Starting phenix.real_space_refine on Wed Jun 25 02:55:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yve_34124/06_2025/7yve_34124.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yve_34124/06_2025/7yve_34124.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yve_34124/06_2025/7yve_34124.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yve_34124/06_2025/7yve_34124.map" model { file = "/net/cci-nas-00/data/ceres_data/7yve_34124/06_2025/7yve_34124.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yve_34124/06_2025/7yve_34124.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.036 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 123 5.16 5 C 18542 2.51 5 N 4804 2.21 5 O 5540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 141 residue(s): 2.40s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29009 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 7725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7725 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 174 Chain: "B" Number of atoms: 7725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7725 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 174 Chain: "A" Number of atoms: 7725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7725 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 174 Chain: "H" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "I" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 956 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "K" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "L" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 956 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "N" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "O" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 956 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 18.00, per 1000 atoms: 0.62 Number of scatterers: 29009 At special positions: 0 Unit cell: (167.28, 204.18, 177.94, 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 123 16.00 O 5540 8.00 N 4804 7.00 C 18542 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.06 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.07 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.06 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.06 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.01 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.06 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.05 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.01 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.05 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.05 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.05 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 89 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 97 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 97 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 89 " distance=2.02 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 97 " distance=2.04 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: 6.51 Conformation dependent library (CDL) restraints added in 3.7 seconds 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7014 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 55 sheets defined 22.1% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.74 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 368 removed outlier: 4.037A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU C 368 " --> pdb=" O TYR C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 364 through 368' Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.644A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 388' Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 417 through 422 removed outlier: 3.522A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 417 through 422' Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.678A pdb=" N ASP C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 438 through 443' Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.573A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.578A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.859A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.579A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.158A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.694A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.671A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.132A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.925A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.984A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.604A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.602A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.106A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.685A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.105A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.874A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.526A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.204A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.515A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 4.030A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.570A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.570A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.017A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.603A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.935A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.891A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 84 removed outlier: 4.013A pdb=" N ASP H 83 " --> pdb=" O ARG H 80 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLU H 84 " --> pdb=" O SER H 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 80 through 84' Processing helix chain 'I' and resid 63 through 66 Processing helix chain 'I' and resid 88 through 92 removed outlier: 3.503A pdb=" N THR I 92 " --> pdb=" O PRO I 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 84 removed outlier: 4.040A pdb=" N ASP K 83 " --> pdb=" O ARG K 80 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLU K 84 " --> pdb=" O SER K 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 80 through 84' Processing helix chain 'L' and resid 63 through 66 Processing helix chain 'L' and resid 75 through 77 No H-bonds generated for 'chain 'L' and resid 75 through 77' Processing helix chain 'L' and resid 88 through 92 Processing helix chain 'N' and resid 80 through 84 removed outlier: 3.868A pdb=" N ASP N 83 " --> pdb=" O ARG N 80 