t) cc_final: 0.9394 (p) REVERT: A 1198 MET cc_start: 0.8108 (mpp) cc_final: 0.7877 (mpp) REVERT: B 252 MET cc_start: 0.9156 (mtm) cc_final: 0.8818 (mtm) REVERT: B 291 MET cc_start: 0.9407 (mmm) cc_final: 0.9154 (mmm) REVERT: B 372 MET cc_start: 0.8674 (mmm) cc_final: 0.8230 (mmm) REVERT: B 397 MET cc_start: 0.8616 (mtm) cc_final: 0.8192 (mtp) REVERT: B 849 ASP cc_start: 0.9281 (m-30) cc_final: 0.9021 (m-30) REVERT: B 879 LEU cc_start: 0.9235 (mt) cc_final: 0.8894 (pt) REVERT: B 889 PHE cc_start: 0.8240 (p90) cc_final: 0.7496 (p90) REVERT: B 917 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8613 (mt-10) REVERT: B 1109 SER cc_start: 0.9738 (t) cc_final: 0.9312 (p) REVERT: B 1112 VAL cc_start: 0.9624 (t) cc_final: 0.9408 (p) REVERT: B 1120 MET cc_start: 0.9083 (ttm) cc_final: 0.8241 (ttm) REVERT: B 1198 MET cc_start: 0.8181 (mpp) cc_final: 0.7940 (mpp) REVERT: C 180 LEU cc_start: 0.8858 (mm) cc_final: 0.8294 (tp) REVERT: C 254 LEU cc_start: 0.8481 (tp) cc_final: 0.8242 (tp) REVERT: C 291 MET cc_start: 0.9459 (mmm) cc_final: 0.9124 (mmm) REVERT: C 296 SER cc_start: 0.8956 (m) cc_final: 0.8556 (p) REVERT: C 303 GLN cc_start: 0.9291 (OUTLIER) cc_final: 0.8781 (tm-30) REVERT: C 397 MET cc_start: 0.8866 (mtm) cc_final: 0.8505 (mtm) REVERT: C 547 LYS cc_start: 0.9168 (ttpt) cc_final: 0.8932 (mmtm) REVERT: C 849 ASP cc_start: 0.9118 (m-30) cc_final: 0.8831 (m-30) REVERT: C 863 ASP cc_start: 0.9042 (m-30) cc_final: 0.8710 (t0) REVERT: C 874 MET cc_start: 0.9276 (ptm) cc_final: 0.8925 (ptp) REVERT: C 952 SER cc_start: 0.9608 (t) cc_final: 0.9364 (p) REVERT: C 971 TYR cc_start: 0.9431 (m-10) cc_final: 0.8884 (m-80) REVERT: C 1109 SER cc_start: 0.9662 (t) cc_final: 0.9328 (p) outliers start: 1 outliers final: 0 residues processed: 187 average time/residue: 0.1456 time to fit residues: 47.0278 Evaluate side-chains 125 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: [328, 214, 47, 279, 282, 81, 345, 250, 45, 219, 259] chunk 328 optimal weight: 9.9990 chunk 214 optimal weight: 9.9990 chunk 47 optimal weight: 20.0000 chunk 279 optimal weight: 2.9990 chunk 282 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 345 optimal weight: 7.9990 chunk 250 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 219 optimal weight: 5.9990 chunk 259 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN A 609 ASN B 859 ASN ** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.066653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.050055 restraints weight = 90044.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.052159 restraints weight = 46548.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.053647 restraints weight = 29829.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.054685 restraints weight = 21773.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.055407 restraints weight = 17463.327| |-----------------------------------------------------------------------------| r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 28140 Z= 0.221 Angle : 0.582 9.498 38358 Z= 0.311 Chirality : 0.043 0.238 4320 Planarity : 0.004 0.046 4938 Dihedral : 4.544 30.397 3819 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.14), residues: 3489 helix: 1.31 (0.20), residues: 729 sheet: -0.63 (0.21), residues: 615 loop : -1.82 (0.12), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 272 TYR 0.019 0.001 TYR B 274 PHE 0.016 0.002 PHE A 776 TRP 0.010 0.001 TRP C 586 HIS 0.004 0.001 HIS A1142 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.22 (28077) covalent geometry : angle 0.57817 / 0.31 (38232) SS BOND : bond 0.00255 / 0.17 ( 63) SS BOND : angle 1.27882 / 0.88 ( 126) hydrogen bonds : bond 0.06400 / 4.15 ( 857) hydrogen bonds : angle 5.45887 / 3.82 ( 2382) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: A 252 MET cc_start: 0.9160 (mtm) cc_final: 0.8480 (pmm) REVERT: A 291 MET cc_start: 0.9444 (mmm) cc_final: 0.9111 (mmm) REVERT: A 295 MET cc_start: 0.8627 (tpt) cc_final: 0.8200 (tpp) REVERT: A 849 ASP cc_start: 0.9177 (m-30) cc_final: 0.8880 (m-30) REVERT: A 865 THR cc_start: 0.9648 (m) cc_final: 0.9318 (p) REVERT: A 877 VAL cc_start: 0.9589 (t) cc_final: 0.9380 (p) REVERT: A 1109 SER cc_start: 0.9627 (t) cc_final: 0.9198 (p) REVERT: A 1198 MET cc_start: 0.8098 (mpp) cc_final: 0.7860 (mpp) REVERT: B 252 MET cc_start: 0.9128 (mtm) cc_final: 0.8895 (mtm) REVERT: B 291 MET cc_start: 0.9413 (mmm) cc_final: 0.9151 (mmm) REVERT: B 397 MET cc_start: 0.8655 (mtm) cc_final: 0.8383 (mtp) REVERT: B 813 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8296 (mm-30) REVERT: B 849 ASP cc_start: 0.9265 (m-30) cc_final: 0.9011 (m-30) REVERT: B 874 MET cc_start: 0.9230 (ptp) cc_final: 0.8791 (ptt) REVERT: B 879 LEU cc_start: 0.9307 (mt) cc_final: 0.8953 (pt) REVERT: B 889 PHE cc_start: 0.8293 (p90) cc_final: 0.7579 (p90) REVERT: B 917 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8644 (mt-10) REVERT: B 1109 SER cc_start: 0.9757 (t) cc_final: 0.9322 (p) REVERT: B 1120 MET cc_start: 0.9054 (ttm) cc_final: 0.8203 (ttm) REVERT: B 1198 MET cc_start: 0.8202 (mpp) cc_final: 0.7957 (mpp) REVERT: C 180 LEU cc_start: 0.8840 (mm) cc_final: 0.8173 (tp) REVERT: C 252 MET cc_start: 0.9056 (mtm) cc_final: 0.8505 (pmm) REVERT: C 291 MET cc_start: 0.9474 (mmm) cc_final: 0.9146 (mmm) REVERT: C 296 SER cc_start: 0.9005 (m) cc_final: 0.8638 (p) REVERT: C 397 MET cc_start: 0.8895 (mtm) cc_final: 0.8564 (mtm) REVERT: C 547 LYS cc_start: 0.9179 (ttpt) cc_final: 0.8942 (mmtm) REVERT: C 849 ASP cc_start: 0.9099 (m-30) cc_final: 0.8824 (m-30) REVERT: C 863 ASP cc_start: 0.9060 (m-30) cc_final: 0.8728 (t0) REVERT: C 874 MET cc_start: 0.9325 (ptm) cc_final: 0.8742 (ptp) REVERT: C 952 SER cc_start: 0.9638 (t) cc_final: 0.9396 (p) REVERT: C 971 TYR cc_start: 0.9414 (m-10) cc_final: 0.8817 (m-80) REVERT: C 1109 SER cc_start: 0.9629 (t) cc_final: 0.9119 (p) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1459 time to fit residues: 39.4518 Evaluate side-chains 119 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: [156, 101, 263, 212, 68, 307, 280, 29, 82, 294, 241] chunk 156 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 263 optimal weight: 1.9990 chunk 212 optimal weight: 0.9980 chunk 68 optimal weight: 0.0270 chunk 307 optimal weight: 0.0670 chunk 280 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 294 optimal weight: 9.9990 chunk 241 optimal weight: 7.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 ASN A 218 GLN A 609 ASN ** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 705 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.069263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.052660 restraints weight = 88241.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.054866 restraints weight = 44795.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.056409 restraints weight = 28351.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.057483 restraints weight = 20521.