Starting phenix.real_space_refine on Mon Aug 25 03:52:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h3e_34465/08_2025/8h3e_34465_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h3e_34465/08_2025/8h3e_34465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8h3e_34465/08_2025/8h3e_34465_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h3e_34465/08_2025/8h3e_34465_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h3e_34465/08_2025/8h3e_34465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h3e_34465/08_2025/8h3e_34465.map" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.122 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 114 5.16 5 C 15933 2.51 5 N 4131 2.21 5 O 4779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24957 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8227 Classifications: {'peptide': 1053} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1001} Chain breaks: 6 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 8227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8227 Classifications: {'peptide': 1053} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1001} Chain breaks: 6 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 8227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8227 Classifications: {'peptide': 1053} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1001} Chain breaks: 6 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 92 Unusual residues: {'NAG': 5, 'Q83': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 92 Unusual residues: {'NAG': 5, 'Q83': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 92 Unusual residues: {'NAG': 5, 'Q83': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Residues with excluded nonbonded symmetry interactions: 197 residue: pdb=" N THR A 33 " occ=0.77 ... (5 atoms not shown) pdb=" CG2 THR A 33 " occ=0.46 residue: pdb=" N HIS A 69 " occ=0.34 ... (8 atoms not shown) pdb=" NE2 HIS A 69 " occ=0.55 residue: pdb=" N VAL A 70 " occ=0.38 ... (5 atoms not shown) pdb=" CG2 VAL A 70 " occ=0.64 residue: pdb=" N THR A 76 " occ=0.73 ... (5 atoms not shown) pdb=" CG2 THR A 76 " occ=0.80 residue: pdb=" N LYS A 77 " occ=0.76 ... (7 atoms not shown) pdb=" NZ LYS A 77 " occ=0.97 residue: pdb=" N ASP A 80 " occ=0.59 ... (6 atoms not shown) pdb=" OD2 ASP A 80 " occ=0.57 residue: pdb=" N ASN A 81 " occ=0.73 ... (6 atoms not shown) pdb=" ND2 ASN A 81 " occ=0.77 residue: pdb=" N SER A 98 " occ=0.66 ... (4 atoms not shown) pdb=" OG SER A 98 " occ=0.86 residue: pdb=" N THR A 109 " occ=0.76 ... (5 atoms not shown) pdb=" CG2 THR A 109 " occ=0.53 residue: pdb=" N ASP A 111 " occ=0.62 ... (6 atoms not shown) pdb=" OD2 ASP A 111 " occ=0.61 residue: pdb=" N ASP A 138 " occ=0.60 ... (6 atoms not shown) pdb=" OD2 ASP A 138 " occ=0.53 residue: pdb=" N TYR A 144 " occ=0.58 ... (10 atoms not shown) pdb=" OH TYR A 144 " occ=0.54 ... (remaining 185 not shown) Time building chain proxies: 6.19, per 1000 atoms: 0.25 Number of scatterers: 24957 At special positions: 0 Unit cell: (145.34, 146.2, 180.6, 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 114 16.00 O 4779 8.00 N 4131 7.00 C 15933 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 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 B 131 " - pdb=" SG CYS B 166 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 331 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 331 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 331 " Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5910 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 45 sheets defined 21.0% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 296 through 304 removed outlier: 3.959A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.960A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 343' Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.829A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.619A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.836A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 410' Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.945A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 417 through 422' Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.104A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.636A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 760 through 778 removed outlier: 3.947A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL A 772 " --> pdb=" O THR A 768 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 823 removed outlier: 3.682A pdb=" N LEU A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 818 through 823' Processing helix chain 'A' and resid 850 through 855 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.840A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 873 " --> pdb=" O MET A 869 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 874 " --> pdb=" O ILE A 870 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 877 " --> pdb=" O TYR A 873 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 879 " --> pdb=" O SER A 875 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER A 884 " --> pdb=" O GLY A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.660A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG A 905 " --> pdb=" O GLN A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.005A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 932 Processing helix chain 'A' and resid 932 through 939 removed outlier: 4.497A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 954 Processing helix chain 'A' and resid 959 through 965 removed outlier: 4.044A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 removed outlier: 3.566A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 976 through 981' Processing helix chain 'A' and resid 985 through 1001 removed outlier: 4.164A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1015 removed outlier: 3.784A pdb=" N THR A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1032 removed outlier: 3.719A pdb=" N SER A1021 " --> pdb=" O GLU A1017 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER A1030 " --> pdb=" O ALA A1026 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU A1031 " --> pdb=" O THR A1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 304 removed outlier: 