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU N 84 " --> pdb=" O SER N 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 80 through 84' Processing helix chain 'O' and resid 63 through 66 Processing helix chain 'O' and resid 75 through 77 No H-bonds generated for 'chain 'O' and resid 75 through 77' Processing helix chain 'O' and resid 88 through 92 removed outlier: 3.640A pdb=" N THR O 92 " --> pdb=" O PRO O 89 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.533A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 5.551A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.553A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.664A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.488A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.588A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 357 through 358 Processing sheet with id=AA8, first strand: chain 'C' and resid 391 through 392 removed outlier: 3.595A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 453 through 454 Processing sheet with id=AB1, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.990A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 702 through 703 Processing sheet with id=AB3, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.161A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 1047 through 1050 removed outlier: 6.801A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.495A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 788 through 789 removed outlier: 6.026A pdb=" N ILE C 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.401A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 30 through 31 Processing sheet with id=AB9, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.541A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.990A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 63 through 66 removed outlier: 3.503A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.586A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.204A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.620A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.522A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.887A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.160A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1047 through 1050 removed outlier: 5.610A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 788 through 789 removed outlier: 6.036A pdb=" N ILE B 788 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.482A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.571A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 63 through 66 removed outlier: 3.548A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.797A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.471A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.847A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.921A pdb=" N CYS A 525 " --> pdb=" O CYS A 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.119A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.018A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.018A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.509A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AE8, first strand: chain 'H' and resid 46 through 49 removed outlier: 6.800A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.944A pdb=" N THR I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 59 through 61 removed outlier: 4.971A pdb=" N TRP I 49 " --> pdb=" O ARG I 40 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG I 40 " --> pdb=" O TRP I 49 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL I 36 " --> pdb=" O ILE I 53 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE I 112 " --> pdb=" O HIS I 99 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 59 through 61 removed outlier: 4.971A pdb=" N TRP I 49 " --> pdb=" O ARG I 40 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG I 40 " --> pdb=" O TRP I 49 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL I 36 " --> pdb=" O ILE I 53 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AF4, first strand: chain 'K' and resid 46 through 49 removed outlier: 6.805A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA K 90 " --> pdb=" O TYR K 35 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER K 98 " --> pdb=" O ASP K 93 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 3 through 5 Processing sheet with id=AF6, first strand: chain 'L' and resid 11 through 12 removed outlier: 6.889A pdb=" N VAL L 36 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N LEU L 52 " --> pdb=" O VAL L 36 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N TRP L 38 " --> pdb=" O LEU L 50 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 18 through 23 Processing sheet with id=AF8, first strand: chain 'N' and resid 34 through 36 Processing sheet with id=AF9, first strand: chain 'O' and resid 3 through 5 Processing sheet with id=AG1, first strand: chain 'O' and resid 11 through 12 removed outlier: 6.151A pdb=" N ARG O 40 " --> pdb=" O TRP O 49 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N TRP O 49 " --> pdb=" O ARG O 40 " (cutoff:3.500A) 1119 hydrogen bonds defined for protein. 2958 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: 14.04 Time building geometry restraints manager: 7.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 8501 1.33 - 1.47: 9191 1.47 - 1.60: 11860 1.60 - 1.74: 14 1.74 - 1.88: 139 Bond restraints: 29705 Sorted by residual: bond pdb=" C PRO A 862 " pdb=" O PRO A 862 " ideal model delta sigma weight residual 1.240 1.196 0.044 1.12e-02 7.97e+03 1.54e+01 bond pdb=" CB CYS B 649 " pdb=" SG CYS B 649 " ideal model delta sigma weight residual 1.808 1.690 0.118 3.30e-02 9.18e+02 1.28e+01 bond pdb=" C PRO B 862 " pdb=" O PRO B 862 " ideal model delta sigma weight residual 1.240 1.201 0.039 1.12e-02 7.97e+03 1.24e+01 bond pdb=" C PRO A 863 " pdb=" O PRO A 863 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.30e-02 5.92e+03 1.05e+01 bond pdb=" CB CYS A 649 " pdb=" SG CYS A 649 " ideal model delta sigma weight residual 1.808 1.703 0.105 3.30e-02 9.18e+02 1.02e+01 ... (remaining 29700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 39148 2.96 - 5.92: 1298 5.92 - 8.88: 93 8.88 - 11.83: 21 11.83 - 14.79: 7 Bond angle restraints: 40567 Sorted by residual: angle pdb=" N PRO C 330 " pdb=" CA PRO C 330 " pdb=" C PRO C 330 " ideal model delta sigma weight residual 111.26 122.06 -10.80 1.63e+00 3.76e-01 4.39e+01 angle pdb=" CA CYS C 538 " pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " ideal