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.058226 restraints weight = 16346.502| |-----------------------------------------------------------------------------| r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 28140 Z= 0.103 Angle : 0.479 8.446 38358 Z= 0.261 Chirality : 0.042 0.243 4320 Planarity : 0.004 0.046 4938 Dihedral : 4.165 30.453 3819 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.14), residues: 3489 helix: 1.58 (0.20), residues: 735 sheet: -0.48 (0.21), residues: 615 loop : -1.66 (0.13), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1063 TYR 0.016 0.001 TYR B 274 PHE 0.011 0.001 PHE A 294 TRP 0.008 0.001 TRP B 655 HIS 0.005 0.001 HIS B 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (28077) covalent geometry : angle 0.47511 / 0.26 (38232) SS BOND : bond 0.00178 / 0.12 ( 63) SS BOND : angle 1.10026 / 0.77 ( 126) hydrogen bonds : bond 0.05663 / 3.66 ( 857) hydrogen bonds : angle 5.08635 / 3.56 ( 2382) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 MET cc_start: 0.9370 (mmm) cc_final: 0.9030 (mmm) REVERT: A 295 MET cc_start: 0.8598 (tpt) cc_final: 0.8102 (tpp) REVERT: A 849 ASP cc_start: 0.9242 (m-30) cc_final: 0.8959 (m-30) REVERT: A 865 THR cc_start: 0.9586 (m) cc_final: 0.9264 (p) REVERT: A 877 VAL cc_start: 0.9631 (t) cc_final: 0.9428 (p) REVERT: A 1109 SER cc_start: 0.9692 (t) cc_final: 0.9329 (p) REVERT: A 1112 VAL cc_start: 0.9626 (t) cc_final: 0.9357 (p) REVERT: A 1198 MET cc_start: 0.8135 (mpp) cc_final: 0.7887 (mpp) REVERT: B 252 MET cc_start: 0.9189 (mtm) cc_final: 0.8897 (mtm) REVERT: B 291 MET cc_start: 0.9431 (mmm) cc_final: 0.9123 (mmm) REVERT: B 397 MET cc_start: 0.8637 (mtm) cc_final: 0.8310 (mtp) REVERT: B 813 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8148 (mm-30) REVERT: B 849 ASP cc_start: 0.9268 (m-30) cc_final: 0.9017 (m-30) REVERT: B 879 LEU cc_start: 0.9278 (mt) cc_final: 0.8965 (pt) REVERT: B 889 PHE cc_start: 0.8185 (p90) cc_final: 0.7436 (p90) REVERT: B 917 GLU cc_start: 0.8951 (mt-10) cc_final: 0.8590 (mt-10) REVERT: B 946 ASP cc_start: 0.8461 (t70) cc_final: 0.8143 (t70) REVERT: B 1109 SER cc_start: 0.9698 (t) cc_final: 0.9256 (p) REVERT: B 1120 MET cc_start: 0.9081 (ttm) cc_final: 0.8097 (ttm) REVERT: B 1198 MET cc_start: 0.8138 (mpp) cc_final: 0.7858 (mpp) REVERT: C 118 MET cc_start: 0.9254 (mpp) cc_final: 0.9044 (mmt) REVERT: C 180 LEU cc_start: 0.8835 (mm) cc_final: 0.8175 (tp) REVERT: C 252 MET cc_start: 0.9123 (mtm) cc_final: 0.8894 (mtm) REVERT: C 291 MET cc_start: 0.9444 (mmm) cc_final: 0.9069 (mmm) REVERT: C 295 MET cc_start: 0.8599 (tpp) cc_final: 0.8253 (tpp) REVERT: C 296 SER cc_start: 0.8725 (m) cc_final: 0.8281 (p) REVERT: C 397 MET cc_start: 0.8987 (mtm) cc_final: 0.8568 (mtm) REVERT: C 547 LYS cc_start: 0.9198 (ttpt) cc_final: 0.8933 (mmtm) REVERT: C 849 ASP cc_start: 0.9111 (m-30) cc_final: 0.8847 (m-30) REVERT: C 863 ASP cc_start: 0.9041 (m-30) cc_final: 0.8708 (t0) REVERT: C 874 MET cc_start: 0.9295 (ptm) cc_final: 0.9000 (ptp) REVERT: C 952 SER cc_start: 0.9595 (t) cc_final: 0.9349 (p) REVERT: C 971 TYR cc_start: 0.9401 (m-10) cc_final: 0.8931 (m-80) REVERT: C 1007 MET cc_start: 0.8270 (mmm) cc_final: 0.8049 (mmm) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1423 time to fit residues: 44.7619 Evaluate side-chains 126 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: [76, 78, 43, 261, 80, 119, 138, 167, 340, 126, 242] chunk 76 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 261 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 119 optimal weight: 0.0670 chunk 138 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 340 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 chunk 242 optimal weight: 7.