3.976A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.959A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 337 through 343' Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.823A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.600A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.851A pdb=" N GLN B 409 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 406 through 410' Processing helix chain 'B' and resid 417 through 422 removed outlier: 3.985A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN B 422 " --> pdb=" O ILE B 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 417 through 422' Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.115A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.606A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 760 through 778 removed outlier: 3.889A pdb=" N ILE B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA B 771 " --> pdb=" O LEU B 767 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL B 772 " --> pdb=" O THR B 768 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 823 removed outlier: 3.691A pdb=" N LEU B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE B 823 " --> pdb=" O GLU B 819 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 818 through 823' Processing helix chain 'B' and resid 850 through 856 removed outlier: 3.665A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 removed outlier: 4.016A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR B 873 " --> pdb=" O MET B 869 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR B 874 " --> pdb=" O ILE B 870 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA B 876 " --> pdb=" O GLN B 872 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 879 " --> pdb=" O SER B 875 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR B 881 " --> pdb=" O LEU B 877 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER B 884 " --> pdb=" O GLY B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.650A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.041A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 932 Processing helix chain 'B' and resid 932 through 939 removed outlier: 4.490A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 954 Processing helix chain 'B' and resid 959 through 965 removed outlier: 4.074A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 981 removed outlier: 3.604A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 976 through 981' Processing helix chain 'B' and resid 985 through 1001 removed outlier: 4.167A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1002 through 1015 removed outlier: 3.823A pdb=" N THR B1006 " --> pdb=" O GLN B1002 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL B1008 " --> pdb=" O LEU B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1032 removed outlier: 3.675A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER B1030 " --> pdb=" O ALA B1026 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU B1031 " --> pdb=" O THR B1027 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 304 removed outlier: 3.978A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.913A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN C 343 " --> pdb=" O GLY C 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 337 through 343' Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.789A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.843A pdb=" N GLN C 409 " --> pdb=" O GLU C 406 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 406 through 410' Processing helix chain 'C' and resid 417 through 422 removed outlier: 3.941A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) removed outlier: 3.665A 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 616 through 620 removed outlier: 4.107A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.590A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) 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 760 through 778 removed outlier: 3.917A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA C 771 " --> pdb=" O LEU C 767 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL C 772 " --> pdb=" O THR C 768 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 823 removed outlier: 3.665A pdb=" N LEU C 822 " --> pdb=" O ILE C 818 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE C 823 " --> pdb=" O GLU C 819 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 818 through 823' Processing helix chain 'C' and resid 850 through 855 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.833A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR C 874 " --> pdb=" O ILE C 870 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER C 875 " --> pdb=" O ALA C 871 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA C 876 " --> pdb=" O GLN C 872 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU C 877 " --> pdb=" O TYR C 873 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA C 879 " --> pdb=" O SER C 875 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER C 884 " --> pdb=" O GLY C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.655A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG C 905 " --> pdb=" O GLN C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.019A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 932 Processing helix chain 'C' and resid 932 through 939 removed outlier: 4.489A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 954 removed outlier: 3.778A pdb=" N ASP C 950 " --> pdb=" O GLY C 946 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 965 removed outlier: 4.062A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 981 removed outlier: 3.646A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 976 through 981' Processing helix chain 'C' and resid 985 through 1001 removed outlier: 4.375A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1002 through 1032 removed outlier: 3.815A pdb=" N THR C1006 " --> pdb=" O GLN C1002 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL C1008 " --> pdb=" O LEU C1004 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE C1018 " --> pdb=" O ARG C1014 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG C1019 " --> pdb=" O ALA C1015 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU C1031 " --> pdb=" O THR C1027 