model delta sigma weight residual 114.40 129.19 -14.79 2.30e+00 1.89e-01 4.14e+01 angle pdb=" CA CYS A 391 " pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " ideal model delta sigma weight residual 114.40 128.48 -14.08 2.30e+00 1.89e-01 3.75e+01 angle pdb=" N GLY C 526 " pdb=" CA GLY C 526 " pdb=" C GLY C 526 " ideal model delta sigma weight residual 112.34 124.63 -12.29 2.04e+00 2.40e-01 3.63e+01 angle pdb=" CA CYS C 391 " pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " ideal model delta sigma weight residual 114.40 128.02 -13.62 2.30e+00 1.89e-01 3.51e+01 ... (remaining 40562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 16472 18.05 - 36.09: 1198 36.09 - 54.14: 237 54.14 - 72.19: 68 72.19 - 90.24: 19 Dihedral angle restraints: 17994 sinusoidal: 7083 harmonic: 10911 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -9.27 -76.73 1 1.00e+01 1.00e-02 7.40e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 168.48 -75.48 1 1.00e+01 1.00e-02 7.19e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -11.47 -74.53 1 1.00e+01 1.00e-02 7.04e+01 ... (remaining 17991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 3487 0.080 - 0.160: 1100 0.160 - 0.240: 128 0.240 - 0.320: 17 0.320 - 0.400: 3 Chirality restraints: 4735 Sorted by residual: chirality pdb=" CA CYS A 391 " pdb=" N CYS A 391 " pdb=" C CYS A 391 " pdb=" CB CYS A 391 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" CA CYS A 760 " pdb=" N CYS A 760 " pdb=" C CYS A 760 " pdb=" CB CYS A 760 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CA CYS C 379 " pdb=" N CYS C 379 " pdb=" C CYS C 379 " pdb=" CB CYS C 379 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 4732 not shown) Planarity restraints: 5188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 526 " -0.070 5.00e-02 4.00e+02 1.05e-01 1.78e+01 pdb=" N PRO B 527 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 377 " -0.032 2.00e-02 2.50e+03 3.04e-02 1.61e+01 pdb=" CG PHE C 377 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 PHE C 377 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE C 377 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE C 377 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 377 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE C 377 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 526 " -0.055 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO A 527 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " -0.046 5.00e-02 4.00e+02 ... (remaining 5185 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 254 2.57 - 3.15: 24787 3.15 - 3.73: 40744 3.73 - 4.32: 57245 4.32 - 4.90: 99659 Nonbonded interactions: 222689 Sorted by model distance: nonbonded pdb=" OG1 THR K 5 " pdb=" OG SER K 23 " model vdw 1.983 3.040 nonbonded pdb=" O GLY I 33 " pdb=" NH1 ARG I 100 " model vdw 2.087 3.120 nonbonded pdb=" O6 NAG B1301 " pdb=" O6 NAG B1312 " model vdw 2.090 3.040 nonbonded pdb=" ND2 ASN B 450 " pdb=" OD2 ASP O 56 " model vdw 2.096 3.120 nonbonded pdb=" ND2 ASN C1134 " pdb=" O7 NAG C1304 " model vdw 2.102 3.120 ... (remaining 222684 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 1146 or resid 1301 through 1311)) selection = (chain 'B' and (resid 27 through 1146 or resid 1301 through 1311)) selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'N' } ncs_group { reference = chain 'I' selection = chain 'L' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.250 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 68.540 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 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 : 0.017 0.132 29750 Z= 0.728 Angle : 1.254 14.792 40657 Z= 0.686 Chirality : 0.074 0.400 4735 Planarity : 0.007 0.105 5188 Dihedral : 13.192 90.236 10845 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.04 % Favored : 94.61 % Rotamer: Outliers : 1.49 % Allowed : 8.19 % Favored : 90.32 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.12), residues: 3708 helix: 0.03 (0.20), residues: 669 sheet: -1.26 (0.14), residues: 1054 loop : -2.34 (0.12), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.005 TRP A1102 HIS 0.025 0.003 HIS N 50 PHE 0.070 0.005 PHE C 377 TYR 0.053 0.004 TYR C 495 ARG 0.027 0.002 ARG A 905 Details of bonding type rmsd hydrogen bonds : bond 0.20786 ( 1101) hydrogen bonds : angle 7.99226 ( 2958) SS BOND : bond 0.01380 ( 45) SS BOND : angle 4.63900 ( 90) covalent geometry : bond 0.01746 (29705) covalent geometry : angle 1.23644 (40567) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 272 time to evaluate : 3.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 509 ARG cc_start: 0.6393 (mtt180) cc_final: 0.5805 (mtt180) REVERT: B 574 ASP cc_start: 0.8116 (t70) cc_final: 0.7902 (t0) REVERT: B 858 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9035 (mt) REVERT: A 102 ARG cc_start: 0.6713 (mtt180) cc_final: 0.6486 (mtt-85) REVERT: A 518 LEU cc_start: 0.2421 (OUTLIER) cc_final: 0.1862 (tp) REVERT: H 79 LEU cc_start: 0.5701 (OUTLIER) cc_final: 0.5349 (pp) REVERT: I 87 MET cc_start: 0.2361 (tpt) cc_final: -0.0337 (ptt) REVERT: K 63 PHE cc_start: 0.7782 (m-80) cc_final: 0.7479 (m-80) REVERT: L 38 TRP cc_start: 0.7443 (m100) cc_final: 0.7014 (m100) REVERT: L 53 ILE cc_start: 0.8695 (tt) cc_final: 0.8489 (tp) REVERT: L 61 TYR cc_start: 0.8105 (m-80) cc_final: 0.7642 (m-80) REVERT: L 62 ASN cc_start: 0.8245 (t0) cc_final: 0.7726 (t0) REVERT: L 73 LYS cc_start: 0.8674 (pttt) cc_final: 0.7986 (pttm) REVERT: L 111 GLU cc_start: 0.8556 (tp30) cc_final: 0.8271 (tp30) REVERT: N 96 LEU cc_start: 0.8950 (mm) cc_final: 0.8690 (mp) REVERT: N 106 LYS cc_start: 0.9020 (tppt) cc_final: 0.8714 (mmmt) outliers start: 45 outliers final: 20 residues processed: 311 average time/residue: 0.4662 time to fit residues: 219.0134 Evaluate side-chains 196 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 3.