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN A 429 ASN A 609 ASN B 859 ASN ** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 810 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.073223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.056119 restraints weight = 88317.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.058334 restraints weight = 45365.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.059889 restraints weight = 28939.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.060959 restraints weight = 21069.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.061715 restraints weight = 16834.141| |-----------------------------------------------------------------------------| r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 28140 Z= 0.101 Angle : 0.464 8.249 38358 Z= 0.251 Chirality : 0.041 0.201 4320 Planarity : 0.003 0.046 4938 Dihedral : 3.968 26.921 3819 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.14), residues: 3489 helix: 1.81 (0.20), residues: 729 sheet: -0.35 (0.21), residues: 618 loop : -1.54 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 475 TYR 0.018 0.001 TYR A 971 PHE 0.012 0.001 PHE B 223 TRP 0.009 0.001 TRP B 348 HIS 0.004 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (28077) covalent geometry : angle 0.46110 / 0.25 (38232) SS BOND : bond 0.00184 / 0.13 ( 63) SS BOND : angle 0.98157 / 0.69 ( 126) hydrogen bonds : bond 0.05224 / 3.36 ( 857) hydrogen bonds : angle 4.88996 / 3.42 ( 2382) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 MET cc_start: 0.9332 (mmm) cc_final: 0.8992 (mmm) REVERT: A 295 MET cc_start: 0.8593 (tpt) cc_final: 0.8343 (tpp) REVERT: A 849 ASP cc_start: 0.9183 (m-30) cc_final: 0.8922 (m-30) REVERT: A 865 THR cc_start: 0.9639 (m) cc_final: 0.9322 (p) REVERT: A 1112 VAL cc_start: 0.9679 (t) cc_final: 0.9433 (p) REVERT: B 252 MET cc_start: 0.9055 (mtm) cc_final: 0.8811 (mtm) REVERT: B 291 MET cc_start: 0.9372 (mmm) cc_final: 0.9042 (mmm) REVERT: B 397 MET cc_start: 0.8533 (mtm) cc_final: 0.8270 (mtp) REVERT: B 813 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8137 (mm-30) REVERT: B 849 ASP cc_start: 0.9200 (m-30) cc_final: 0.8970 (m-30) REVERT: B 865 THR cc_start: 0.9589 (m) cc_final: 0.9343 (p) REVERT: B 879 LEU cc_start: 0.9321 (mt) cc_final: 0.9020 (pt) REVERT: B 889 PHE cc_start: 0.8206 (p90) cc_final: 0.7480 (p90) REVERT: B 917 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8507 (mt-10) REVERT: B 946 ASP cc_start: 0.8440 (t70) cc_final: 0.8179 (t70) REVERT: B 1120 MET cc_start: 0.9017 (ttm) cc_final: 0.8145 (ttm) REVERT: B 1127 VAL cc_start: 0.8619 (t) cc_final: 0.8414 (t) REVERT: B 1198 MET cc_start: 0.8080 (mpp) cc_final: 0.7863 (mpp) REVERT: C 180 LEU cc_start: 0.8808 (mm) cc_final: 0.8102 (tp) REVERT: C 252 MET cc_start: 0.9027 (mtm) cc_final: 0.8790 (mtm) REVERT: C 291 MET cc_start: 0.9445 (mmm) cc_final: 0.9062 (mmm) REVERT: C 295 MET cc_start: 0.8703 (tpp) cc_final: 0.8325 (tpp) REVERT: C 296 SER cc_start: 0.8713 (m) cc_final: 0.8290 (p) REVERT: C 397 MET cc_start: 0.8830 (mtm) cc_final: 0.8486 (mtm) REVERT: C 547 LYS cc_start: 0.9161 (ttpt) cc_final: 0.8931 (mmtm) REVERT: C 849 ASP cc_start: 0.9047 (m-30) cc_final: 0.8809 (m-30) REVERT: C 863 ASP cc_start: 0.8996 (m-30) cc_final: 0.8664 (t0) REVERT: C 874 MET cc_start: 0.9092 (ptm) cc_final: 0.8696 (ptp) REVERT: C 952 SER cc_start: 0.9540 (t) cc_final: 0.9327 (p) REVERT: C 971 TYR cc_start: 0.9389 (m-10) cc_final: 0.8881 (m-80) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1391 time to fit residues: 43.7012 Evaluate