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.709A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.361A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 154 through 164 removed outlier: 9.718A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 11.723A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 10.035A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.739A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 13.656A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.811A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.664A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 241 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.638A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.795A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.795A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL A 395 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N SER A 514 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA A 397 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL A 512 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N SER A 399 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL A 510 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL A 401 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TYR A 508 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.598A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 539 through 543 removed outlier: 3.670A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.682A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 714 removed outlier: 3.715A pdb=" N ILE A 712 " --> pdb=" O PHE A1075 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A1096 " --> pdb=" O PHE A1103 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.662A pdb=" N ALA A1070 " --> pdb=" O ASN A 717 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.807A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.578A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.712A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 263 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.365A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 154 through 160 removed outlier: 9.706A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 11.707A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 10.044A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.749A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 13.648A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.797A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 241 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 313 removed outlier: 3.666A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.787A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.787A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL B 395 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N SER B 514 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA B 397 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL B 512 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER B 399 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL B 510 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL B 401 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N TYR B 508 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.586A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 539 through 543 removed outlier: 3.668A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.631A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 712 through 714 removed outlier: 3.730A pdb=" N ILE B 712 " --> pdb=" O PHE B1075 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B1096 " --> pdb=" O PHE B1103 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 717 through 728 removed outlier: 3.649A pdb=" N ALA B1070 " --> pdb=" O ASN B 717 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.569A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.531A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.338A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 154 through 160 removed outlier: 9.654A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 11.688A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 10.033A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.744A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 13.702A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.804A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.647A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 313 removed outlier: 3.673A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.797A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.797A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL C 395 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N SER C 514 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA C 397 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL C 512 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER C 399 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL C 510 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL C 401 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TYR C 508 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.590A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 539 through 543 removed outlier: 3.648A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 714 removed outlier: 3.794A pdb=" N ILE C 712 " --> pdb=" O PHE C1075 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL C1096 " --> pdb=" O PHE C1103 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 717 through 728 removed outlier: 3.679A pdb=" N ALA C1070 " --> pdb=" O ASN C 717 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.602A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) 650 hydrogen bonds defined for protein. 