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain I residue 13 ARG Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain N residue 38 HIS Chi-restraints excluded: chain O residue 120 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 0.5980 chunk 284 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 191 optimal weight: 0.8980 chunk 151 optimal weight: 7.9990 chunk 293 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 178 optimal weight: 0.9980 chunk 218 optimal weight: 0.9980 chunk 340 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 439 ASN C 544 ASN C 657 ASN C1134 ASN B 188 ASN B 331 ASN B 657 ASN B 755 GLN B 762 GLN B1074 ASN B1088 HIS B1134 ASN A 439 ASN ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN A1134 ASN H 6 GLN I 16 GLN ** I 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN L 41 GLN L 86 ASN N 6 GLN N 38 HIS N 54 GLN O 41 GLN O 99 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.121834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.082500 restraints weight = 67134.806| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.50 r_work: 0.3156 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 29750 Z= 0.140 Angle : 0.637 9.753 40657 Z= 0.333 Chirality : 0.046 0.192 4735 Planarity : 0.005 0.055 5188 Dihedral : 6.829 58.613 4826 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.75 % Favored : 95.12 % Rotamer: Outliers : 1.88 % Allowed : 11.50 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.13), residues: 3708 helix: 1.28 (0.21), residues: 675 sheet: -0.63 (0.15), residues: 1046 loop : -1.82 (0.12), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 99 HIS 0.008 0.001 HIS O 104 PHE 0.017 0.001 PHE L 24 TYR 0.016 0.001 TYR H 35 ARG 0.007 0.001 ARG O 100 Details of bonding type rmsd hydrogen bonds : bond 0.05251 ( 1101) hydrogen bonds : angle 5.87757 ( 2958) SS BOND : bond 0.00774 ( 45) SS BOND : angle 2.66625 ( 90) covalent geometry : bond 0.00308 (29705) covalent geometry : angle 0.62521 (40567) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 241 time to evaluate : 3.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 754 LEU cc_start: 0.9689 (OUTLIER) cc_final: 0.9455 (mm) REVERT: B 198 ASP cc_start: 0.8298 (t0) cc_final: 0.8053 (t0) REVERT: B 574 ASP cc_start: 0.8601 (t70) cc_final: 0.8287 (t0) REVERT: B 950 ASP cc_start: 0.8832 (m-30) cc_final: 0.8611 (m-30) REVERT: A 102 ARG cc_start: 0.6992 (mtt180) cc_final: 0.6616 (mmm-85) REVERT: I 87 MET cc_start: 0.1685 (tpt) cc_final: -0.0689 (ptt) REVERT: K 28 ASN cc_start: 0.7599 (p0) cc_final: 0.7228 (p0) REVERT: K 55 ARG cc_start: 0.7416 (mtp-110) cc_final: 0.7119 (ttm-80) REVERT: K 93 ASP cc_start: 0.8312 (t0) cc_final: 0.8055 (t70) REVERT: L 13 ARG cc_start: 0.8935 (mpp-170) cc_final: 0.8212 (tpp80) REVERT: L 38 TRP cc_start: 0.7569 (m100) cc_final: 0.6840 (m100) REVERT: L 40 ARG cc_start: 0.7542 (ptt180) cc_final: 0.7209 (ptm160) REVERT: L 61 TYR cc_start: 0.8458 (m-80) cc_final: 0.8063 (m-80) REVERT: L 62 ASN cc_start: 0.8582 (t0) cc_final: 0.8124 (t0) REVERT: L 86 ASN cc_start: 0.8403 (OUTLIER) cc_final: 0.8128 (p0) REVERT: L 111 GLU cc_start: 0.8710 (tp30) cc_final: 0.8507 (tp30) REVERT: N 82 GLU cc_start: 0.8334 (pm20) cc_final: 0.7776 (pp20) REVERT: N 84 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7935 (mt-10) REVERT: N 106 LYS cc_start: 0.9022 (tppt) cc_final: 0.8639 (mmmt) outliers start: 57 outliers final: 26 residues processed: 289 average time/residue: 0.4250 time to fit residues: 198.7147 Evaluate side-chains 219 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 4.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain O residue 99 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 336 optimal weight: 40.0000 chunk 174 optimal weight: 1.9990 chunk 247 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 194 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 250 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 chunk 298 optimal weight: 3.9990 chunk 252 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 394 ASN C1002 GLN ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 99 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.120701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.081092 restraints weight = 67127.662| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 3.50 r_work: 0.3125 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 29750 Z= 0.154 Angle : 0.604 11.269 40657 Z= 0.315 Chirality : 0.045 0.201 4735 Planarity : 0.004 0.051 5188 Dihedral : 6.179 59.646 4800 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.29 % Favored : 94.66 % Rotamer: Outliers : 3.17 % Allowed : 12.16 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.13), residues: 3708 helix: 1.74 (0.21), residues: 669 sheet: -0.31 (0.15), residues: 1045 loop : -1.62 (0.13), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 353 HIS 0.006 0.001 HIS N 50 PHE 0.018 0.001 PHE B 375 TYR 0.020 0.001 TYR A 170 ARG 0.008 0.000 ARG O 100 Details of bonding type rmsd hydrogen bonds : bond 0.04966 ( 1101) hydrogen bonds : angle 5.51757 ( 2958) SS BOND : bond 0.00621 ( 45) SS BOND : angle 2.69668 ( 90) covalent geometry : bond 0.00363 (29705) covalent geometry : angle 0.59159 (40567) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 211 time to evaluate : 3.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 394 ASN cc_start: 0.6143 (OUTLIER) cc_final: 0.5928 (t0) REVERT: C 754 LEU cc_start: 0.9684 (OUTLIER) cc_final: 0.9459 (mm) REVERT: C 950 ASP cc_start: 0.8797 (m-30) cc_final: 0.8573 (m-30) REVERT: B 198 ASP cc_start: 0.8328 (t0) cc_final: 0.8050 (t0) REVERT: B 574 ASP cc_start: 0.8565 (t70) cc_final: 0.8248 (t0) REVERT: B 950 ASP cc_start: 0.8827 (m-30) cc_final: 0.8506 (m-30) REVERT: A 102 ARG cc_start: 0.6900 (mtt180) cc_final: 0.6509 (mmm-85) REVERT: I 87 MET cc_start: 0.1587 (tpt) cc_final: -0.0690 (ptt) REVERT: I 121 VAL cc_start: 0.5842 (OUTLIER) cc_final: 0.5285 (p) REVERT: K 28 ASN cc_start: 0.7684 (p0) cc_final: 0.7120 (p0) REVERT: K 55 ARG cc_start: 0.7354 (mtp-110) cc_final: 0.7002 (mtp180) REVERT: K 80 ARG cc_start: 0.8764 (mmm-85) cc_final: 0.8502 (mtp85) REVERT: K 93 ASP cc_start: 0.8267 (t0) cc_final: 0.8017 (t70) REVERT: L 13 ARG cc_start: 0.8960 (mpp-170) cc_final: 0.8246 (tpp80) REVERT: L 38 TRP cc_start: 0.7493 (m100) cc_final: 0.6675 (m100) REVERT: L 61 TYR cc_start: 0.8522 (m-80) cc_final: 0.8117 (m-80) REVERT: L 62 ASN cc_start: 0.8655 (t0) cc_final: 0.8247 (t0) REVERT: L 86 ASN cc_start: 0.8449 (m-40) cc_final: 0.8140 (p0) REVERT: N 82 GLU cc_start: 0.8369 (pm20) cc_final: 0.7882 (pp20) REVERT: N 106 LYS cc_start: 0.9072 (tppt) cc_final: 0.8680 (mmmt) REVERT: O 18 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7689 (mm) outliers start: 96 outliers final: 55 residues processed: 293 average time/residue: 0.3927 time to fit residues: 188.3163 Evaluate side-chains 253 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 194 time to evaluate : 3.