side-chains 127 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: [155, 224, 285, 347, 311, 183, 64, 27, 255, 30, 26] chunk 155 optimal weight: 0.0170 chunk 224 optimal weight: 0.7980 chunk 285 optimal weight: 4.9990 chunk 347 optimal weight: 2.9990 chunk 311 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 255 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN A 609 ASN ** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.073719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.056652 restraints weight = 88623.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.058881 restraints weight = 45506.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.060442 restraints weight = 28972.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.061484 restraints weight = 21082.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.062293 restraints weight = 16870.129| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 28140 Z= 0.093 Angle : 0.454 7.614 38358 Z= 0.245 Chirality : 0.041 0.233 4320 Planarity : 0.003 0.045 4938 Dihedral : 3.852 30.502 3819 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.14), residues: 3489 helix: 1.88 (0.20), residues: 729 sheet: -0.26 (0.21), residues: 654 loop : -1.48 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1063 TYR 0.013 0.001 TYR B 274 PHE 0.010 0.001 PHE A 968 TRP 0.007 0.001 TRP A 188 HIS 0.004 0.000 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.09 (28077) covalent geometry : angle 0.45094 / 0.24 (38232) SS BOND : bond 0.00164 / 0.11 ( 63) SS BOND : angle 0.96007 / 0.66 ( 126) hydrogen bonds : bond 0.04948 / 3.18 ( 857) hydrogen bonds : angle 4.78642 / 3.35 ( 2382) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: A 188 TRP cc_start: 0.8817 (p-90) cc_final: 0.7899 (p-90) REVERT: A 291 MET cc_start: 0.9294 (mmm) cc_final: 0.8960 (mmm) REVERT: A 295 MET cc_start: 0.8580 (tpt) cc_final: 0.8317 (tpp) REVERT: A 813 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8138 (mm-30) REVERT: A 849 ASP cc_start: 0.9167 (m-30) cc_final: 0.8900 (m-30) REVERT: A 865 THR cc_start: 0.9584 (m) cc_final: 0.9242 (p) REVERT: A 1112 VAL cc_start: 0.9669 (t) cc_final: 0.9424 (p) REVERT: A 1198 MET cc_start: 0.9086 (mtm) cc_final: 0.7940 (mpp) REVERT: B 252 MET cc_start: 0.9054 (mtm) cc_final: 0.8802 (mtm) REVERT: B 291 MET cc_start: 0.9364 (mmm) cc_final: 0.9025 (mmm) REVERT: B 376 MET cc_start: 0.8775 (mmp) cc_final: 0.8366 (mmp) REVERT: B 397 MET cc_start: 0.8539 (mtm) cc_final: 0.8224 (mtp) REVERT: B 813 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8134 (mm-30) REVERT: B 849 ASP cc_start: 0.9206 (m-30) cc_final: 0.8971 (m-30) REVERT: B 865 THR cc_start: 0.9579 (m) cc_final: 0.9328 (p) REVERT: B 874 MET cc_start: 0.8899 (ptp) cc_final: 0.8553 (ptt) REVERT: B 879 LEU cc_start: 0.9307 (mt) cc_final: 0.9020 (pt) REVERT: B 889 PHE cc_start: 0.8166 (p90) cc_final: 0.7429 (p90) REVERT: B 917 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8487 (mt-10) REVERT: B 946 ASP cc_start: 0.8447 (t70) cc_final: 0.8224 (t70) REVERT: B 1120 MET cc_start: 0.9029 (ttm) cc_final: 0.8162 (ttm) REVERT: B 1198 MET cc_start: 0.8083 (mpp) cc_final: 0.7861 (mpp) REVERT: C 180 LEU cc_start: 0.8807 (mm) cc_final: 0.8116 (tp) REVERT: C 252 MET cc_start: 0.9034 (mtm) cc_final: 0.8787 (mtm) REVERT: C 291 MET cc_start: 0.9426 (mmm) cc_final: 0.9056 (mmm) REVERT: C 295 MET cc_start: 0.8649 (tpp) cc_final: 0.8330 (tpp) REVERT: C 296 SER cc_start: 0.8701 (m) cc_final: 0.8262 (p) REVERT: C 397 MET cc_start: 0.8787 (mtm) cc_final: 0.8439 (mtm) REVERT: C 547 LYS cc_start: 0.9123 (ttpt) cc_final: 0.8894 (mmtm) REVERT: C 849 ASP cc_start: 0.9023 (m-30) cc_final: 0.8795 (m-30) REVERT: C 863 ASP cc_start: 0.8995 (m-30) cc_final: 0.8632 (t0) REVERT: C 874 MET cc_start: 0.9061 (ptm) cc_final: 0.8667 (ptp) REVERT: C 952 SER cc_start: 0.9532 (t) cc_final: 0.9322 (p) REVERT: C 971 TYR cc_start: 0.9388 (m-10) cc_final: 0.8874 (m-80) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1419 time to fit residues: 43.6731 Evaluate side-chains 123 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: [29, 330, 267, 90, 127, 162, 244, 263, 155, 256, 62] chunk 29 optimal weight: 3.9990 chunk 330 optimal weight: 1.9990 chunk 267 optimal weight: 7.9990 chunk 90 optimal weight: 0.0870 chunk 127 optimal weight: 0.8980 chunk 162 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 263 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 256 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN B 859 ASN ** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.072663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.055544 restraints weight = 89074.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.057733 restraints weight = 46063.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.059283 restraints weight = 29487.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.060336 restraints weight = 21478.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.061105 restraints weight = 17211.802| |-----------------------------------------------------------------------------| r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28140 Z= 0.132 Angle : 0.477 7.447 38358 Z= 0.257 Chirality : 0.042 0.230 4320 Planarity : 0.003 0.045 4938 Dihedral : 3.912 29.098 3819 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.14), residues: 3489 helix: 1.91 (0.20), residues: 729 sheet: -0.29 (0.21), residues: 618 loop : -1.47 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 272 TYR 0.026 0.001 TYR A 971 PHE 0.012 0.001 PHE A 968 TRP 0.010 0.001 TRP A 188 HIS 0.004 0.001 HIS A1142 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (28077) covalent geometry : angle 0.47390 / 0.26 (38232) SS BOND : bond 0.00203 / 0.15 ( 63) SS BOND : angle 1.00820 / 0.70 ( 126) hydrogen bonds : bond 0.05120 / 3.30 ( 857) hydrogen bonds : angle 4.81504 / 3.37 ( 2382) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 TRP cc_start: 0.8771 (p-90) cc_final: 0.8003 (p-90) REVERT: A 269 LEU cc_start: 0.8774 (mt) cc_final: 0.8541 (mt) REVERT: A 291 MET cc_start: 0.9358 (mmm) cc_final: 0.8986 (mmm) REVERT: A 295 MET cc_start: 0.8634 (tpt) cc_final: 0.8391 (tpp) REVERT: A 813 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8308 (mm-30) REVERT: A 849 ASP cc_start: 0.9191 (m-30) cc_final: 0.8917 (m-30) REVERT: A 865 THR cc_start: 0.9490 (m) cc_final: 0.9154 (p) REVERT: A 1112 VAL cc_start: 0.9646 (t) cc_final: 0.9409 (p) REVERT: A 1198 MET cc_start: 0.9151 (mtm) cc_final: 0.7866 (mpp) REVERT: B 252 MET cc_start: 0.9162 (mtm) cc_final: 0.8892 (mtm) REVERT: B 291 MET cc_start: 0.9402 (mmm) cc_final: 0.9041 (mmm) REVERT: B 397 MET cc_start: 0.8665 (mtm) cc_final: 0.8320 (mtp) REVERT: B 813 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8211 (mm-30) REVERT: B 849 ASP cc_start: 0.9261 (m-30) cc_final: 0.9024 (m-30) REVERT: B 865 THR cc_start: 0.9528 (m) cc_final: 0.9278 (p) REVERT: B 874 MET cc_start: 0.9120 (ptp) cc_final: 0.8630 (ptt) REVERT: B 879 LEU cc_start: 0.9294 (mt) cc_final: 0.8985 (pt) REVERT: B 889 PHE cc_start: 0.8143 (p90) cc_final: 0.7364 (p90) REVERT: B 917 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8562 (mt-10) REVERT: B 946 ASP cc_start: 0.8458 (t70) cc_final: 0.8183 (t70) REVERT: B 1120 MET cc_start: 0.9120 (ttm) cc_final: 0.8194 (ttm) REVERT: B 1198 MET cc_start: 0.8120 (mpp) cc_final: 0.7839 (mpp) REVERT: C 252 MET cc_start: 0.9160 (mtm) cc_final: 0.8852 (mtm) REVERT: C 291 MET cc_start: 0.9449 (mmm) cc_final: 0.9028 (mmm) REVERT: C 295 MET cc_start: 0.8693 (tpp) cc_final: 0.8343 (tpp) REVERT: C 296 SER cc_start: 0.8743 (m) cc_final: 0.8286 (p) REVERT: C 397 MET cc_start: 0.8982 (mtm) cc_final: 0.8522 (mtm) REVERT: C 547 LYS cc_start: 0.9173 (ttpt) cc_final: 0.8900 (mmtm) REVERT: C 849 ASP cc_start: 0.9102 (m-30) cc_final: 0.8849 (m-30) REVERT: C 863 ASP cc_start: 0.9035 (m-30) cc_final: 0.8793 (t0) REVERT: C 874 MET cc_start: 0.9143 (ptm) cc_final: 0.8794 (ptp) REVERT: C 952 SER cc_start: 0.9594 (t) cc_final: 0.9348 (p) REVERT: C 971 TYR cc_start: 0.9413 (m-10) cc_final: 0.8895 (m-80) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1408 time to fit residues: 41.1753 Evaluate side-chains 127 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: [256, 116, 233, 194, 195, 305, 345, 328, 261, 262, 58] chunk 256 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 233 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 chunk 195 optimal weight: 0.8980 chunk 305 optimal weight: 0.9980 chunk 345 optimal weight: 2.9990 chunk 328 optimal weight: 9.9990 chunk 261 optimal weight: 1.9990 chunk 262 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN ** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.072878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.055798 restraints weight = 89350.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.058001 restraints weight = 46221.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.059555 restraints weight = 29576.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.060636 restraints weight = 21536.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.061381 restraints weight = 17215.420| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28140 Z= 0.120 Angle : 0.472 7.333 38358 Z= 0.253 Chirality : 0.041 0.217 4320 Planarity : 0.003 0.045 4938 Dihedral : 3.883 28.193 3819 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.14), residues: 3489 helix: 1.92 (0.20), residues: 729 sheet: -0.30 (0.21), residues: 618 loop : -1.45 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1133 TYR 0.027 0.001 TYR A 971 PHE 0.016 0.001 PHE A 968 TRP 0.006 0.001 TRP B 655 HIS 0.004 0.001 HIS A1142 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (28077) covalent geometry : angle 0.46916 / 0.25 (38232) SS BOND : bond 0.00186 / 0.13 ( 63) SS BOND : angle 0.94434 / 0.65 ( 126) hydrogen bonds : bond 0.05121 / 3.30 ( 857) hydrogen bonds : angle 4.81146 / 3.37 ( 2382) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 TRP cc_start: 0.8859 (p-90) cc_final: 0.8089 (p-90) REVERT: A 269 LEU cc_start: 0.8708 (mt) cc_final: 0.8484 (mt) REVERT: A 291 MET cc_start: 0.9301 (mmm) cc_final: 0.8952 (mmm) REVERT: A 295 MET cc_start: 0.8621 (tpt) cc_final: 0.8360 (tpp) REVERT: A 813 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8307 (mm-30) REVERT: A 849 ASP cc_start: 0.9128 (m-30) cc_final: 0.8855 (m-30) REVERT: A 865 THR cc_start: 0.9540 (m) cc_final: 0.9200 (p) REVERT: A 1112 VAL cc_start: 0.9681 (t) cc_final: 0.9455 (p) REVERT: A 1198 MET cc_start: 0.9149 (mtm) cc_final: 0.7929 (mpp) REVERT: B 252 MET cc_start: 0.9050 (mtm) cc_final: 0.8848 (mtm) REVERT: B 291 MET cc_start: 