1734 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.27 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4092 1.30 - 1.43: 7074 1.43 - 1.56: 14216 1.56 - 1.69: 1 1.69 - 1.82: 144 Bond restraints: 25527 Sorted by residual: bond pdb=" C12 Q83 C1301 " pdb=" C13 Q83 C1301 " ideal model delta sigma weight residual 1.387 1.540 -0.153 2.00e-02 2.50e+03 5.84e+01 bond pdb=" C12 Q83 B1301 " pdb=" C13 Q83 B1301 " ideal model delta sigma weight residual 1.387 1.540 -0.153 2.00e-02 2.50e+03 5.81e+01 bond pdb=" C12 Q83 A1301 " pdb=" C13 Q83 A1301 " ideal model delta sigma weight residual 1.387 1.539 -0.152 2.00e-02 2.50e+03 5.81e+01 bond pdb=" C14 Q83 C1301 " pdb=" C15 Q83 C1301 " ideal model delta sigma weight residual 1.387 1.523 -0.136 2.00e-02 2.50e+03 4.65e+01 bond pdb=" C14 Q83 A1301 " pdb=" C15 Q83 A1301 " ideal model delta sigma weight residual 1.387 1.523 -0.136 2.00e-02 2.50e+03 4.59e+01 ... (remaining 25522 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 33674 1.31 - 2.62: 815 2.62 - 3.92: 191 3.92 - 5.23: 35 5.23 - 6.54: 10 Bond angle restraints: 34725 Sorted by residual: angle pdb=" C THR C 315 " pdb=" CA THR C 315 " pdb=" CB THR C 315 " ideal model delta sigma weight residual 116.54 110.00 6.54 1.15e+00 7.56e-01 3.23e+01 angle pdb=" CA ALA C 706 " pdb=" C ALA C 706 " pdb=" O ALA C 706 " ideal model delta sigma weight residual 122.13 116.75 5.38 1.13e+00 7.83e-01 2.27e+01 angle pdb=" CA ALA B 706 " pdb=" C ALA B 706 " pdb=" O ALA B 706 " ideal model delta sigma weight residual 122.37 117.09 5.28 1.15e+00 7.56e-01 2.11e+01 angle pdb=" CA ALA A 706 " pdb=" C ALA A 706 " pdb=" O ALA A 706 " ideal model delta sigma weight residual 122.37 117.16 5.21 1.15e+00 7.56e-01 2.05e+01 angle pdb=" CA PRO C1140 " pdb=" N PRO C1140 " pdb=" CD PRO C1140 " ideal model delta sigma weight residual 112.00 105.80 6.20 1.40e+00 5.10e-01 1.96e+01 ... (remaining 34720 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 13255 17.93 - 35.86: 1634 35.86 - 53.79: 398 53.79 - 71.72: 94 71.72 - 89.65: 27 Dihedral angle restraints: 15408 sinusoidal: 6219 harmonic: 9189 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 176.62 -83.62 1 1.00e+01 1.00e-02 8.53e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 176.56 -83.56 1 1.00e+01 1.00e-02 8.52e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 175.86 -82.86 1 1.00e+01 1.00e-02 8.41e+01 ... (remaining 15405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 3605 0.081 - 0.162: 350 0.162 - 0.242: 6 0.242 - 0.323: 4 0.323 - 0.404: 1 Chirality restraints: 3966 Sorted by residual: chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C 343 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C1 NAG A1306 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1306 " pdb=" O5 NAG A1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 3963 not shown) Planarity restraints: 4500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 705 " -0.023 2.00e-02 2.50e+03 4.44e-02 1.97e+01 pdb=" C VAL C 705 " 0.077 2.00e-02 2.50e+03 pdb=" O VAL C 705 " -0.028 2.00e-02 2.50e+03 pdb=" N ALA C 706 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C1139 " -0.073 5.00e-02 4.00e+02 1.07e-01 1.84e+01 pdb=" N PRO C1140 " 0.186 5.00e-02 4.00e+02 pdb=" CA PRO C1140 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO C1140 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 894 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.79e+00 pdb=" C LEU B 894 " -0.042 2.00e-02 2.50e+03 pdb=" O LEU B 894 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN B 895 " 0.014 2.00e-02 2.50e+03 ... (remaining 4497 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 87 2.55 - 3.14: 17703 3.14 - 3.72: 31819 3.72 - 4.31: 44564 4.31 - 4.90: 81567 Nonbonded interactions: 175740 Sorted by model distance: nonbonded pdb=" OH TYR C 91 " pdb=" OE1 GLU C 191 " model vdw 1.960 3.040 nonbonded pdb=" OH TYR B 91 " pdb=" OE1 GLU B 191 " model vdw 1.960 3.040 nonbonded pdb=" OH TYR A 91 " pdb=" OE1 GLU A 191 " model vdw 1.970 3.040 nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 1.972 3.040 nonbonded pdb=" OG1 THR A 323 " pdb=" OE1 GLU A 324 " model vdw 2.011 3.040 ... (remaining 175735 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.80 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: 7.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 25.220 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 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 : 0.005 0.153 25581 Z= 0.222 Angle : 0.530 6.972 34848 Z= 0.292 Chirality : 0.045 0.404 3966 Planarity : 0.004 0.107 4485 Dihedral : 16.698 89.648 9381 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.22 % Allowed : 25.95 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.27 (0.14), residues: 3117 helix: -1.25 (0.22), residues: 588 sheet: -0.43 (0.20), residues: 708 loop : -2.12 (0.13), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 454 TYR 0.016 0.001 TYR A 707 PHE 0.012 0.001 PHE B 592 TRP 0.008 0.001 TRP A 436 HIS 0.002 0.001 HIS A 625 Details of bonding type rmsd covalent geometry : bond 0.00452 (25527) covalent geometry : angle 0.52081 (34725) SS BOND : bond 0.00206 ( 39) SS BOND : angle 0.99190 ( 78) hydrogen bonds : bond 0.28048 ( 644) hydrogen bonds : angle 8.20490 ( 1734) link_NAG-ASN : bond 0.00558 ( 15) link_NAG-ASN : angle 2.61199 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 1.216 Fit side-chains revert: symmetry clash REVERT: A 624 ILE cc_start: 0.8339 (mt) cc_final: 0.7691 (mm) outliers start: 6 outliers final: 2 residues processed: 96 average time/residue: 0.1777 time to fit residues: 28.0426 Evaluate side-chains 87 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain C residue 343 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.3980 chunk 298 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 703 ASN A 804 GLN A 935 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 935 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 935 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.078873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.066188 restraints weight = 62847.576| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.17 r_work: 0.2924 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 633 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 668 | |-----------------------------------------------------------------------------| r_final: 0.2849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25581 Z= 0.155 Angle : 0.606 10.254 34848 Z= 0.319 Chirality : 0.050 0.355 3966 Planarity : 0.004 0.046 4485 Dihedral : 6.325 54.674 3753 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.09 % Allowed : 24.42 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.20 (0.14), residues: 3117 helix: -1.43 (0.21), residues: 609 sheet: -0.07 (0.20), residues: 666 loop : -2.10 (0.13), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1000 TYR 0.014 0.001 TYR A1067 PHE 0.016 0.001 PHE C1121 TRP 