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 89 CYS Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 99 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 86 optimal weight: 4.9990 chunk 371 optimal weight: 6.9990 chunk 209 optimal weight: 3.9990 chunk 354 optimal weight: 0.1980 chunk 321 optimal weight: 40.0000 chunk 361 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 266 optimal weight: 0.9980 chunk 44 optimal weight: 0.3980 chunk 29 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 394 ASN C 603 ASN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 99 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.118432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.078970 restraints weight = 67516.954| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 3.42 r_work: 0.3037 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 29750 Z= 0.136 Angle : 0.583 14.343 40657 Z= 0.302 Chirality : 0.044 0.195 4735 Planarity : 0.004 0.048 5188 Dihedral : 5.835 59.467 4799 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.31 % Favored : 94.66 % Rotamer: Outliers : 2.97 % Allowed : 13.48 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.13), residues: 3708 helix: 1.88 (0.21), residues: 668 sheet: -0.11 (0.15), residues: 1038 loop : -1.49 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.005 0.001 HIS N 50 PHE 0.015 0.001 PHE B 375 TYR 0.016 0.001 TYR A 170 ARG 0.006 0.000 ARG K 17 Details of bonding type rmsd hydrogen bonds : bond 0.04642 ( 1101) hydrogen bonds : angle 5.34715 ( 2958) SS BOND : bond 0.00641 ( 45) SS BOND : angle 2.59734 ( 90) covalent geometry : bond 0.00319 (29705) covalent geometry : angle 0.57112 (40567) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 209 time to evaluate : 5.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 394 ASN cc_start: 0.6025 (OUTLIER) cc_final: 0.5768 (t0) REVERT: C 754 LEU cc_start: 0.9711 (OUTLIER) cc_final: 0.9468 (mm) REVERT: C 950 ASP cc_start: 0.8887 (m-30) cc_final: 0.8656 (m-30) REVERT: B 198 ASP cc_start: 0.8333 (t0) cc_final: 0.8012 (t0) REVERT: B 574 ASP cc_start: 0.8612 (t70) cc_final: 0.8285 (t0) REVERT: B 950 ASP cc_start: 0.8927 (m-30) cc_final: 0.8612 (m-30) REVERT: A 979 ASP cc_start: 0.8497 (t0) cc_final: 0.8049 (t0) REVERT: A 983 ARG cc_start: 0.8474 (ptt-90) cc_final: 0.8227 (ptt-90) REVERT: I 87 MET cc_start: 0.1743 (tpt) cc_final: -0.0511 (ptt) REVERT: K 28 ASN cc_start: 0.7509 (p0) cc_final: 0.7012 (p0) REVERT: K 55 ARG cc_start: 0.7301 (mtp-110) cc_final: 0.6991 (mtm110) REVERT: K 93 ASP cc_start: 0.8207 (t0) cc_final: 0.7986 (t70) REVERT: L 13 ARG cc_start: 0.8938 (mpp-170) cc_final: 0.8222 (tpp80) REVERT: L 38 TRP cc_start: 0.7394 (m100) cc_final: 0.6516 (m100) REVERT: L 61 TYR cc_start: 0.8427 (m-80) cc_final: 0.7922 (m-80) REVERT: L 62 ASN cc_start: 0.8695 (t0) cc_final: 0.8249 (t0) REVERT: L 68 ARG cc_start: 0.7450 (ttt180) cc_final: 0.6609 (ttt180) REVERT: L 86 ASN cc_start: 0.8480 (m-40) cc_final: 0.8131 (p0) REVERT: L 87 MET cc_start: 0.6684 (mmm) cc_final: 0.6480 (mmm) REVERT: N 82 GLU cc_start: 0.8467 (pm20) cc_final: 0.7991 (pp20) REVERT: N 106 LYS cc_start: 0.9106 (tppt) cc_final: 0.8646 (mmmt) REVERT: N 109 VAL cc_start: 0.8510 (OUTLIER) cc_final: 0.8176 (m) REVERT: O 18 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7744 (mm) outliers start: 90 outliers final: 60 residues processed: 286 average time/residue: 0.3910 time to fit residues: 184.1316 Evaluate side-chains 260 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 196 time to evaluate : 3.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 89 CYS Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain N residue 38 HIS Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 99 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 240 optimal weight: 1.9990 chunk 233 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 341 optimal weight: 10.0000 chunk 343 optimal weight: 5.9990 chunk 373 optimal weight: 0.8980 chunk 228 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 168 optimal weight: 0.1980 chunk 236 optimal weight: 0.0010 chunk 113 optimal weight: 5.9990 overall best weight: 1.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 394 ASN C 957 GLN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** 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 = 0.3852 r_free = 0.3852 target = 0.118136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.078711 restraints weight = 67071.560| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.41 r_work: 0.3086 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 29750 Z= 0.143 Angle : 0.575 13.270 40657 Z= 0.299 Chirality : 0.044 0.192 4735 Planarity : 0.004 0.047 5188 Dihedral : 5.635 56.723 4797 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.42 % Favored : 94.55 % Rotamer: Outliers : 3.34 % Allowed : 13.71 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.14), residues: 3708 helix: 1.93 (0.21), residues: 669 sheet: 0.04 (0.16), residues: 1030 loop : -1.37 (0.13), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.005 0.001 HIS A 519 PHE 0.019 0.001 PHE B 375 TYR 0.016 0.001 TYR B1067 ARG 0.010 0.000 ARG B 983 Details of bonding type rmsd hydrogen bonds : bond 0.04577 ( 1101) hydrogen bonds : angle 5.24894 ( 2958) SS BOND : bond 0.00598 ( 45) SS BOND : angle 2.53492 ( 90) covalent geometry : bond 0.00336 (29705) covalent geometry : angle 0.56271 (40567) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 209 time to evaluate : 3.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 754 LEU cc_start: 0.9688 (OUTLIER) cc_final: 0.9448 (mm) REVERT: C 950 ASP cc_start: 0.8812 (m-30) cc_final: 0.8602 (m-30) REVERT: B 198 ASP cc_start: 0.8295 (t0) cc_final: 0.7948 (t0) REVERT: B 574 ASP cc_start: 0.8621 (t70) cc_final: 0.8292 (t0) REVERT: B 950 ASP cc_start: 0.8859 (m-30) cc_final: 0.8566 (m-30) REVERT: A 238 PHE cc_start: 0.7759 (OUTLIER) cc_final: 0.7376 (p90) REVERT: A 979 ASP cc_start: 0.8486 (t0) cc_final: 0.8173 (t0) REVERT: I 87 MET cc_start: 0.1699 (tpt) cc_final: -0.0490 (ptt) REVERT: K 28 ASN cc_start: 0.7540 (p0) cc_final: 0.7042 (p0) REVERT: K 55 ARG cc_start: 0.7333 (mtp-110) cc_final: 0.7021 (mtm110) REVERT: K 80 ARG cc_start: 0.8725 (mmm-85) cc_final: 0.8440 (mtp85) REVERT: L 13 ARG cc_start: 0.8940 (mpp-170) cc_final: 0.8221 (tpp80) REVERT: L 38 TRP cc_start: 0.7405 (m100) cc_final: 0.6520 (m100) REVERT: L 61 TYR cc_start: 0.8384 (m-80) cc_final: 0.7841 (m-80) REVERT: L 62 ASN cc_start: 0.8756 (t0) cc_final: 0.8256 (t0) REVERT: L 68 ARG cc_start: 0.7473 (ttt180) cc_final: 0.6523 (ttt180) REVERT: L 73 LYS cc_start: 0.8396 (pttm) cc_final: 0.8056 (ptpt) REVERT: L 86 ASN cc_start: 0.8451 (m-40) cc_final: 0.8088 (p0) REVERT: N 82 GLU cc_start: 0.8424 (pm20) cc_final: 0.8025 (pp20) REVERT: N 106 LYS cc_start: 0.9123 (tppt) cc_final: 0.8658 (mmmt) outliers start: 101 outliers final: 70 residues processed: 294 average time/residue: 0.4101 time to fit residues: 198.4129 Evaluate side-chains 267 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 195 time to evaluate : 3.