0.9364 (mmm) cc_final: 0.9020 (mmm) REVERT: B 397 MET cc_start: 0.8572 (mtm) cc_final: 0.8278 (mtp) REVERT: B 813 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8176 (mm-30) REVERT: B 849 ASP cc_start: 0.9206 (m-30) cc_final: 0.8972 (m-30) REVERT: B 865 THR cc_start: 0.9591 (m) cc_final: 0.9340 (p) REVERT: B 874 MET cc_start: 0.9049 (ptp) cc_final: 0.8614 (ptt) REVERT: B 879 LEU cc_start: 0.9333 (mt) cc_final: 0.9059 (pt) REVERT: B 889 PHE cc_start: 0.8169 (p90) cc_final: 0.7426 (p90) REVERT: B 917 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8457 (mt-10) REVERT: B 946 ASP cc_start: 0.8464 (t70) cc_final: 0.8242 (t70) REVERT: B 1120 MET cc_start: 0.9035 (ttm) cc_final: 0.8166 (ttm) REVERT: B 1198 MET cc_start: 0.8063 (mpp) cc_final: 0.7849 (mpp) REVERT: C 252 MET cc_start: 0.9067 (mtm) cc_final: 0.8814 (mtm) REVERT: C 291 MET cc_start: 0.9417 (mmm) cc_final: 0.9053 (mmm) REVERT: C 295 MET cc_start: 0.8712 (tpp) cc_final: 0.8380 (tpp) REVERT: C 296 SER cc_start: 0.8754 (m) cc_final: 0.8317 (p) REVERT: C 547 LYS cc_start: 0.9139 (ttpt) cc_final: 0.8901 (mmtm) REVERT: C 849 ASP cc_start: 0.9039 (m-30) cc_final: 0.8801 (m-30) REVERT: C 863 ASP cc_start: 0.8998 (m-30) cc_final: 0.8659 (t0) REVERT: C 874 MET cc_start: 0.9087 (ptm) cc_final: 0.8683 (ptp) REVERT: C 879 LEU cc_start: 0.9406 (mt) cc_final: 0.9016 (pt) REVERT: C 946 ASP cc_start: 0.8479 (t0) cc_final: 0.8267 (t70) REVERT: C 952 SER cc_start: 0.9541 (t) cc_final: 0.9332 (p) REVERT: C 971 TYR cc_start: 0.9410 (m-10) cc_final: 0.8874 (m-80) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1361 time to fit residues: 40.1203 Evaluate side-chains 125 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: [325, 104, 28, 57, 340, 92, 37, 315, 257, 297, 299] chunk 325 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 57 optimal weight: 8.9990 chunk 340 optimal weight: 0.8980 chunk 92 optimal weight: 0.0770 chunk 37 optimal weight: 6.9990 chunk 315 optimal weight: 2.9990 chunk 257 optimal weight: 10.0000 chunk 297 optimal weight: 7.9990 chunk 299 optimal weight: 7.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN B 859 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.073738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.056672 restraints weight = 88096.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.058903 restraints weight = 45442.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.060472 restraints weight = 28987.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.061552 restraints weight = 21030.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.062325 restraints weight = 16793.681| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 28140 Z= 0.093 Angle : 0.450 7.383 38358 Z= 0.242 Chirality : 0.041 0.203 4320 Planarity : 0.003 0.045 4938 Dihedral : 3.758 27.195 3819 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.14), residues: 3489 helix: 2.00 (0.20), residues: 729 sheet: -0.23 (0.21), residues: 618 loop : -1.39 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 272 TYR 0.036 0.001 TYR A 971 PHE 0.013 0.001 PHE A 968 TRP 0.006 0.001 TRP A 188 HIS 0.004 0.000 HIS A1142 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 (28077) covalent geometry : angle 0.44827 / 0.24 (38232) SS BOND : bond 0.00167 / 0.12 ( 63) SS BOND : angle 0.84913 / 0.58 ( 126) hydrogen bonds : bond 0.04858 / 3.12 ( 857) hydrogen bonds : angle 4.71571 / 3.31 ( 2382) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3421.81 seconds wall clock time: 60 minutes 26.97 seconds (3626.97 seconds total)