0.013 0.001 TRP C 436 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00361 (25527) covalent geometry : angle 0.58961 (34725) SS BOND : bond 0.00449 ( 39) SS BOND : angle 1.23048 ( 78) hydrogen bonds : bond 0.05207 ( 644) hydrogen bonds : angle 5.46496 ( 1734) link_NAG-ASN : bond 0.01059 ( 15) link_NAG-ASN : angle 3.64447 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 90 time to evaluate : 0.685 Fit side-chains REVERT: A 287 ASP cc_start: 0.8828 (OUTLIER) cc_final: 0.8612 (m-30) REVERT: A 529 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7479 (mtmm) REVERT: A 584 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8565 (mm) REVERT: A 624 ILE cc_start: 0.8414 (mt) cc_final: 0.7770 (mm) REVERT: A 703 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.8198 (m110) REVERT: A 955 ASN cc_start: 0.9267 (m-40) cc_final: 0.8534 (m110) REVERT: A 1138 TYR cc_start: 0.8715 (t80) cc_final: 0.8455 (t80) REVERT: B 287 ASP cc_start: 0.8884 (OUTLIER) cc_final: 0.8625 (m-30) REVERT: B 529 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.6743 (tttp) REVERT: C 102 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8042 (mmt180) REVERT: C 1138 TYR cc_start: 0.8769 (t80) cc_final: 0.8358 (t80) outliers start: 85 outliers final: 47 residues processed: 168 average time/residue: 0.1459 time to fit residues: 40.7746 Evaluate side-chains 139 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 85 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 1073 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 153 optimal weight: 1.9990 chunk 299 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 chunk 305 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 266 optimal weight: 5.9990 chunk 134 optimal weight: 0.7980 chunk 289 optimal weight: 0.9980 chunk 124 optimal weight: 0.2980 chunk 84 optimal weight: 5.9990 chunk 214 optimal weight: 9.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.080112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.066712 restraints weight = 62132.961| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.17 r_work: 0.2942 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 668 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 711 | |-----------------------------------------------------------------------------| r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25581 Z= 0.114 Angle : 0.538 10.004 34848 Z= 0.281 Chirality : 0.047 0.350 3966 Planarity : 0.004 0.041 4485 Dihedral : 5.696 54.268 3751 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.28 % Allowed : 24.64 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.97 (0.14), residues: 3117 helix: -1.24 (0.21), residues: 609 sheet: 0.05 (0.19), residues: 735 loop : -2.01 (0.13), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1000 TYR 0.013 0.001 TYR A1067 PHE 0.015 0.001 PHE C1121 TRP 0.012 0.001 TRP C 436 HIS 0.005 0.001 HIS A 625 Details of bonding type rmsd covalent geometry : bond 0.00256 (25527) covalent geometry : angle 0.52153 (34725) SS BOND : bond 0.00342 ( 39) SS BOND : angle 0.92881 ( 78) hydrogen bonds : bond 0.03888 ( 644) hydrogen bonds : angle 4.96088 ( 1734) link_NAG-ASN : bond 0.00998 ( 15) link_NAG-ASN : angle 3.61961 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 93 time to evaluate : 1.010 Fit side-chains REVERT: A 176 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7064 (mp) REVERT: A 955 ASN cc_start: 0.9205 (m-40) cc_final: 0.8427 (m110) REVERT: A 1138 TYR cc_start: 0.8690 (t80) cc_final: 0.8408 (t80) REVERT: B 287 ASP cc_start: 0.8785 (OUTLIER) cc_final: 0.8551 (m-30) REVERT: B 529 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.6793 (tttp) REVERT: B 1142 GLN cc_start: 0.7214 (OUTLIER) cc_final: 0.6826 (tp-100) REVERT: C 287 ASP cc_start: 0.8791 (OUTLIER) cc_final: 0.8519 (m-30) REVERT: C 1138 TYR cc_start: 0.8784 (t80) cc_final: 0.8361 (t80) REVERT: C 1142 GLN cc_start: 0.7246 (OUTLIER) cc_final: 0.6967 (tp40) outliers start: 90 outliers final: 54 residues processed: 176 average time/residue: 0.1735 time to fit residues: 50.2776 Evaluate side-chains 141 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 81 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 1142 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 270 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 263 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 207 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 244 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.078934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.064748 restraints weight = 61109.309| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.24 r_work: 0.2900 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 711 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 782 | |-----------------------------------------------------------------------------| r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25581 Z= 0.150 Angle : 0.582 10.385 34848 Z= 0.305 Chirality : 0.049 0.420 3966 Planarity : 0.004 0.044 4485 Dihedral : 5.760 53.847 3750 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.93 % Allowed : 24.27 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.01 (0.14), residues: 3117 helix: -1.33 (0.21), residues: 609 sheet: 0.20 (0.20), residues: 702 loop : -2.05 (0.13), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 214 TYR 0.014 0.001 TYR A1067 PHE 0.016 0.001 PHE A1121 TRP 0.011 0.001 TRP C 436 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00352 (25527) covalent geometry : angle 0.56392 (34725) SS BOND : bond 0.00415 ( 39) SS BOND : angle 1.24669 ( 78) hydrogen bonds : bond 0.04563 ( 644) hydrogen bonds : angle 4.97535 ( 1734) link_NAG-ASN : bond 0.00997 ( 15) link_NAG-ASN : angle 3.78262 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 85 time to evaluate : 1.034 Fit side-chains REVERT: A 176 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7211 (mp) REVERT: A 287 ASP cc_start: 0.8844 (OUTLIER) cc_final: 0.8605 (m-30) REVERT: A 529 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7660 (mtmm) REVERT: A 584 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8481 (mm) REVERT: A 624 ILE cc_start: 0.8400 (mt) cc_final: 0.7725 (mm) REVERT: A 955 ASN cc_start: 0.9223 (m-40) cc_final: 0.8498 (m110) REVERT: A 1138 TYR cc_start: 0.8752 (t80) cc_final: 0.8497 (t80) REVERT: B 287 ASP cc_start: 0.8837 (OUTLIER) cc_final: 0.8588 (m-30) REVERT: B 529 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.6828 (tttp) REVERT: C 287 ASP cc_start: 0.8838 (OUTLIER) cc_final: 0.8572 (m-30) REVERT: C 471 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8026 (mp0) REVERT: C 1138 TYR cc_start: 0.8776 (t80) cc_final: 0.8398 (t80) outliers start: 108 outliers final: 73 residues processed: 187 average time/residue: 0.1533 time to fit residues: 48.0887 Evaluate side-chains 161 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 80 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 112 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 232 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 259 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 308 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.080774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.066014 restraints weight = 60184.564| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.29 r_work: 0.2928 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 782 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 903 | |-----------------------------------------------------------------------------| r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25581 Z= 0.106 Angle : 0.518 10.058 34848 Z= 0.268 Chirality : 0.047 0.350 3966 Planarity : 0.004 0.043 4485 Dihedral : 5.377 54.392 3750 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.89 % Allowed : 24.45 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.14), residues: 3117 helix: -1.08 (0.22), residues: 609 sheet: 0.07 (0.20), residues: 699 loop : -1.94 (0.13), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 214 TYR 0.012 0.001 TYR A1067 PHE 0.014 0.001 PHE C1121 TRP 0.011 0.001 TRP C 436 HIS 0.002 0.000 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00238 (25527) covalent geometry : angle 0.50066 (34725) SS BOND : bond 0.00310 ( 39) SS BOND : angle 0.92531 ( 78) hydrogen bonds : bond 0.03337 ( 644) hydrogen bonds : angle 4.69550 ( 1734) link_NAG-ASN : bond 0.00957 ( 15) link_NAG-ASN : angle 3.57137 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 85 time to evaluate : 1.063 Fit side-chains revert: symmetry clash REVERT: A 176 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7161 (mp) REVERT: A 287 ASP cc_start: 0.8794 (OUTLIER) cc_final: 0.8584 (m-30) REVERT: A 529 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7678 (mtmm) REVERT: A 584 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8458 (mm) REVERT: A 624 ILE cc_start: 0.8337 (mt) cc_final: 0.7671 (mm) REVERT: A 955 ASN cc_start: 0.9153 (m-40) cc_final: 0.8385 (m110) REVERT: A 1138 TYR cc_start: 0.8724 (t80) cc_final: 0.8467 (t80) REVERT: B 122 ASN cc_start: 0.8359 (p0) cc_final: 0.7401 (p0) REVERT: B 529 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.6832 (tttp) REVERT: C 287 ASP cc_start: 0.8782 (OUTLIER) cc_final: 0.8521 (m-30) REVERT: C 471 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7975 (mp0) REVERT: C 1138 TYR cc_start: 0.8763 (t80) cc_final: 0.8383 (t80) outliers start: 107 outliers final: 80 residues processed: 187 average time/residue: 0.1527 time to fit residues: 48.5368 Evaluate side-chains 170 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 83 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 123 optimal weight: 2.9990 chunk 163 optimal weight: 9.9990 chunk 202 optimal weight: 0.9980 chunk 159 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 133 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.079292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.063979 restraints weight = 59557.143| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.01 r_work: 0.2889 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 903 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1007 | |-----------------------------------------------------------------------------| r_final: 0.2823 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 25581 Z= 0.154 Angle : 0.578 10.313 34848 Z= 0.303 Chirality : 0.049 0.477 3966 Planarity : 0.004 0.046 4485 Dihedral : 5.653 53.807 3750 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 4.37 % Allowed : 24.38 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.96 (0.14), residues: 3117 helix: -1.21 (0.21), residues: 609 sheet: 0.11 (0.19), residues: 735 loop : -2.04 (0.13), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 214 TYR 0.014 0.001 TYR A1067 PHE 0.017 0.001 PHE A1121 TRP 0.010 0.001 TRP B 436 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00367 (25527) covalent geometry : angle 0.56002 (34725) SS BOND : bond 0.00412 ( 39) SS BOND : angle 1.21990 ( 78) hydrogen bonds : bond 0.04480 ( 644) hydrogen bonds : angle 4.85984 ( 1734) link_NAG-ASN : bond 0.00986 ( 15) link_NAG-ASN : angle 3.77568 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 83 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7168 (mp) REVERT: A 287 ASP cc_start: 0.8907 (OUTLIER) cc_final: 0.8668 (m-30) REVERT: A 529 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7750 (mtmm) REVERT: A 584 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8432 (mm) REVERT: A 624 ILE cc_start: 0.8370 (mt) cc_final: 0.7650 (mm) REVERT: A 955 ASN cc_start: 0.9221 (m-40) cc_final: 0.8513 (m110) REVERT: A 1138 TYR cc_start: 0.8762 (t80) cc_final: 0.8541 (t80) REVERT: B 287 ASP cc_start: 0.8844 (OUTLIER) cc_final: 0.8597 (m-30) REVERT: B 529 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.6840 (tttp) REVERT: B 625 HIS cc_start: 0.7258 (OUTLIER) cc_final: 0.6151 (p-80) REVERT: B 1142 GLN cc_start: 0.7220 (OUTLIER) cc_final: 0.6849 (tp-100) REVERT: C 287 ASP cc_start: 0.8869 (OUTLIER) cc_final: 0.8609 (m-30) REVERT: C 471 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7998 (mp0) REVERT: C 1138 TYR cc_start: 0.8766 (t80) cc_final: 0.8438 (t80) outliers start: 120 outliers final: 101 residues processed: 196 average time/residue: 0.1552 time to fit residues: 50.8202 Evaluate side-chains 191 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 80 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 104 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 276 optimal weight: 1.9990 chunk 5 optimal weight: 0.0040 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 163 optimal weight: 3.9990 chunk 279 optimal