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 89 CYS Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain N residue 38 HIS Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 99 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 94 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 243 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 220 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 338 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 211 optimal weight: 9.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 ASN A1005 GLN ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 16 GLN O 99 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.125715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.087365 restraints weight = 69701.959| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 3.15 r_work: 0.3155 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 29750 Z= 0.135 Angle : 0.564 14.134 40657 Z= 0.293 Chirality : 0.044 0.195 4735 Planarity : 0.004 0.046 5188 Dihedral : 5.416 56.886 4797 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.34 % Favored : 94.63 % Rotamer: Outliers : 3.04 % Allowed : 14.40 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.14), residues: 3708 helix: 1.96 (0.21), residues: 669 sheet: 0.12 (0.16), residues: 1029 loop : -1.24 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.005 0.001 HIS A 519 PHE 0.017 0.001 PHE B 375 TYR 0.015 0.001 TYR B1067 ARG 0.005 0.000 ARG C 357 Details of bonding type rmsd hydrogen bonds : bond 0.04432 ( 1101) hydrogen bonds : angle 5.15832 ( 2958) SS BOND : bond 0.00618 ( 45) SS BOND : angle 2.44296 ( 90) covalent geometry : bond 0.00318 (29705) covalent geometry : angle 0.55227 (40567) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 205 time to evaluate : 3.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 754 LEU cc_start: 0.9661 (OUTLIER) cc_final: 0.9427 (mm) REVERT: B 198 ASP cc_start: 0.8263 (t0) cc_final: 0.7916 (t0) REVERT: B 574 ASP cc_start: 0.8557 (t70) cc_final: 0.8248 (t0) REVERT: B 950 ASP cc_start: 0.8762 (m-30) cc_final: 0.8519 (m-30) REVERT: A 238 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7336 (p90) REVERT: A 979 ASP cc_start: 0.8496 (t0) cc_final: 0.8215 (t0) REVERT: H 49 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8327 (mm) REVERT: H 54 GLN cc_start: 0.6336 (mt0) cc_final: 0.6022 (tp40) REVERT: I 87 MET cc_start: 0.1988 (tpt) cc_final: -0.0258 (ptt) REVERT: K 28 ASN cc_start: 0.7354 (p0) cc_final: 0.6956 (p0) REVERT: K 32 ASN cc_start: 0.8378 (m-40) cc_final: 0.8044 (m110) REVERT: K 55 ARG cc_start: 0.7197 (mtp-110) cc_final: 0.6849 (mtm110) REVERT: K 80 ARG cc_start: 0.8721 (mmm-85) cc_final: 0.8431 (mtp85) REVERT: L 13 ARG cc_start: 0.8942 (mpp-170) cc_final: 0.8209 (tpp80) REVERT: L 38 TRP cc_start: 0.7398 (m100) cc_final: 0.6549 (m100) REVERT: L 61 TYR cc_start: 0.8389 (m-80) cc_final: 0.7556 (m-10) REVERT: L 62 ASN cc_start: 0.8817 (t0) cc_final: 0.8213 (t0) REVERT: L 68 ARG cc_start: 0.7460 (ttt180) cc_final: 0.6445 (ttt180) REVERT: L 73 LYS cc_start: 0.8360 (pttm) cc_final: 0.8031 (ptpt) REVERT: L 86 ASN cc_start: 0.8407 (m-40) cc_final: 0.8116 (p0) REVERT: N 82 GLU cc_start: 0.8418 (pm20) cc_final: 0.8074 (pp20) REVERT: N 106 LYS cc_start: 0.9114 (tppt) cc_final: 0.8671 (mmmt) outliers start: 92 outliers final: 70 residues processed: 283 average time/residue: 0.4736 time to fit residues: 223.8946 Evaluate side-chains 263 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 190 time to evaluate : 2.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 89 CYS Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain N residue 38 HIS Chi-restraints excluded: chain O residue 99 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 153 optimal weight: 5.9990 chunk 347 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 287 optimal weight: 4.9990 chunk 245 optimal weight: 4.9990 chunk 128 optimal weight: 0.0570 chunk 139 optimal weight: 0.6980 chunk 228 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN L 99 HIS O 99 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.126779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.088528 restraints weight = 69630.440| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.18 r_work: 0.3178 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 29750 Z= 0.110 Angle : 0.549 13.453 40657 Z= 0.286 Chirality : 0.043 0.184 4735 Planarity : 0.004 0.043 5188 Dihedral : 5.165 59.259 4797 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.07 % Favored : 94.90 % Rotamer: Outliers : 2.91 % Allowed : 15.03 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.14), residues: 3708 helix: 2.09 (0.21), residues: 660 sheet: 0.22 (0.16), residues: 1029 loop : -1.14 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.008 0.001 HIS O 99 PHE 0.021 0.001 PHE B 375 TYR 0.012 0.001 TYR A 170 ARG 0.012 0.000 ARG B 983 Details of bonding type rmsd hydrogen bonds : bond 0.04103 ( 1101) hydrogen bonds : angle 5.02629 ( 2958) SS BOND : bond 0.00574 ( 45) SS BOND : angle 2.26012 ( 90) covalent geometry : bond 0.00248 (29705) covalent geometry : angle 0.53942 (40567) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 209 time to evaluate : 3.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 754 LEU cc_start: 0.9663 (OUTLIER) cc_final: 0.9403 (mm) REVERT: B 198 ASP cc_start: 0.8271 (t0) cc_final: 0.7883 (t0) REVERT: B 574 ASP cc_start: 0.8561 (t70) cc_final: 0.8241 (t0) REVERT: B 950 ASP cc_start: 0.8754 (m-30) cc_final: 0.8500 (m-30) REVERT: A 238 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.7495 (p90) REVERT: A 979 ASP cc_start: 0.8462 (t0) cc_final: 0.7923 (t0) REVERT: A 983 ARG cc_start: 0.8453 (ptt-90) cc_final: 0.8080 (ptt-90) REVERT: H 49 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8536 (mm) REVERT: H 54 GLN cc_start: 0.6328 (mt0) cc_final: 0.6055 (tp40) REVERT: I 87 MET cc_start: 0.1828 (tpt) cc_final: -0.0238 (ptt) REVERT: K 32 ASN cc_start: 0.8342 (m-40) cc_final: 0.8037 (m110) REVERT: L 13 ARG cc_start: 0.8930 (mpp-170) cc_final: 0.8239 (tpp80) REVERT: L 38 TRP cc_start: 0.7413 (m100) cc_final: 0.6520 (m100) REVERT: L 61 TYR cc_start: 0.8446 (m-80) cc_final: 0.7669 (m-10) REVERT: L 62 ASN cc_start: 0.8793 (t0) cc_final: 0.8394 (t0) REVERT: L 68 ARG cc_start: 0.7535 (ttt180) cc_final: 0.6718 (ttt180) REVERT: L 86 ASN cc_start: 0.8498 (m-40) cc_final: 0.8182 (p0) REVERT: N 82 GLU cc_start: 0.8393 (pm20) cc_final: 0.8058 (pp20) REVERT: N 106 LYS cc_start: 0.9098 (tppt) cc_final: 0.8720 (mmmt) outliers start: 88 outliers final: 70 residues processed: 279 average time/residue: 0.3861 time to fit residues: 178.2093 Evaluate side-chains 266 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 193 time to evaluate : 3.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 89 CYS Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 38 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 348 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 321 optimal weight: 4.9990 chunk 250 optimal weight: 8.9990 chunk 303 optimal weight: 4.9990 chunk 185 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 273 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 358 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 207 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 957 GLN ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 ASN ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 1 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.117869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.078203 restraints weight = 67787.387| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.46 r_work: 0.3010 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 29750 Z= 0.269 Angle : 0.658 13.909 40657 Z= 0.343 Chirality : 0.047 0.195 4735 Planarity : 0.005 0.051 5188 Dihedral : 5.687 59.525 4797 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.91 % Favored : 94.07 % Rotamer: Outliers : 3.14 % Allowed : 15.43 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.14), residues: 3708 helix: 1.83 (0.21), residues: 662 sheet: -0.01 (0.16), residues: 1056 loop : -1.30 (0.13), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1102 HIS 0.010 0.001 HIS L 99 PHE 0.022 0.002 PHE A 92 TYR 0.024 0.002 TYR B1067 ARG 0.008 0.001 ARG K 55 Details of bonding type rmsd hydrogen bonds : bond 0.05633 ( 1101) hydrogen bonds : angle 5.39264 ( 2958) SS BOND : bond 0.00660 ( 45) SS BOND : angle 2.78032 ( 90) covalent geometry : bond 0.00650 (29705) covalent geometry : angle 0.64581 (40567) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 191 time to evaluate : 3.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 339 ASP cc_start: 0.8628 (m-30) cc_final: 0.8238 (t70) REVERT: C 754 LEU cc_start: 0.9698 (OUTLIER) cc_final: 0.9462 (mm) REVERT: B 198 ASP cc_start: 0.8618 (t0) cc_final: 0.8193 (t0) REVERT: B 574 ASP cc_start: 0.8625 (t70) cc_final: 0.8303 (t0) REVERT: B 950 ASP cc_start: 0.8853 (m-30) cc_final: 0.8646 (m-30) REVERT: A 238 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.7368 (p90) REVERT: A 979 ASP cc_start: 0.8508 (t0) cc_final: 0.7924 (t0) REVERT: A 983 ARG cc_start: 0.8479 (ptt-90) cc_final: 0.8097 (ptt-90) REVERT: H 49 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8586 (mm) REVERT: H 54 GLN cc_start: 0.6332 (mt0) cc_final: 0.6034 (tp40) REVERT: I 87 MET cc_start: 0.2161 (tpt) cc_final: -0.0316 (ptp) REVERT: K 55 ARG cc_start: 0.7472 (mtm110) cc_final: 0.7057 (mtp180) REVERT: K 80 ARG cc_start: 0.8610 (mmm-85) cc_final: 0.8392 (mtp85) REVERT: L 13 ARG cc_start: 0.8896 (mpp-170) cc_final: 0.8149 (tpp80) REVERT: L 38 TRP cc_start: 0.7492 (m100) cc_final: 0.6672 (m100) REVERT: L 45 LYS cc_start: 0.8772 (mmtm) cc_final: 0.8569 (mtmt) REVERT: L 61 TYR cc_start: 0.8512 (m-80) cc_final: 0.7965 (m-10) REVERT: N 82 GLU cc_start: 0.8538 (pm20) cc_final: 0.8091 (pp20) REVERT: N 106 LYS cc_start: 0.9140 (tppt) cc_final: 0.8742 (mmmt) REVERT: O 13 ARG cc_start: 0.9014 (mmm-85) cc_final: 0.8265 (mmp-170) REVERT: O 58 ASP cc_start: 0.8545 (t0) cc_final: 0.8307 (t0) outliers start: 95 outliers final: 75 residues processed: 271 average time/residue: 0.3890 time to fit residues: 175.2289 Evaluate side-chains 261 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 183 time to evaluate : 3.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 89 CYS Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 38 HIS Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 121 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 328 optimal weight: 9.9990 chunk 339 optimal weight: 9.9990 chunk 198 optimal weight: 0.7980 chunk 282 optimal weight: 0.2980 chunk 289 optimal weight: 0.0270 chunk 137 optimal weight: 0.9990 chunk 301 optimal weight: 1.9990 chunk 252 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 364 optimal weight: 2.9990 chunk 235 optimal weight: 0.0070 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 394 ASN C 544 ASN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.126557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.088485 restraints weight = 69802.299| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.14 r_work: 0.3188 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 29750 Z= 0.102 Angle : 0.555 12.826 40657 Z= 0.288 Chirality : 0.044 0.178 4735 Planarity : 0.004 0.046 5188 Dihedral : 5.054 59.913 4797 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.69 % Favored : 95.28 % Rotamer: Outliers : 2.54 % Allowed : 16.25 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.14), residues: 3708 helix: 2.11 (0.21), residues: 653 sheet: 0.22 (0.16), residues: 1025 loop : -1.11 (0.13), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 436 HIS 0.005 0.001 HIS A 519 PHE 0.021 0.001 PHE B 375 TYR 0.013 0.001 TYR A 170 ARG 0.013 0.000 ARG B 983 Details of bonding type rmsd hydrogen bonds : bond 0.03960 ( 1101) hydrogen bonds : angle 4.98624 ( 2958) SS BOND : bond 0.00557 ( 45) SS BOND : angle 2.21386 ( 90) covalent geometry : bond 0.00222 (29705) covalent geometry : angle 0.54594 (40567) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 209 time to evaluate : 3.