weight: 0.8980 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.080005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.064324 restraints weight = 59168.034| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.25 r_work: 0.2891 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1007 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1099 | |-----------------------------------------------------------------------------| r_final: 0.2829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25581 Z= 0.131 Angle : 0.550 10.192 34848 Z= 0.287 Chirality : 0.048 0.434 3966 Planarity : 0.004 0.045 4485 Dihedral : 5.533 54.136 3750 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.55 % Allowed : 24.60 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.98 (0.14), residues: 3117 helix: -1.14 (0.21), residues: 609 sheet: 0.05 (0.20), residues: 660 loop : -1.98 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.013 0.001 TYR A1067 PHE 0.015 0.001 PHE C1121 TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00304 (25527) covalent geometry : angle 0.53244 (34725) SS BOND : bond 0.00358 ( 39) SS BOND : angle 1.06111 ( 78) hydrogen bonds : bond 0.03948 ( 644) hydrogen bonds : angle 4.73103 ( 1734) link_NAG-ASN : bond 0.00958 ( 15) link_NAG-ASN : angle 3.71698 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 80 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7173 (mp) REVERT: A 287 ASP cc_start: 0.8906 (OUTLIER) cc_final: 0.8687 (m-30) REVERT: A 529 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7753 (mtmm) REVERT: A 584 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8388 (mm) REVERT: A 624 ILE cc_start: 0.8334 (mt) cc_final: 0.7605 (mm) REVERT: A 955 ASN cc_start: 0.9208 (m-40) cc_final: 0.8495 (m110) REVERT: A 1142 GLN cc_start: 0.7246 (OUTLIER) cc_final: 0.6959 (tp-100) REVERT: B 287 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8596 (m-30) REVERT: B 529 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.6758 (tttp) REVERT: B 625 HIS cc_start: 0.7278 (OUTLIER) cc_final: 0.6173 (p-80) REVERT: B 1142 GLN cc_start: 0.7219 (OUTLIER) cc_final: 0.6867 (tp-100) REVERT: C 287 ASP cc_start: 0.8881 (OUTLIER) cc_final: 0.8626 (m-30) REVERT: C 471 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7968 (mp0) REVERT: C 1138 TYR cc_start: 0.8763 (t80) cc_final: 0.8433 (t80) REVERT: C 1142 GLN cc_start: 0.7124 (OUTLIER) cc_final: 0.6895 (tp40) outliers start: 125 outliers final: 103 residues processed: 198 average time/residue: 0.1599 time to fit residues: 53.2119 Evaluate side-chains 195 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 80 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1142 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 307 optimal weight: 4.9990 chunk 162 optimal weight: 0.0000 chunk 140 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 182 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.078531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.062982 restraints weight = 58772.575| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.32 r_work: 0.2850 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1099 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1128 | |-----------------------------------------------------------------------------| r_final: 0.2791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 25581 Z= 0.210 Angle : 0.644 10.562 34848 Z= 0.339 Chirality : 0.051 0.444 3966 Planarity : 0.005 0.048 4485 Dihedral : 5.975 53.732 3750 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 4.80 % Allowed : 24.67 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.09 (0.14), residues: 3117 helix: -1.45 (0.20), residues: 615 sheet: 0.15 (0.19), residues: 720 loop : -2.11 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.014 0.002 TYR A1067 PHE 0.021 0.002 PHE A1121 TRP 0.010 0.002 TRP B 436 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00510 (25527) covalent geometry : angle 0.62585 (34725) SS BOND : bond 0.00538 ( 39) SS BOND : angle 1.51349 ( 78) hydrogen bonds : bond 0.05397 ( 644) hydrogen bonds : angle 4.98213 ( 1734) link_NAG-ASN : bond 0.00964 ( 15) link_NAG-ASN : angle 3.83481 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 82 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.7288 (t80) cc_final: 0.7000 (t80) REVERT: A 176 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7194 (mp) REVERT: A 287 ASP cc_start: 0.8968 (OUTLIER) cc_final: 0.8727 (m-30) REVERT: A 529 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7763 (mtmm) REVERT: A 584 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8375 (mm) REVERT: B 287 ASP cc_start: 0.8974 (OUTLIER) cc_final: 0.8711 (m-30) REVERT: B 529 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7656 (mtmm) REVERT: B 625 HIS cc_start: 0.7297 (OUTLIER) cc_final: 0.6172 (p-80) REVERT: C 177 MET cc_start: 0.7344 (ttm) cc_final: 0.7120 (ttm) REVERT: C 471 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8056 (mp0) REVERT: C 1138 TYR cc_start: 0.8749 (t80) cc_final: 0.8482 (t80) outliers start: 132 outliers final: 106 residues processed: 206 average time/residue: 0.1527 time to fit residues: 53.5487 Evaluate side-chains 196 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 82 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 33 optimal weight: 2.9990 chunk 258 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 173 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 261 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 252 optimal weight: 8.9990 chunk 155 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.079331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.063659 restraints weight = 58593.243| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.34 r_work: 0.2865 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1128 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1185 | |-----------------------------------------------------------------------------| r_final: 0.2805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25581 Z= 0.153 Angle : 0.587 10.960 34848 Z= 0.307 Chirality : 0.049 0.489 3966 Planarity : 0.005 0.047 4485 Dihedral : 5.809 54.224 3750 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.33 % Allowed : 25.07 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.04 (0.14), residues: 3117 helix: -1.38 (0.21), residues: 615 sheet: 0.22 (0.19), residues: 705 loop : -2.09 (0.13), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 214 TYR 0.014 0.001 TYR A1067 PHE 0.017 0.001 PHE A1121 TRP 0.012 0.001 TRP C 436 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00361 (25527) covalent geometry : angle 0.56746 (34725) SS BOND : bond 0.00418 ( 39) SS BOND : angle 1.22945 ( 78) hydrogen bonds : bond 0.04472 ( 644) hydrogen bonds : angle 4.81850 ( 1734) link_NAG-ASN : bond 0.01008 ( 15) link_NAG-ASN : angle 4.00784 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 83 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.7366 (t80) cc_final: 0.7044 (t80) REVERT: A 176 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7248 (mp) REVERT: A 287 ASP cc_start: 0.8989 (OUTLIER) cc_final: 0.8751 (m-30) REVERT: A 529 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7739 (mtmm) REVERT: A 584 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8364 (mm) REVERT: B 274 THR cc_start: 0.9226 (OUTLIER) cc_final: 0.9007 (t) REVERT: B 287 ASP cc_start: 0.8942 (OUTLIER) cc_final: 0.8695 (m-30) REVERT: B 529 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7676 (mtmm) REVERT: B 625 HIS cc_start: 0.7287 (OUTLIER) cc_final: 0.6167 (p-80) REVERT: B 1142 GLN cc_start: 0.7165 (OUTLIER) cc_final: 0.6788 (tp-100) REVERT: C 471 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.7994 (mp0) REVERT: C 1138 TYR cc_start: 0.8740 (t80) cc_final: 0.8472 (t80) outliers start: 119 outliers final: 107 residues processed: 195 average time/residue: 0.1602 time to fit residues: 52.7768 Evaluate side-chains 196 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 79 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 132 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 185 optimal weight: 0.9980 chunk 228 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 162 optimal weight: 6.9990 chunk 57 optimal weight: 0.0970 chunk 177 optimal weight: 0.9980 chunk 245 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 overall best weight: 0.8178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 207 HIS ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.081334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.065234 restraints weight = 58264.890| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.24 r_work: 0.2909 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1185 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1262 | |-----------------------------------------------------------------------------| r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25581 Z= 0.101 Angle : 0.515 10.401 34848 Z= 0.265 Chirality : 0.047 0.438 3966 Planarity : 0.004 0.044 4485 Dihedral : 5.363 54.500 3750 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.93 % Allowed : 25.44 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.90 (0.14), residues: 3117 helix: -1.10 (0.21), residues: 615 sheet: 0.09 (0.20), residues: 687 loop : -1.94 (0.13), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.013 0.001 TYR A1067 PHE 0.013 0.001 PHE C1121 TRP 0.011 0.001 TRP C 436 HIS 0.002 0.000 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00229 (25527) covalent geometry : angle 0.49566 (34725) SS BOND : bond 0.00281 ( 39) SS BOND : angle 0.84461 ( 78) hydrogen bonds : bond 0.03190 ( 644) hydrogen bonds : angle 4.53926 ( 1734) link_NAG-ASN : bond 0.00997 ( 15) link_NAG-ASN : angle 3.86884 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 83 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7202 (mp) REVERT: A 529 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7750 (mtmm) REVERT: A 584 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8281 (mm) REVERT: A 624 ILE cc_start: 0.8354 (mt) cc_final: 0.7647 (mm) REVERT: A 955 ASN cc_start: 0.9194 (m-40) cc_final: 0.8480 (m110) REVERT: B 274 THR cc_start: 0.9164 (OUTLIER) cc_final: 0.8958 (t) REVERT: B 287 ASP cc_start: 0.8873 (OUTLIER) cc_final: 0.8624 (m-30) REVERT: B 529 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.6710 (tttp) REVERT: B 625 HIS cc_start: 0.7272 (OUTLIER) cc_final: 0.6161 (p-80) REVERT: B 1142 GLN cc_start: 0.7154 (OUTLIER) cc_final: 0.6808 (tp40) REVERT: C 287 ASP cc_start: 0.8900 (OUTLIER) cc_final: 0.8644 (m-30) REVERT: C 471 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7921 (mp0) REVERT: C 1138 TYR cc_start: 0.8767 (t80) cc_final: 0.8501 (t80) outliers start: 108 outliers final: 93 residues processed: 186 average time/residue: 0.1591 time to fit residues: 49.2502 Evaluate side-chains 178 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 75 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 263 optimal weight: 0.5980 chunk 271 optimal weight: 3.9990 chunk 209 optimal weight: 5.9990 chunk 300 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 chunk 297 optimal weight: 0.7980 chunk 301 optimal weight: 3.9990 chunk 307 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.079418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.063431 restraints weight = 58350.134| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.25 r_work: 0.2859 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1262 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1290 | |-----------------------------------------------------------------------------| r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 25581 Z= 0.166 Angle : 0.593 10.584 34848 Z= 0.310 Chirality : 0.049 0.451 3966 Planarity : 0.004 0.047 4485 Dihedral : 5.715 53.871 3750 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.93 % Allowed : 25.58 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.99 (0.14), residues: 3117 helix: -1.27 (0.21), residues: 615 sheet: 0.16 (0.19), residues: 735 loop : -2.07 (0.13), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 214 TYR 0.013 0.001 TYR A1067 PHE 0.018 0.001 PHE A1121 TRP 0.011 0.001 TRP B 436 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00397 (25527) covalent geometry : angle 0.57441 (34725) SS BOND : bond 0.00439 ( 39) SS BOND : angle 1.24548 ( 78) hydrogen bonds : bond 0.04648 ( 644) hydrogen bonds : angle 4.78297 ( 1734) link_NAG-ASN : bond 0.00977 ( 15) link_NAG-ASN : angle 3.91626 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6303.54 seconds wall clock time: 108 minutes 43.20 seconds (6523.20 seconds total)