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 754 LEU cc_start: 0.9653 (OUTLIER) cc_final: 0.9380 (mm) REVERT: B 198 ASP cc_start: 0.8341 (t0) cc_final: 0.7929 (t0) REVERT: B 574 ASP cc_start: 0.8592 (t70) cc_final: 0.8259 (t0) REVERT: B 950 ASP cc_start: 0.8742 (m-30) cc_final: 0.8505 (m-30) REVERT: A 238 PHE cc_start: 0.7891 (OUTLIER) cc_final: 0.7397 (p90) REVERT: A 979 ASP cc_start: 0.8454 (t0) cc_final: 0.8142 (t0) REVERT: H 49 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8451 (mm) REVERT: H 54 GLN cc_start: 0.6310 (mt0) cc_final: 0.5984 (tp40) REVERT: I 87 MET cc_start: 0.1881 (tpt) cc_final: -0.0341 (ptp) REVERT: K 32 ASN cc_start: 0.8384 (m-40) cc_final: 0.8082 (m110) REVERT: K 55 ARG cc_start: 0.7564 (mtm110) cc_final: 0.7128 (mtp180) REVERT: L 13 ARG cc_start: 0.8932 (mpp-170) cc_final: 0.8299 (tpp80) REVERT: L 38 TRP cc_start: 0.7442 (m100) cc_final: 0.6665 (m100) REVERT: L 61 TYR cc_start: 0.8605 (m-80) cc_final: 0.7865 (m-80) REVERT: L 62 ASN cc_start: 0.8870 (t0) cc_final: 0.8639 (t0) REVERT: L 68 ARG cc_start: 0.7585 (ttt180) cc_final: 0.7281 (ttt180) REVERT: N 82 GLU cc_start: 0.8481 (pm20) cc_final: 0.8095 (pp20) REVERT: N 83 ASP cc_start: 0.8990 (m-30) cc_final: 0.8609 (m-30) REVERT: N 106 LYS cc_start: 0.9104 (tppt) cc_final: 0.8739 (mmmt) REVERT: O 13 ARG cc_start: 0.9039 (mmm-85) cc_final: 0.8445 (mmp-170) REVERT: O 58 ASP cc_start: 0.8447 (t0) cc_final: 0.8231 (t0) outliers start: 77 outliers final: 57 residues processed: 274 average time/residue: 0.3816 time to fit residues: 172.5453 Evaluate side-chains 256 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 196 time to evaluate : 3.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 89 CYS Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 38 HIS Chi-restraints excluded: chain O residue 121 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 370 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 209 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 213 optimal weight: 0.9980 chunk 288 optimal weight: 2.9990 chunk 118 optimal weight: 0.3980 chunk 30 optimal weight: 8.9990 chunk 180 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 272 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 957 GLN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.120823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.081622 restraints weight = 67726.938| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 3.45 r_work: 0.3161 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 29750 Z= 0.113 Angle : 0.555 12.826 40657 Z= 0.288 Chirality : 0.044 0.211 4735 Planarity : 0.004 0.061 5188 Dihedral : 4.939 59.340 4796 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.99 % Favored : 94.98 % Rotamer: Outliers : 2.28 % Allowed : 16.65 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.14), residues: 3708 helix: 2.18 (0.21), residues: 654 sheet: 0.25 (0.16), residues: 1028 loop : -1.05 (0.13), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.005 0.001 HIS A 519 PHE 0.022 0.001 PHE L 112 TYR 0.012 0.001 TYR A 170 ARG 0.014 0.000 ARG B 983 Details of bonding type rmsd hydrogen bonds : bond 0.04031 ( 1101) hydrogen bonds : angle 4.93857 ( 2958) SS BOND : bond 0.00520 ( 45) SS BOND : angle 2.22853 ( 90) covalent geometry : bond 0.00260 (29705) covalent geometry : angle 0.54543 (40567) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 199 time to evaluate : 3.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 754 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9380 (mm) REVERT: B 198 ASP cc_start: 0.8315 (t0) cc_final: 0.7921 (t0) REVERT: B 574 ASP cc_start: 0.8567 (t70) cc_final: 0.8271 (t0) REVERT: B 950 ASP cc_start: 0.8751 (m-30) cc_final: 0.8510 (m-30) REVERT: A 238 PHE cc_start: 0.7867 (OUTLIER) cc_final: 0.7388 (p90) REVERT: A 979 ASP cc_start: 0.8415 (t0) cc_final: 0.8050 (t0) REVERT: H 49 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8565 (mm) REVERT: H 54 GLN cc_start: 0.6283 (mt0) cc_final: 0.6006 (tp40) REVERT: I 87 MET cc_start: 0.1724 (tpt) cc_final: -0.0489 (ptp) REVERT: K 32 ASN cc_start: 0.8331 (m-40) cc_final: 0.7971 (m110) REVERT: K 55 ARG cc_start: 0.7500 (mtm110) cc_final: 0.7054 (mtp180) REVERT: K 80 ARG cc_start: 0.8503 (mtp85) cc_final: 0.8200 (mtp-110) REVERT: L 13 ARG cc_start: 0.9028 (mpp-170) cc_final: 0.8211 (tpp80) REVERT: L 38 TRP cc_start: 0.7438 (m100) cc_final: 0.6605 (m100) REVERT: L 39 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.7859 (tp) REVERT: L 61 TYR cc_start: 0.8580 (m-80) cc_final: 0.7886 (m-80) REVERT: L 62 ASN cc_start: 0.8894 (t0) cc_final: 0.8635 (t0) REVERT: L 68 ARG cc_start: 0.7699 (ttt180) cc_final: 0.7455 (ttt180) REVERT: N 82 GLU cc_start: 0.8424 (pm20) cc_final: 0.8108 (pp20) REVERT: N 106 LYS cc_start: 0.9114 (tppt) cc_final: 0.8717 (mmmt) REVERT: O 13 ARG cc_start: 0.9059 (mmm-85) cc_final: 0.8480 (mmp-170) REVERT: O 58 ASP cc_start: 0.8439 (t0) cc_final: 0.8217 (t0) outliers start: 69 outliers final: 60 residues processed: 257 average time/residue: 0.3865 time to fit residues: 163.9317 Evaluate side-chains 257 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 193 time to evaluate : 2.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 89 CYS Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 38 HIS Chi-restraints excluded: chain O residue 121 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 202 optimal weight: 3.9990 chunk 351 optimal weight: 9.9990 chunk 172 optimal weight: 0.8980 chunk 1 optimal weight: 0.1980 chunk 19 optimal weight: 0.4980 chunk 357 optimal weight: 0.0270 chunk 296 optimal weight: 2.9990 chunk 352 optimal weight: 0.4980 chunk 332 optimal weight: 0.9990 chunk 316 optimal weight: 50.0000 chunk 74 optimal weight: 0.5980 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1074 ASN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 ASN ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.122515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.083613 restraints weight = 67591.186| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.46 r_work: 0.3204 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 29750 Z= 0.096 Angle : 0.537 12.551 40657 Z= 0.278 Chirality : 0.043 0.175 4735 Planarity : 0.004 0.056 5188 Dihedral : 4.648 56.432 4796 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.83 % Favored : 95.15 % Rotamer: Outliers : 2.18 % Allowed : 16.78 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.14), residues: 3708 helix: 2.32 (0.21), residues: 648 sheet: 0.33 (0.16), residues: 1063 loop : -0.96 (0.14), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.005 0.001 HIS A 519 PHE 0.022 0.001 PHE B 375 TYR 0.013 0.001 TYR A 170 ARG 0.013 0.000 ARG B 983 Details of bonding type rmsd hydrogen bonds : bond 0.03573 ( 1101) hydrogen bonds : angle 4.77678 ( 2958) SS BOND : bond 0.00479 ( 45) SS BOND : angle 1.99027 ( 90) covalent geometry : bond 0.00210 (29705) covalent geometry : angle 0.52928 (40567) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17184.11 seconds wall clock time: 300 minutes 56.51 seconds (18056.51 seconds total)